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Micro Lung Empyema


    1. Thermometry: normal range = 35.6 – 38.2 (mean = 36.8); ♀ = 36.9; ♂=36.7; max = 37.7; 2-12 min eqlib
           a. Observer variability: 25% glass therm=inaccur after 8 mo; region diff in mouth >w/elec therm
                    i. oral temps vary by ~0.95C from rear sublingual pocket to area beneath frenum
                   ii. temp ↑er w/smoking/mastication; rapid breathing = ↓oral temp but not rectal (Δ0.71)
           b. Anatomic variability: core temp (adults) is 0.2C ↓er < rectal temp & 0.4C ↑er > oral
           c. Physio variables: older=colder; ovulation ↑temp by 0.5; ↓est=6am & ↑est=4-6pm
    2. Pathophysiology of fever – Hypothalamic thermoreg center = preoptic nucl of ant hypothal!
           a. ant hypothal sends signal to post hypothal which is regulatory pt (post will Δ environment)
           b. Definition: state of altered core temp (set pt), often (not always) part of defens respons to foreign
                    i. **ALTERATION in HYPOTHALAMIC SET POINT**
           c. Reg (vasodil, sweating; vasocnstrx, shiver; Δbehavior); Temp dysregulation =
                 Hypothermia                                                 Hyperthermia
Xposr; aging; sepsis (severe infxn); CHF; OD; Heat stroke; hypothal lesion (rare b/c dead); malignant
hypoglyc; renal/hepatic failure                    hypertherm; thyrotoxicosis; anticholinergic blockage; exercise
           d. Exog pyrogens  Host cell (mononuc phag)  Endogenous Pyrogens (IL-1)  BBB  ANT
               hypthal  arachadonic acid  thromboxanes/prostaglandins  cAMP POST hypthal
               vasomotor center  symp efferents vasocnstrxn  FEVER
Exogen Pyrogens (syn endog pyr from phago cell)            Endog Pyrogens (bind to endothel cells in ant hypthal)
Microbes (virus/bact/spirochetes/yesast) & products        IL-1, TNF, γ-IFN (syn –not stored- by mononuc phago
(endotox, exotox, bact cell wall); Ag-Ab cmplx;            cells in response to stim by exog pyr); can cross BBB.
activated compl components; Inflam agents (Bile salts, IL1 sources = mononuc phago, myelomonocytic
etiocholanonlone, C5a, Urate, PHA, bleomycin)              leukemia cells, renal carcinoma, langerhans, keratincyt
                    i. Endog also found in blood w/out fever
           e. &/OR: local inflame activates thermosensitive neurons that stim thermoreg center  ↑body temp
           f. Treatment: Antipyretics (apirin-ASA, acetaminophen, NSAIDs); Glucocorticosteroids
                    i. Rationale for Antipyr
                           1. relief of discomfort (sponge baths = ↑discomfort)—antipyr =analgesic–pain relief
                           2. ↓mortality (raising temp in mice artificially ↑survival rate);
                           3. ↓morbidity – acetaminophen ↑crusting time in kids w/varicella & ↑symptoms
                           4. prevent febrile seizure – ibuprofen & prophylactic acetaminophen in kids =no diff
                           5. ↓cognitive impair (no data), improve outcome for pt w/stroke/brain injury;
                           6. ↓metab demands in pt w/severe CV dz (pts need to be paralyzed to prevent shiver)
                   ii. Bad fx of antipyr = external cooling (potential to cause coronary vasospasm thru cold
                       pressor resp); ↓in heat-shock proteins; + side fx
                  iii. NO cooling baths/blankets! (b/c in fever set-pt Δs so blankets make inappro body resp)
           g. Benefits of Fever:
                    i. ↑Ig syn; T-cell act; ↑cytokine prodxn; ↑NK act; ↑phago act; ↓microb growth, ↓virus replc
    3. Components of the Acute Phase Response
           a. Thermoregulator (fever)
           b. Anti-infective – pro-inflam cytokine (IL1, TNFα, IL6), ICAM-1, phagos, compl prot
           c. Anti-inflammatory – anti-inflam cytokines (IL4, IL10), ACTH, haptoglobin, protease inhibitors
                    i. b/c acute resp needs to be turned off & 2ndly b/c most inflm= local avoid systemic resp
           d. Metabolic – cortisol, gluconeogenesis, lipolysis, catecholamines
           e. Procoagulant – fibrinogen, clot of infxn
    4. Fever of unknown origin (FUO): ill >3wks; temp>38.4 severl xs; uncertain diag after 1wk of study
           a. Infxn (40%) – gen infxn hard to diagnose (ie. occult Tb, endocarditis, viral or abscess in abd)
           b. Neoplasia (25%) – some tumors w/fever (hematologic malign –not myeloma, hypernephroma)
           c. Collagen vasc dz (15%) –systemic lupus erythmatosus, po.lyarteritis nodosa, vasculitis, etc
           d. Misc – inflame bowel dz, sarcoid, drug fever, factitious fever;
Bacterial Classification & Structure
   1. Classification schemes for bacteria. *bacteria are prokaryotic (lack introns/nuc/orgnls, have cell wall)*
           a. given genus/species name based on morph, physio, biochem, genetics (bergey’s-non natural)
   2. Recog & classify bacteria according to classification schemes
           a. Classification based on Morphology:
                    i. Stain: *Gram + = purple* & *Gram – = pink* (10s/stain; exam w/oil immers @ 100X)
                           1. procedures: heat fix cell to slidestain w/crystal violetwashstain w/Grams I
                               washdecolor w/et-OHcounterstain w/safranin (pink)wash/air dryexam
                   ii. shape: Bacil=rod; Cocci=sphere; Coc-bac=short rod; Spirochete=spiral; vibrium=comma
                  iii. Arrang: streptobac/coc (chain); staphylococ (cluster); diplococ (pair); sarcinae (tetra)
           b. Classification based on Biochem & Physio:
                    i. type of metab (anaerobic vs aerobic vs fermentation); nutrients used; metab by-prodx;
                       temp, pH & salt tolerance
           c. Classification based on Genetics: (helps classify based on relatedness via rDNA)
                    i. G & C content in DNA; DNA fingerprint by restrxn fragment length polymorph (RFLP);
                       PCR of specific genes; rDNA sequencing
   3. basic structure of bacterial cells: (cell membrane + cell wall)
           a. Cytoplasmic membrane (gram + = 1 membrane; gram - = 2membr)
                    i. fnx: Osmotic barrier (keeps H20 @ right [C]; site of chromosome attachment; E gen
                       (w/out mito); cell wall syn; selective perm & trans of metab
                   ii. transport mechanisms:
                           1. Facilitated Diffusion – uses carrier molecules (permease); sub mv along [C] grad;
                               NO E required; chem. modifictn w/in cell can allow accum against apparent grad
                           2. Active Transport – requires specific permease; sub mvs against [C] grad; req E;
                                   a. 1o active trans driven by ATP hydrolysis
                                   b. 2o active trans driven by ion flux ax membr
                           3. Group translocation – sugar transport ax membr; substrate phosphorylated by
                               carrier & rel into cytoplasm; accumulate sugars against [C]grad; NO E required
           b. Periplasmic Space: space btwn inner & outer members of Gram – bacteria
                    i. contains enz that breakdown big molecules into constituent parts for transport into cell
                   ii. some strains concentrate antibiotic hydrolases in periplasmic space
           c. Cell Wall (aka murein sacculus): diff btwn gram + & -; all bact except mycoplasms/halophiles
                           1. prevents osmotic lysis; surrounds cell/provides rigidity; mostly of peptidoglycans
                   ii. Constituents
                           1. peptidoglycan – overlapping lattice of 2 sugars x-linked by aa bridges
                                   a. sugars = NAG & NAM; pepglyc are only found in bacterial wall
                           2. teichoic acid/lipoteichoic acids – (lipo =major Ag-ic determinants in *gram +*)
                                   a. teichoic = chains of 30glycerol/ribitol-P attached to cell wall
                                            i. attached to NAM in cell wall; affect ability of cell to take up DNA
                                           ii. involved in adhesion-required for virulence (cause of sepsis)
                                   b. Lipoteich= attached to lipids in cyto membr & thru cell wall to EC environ
                  iii. Synthesis – several antibiotics interfere w/syn
                           1. vancomycin & Ristocetin – block disacch addition to growing wall
                           2. bacitracin – prevents regen of disacch carrier
                           3. Penicillin/cephalosporins – prevent x-linking (but not syn)
           d. Outer Membrane *only in gram – * same compos as cyto membr (anchored to wall by braun)
                    i. Constituents (proteins like porins/channels float in lipid bilayer)
                           1. LPS (endotoxin)
                                   a. O-Ag (o-polysacc) – repeat polysac; char type for each bact (can xprs >1)
                                            i. adherence rcptr (adhere to our membr); resistance to phagocytosis
                                           ii. phage rcptr (bad for bact b/c this is where virus attack)
                                    b. Core (fnx = connect lipid A to O-Ag)
                                              i. outer – variable; sugars/aa (haptose); connects w/O-Ag
                                             ii. inner – mostly KDO-connects to inner core & lipid A
                                    c. Lipid A – glycophospholipid; conx inner core; float outside of outer memb
                                    d. Clinical importance –
                                              i. free LPS is toxic to mammals (act alt compl; acts as pyogen-fever;
                                                 responsible for sepsis, dissemin intravasc coag-DIC, shock; lipid A
                                                 is B cell mitogen (b cells grow)
                                             ii. does this by causing host cell to prod abn amts of mol that reg vasc
                                                 perm, BP, coag & immune response (im sys kills what it shouldn’t)
                           2. Channels – responsible for uptake of material (nutrients) from environ
                                    a. Porins – trimeric prot; form H2O filled chan thru membr;
                                              i. pass of sm ions/hydrophil (ie. E.coli include OmpF, OmpC, PhoE)
                                    b. Porin-lik protein – (lamb in E.coli) maltose trans; rcptr for phage λ (virus)
                                    c. TonB-dep rcptr–link to E-dep prot TonB; ↑ly spec for scarce mol (vitB12)
                                              i. not well characterized
                   ii. Fnx – sel barrier; – charge; phage rcptr; patho prop; stabil mating; keep enz in periplsm
             e. Cell Appendages
                    i. Flagella – *mostly gram -* for mvmt; made of flagellin; arr diff in diff species; anch to
                       membr by cmplx molec machinery; rotates CCW like a propeller up to 300x/sec
                           1. driv=p+ pump; monotrichous (1), lophotrich (1 tuft), amphitrich (2 tuft), peritrich
                           2. Chemotaxis (mv twd/away chem.): chemoattractant vs Chemorepellent
                                    a. chemoattract = longer runs; net mvmt twd
                                    b. chemorepel = rotate CW  tumbles aimlessly
                   ii. Pili (fimbriae) – hollow hairlike, made of pilin (1-100/cell)
                           1. Common (somat) = ↑#/cell; adhes (colonize muc surf); may prevent phagtosis
                           2. Sex - *mostly gram –* few/♂; genes for syn encoded on extrachrom DNA
                                (Fertility [F] factor or conj factors); facilitates trans of F factor to non-fertile cells
             f. Other strx
                    i. Capsules & slime layers – mucopolysac layer surround cell; slime=loose caps (spec stain)
                           1. Fnx = resist phagocytosis; adher (oral streptococ); prevents dessication
                   ii. Endospores – dormant, ↑ly resist cells formed by some **gram +**; last >300yrs
                           1. hard to kill, survive hrs of boiling; autoclave for 10-15min @121C
                           2. Bacillus (cereus, subtilis, anthracis); Clostridium (botulinum, tetani, perfringes)
                           3. Core (cytoplasm w/chrom); Cell membr; Thin Cell wall; Exosporium (outer layer)
                           4. Cortex – concent layer of pep-gly w/unusual x-links
                                    a. DPA – Ca chelator; causes dehyd of cortex –resist boiling; >15%cell wt
                           5. Spore Coats (outer/inner) - ↑ly disulf bonded; resist to chem.
                           6. Sporulation (form spore)– induced by starv, ↑cell density, stationary growth phase
                           7. Germination (90min; 3stages): activatn – heat/chem.; active L-ala rcptr
                                (protease); initiation – xpsr to L-ala act proteasesact cortex lytic enz
                                (degen of cortex & rehyd); Outgrowth – resume vegetative growth
                              Gram +                                                       Gram –
Wall     -multi peptidoglyc layers (stacked); ↑ly x-                  -Single layer of peptidoglycan; Braun’s lipoprot
         linked w/in & btwn layers; peptidogly may
peptidogly                                                            anchors outer membr to cell wall; xlink w/in
         contain several alt @position 3allows more                  -NAM side chane w/unique aa: (D-glutamate,
         x-link than w/gram – (very rigid strx)                       D-ala xlink w/meso-DAP = penultimate aa)
Membrane Single membrane in cell envelope                             2 membranes in cell envelope; *outer membr*
Staining Blue/Purple: crystal violet/I trap in cell wall              Pink: Cell wall perm after et-OH tx which
         (dehyd w/et-OH tx)                                           washes out purple color; counterstain=pink
Other    Wall-Teichoic & lipotechoic acids; Endospores                Flagella, sex pili
Bacterial Genetics Lecture
Intro: (purines = A & G; Pyrimidines = C, T, U; G≡Cstronger bond; A=T – opposite but complementary pairing of strands)
      -DNA strands = complementary & anti-parallel
      -mRNA – RNA copy of DNA + top strand; tRNA – carries aa; rRNA- strxl component of ribosomes
      *Central Dogma* Replication (copy of DNA) transcription (mRNA copy-xprsn); Translation-prot syn
      Genetic Code: Codon = triplet of 3bases = complementary to anti-codon of tRNA; each encodes spec aa (1start–AUG=met)
              o 64 codon = 20 aa-b/c code degenerate (some aa encode by >1codon); Stop codons = end transltn: TAA, TAG, TGA
    1. Bacterial DNA (2types=chrm & plasmid)
          a. Chromosome: 1 double-stranded DNA molec; 1copy/cell (haploid); attached to cell membrane
                    i. variable & conserved regions
          b. Plasmids: small, closed circ extrachrm DNA; many copies/cell; replicates indep of chrm;
                    i. useful as vectors for recombo DNA
          c. Gene structure (genes are nucleic acid seq that encode polypep, tRNA, rRNA)
                    i. Promotor (rna polymerase binding site); Operators (repressor binding site); Coding
                       Region (encodes strxl genes); Terminator Signals (strong & weak)
                   ii. Bact genes=very efficient (NO introns; some overlap; some contain genes on both strand)
          d. Replication (occurs continly, starting @ origin of repl & cont in both directions-50000bp/min)
                           1. semi-conservative – each new helix has ori strand & new strand
                   ii. Replicon (dna seq that repl autonom) – has origin of repl (oriC); includes chrm, plasmids
                       & virus (bacteriophages)
                 iii. Nonreplicon (dna seq can’t repl auton)–NO ori of repl; repl only if recombo into replicon
                  iv. Steps: Helicase unwinds dnadna primase syn short seq-spec rna primerdna poly III
                       extends primer in 5-3 directionleading strand syn contin; laggin syn in okazaki frag
                       dna polymerase I excises rna primer & fills in gaps
    2. Mutations (Δin nucleotide seq)
          a. Mechanism by which they occur:
                    i. Inherent Errors (rare- 1/cycle = 1/10^7bp) –b/c rapid repl can get lots mut even @↓rate
                   ii. Mutagens (physical = UV light; Chemical=modify dna covalently/intercalatemisread)
          b. Types:
                    i. Transition – Δpurine  another purine (AG) OR pyrimanother pyrim (CT)
                   ii. Transversion – Δ purine pyrim (GC OR TA) …[less common]
                 iii. Insertions – insert extra dna
                  iv. Deletions – remove dna
          c. Consequences/fx on bacteria
                    i. Synonymous/silent – Δdna seq, but NO fx on aa seq (happens b/c of degenerative nature)
                   ii. Nonsynonymous/missense – dna Δs that alter aa seq; may fx fnx of prot
                 iii. Nonsense – Δstop codon  truncated prot; usually fx fnx
                  iv. Frameshift – Δ reading frame (~caused by indels); ~insert stop codon (unless multi of 3)
                   v. Null – any mut that destroys fnx of protein (same as nonsynonymous)
                  vi. Reversions – restore original dna seq
                 vii. Supressors – 2nd mutation @ diff site that restore prot fnx
          d. DNA repair mech (bact have mec that can fix mutation if they aren’t too bad):
                    i. Proofreading – dna polymerase removes error during repl (very common & successful)
                   ii. Direct dna repair – enz repair damaged base (ie. photolyase repairs UV damage)
                 iii. excision repair – damaged stretch of dna is removed & repaired
                  iv. Recombinational–destroyed template; prot recA uses piece of sis chrm to replace damage
                   v. SOS repair – global resp to severe damage; recombo replaces large stretch of dna/lesions
                  vi. Error prone repair – LAST RESORT; no template is available; not very effective
   3. bacteria xΔ DNA mech & importance of DNA xΔ for bacteria;
   Recombination!! (integr dna into genome)=
         a. Homologous–foreign gene insert in area of simil seq; vs Heterologous–forn gene insert anywhere
      Types of Recombination
         b. Generalized recombo – donor dna has seq w/homol to section of recip dna; mediated by recA
         c. Site-Spec Recombo – intro of dna into spec site in replicon
                  i. ie. phage λ inserts btwn gal & bio genes on E.coli chrm
         d. Transposition Recombo – small mobile dna elements (transposons/Tn element) mv from site to
             site or w/in/btwn replicons; insertion of transposon INACTIVATES gene
                  i. Tn = nonreplicons that often encode virulence/antibiotic factors; 3 types:
                          1. Insertion Sequences (IS element) – encode 1 gene=transposase
                                 a. small (700-1500bp); have terminal inverted repeats
                          2. Composite Tn – encode multi genes; have insertion seq on each end
                                 a. often encode virulence or resistance genes; 20-40kbp [ie. Tn1681 (E.coli
                                      heatstable enterotox); Tn10 (tetracycl resist); Tn5 (kanamycin resist)]
                         3. TnA type – several genes (Tnases, resolvases, others); have term invert repeats;
                             NO IS seq; ie. Tn A = encodes ampicillin resistance
Conjugation!! (xΔ dna from on bact to another thru conjugal bridge/sex pilus) **primarily in Gram – enteric**
          a. Transfer of plasmid DNA (need F+ donor cell & F- rcp cell)
                  a. F+ bact = 1big plasmid (F factor); 100kbp encod>60genes (25traA & traB genes)
                          i. traA-encodes sex pilus; 12 other tra ctrl pilus xprsn
                         ii. F fact has ori of repl (oriV); 2F+ cell cant mate (traT/traS encode surf xclusn prot)
                  b. 1-way trans of dna to rcp (genes pass @ same rate/order); other dnas + copy F plasmid
                     transferred  results in 2F+ cells (donor retains copy); need 10min to trans all F plasmid
          b. Transfer of chrml DNA (need Hfr-↑freq of recombo-donor w/F plasmid integr in chrm)
                  a. Hfr mates w/F-: copy of chrm transferred; need 100min; rare b/c conj bridge easy broken;
                     some dna makes it into rcp (if homol to rcp chrm-can be incorp by recombo)
                          i. if not incorp-DNA will be LOST & rcp stays nonfertile
          c. Transfer of Plasmid & chrml DNA (aka F/sex-duction) --sloppy excisions--
                  a. need F’ w/plasmid excised from Hfr cell that has F factor + genes adj to it on chrm)
                  b. F’ trans F factor + chrm piece  Fertile cell, stably diploid for some chrm genes
          d. Imp of Conj:
                  a. Trans of resist-R-factors – R fact – plasmids encod genes for antibiotic resist; clinic imp
                  b. Transfer of virulence fact (toxin genes) & molec bio (mapping chrm)
Transformation: (5-20 genes) uptake of naked dna by bact; acct for large amt of gene transfer; **Gram + **
          a. Competence – ability to be transformed; dep on presence of peptide competence factor
                  a. not in gram– but can be made competent if tx w/chem. ie. E.coli & genetic engineering
                          i. ie. E.coli tx w/CaCl2 – uptake (dna) of ds circular molecules is most efficient
Transduction: bacteriophage-med xΔ of DNA; Bactphage Primer: (bactphag=host-spec virus infx bact; 2types)
          a. Lytic phages – produce new phag w/in bact; usually lyse cell to release new phage
          b. Temperate phages – insert dna into host bact’s chrm; may/not lyse cell (aka lysogenic phages)
                  a. can enter lytic cycle from lysogenic pathway
   Types of Transduction
          a. Generalized (bacterial genes introduced into another bact randomly by (via) bactphage)
                  a. Lytic Phages – chop up chrm during infx; sometime bact dna piece co-pack w/phag dna
                          i. when next cell infx, dna may recombo
                  b. Lysogenic phages–insert dna into bact chrm randomly; excise=take piece of chrm w/them
                          i. phage head packed w/both phage & bact dna; phage genome incomplete 
                                 1. infect another cell; no new phage made; bact dna recomb w/new chrm
                                          a. recombines to get new dna
          b. Speciailzed (phages that always insert @same place in chrm, ie phage λ)
                  a. excision errorsinclusion of adj bact genes in phage dna
       c. Imp of Transdxn:
             a. Dissemination of R factors – R fact trans by transdxn; imp in *Gram +* b/c lack conj
                     i. S.aureus – multi-drug resistance is carried on plasmids transferred by transdxn

              b. Phage conversion – let some bact make toxins; toxin gene=part of phage genome (as Tn)
                      i. C. diphtheriae (dip toxin) made only when bact infx w/lysogenic phage w/gene
              c. Molec Bio – gene mapping & as cloning vectors (close linked genes transducer >freq)
4. Regulation of Gene xprsn (transcripton of mRNA from dna template) & diff btwn + & – regul mech
      a. Transxpn – bact = 1rna polymerase: transxn ctrld by promoters & operators & linked to transltn
      b. many bact genes arranged as operons; genes of metab pathway grpd in operons; operon =…
               i. gene grp under ctrl of 1promoter, transxd 2gether into long polycistronic-polygene-mess
      c. Regulation –
               i. +ly ctrld operons – inducible & usually catabolic; ie. lac(tose) operon in E.coli
                     1. Plac=lac promo; O=lac operat; z=βgalactosidase; y=lac permease; a=transacetylase
                             a. z,y,a = strxl genes
                             b. R = repressor –not part of lac operon; under ctrl of own promoter Pi
                     2. NO lactose – R bind to O & block access to Plac by rna polymer prevent transxn
                     3. W/lactos – sm amt of natural inducer allolactose formed allolac binds to R,
                          INACT it (R can’t bind to operator) rna poly binds to Plac transx strxl genes
                             a. **w/lactose** genes required for it’s uses are turned ON!!
              ii. —ly ctrld operons = repressible & usually anabolic; ie. Tryptophan operon
                     1. Trp operon encodes for genes needed for syn of trp
                     2. P=promoter; O=operator; E,D,C,B,A=strxl genes; R=own prom; inact @↓trp
                     3. ↑↑↑trp = trp binds to R & act it R bind to O, block dna poly access to P/trnsx
                             a. DOWN reg of gene xpsn by prod of pathway = feedback inhibition
                             b. ** if you already have trp then you don’t need to make more**
                     4. ↓↓↓trp = not enough trp to bind R; R=inact; rna poly binds to Ptrnsxn/trnsltn
                             a. **make trp if the cell needs it**
5. Mechanisms of antibiotic resistance in bacteria – bact can resist antibiotics by 2 mech
      a. Non-genetic Resistance – spp inherently resist to drug; spp insensitive to drug
               i. can be due to strxl diff (ie. cell wall);
              ii. some bact have modifying enz that destroy drug
             iii. spp may lack drug target
      b. Genetic Mech – heritable Δs make it drug resist; mech = …
               i. Mutation in target gene – either strxl or regulatory
                     1. alteration of ribos binding sites (tetracycline, aminoglycosides, macrolides)
                     2. mutation in gyrA gene prevents binding of nalidixic acid to dna gyrase
                     3. mutations in regulatory genes result in hyperprodxn of β-lactamase (penicillinase)
              ii. Acquired Resistance Factors – acquired by conj, transformation, transduction
                     1. most common R factors are plasmids
                     2. transfer of R factors can occur both w/in & btwn spp
                     3. TEM-1penicilinase gene originated in enteric bacteria; but transferd to gonococci
                     4. recently reported transfer btwn **Gram +** & **Gram –** spp
                     5. ie. plasmid-encoded R factors =
                             a. Tn3 (amp resistance); Tn10 (Tet resistance); Tn917 (erythromycin)
Bacterial Pathogenesis
     Pathogen = org that causes dz; Pathogenesis = process by which patho causes dz
     Normal Flora = live in habitats external to body (GI, ↑er respiratory, skin); mostly harmless;
             o usually benefit /neutral for host; but can cause dz if get into wrong place
     Virulent bact = grow @expense of host; use genetic factors (virulence factors) to cause damage/dz
     Opportunistic = cause dz only in susceptible individuals or get in wrong place (ie. pseudomonas in burn pt)
     Symptoms dep on: area fxd; host factors (innate resist, pre-exist condition, previous xposr); inoculum size; virulence of bact
Stages of Infxn (entry; adhes/multi/coloniz; invasion/spread) & Mech involved w/bacterial infxn
     1. Entry – bact must cross natural defense mech/barriers: skin, mucus, ciliated epithelium, antibact secr
           a. Passive mech (w/out x-ing epi barriers): Inhalation & Ingestion
                    i. Inhalation: org in aerosol drop/dust partic; deep in lung & adhere to epi (escape ciliation)
                   ii. Ingestion (of contam food/H2O) – bact must survive stomach acid (↓inoc size million Xs)
                           1. SI = panc enz & strong peristalsis; LI=more conducive, but still need adher mech
                           2. toxin-making bact in intest can produce dz w/out entering body, ie cholera/Ecoli
           b. Penetration Mech (entry thru barrier) – thru mucosal epi; OR require opening (ie. break in skin)
                    i. Active Penetration – (rcptr-med) bind to host cell rcptr & internalize; virus & some bact
                   ii. Cell-mediated – host immune cell internalize bact & carries them into body
                  iii. Trauma – wounds, cuts, etc; Clostridium spp = notorious
                  iv. Arthropod bites – bact = Yersinia pestis (plaque), Borrelia spp. (lyme dz), Erlichia spp
                           1. also other parasites including viruses, protozoa & worms
                   v. Sex Trans–venereal dz-Treponem pallidum, Neisser gonorrhoeae, Chlamyd trachomatis
     2. Ways in which bacteria cause dz: Adhesion, Multiplication, Colonization
           a. the ability to colonize dep on:
                    i. ability to Adhere (involves bacterial adhesin & host rcptr)
                           1. Adhesin – mol that bind to host tissue rcptr; prot @tip of pili;
                                   a. they are often lectins (ie. bind to carbs)
                           2. some are on bact cell surf (ie. Invasins) that recog host cell integrins
                                   a. Streptococ pyogen use lipoteich & F prot to bind to fibronectin on cell surf
                           3. Biofilms, slime, capsules – help bact adhere to muc dental plaque=biofilm
                   ii. specif Growth req-ment (aka *Tissue Tropism =bact clnz sites that meet growth needs)
                           1. conditions = pH, temp, nutrients; tissue trop med by presence of adhesins
                                   a. bact xprs adhesins specific for rcptrs in permissive sites
                                   b. colonization of sites by normal flora help prevent coliniz by new spp
                                           i. BUT bact in sterile/abandoned sites don’t have this competition
                           2. *Acquire Fe* (limiting step b/c host has ↑affinity Fe-binding prot↓free Fe)
                                   a. bact mech = Fe rcptr, chelators, lysis of cells to release Fe
                  iii. defects in host Defense mech (multiplication of bact to cause dz)
           b. once adhered, bact multi b4 dz symp appear; Incubation Pd=from infxn timesymp appearance
                    i. during incub, bact overcome host defense mech & multi to pop size that causes dz
How bacteria evade host defense Mechanisms
     3. Invasion & Spread (Vibrio cholerae = epi surf; Shigella=x-epi, stay local; Salmonella typhi=systemic)
           a. Production/release of factors (*Invasins*-generally enz) that breakdown host defense!
                    i. Invasins –act locally to damage host cells & promote growth/spread of bac (dz patho)
           b. enteric bact have invasins that allow them to bind to intest cells-envag/swallow bact
                    i. once inside, bact can infx adj cells (ie. Shigella) or enter bloodstream (Salmonella)
           c. Invasins diff from exotox in that they act locally, NOT cytotoxic, & ↓potent; Types = …
                    i. Spreading Factors – fx physical prop of tissues, facil spread of bact
                           1. hyaluronidase – (―orig‖ spread factor), in staph, strep, clostridia; break↓ CT
                           2. collagenase – clostridium – degrades collagen
                           3. neruaminadase – breaks down neruaminic (sialic) acid in epi of intest muc
                                   a. prod by enteric bact (ie. Vibrio cholera & Shigella)
                           4. strepto/staphlokinase – conv plasminogenplasmin-digests fibrin *prevent Clot*
             ii. Hemolysins & Leucolysins – attack cell membr to kill clls
                     1. some hemolysins = pore forming prot (αtoxin from staph);
                     2. other hemolysins = phospholipases/lecithinases – breakdown membr lipids
                     3. leucocidins/streptolysin = invasions; considered to be exotoxins
           iii. Coagulase – converts fibrinogen to fibrin, *causes Clotting* (made by patho Staph)
                     1. surrounds leion to possibly protect bact from immune response
            iv. Extracell digestive enz – may have 2ndary role in invasion/pathosis (prote-/lip-/nucle-ases)
             v. Locally acting toxins – adenylate cyclases (help invasn); ↑cAMP, fx cell perm
                     1. Edema factor (EF) from B.anthracis & Bordetella pertussis toxin
            vi. Endocytosis inducers
4. Survival in the Host (normal def = Ab binds to cell rcptr for phagocyteswallowfuse w/lysosome)
     a. Avoiding contact w/phagocytes – don’t inflam, avoid them, inhibit phagocyte chemotax, hide
              i. some cover selves w/host mol (Staph & fibrin) or capsule that in non-immunogenic
     b. Inhibit Engulfment – cell wall components that inhib ingestion
              i. polysacch capsule; Mprot & fimbriae (grp A strep); surface slime (Pseudomonas
                 aeruginosa); depolmerz actin (prevent engulf-Yersinia); O Ag of LPS; Prot A (S. aureus)
     c. Survival inside phagocyte – intracell parasites of neutrophils or Mphages
              i. inihibit phagosome-lysosome fusion – prevent discharge of lysosomal hydrolyases into
                 phagosome (Salmonella, Mycobacteria, Legionella, Chlamydiae)
             ii. Resistance to lysosomal enzyme – protected by surf components of rel substances
                     1. Bacillus anthracis, Mycobacterium tuberculosis, Staphylococcus aureus
           iii. Escape phagosome – Rickettsias rel PL that liberates them phagosome w/in 30sec
     d. Kill phagocyte (protactive) – some bac make agressins-attack/kill phagocytes (b4/after ingest)
              i. streptolysin- (patho streptococ) bind chol in neutrophils membr rel lysosom enz in cyto
             ii. leukocidin – from staph does same thing; exotoxin A – from Pseudomonas aeruginosa
           iii. most intracell parasites of Mphages eventually kill cell
     e. Avoidig immune response –
              i. Tolerance – Ag-spec ↓in immune resp by host; Ag-ic disguise – bact cover w/host mol;
             ii. Immunosuppression – leprosy & Tb; Intracell habitat – Live w/in cell to avoid xposr;
           iii. induce non-neutralizing Ab; non-specific T-cell response induced by superAg of strep;
            iv. adsorption of Ab of soluble factors rel by bact; Ag-ic variation – ΔAg (fimbriae switch)
             v. ΔAg @ pop level – serotypes xprsing diff Ag
5. Tissue Injury (mech of pathology)
     a. Exotoxins: spp-specific soluble prot actively rel by bac; major determ of virulence; ↑potent/spec
              i. both **Gram + & —**; lethal toxins kill host (ie. anthrax);
             ii. some = very specif cytotox active (attack spec cells/pathway);
           iii. others = broad cytotox (cause nonspec cell death)
            iv. Toxins=strongly Agic, can be neutralized by spec Ab (aka antitoxin)
                     1. many consist of subunit A (bio act) & B (binds to host rcptr, begins transfer of A)
                             a. A is active after rel from B (aka A-B type toxins)
                                     i. ie. cholera, diphtheria, botulism, tetanus, anthrax
                     2. Entry: pore form (hemolysins, PL) by B & rcptr-med uptake (toxin internal in
                         membr-vesic aka endosome—B helps A ax endosome membr)
                     3. ADP-ribos: inactivates host cell
                             a. Diphtheria – catalyz ADP-ribos of host E(long)F-2 interfere w/host prot
                                 syncell death (heart, nerve, kidney) [subunit A from P. aeruginosa]
                             b. Cholera – cataly ADP-ribos of Gscont ↑cAMP synblock Na uptake
                                 stim Cl secr (H2O/elec follow); fluid loss, diarrhea, dehyd
                                     i. [enterotox (C.perfringens, B.cereus, E.coli) + pertussis]
                             c. Anthrax- 2As (Lethal F + EdemaF) share 1B (Protective Ag)
                                     i. PA bind rcptr, cleaved by protease, cr8ting binding site for LF/EF
                                     1. LF –protease; ↓=inhib proinflamimmunosuppression;
                                        ↑=kills Mphagesmassive inflame response & shock
                                     2. EF –adenylate cyclase immunosuppression
       v. Toxoids=detox toxins; retain Agicity & immunizing capacity
              1. formed by tx toxins chem. to inactivate them; used as vaccines against diphtheria
      vi. Modes of Axn:
              1. Cell lysis (hemolysins, PL, pore-forming toxins)
              2. Block prot syn (diphtheria & shiga toxin)
              3. Pharm toxins fx normal cell fnx w/out killing cell
                      a. cholera stime cAMP by enz mod regulatory Gprot
              4. Nervetoxins – botulism, tetanus = peptidases that bind to ganglioside rcptrs
                      a. release of nt/inhibitors
     vii. genes encod toxin prodxn are encoded…
              1. extrachrm on plasmid (anthrax, enterotoxins, tetanus) OR …
              2. lysogenic phages (botulism toxin, diphtheria, shiga-like)
              3. Chrmly encoded (Bordetella AC, cholera, pertussis, exotoxin A, Shiga)
              4. …and can be transferred by genetic xΔ btwn bact
b. Endotoxins: LPS from **Gram –**; ↓potent/specific (than exo); not enz, heatstable; strongly
   Agic (but can’t be converted to toxoids); genereally remain assoc w/cell wall until cell death
       i. lysosome become granulated; release lots of cytokines cell overreactsshock
c. Immunopathy
       i. damage caused by host resp to patho, rather than by patho directly (like LPS)
      ii. tissue damage occurs from toxic fac rel by lymphos, Mphages, neutros in infxn site
     iii. cont generated Ag rel from viable (chonic) bact  chronic immune stim & immunopathy
              1. **chemicals that immune cell use can hurt your own cells too**
Diagnostic Techniques in Microbiology – Basics of Bacterial Identificaiton
    1. Mode of metabolism
            a. Obligate Aerobe (Pseudomonas, Neisseria) – must have O2 in order to gen E
            b. Microaerophilic Aerobe (Campylobacter, Helicobacter) – need ↓er levels of O2
                    i. ↑O2 can be toxic
            c. Faculative Anaerobe (Enterobacteriaceae, Staphylococcus, Haemophilus)
                    i. largest category; can gen E in presence/absence of O2; prefer O2
            d. O2 tolerant Anaerobe (Streptococcus, Enterococcus, few Clostridium)
                    i. fermentation—don’t use O2 (O2 may grow slower, but doesn’t bother them)
            e. Obligate Anaerobe (Bacteroides, most Clostridium) – can’t grow w/O2; only fermentation!
    2. Nutritional Requirements
            a. Growth on chocolate agar
            b. Growth on 5%sheep blood agar
    3. Hemolytic Properties
            a. α – partial
            b. β – complete clearing of blood around cells
            c. γ – nonhemolytic
    4. Stains
          d. Gram positive
                  i. Bacillus (Bacillus, Clostridium)
                 ii. Coccus (Staphylococcus, Streptococcus)
          e. Gram neg
                  i. Bacillus (Enterobacteriaceae, Pseudomonas, Campylobacter, Bacteroides, Haemophilus)
                 ii. Coccus (Neisseria)
          f. Acid-Fast (add acid alcohol that will decolorize all bact xcept acid-fast; stain penetrates wall)
                  i. Completely (Mycobacterium)
                 ii. Partially (Nocardia)
    5. Tests
          g. Catalase
                  i. Positive (Staphylococcus) – look for bubbling on slide
                 ii. Negative (Streptococcus)
          h. Oxidase (reduces O2  H20; last enz in ETC on cyt a3)
                  i. Positive (Neisseria, Campylobacter) – dark blue (oxidase reacts w/ colorless reagent)
                 ii. Negative (Enterobacteriaceae)
          i. Biochemical
                  i. Manual, individually performed tests –
                 ii. Automated –
          j. DNA Probes (used when ↑specific identification of isolates is needed; extremely accurate)
                  i. ie. Neisseria gonorrhoeae in sexually abused children
     1. Taxonomy: Genera of Staphyococcaceae Family
            a. Staphylococcus*, Gemella, Jeotgalicoccus, Macrococcus, Salinicoccus
                     i. *S.aureus, S.epidermidis, S.haemolyticus, S.intermedius, S.lugdunensis,
                        S.saprophyticus, S.schleiferi*
     2. Physiology
          a. Morphology: *Gram +* cocci w/0.5-1.5u diameter
                  a. multiply in 2-D w/incomp separ of daughter cells resulting in formation of clusters
          b. Growth: rapid; sharply defined, smooth, opaque colonies on routine, nonselective media
                  a. Facultatively ANaerobic mode of metabolism
     3. Characteristics
            a. Coagulase Negative Staph:
                     i. usually negative slide coag, negative tube coag, biochem panel to ID spp
     4. ID of Isolates:
            a. Slide Coagulase Test – 2 types: free coag = neg & bound coag = +
                     i. COagulase enz used to convert fibrinogen  Fibrin (+ = clums of stain)
            b. Particle Agglutination works b/c coated with fibrinogen (fibrin) & coated with IgG Ab
     5. Virulence Factors
     6. Epidemiology
     7. Lab Diagnosis
            a. Gram Stain: (+)
            b. Real-Time PCR: Detection of staphylococcal DNA sequences
            c. Microarray testing – simultaneous ID of several staph spp & virulence factors
            d. Culture
                     i. Nonselective media (5%sheep blood agar, chocolate agar)
                    ii. Selective media (mannitol salt agar)
     8. Antimicrobial Resistance
            a. Oxacillin Resistance
                     i. screening isolates for growth on oxacillin-containing agar
                    ii. Dection of mecA gene product by latex particle agglutination
                   iii. Detection of mecA gene by PCR
                   iv. Determination oxacillin MIC
            b. Vancomycin Resistance
                     i. screening isolates for growth on vancomycin-containing agar
                    ii. Determination of vancomycin MIC
            c. Inducible Clindamycin Resistance (streptococci)
                     i. D-zone test
     1. Taxonomy: Genera of the Streptococcaceae & Enterococcaceae Families (*=key spp)
            a. Strep = (Streptococcus*; Abiotrophia; Granulicatella; Lactococcus; Lactovum)
                    i. *S.pyogenes (grpA), S.agalactiae (grp B), S.pneumoniae*
                   ii. *Viridans streptococci (S.bovis, S.mitis, S.mutans, S.sanguis)*
            b. Entero = (Enterococcus **E. faecalis, E.faecium**; Atopobacter; Catellicoccus;
               Melissococcus; Pilibacter; Tetragenococcus; Vagococcus)
     2. Physiology
          c. Morphology: *Gram +* cocci w/0.6-1.0u diameter
                 a. multiply in 1-D w/incomp separ of daughter cells resulting in formation of pairs & chains
          d. Growth: rapid; sharply defined, smooth, translucent colonies on routine, nonselective media
                 a. O2 tolerant anaerobic mode of metabolism
     3. Characteristics
     4. Virulence Factors
     5. Epidemiology
     6. Lab Diagnosis
            a. Gram Stain: (+)
            b. Ag Detection
                    i. Immunochromatography: S. pyogenes, S.agalactiae, S.pneumoniae
                   ii. Optical immunoassay: S.pyogenes
            c. Molec diagnostics
                    i. direct detection of rRNA
                   ii. real-time PCR for detection of amp DNA
            d. Culture
                    i. Nonselective media (5%sheep blood agar, chocolate agar)
                   ii. Selective media (Strep selective agar for S. pyogenes & S.agalactiae)
            e. Ab Detection
                    i. Antistreptolysin O, anti-DNAase – S.pyogenes
     7. Antimicrobial Resistance
            a. Penicillin/cephalosporin Resistance (streptococci) & Ampicillin Resistance (enterococci)
                    i. invitro antimicrobial susceptibility testing
            b. Inducible Clindamycin Resistance (streptococci)
                    i. D-zone test
            c. Vancomycin Resistance (enterococci)
                    i. screening isolates for growth on vancomycin-containing agar
                   ii. invitro antimicrobial susceptibility testing
Endocarditis (↑mean age, related to ↓rheumatic heart dz & ↑importance of degenerative heart dz in elderly)
     1. Endocarditis: infxn of endocardial surf of heart (incl valves, septal defects, mural endocard)
             a. 3 predisposing factors: need abn strx; turbulence; bacteria-sticky
     2. Endarteritis: infxn of arterial endothelium includes infected aneurysms, AV fistulae (uncommon)
     3. Acute bacterial endocarditis (ABE) has more tox/septic; underlying valve is usually normal.
             a. major valve destrcn and ↑mortality……..S. aureus and Enterococcus.
     4. Subacute endocarditis (SBE) slow/indolent course & underlying valve is usually abn. streptococci.
     5. Prosthetic valve endocarditis (PVE) may be acute or subacute.
     6. Culture neg endocarditis: prior antibiotic tx; or when organisms=fastidious/hard to grow in culture.
     7. Hospital acquired endocarditis after invasive dx/tx procedures done in the hospital.
     8. Marantic endocarditis (non-infective endocarditis): lesions that develop on heart valves; w/out infxn.
     1. pathogenesis of infective endocarditis
             a. begins w/underlying damage to heart valve/endocardium tubulence around valve
             b. tissue thromboplastin rel from damaged valvedeposit of fibrin & plateletsmesh on surf
             c. Bacteremia; bacteria adhere to fibrin platelet cmplx  vegetation
             d. ↑er P on L-heart  more turbulence (why veggie more on left)
                      i. *mitral/aortic veggies predom; tricuspid only 0-6%; pulmonic <1%
             e. Predisposing Heart dz: rheumatic heart dz, bicuspid aortic valve, prosthetic heart valve,
                 degenerative lesions (calcific nodular lesions; calcified mitral annulus); congenital heart dz
                      i. Mitral valve prolapse bc causes substantial turbulence (holosystolic murmur present)
                     ii. vent septal defect (VSD)↑Q-grad from L to R vent (↑er P on Lside) w/turbulence
                   iii. ASD ↓grad from L atrium to R atrium (↓risk lesion)
             f. Bacteremia: may orig from diff sources/procedures
                      i. Dental, GI, GU procedures (Streptococci-oral, Enterococci-GI/GU)
                             1. org adhere to fibrin-platelet meshwk by substances on bact surf (ie. Surf
                                 glycoprot, ↑molec weight dextrans, lipoteichoic acid, slime-coag (-) staph)
                             2. stickiest cell surf=more likely to adhere endocarditis
                     ii. bact embedded in veggie; escape hosts immune respns/PMNs & serum bactericidal Ab
     2. common etiologic agents & techniques for diagnosis of infective endocarditis *S. aureus (MRSA)*
             a. Viridans=SBE; resident part of oral flora; bacteremia rel to dental dz/procedures
             b. Grp D strep (enterococci/S. bovis) related to GI/GU manip
                      i. Enterococci  SBE & ABE
                     ii. S. Bovis assoc w/underlying colonic polyps/colon cancer (stool colonization)
             c. S. aureus—most common etiology for ABE
                      i. Freq in drug addicts & methicillin resistant (MRSA);
                     ii. Gram-neg bacilli = rare (except in drug abusers)
             d. For IVDUs-etiologic agents varies from city to city
             e. Sometimes endocarditis caused by org difficult to grow in cult (fastidious) in HACEK grp
                      i. Other fastid: Hemophilus parainfluenzae & nutritionally deficient Strep
             f. Endocarditis in IV drug users involves tricuspid valve (>50%)
                      i. Less hemodynamic compromise; but metastatic lung abscesses more common
             g. Culture-Negative Endocarditis (5-15%) – cult freq neg when there has been prior antibiotics
                      i. Hard to grow: HACEK grp, fungi, rickettsia (Coxiella burnetti/Qfever)
                     ii. Non-infxs (―marantic‖ endocarditis) – seen in inflame syndr
     3. diff in microbio, clinical spectrum & complication of acute, subacute, & prosthetic valve endocarditis
             a. Clinical Manifestations: a febrile illness w/protean clinical manifest
                      i. Systemic sympt: fever, malaise, fatigue, anorexia, and weight loss
                     ii. MSK: arthralgia, back pain, and arthritis are seen in 45%
                   iii. CV: Heart murmurs seen in 85%, but a new/Δing murmur is seen in only < 5%
                    iv. Other: CHF (50%); clubbing (hypertrophic osteoarthropathy); splenomegaly
             b. Periph Manifestations (<50%): conjunctival petecchia, splinter hemorrhages, Osler’s nodes
                (painful nodules on pads of fingers and toes), Janeway lesions (non-tender erythematous
                macules on palms and soles) and Roth’s spots (retinal hemorrhages with/without pale centers
                                          SBE                                             ABE
Develops on         Previously damaged heart valve                     Normal valves
                    Follows dental/dz proced                           org coming from skin/thru IV
Caused by           Viridans Streptococci                              S. aureus
Clinical course     Insidious—lasting weeks-mo                         Abrupt, several days
S/S                 ↓grade fever                                       Toxicity
↓Cardiac Fnx        Gradual                                            Rapid
Mortalitiy          5-15%                                              30-50%
             c. Dx: lab features=leukocytosis, anemia, hematuria; ↑sedimentation rate;
                      i. Can detect rheumatoid factor (40%)
                     ii. Hallmark=continous bacteremia (endovasc focus)
                    iii. 3 blood cultures pick up 90% of cases; lesions detected by ECHO; TEE & TTE
                              1. transesoph echocard (TEE) more sens > Transthoracic echocard (TTE)
                                      a. TEE better esp sens in detecting valve ring abscesses
             d. Prosthetic Valve Endocarditis (PVE) – 3% of valve replacements
                      i. Early: <60 after surg; S.aureus, coag-neg Staph, gram-neg bacilli
                              1. may be relted to IV catheter-related bacteremia/contamination @time of surg
                     ii. Late: >60 after surg; Viridans Strep; acts more like SBE in pathogen/clinical present
      4. principles of tx of infxive endocarditis, incl indications for valve replacement
             a. Tx:
                      i. use ↑dose, IV, bactericidal antibiotics;
                     ii. chose antibiotics based on microbial sensitivities
                    iii. prolonged tx required, duration dep on valve type (native vs prosthetic), & organism
                              1. shorter (2-4wks) for viridans Strep; Longer (4-6 wks) for enterococci, S.aureus
                    iv. Combo therapy w/aminoglycosides-used for synergy
                              1. esp w/enterococci, streptococci w/intermed sensitive, & Pseudomonas
             b. Indications for valve replacement in infective endocarditis:
                      i. Refractory CHF
                     ii. Recurrent systemic embolization
                    iii. Persistent bacteremia
                    iv. Conduction disturbances
                     v. Valve ring abscess
                    vi. Fungal endocarditis
                   vii. Large vegetation size
      5. complications of endocarditis:
             a. Cardio: valve destrxn, valve perforation, heart failure, myocard/valve ring abscess, cndxn abn,
                MI, suppurative pericarditis
             b. Non-cardio: CNS emboli, mycotic aneurysms, arterial emboli, metastatic abscess (brain, lung,
                spleen, kidney) & bony lesions
             c. May see relapse after tx; can also see immune cmplx-med glomerulonephritis in SBE
      6. principles of prevention of infxv endocarditis – imp for ppl w/underlying heart dz!
             a. Giving it dep on nature of underlying heart dz & how likely proceduresustained bacteremia
             b. Recommended for dental proced in ↑risk pt (not mod risk)
             c. Antibiotics directed against oral Strep w/agents (ampicillin, clindamycin, vancomycin)

                   ↑ risk                                     Mod risk                              ↓ risk
Prosthetic valve; prior endocarditis; major   MitralValvProlap (w/murmur/thick       MVP (no murmur); pacemaker;
CHdz; heart transplant w/valve                leaflet); RheumHD; ASeptalHypertrop/   CoronArtBypassGraft, AtrialSeptalD,
abnormalities                                 IdiopathHSubaorticStenosis             other CHD
Neisseria & Moraxella
     1. epidemio, clinical manifestation & methods of dx for Neisseria meningitides & Neisseria gonorrhea
     2. diff modalities of prevention for Neisseria meningitides infxn (chemoprophylaxis & vaccine therapy)
             a. Morphology: Aerobic, diplococci, form non-pigmented, non-hemolytic colonies on choco agar.
                ID based on series of carb ferment; org divided into serogrps & serotypes
                     i. 13 serogrps (based on type of capsular polysac); serotype (based on outer membr prot)
             b. Neisseria meningitidis: only bact meningitis assoc w/epidemics; central Africa=meningitis belt
                     i. seasonal ↑in spring/winter; it is 1 of leading causes of bact meningit in US (serogrp B)
                    ii. Pathogenesis/Immunity: capsul polysac (evade phagocytosis); pili (attach/colonize
                        pharynx); lipopolysac in outer membr (↑vasc damage); outer membr ves/blebs (assoc
                        w/host tissue damage/invad host meninges).
                             1. def in C5-C8 (term compl) ↑↑risk of invasion
                   iii. Clinical: Meningococemia; Meningitis (w/ or w/out meningococcemia); Bacteremia
                             1. Meningococcemia – 1st as ↑er resp infxn w/fever, chills, malaise, weakness,
                                 myalgias, arthralgias, headache, N/V. common=petechial rash-1st as small
                                 discrete lesions on trunk/extremetiesspreads, may coalesceecchymotic lesn
                                     a. rapid progrs dz, assoc w/↑mortal, accomp by vasc collapse (shock)/DIC
                             2. Meningitis w/w/out meningococcemia: abrupt fever, nuchal rigidity, alt MSE
                                     a. (young kids may only have fever/vomit)
                             3. Bacteremia: transient w/out any skin lesions/meningeal signs that resolve quick
                   iv. Tx: 3rd generation cephalosporins (Chloramphenicol-used in US/develping if allerg)
                    v. Prevent: Chemoprophylaxis (for close contacts); Rifampin, ciprofloxacin, ceftriaxone
                             1. tetravalent vaccine for serogrps A,C,Y & W-134 (NOT B)—for travelers,
                                 military recruits, compl deficient pt, asplenics, adolescents (11-12/college)
             c. Neisseria gonorrhea: mostly in asymptomatic pts; peak w/adolescents; transmit via sex
                     i. Pathogenesis: caps polysac, pili, lipo-oligosac. attack fallopian tube ciliated &
                        nonciliated cells (impair bact flushing & create local inflame)
                    ii. Clinical:
                             1. men – infxn restricted to urethra; symptomatic (burning, dysuria, purulent
                                 urethral discharge); Complication=epididymitis, prostatitis, anorectal GC
                             2. women – 1o=cervix (may be asymptom); vaginal discharge, dysuria.
                                 Complications= asc infxn w/tubo-ovarian abscesses, pelvic inflame dz (↑risk
                                 infertile/ectopic preg), bartholinitis
                             3. pt – spread dz w/fever, septic arthrit, rash; +conjunctiv (esp newborn), pharyngit
                   iii. Tx: Ceftriaxone; Quinolones (but ↑ing incidence of resistance)
                             1. complicated dz (dissem infxn/PID) need prolong therapy
     3. epidemiology & clinical manifestations of Moraxella catarrhalis infxn
             a. Microbio: gram neg diplococci, indisting from Neisseria by gram stain;
                     i. prevalence varies w/age; ↑er in adults w/COPD
             b. Pathogenesis: spreads; pts w/otitis: middle ear(Eustachian tube)nasopharynx
             c. Clinical: otitis media, bact sinusitis. ↓er resp infxn (COPD/chron bronch pt); pneumon in old
             d. Tx: (all strains prod β-lactamases)—
                     i. antibiotics: macrolides, quinolones, amoxicillin-clavulanate & cephalosporins
Aerobic Gram-Negative Bacilli
   1. Basic microbio characteristics of aerobic gram-neg bacilli
          a. Morphology & staining. Distinguished by variety of techniques:
                    i. Selective Growth Media (Salmonella, Shigella); Fermentation rxn (fermnt lactos/sugrs);
                       Biochem rxns; Serologic tests; Antibiotic susceptibility patterns (disting isolates);
                   ii. Genetic Analysis: G/C ratio; DNA hybridization; PCR
          b. Molec Techniques used to determine ancestry (esp for nosocomial-hospital-outbreaks):
                    i. pulse-field gel Electrophoresis; Ribotyping; PCR
          c. Trilamellar cell wall:
                    i. inner cytoplasmic membr w/interspersed prot that med microbial resp to external stim
                           1. imperm to polar molec; reg passage of nutr & metabolites
                   ii. Peptidoglycan: 1 molec/layer thick in gram (-)
                 iii. Periplasm space: w/protease, β-lactamase, solut bind enz-trans sug/aa/ions/vit ax space
                  iv. Outer cytoplasmic membr: Outer membr prot (OMPs), fimbriae, flagella; LPS
          d. Ag-ic Strx:
                    i. O-polysac (somatic)-polysac side chains of LPS; (>170 O-Ag for E. coli)
                           1. *smooth strains have polysac side chains & are virulent!*
                           2. *rough strains lack side chains & less virulent*
                   ii. H-Ag (on flagella); anti-H Ab immobilizes motile bacteria
                 iii. K-Ag – Capsular material
          e. Virulence Factor Postulates
                    i. Koch’s postulate:
                           1. organism must be present in al nonhealthy ani, but not in healthy ones
                           2. org must be isolated from dzd animal & grown in pure culture
                           3. pure culture must cause dz in susceptible animals
                           4. pure cult must be recovered from animal & re-grown in pure culture
                   ii. Molecular Koch’s postulates:
                           1. phenotype should be present more often in pathogenic > in non-pathogenic strains
                           2. inactivation of gene in question  ↓virulence
                           3. Restoration of gene  restoration of virulence.
          f. Actual Virulence factors:
                    i. Adhesins – med attachment of microbe to muc surf; oftern=fimbriae
                   ii. Exotoxins =Cytotoxins; Hemolysins; Enterotoxins
                 iii. Endotoxin – LPS
                  iv. Polysac Capsules – INHIB phagocytosis
                   v. Serum Resistance – resistant to lytic axn of compl
                  vi. Siderophore (enterobactin, aerobactin) – Sequester Fe; help bact compete for Fe
                 vii. Ag-ic variation -- xprsn of both K & H Ag can be w/held helping to avoid Ab
                viii. Antimicrobial resistance elements: Plasmids (extrachrm DNA); Inducible enzymes
          g. **Colonization v. Infxn** just bc bact is there doesn’t prove there’s an infxn
                    i. Infxn= single domin org & **evidence of inflam rspns;** Gram-stain more reliable >cult
Question: Is Infection always abnormal?
   2. spectrum of illness assoc w/gram-neg bacillary infxn
          a. Enterobacteriaceae: non-spore forming facultative anaerobes (areorbe)
                    i. widely spread in soil, H2O, mammalian intest; Ferment glcacid+gas; Catalase(+),
                       Oxidase (-); Variable ablility to ferment lactose; part of nl ppl flora – GI/some vaginal
                   ii. Epidemiology: 80% of clinically significant gram-negative isolates
                           1. causes comm-acqrd & nosocomial infxns; Varied antibiotic suscept, w/↑resistance
                 iii. Tribes:
                           1. Escherichiaeae: E. coli-serotype assoc infxn & Shigella-enteric infxn
                                   a. E.coli-UTIs, bacteremia, intraabd infxn, neonat mening
                                           i. most common aerobic gram-neg patho
                                 ii. Nonpathogenic – in intest/rarely cause dz
                                         1. can be patho in pts w/impaired host defens mech
                                iii. Intest patho strains  cause diarrheal syndromes
                                iv. ExPac strains  cuase extraintest dz
                                 v. Spec serotypes assoc w/specific infxn:
                                         1. UTIs: O1, 2, 4, 18, 22 …
                                         2. Meningitis: O1, 6, 7, 16, 18, 83
                                         3. Neonatal Mening: K1
                                         4. Exotoxin prodxn: O6, 8, 15, 20...
                 2. Salmonellae – enteric infxn
                 3. Yersiniae – bubonic plague, enteric infxn.
                         a. Y. pestis – bubonic plague; Zoonotic infxn
                                  i. spread by flea bites, ingest contam food; rat, prairie dog, squirrel
                                 ii. incubation: 2-8days
                                iii. S/S: headache, fever, chills, painful bubo (swollen ln)
                                iv. Clinical Syndromes:
                                         1. Bubonic – acute lympadenitis
                                         2. Septicemic – + blood cult w/out buboes
                                         3. Pneumonic – no bubo; via hematogen spread/inhal; ♀↔♀
                                         4. Cutaneous – postule with eschar, buboes present
                                         5. Meningitis
                                 v. Dx: by aspiration of bubo;
                         b. Y. entercolitica – entercolitis; also bacteremia, liver abscess, endocarditis
                                  i. Reactive polyarthritis, Erythema nodosum
                                 ii. grows @ cold temp ~4C
                         c. Y. pseudotuberculosis – mesenteric (psuedoappendicitis)
                 4. Klebsiellae – UTI, pneumonia, bacteremia, nosocom infxn, post-op mening
                         a. Klebsiella, Enterobacter, Serratia, Proteus = freq cause of nosoc LRTIs
                         b. Klebsiella also occas community acquired LRTI (see Pneumonia section).
                 5. Proteeae (Proteus)– UTIs, soft-tis/wound infxn, bacterem; esp diabetic foot ulcer
b.   Halophilic Vibrios (non-cholera vibrios)
          i. V. vulnificus – rapid progresv cellulitis, bacteremia after wound xposd to contam seaH2O
                 1. Severe sepsis after eating shellfish, esp in pts w/hypochlorhydria.
         ii. V. alginolyticus – cellulitis after sea water exposure.
c.   Aeromonas – xpsr to brackish H2O
          i. A. hydrophilia  soft tissue infxns, frequently w/ulceration; diarrheal syndrome.
         ii. A. sobria – bacteremia and septic shock
d.   Pasturella multocida – normal oropharyngeal flora of domestic & wild animals
          i. after animal bite (esp cat), lick/scratch;
         ii. Rapid onset (hrs) of soft-tissue infxn—sever cellulites; occas respire infxn or bactemia
e.   Brucellosis – zoonotic infxn; worldwide, esp Med basin, Arabian peninsula, India, cntrl/So Amer
          i. B. abortus – cattle, buffalo, camels, yaks; B. suis – swine, reindeer, caribou; B.
             melitensis – goats, sheep, camels; B. canis – dogs
         ii. infxn thru skin abrasn by xpose to infxd animals/carcasses or thru ingest unpasteur dairy.
       iii. Facultative intracell parasite. Multiplies in Mφ. Cell-med immunity neces for resolutn.
        iv. Granuloma formation; Insidious onset with IP 2-8 weeks.
         v. ―undulant‖ fever/sweat/malaise/headache/anorexia/abd pain/diarrhea/constipat, back pain
        vi. Occas: lymphadenopathy, hepatomegaly, splenomegaly
       vii. Focal Dz: Abd, Sk, Neuro, CV; requires prolonged antibiotic therapy
                 1. Abd – pain, vomiting, diarrhea. Liver almost always involved.
                 2. Skeletal – arthritis, sacroiliitis, osteomyelitis, spondylitis, tenosynovitis
                 3. Neuro – meningitis, encephalitis, radiculopathy
f. Francisella tularensis (Tularemia): No. Hemi (except UK) in mammals; 10-50 organisms
       i. rabbits, hares, voles, squirrels, muskrats, beavers, insects, ticks, biting flies, mosquitoes
      ii. Local papule that ulcerates & spreads to regional ln; Focal necrosis w/granuloma formtn
     iii. Spread thru contact w/infxd tissues, bite from infxd insect, ingest contam food, aerosol
     iv. Multi Forms: Ulceroglandular (with papule); Glandular – no skin lesion; Pharyngeal;
          Oculoglandular – eye infxn spread to preauricular nodes; Typhoidal – febrile illness w/no
          obvious source; Pneumonic—aerosols (lab accidents)
      v. Dx: requires enriched media; Serologic tests
g. Bartonellosis: Acute febrile bacteremiapersist asympt bacteremiachronic skin lesions
       i. B. bacilliformis – Oroya fever (Carrion’s dz-med student); Andes mountains (sandfly)
              1. Bact infect rbc ↑fragilityanemia; S/S=Fever, myalgias, arthralgias, headache
              2. Chronic verruga (cutan nodules) after 1-2 mo, can persist for years
      ii. B. henselae (Cat-scratch Dz!) – all age grps; Seasonal: 75% Sept-Feb
              1. follows scratch, bite, lick from cat
              2. enlarged, tender ln w/granulomas & central necrosis; Fever, malaise
              3. rare=encephalopathy, splenomegaly
     iii. Bacillary angiomatosis (B. Quintana & B. henselae);
              1. neovasc prolif in skin/soft tis (can involve viscera)
              2. Skin-colored or red-purple papules that can ulcerate/crust/drain serous fluid
              3. usually/not always in immunocompromised host (esp HIV)
              4. Peliosis hepatitis – blood-filled cysts in liver (related to BA)
h. Others
       i. Acinetobacter – major cause of nosocomial infxn; assoc w/↑level of drug resistance
Enteric Infections
   1. Host defense Mechanisms that are active in prevent enteric infxns
          a. Gastric acidity – markedly ↓ ID50 in pts w/achlorhydria or w/antacids
                   i. ↓ID50 for V. cholerae by 10,000-fold
                  ii. 25% pts w/cholera in Israel had gastric resection
          b. Intestinal Motility – get it out
          c. Enteric Microflora
                   i. Endog bact bind to intest rcptr preventing pathogenic spp from attaching
                  ii. Endog bact produce bacteriocins that interfere w/growth of other species
                 iii. Endog bact use up available nutrients (esp Fe) preventing pathogen growth
                 iv. ↓ing microflora w/antibiotics↓ID50 for pathogenic organisms
                         1. ie. 1dose of streptomycin↓ID50 for S. typhimurium by >100,000-fold
                         2. in 200,000 person Salmonella outbreak in Illinois,
                                 a. 30%=antibiotics in the month before, 6% in controls.
          d. Intestinal IgA. Commonsense—personal hygiene
          e. Neutrophils – neutropenic pts develop a necrotizing infection (typhilitis)
          f. Cell-med immunity – AIDS pts infected w/variety of pathogens assoc w/unrelenting diarrhea
                   i. Cryptosporidia, Isospora, Microsporidia and bacterial pathogens.
          g. Breast milk – lactoferrin, lysozyme, ↓pH, oligosaccharides.
   2. Pathogenesis & pathophysiology of enteric infxns
          a. Epidemiology
                   i. Mortality: Global=2nd to CVdz; leading cause of death amg kids; 4.6-6million/year
                  ii. 13% kids born in parts of Latin America die b4 age 5, primarily due to diarrheal dz
                 iii. more years of potential life loss than any other cause
          b. Historical impact: Leading cause of military death prior to WWI
          c. Enteric Pathogens: Viruses, Bacteria, Fungi (Protozoa), Parasites (Amoebiasis, Giardiasis)
                   i. Viruses: Calciviruses, Astrovirus, Rotavirus
                         1. Caliciviruses (Noroviruses): IP=24-48h; common (by 5th decade=50%pop w/Ab)
                                 a. gastroenteritis – shortlived outbreaks (2-3) days
                                 b. S/S: Abd cramps, followed by nausea, vomiting, watery, non-bloody
                                     diarrhea, malaise, myalgias, ↓grade fever
                                 c. food, H2O, swimming pools; ship outbreaks; shellfish-good transmitters
                                 d. Transmission: fecal-oral vomitus
                                 e. Properties: somewhat heat-resistant (cooking shellfish may not prevent);
                                     RNA virus
                                 f. Dx: immune e- microscopy, ELISA, PCR, can’t cult;
                         2. Astrovirus: IP=3-4 days; duration of illness 5 days (may shed virus upto 35 days)
                                 a. diarrheal illness in kids<3yrs; immunsprsd adult (HIV, bone marrow trns)
                                 b. S/S: Diarrhea, headache, malaise, nausea, vomit uncommon
                                 c. Properties: small RNA virus
                                 d. Dx: ELISA, immune adherence microscopy, PCR, Culture
                         3. Rotavirus: (US) 3.5 million diarrhea, 20 deaths; (devel wrld) 500K-1million death
                                 a. almost all kids infected by 3 (no diff in develpd/develng wrld)
                                 b. no impact shown w/breast feeding
                                 c. SS: fever, vomit (2-3days), diarrhea (4-5days), dehydration
                                 d. Properties: Double stranded RNA virus; 3 grps (A-dz,B,C);
                                           i. inactivated by Cl & gastric acid (pH<2.0)
                                          ii. resistant to most hand-washing agents; can survive long pd time on
                                              hands, in potable H2O & hard surf
                                 e. Dx: ELISA
                                 f. Vaccine: complicated by intussusception
ii. Bacteria: E. coli, Salmonella, Shigella, Campylobacter
       1. Virulence Factors: *bact don’t cause dz just by being there*
               a. Attachment:
                         i. Colonization factor Ag (CFAs/fibriae) – med adher to SI mucosa
                        ii. Potential vaccines – produce Ab directed against CFAs
               b. Toxins:
                         i. Entererotoxins: cyclic nucleotide (promot fluid secrintest lumen)
                                1. Cholera toxin – AB5 structure  cAMP
                                2. Enterotoxigenic E. coli – cAMP, cGMP
                        ii. Prostaglandins – Salmonella;, C. difficile
                       iii. Cytoskeleton altering toxin – C. difficile; some E. coli
                       iv. cytotoxin – Shigella; E. coli O157:H7
                        v. Preformed toxins – S. aureus; B.cereus
       2. In-vitro tests: Ileal loop model=enterotoxin; Sereny test (rabbit conjunctivitis)=
           cytotoxin; HeLa cells & cytotoxicity
       3. Invasive (Fecal Leukocytes usually present) vs. Non invasive
               a. Invasive=invade/destroy epithelial cells
               b. Selective cell destrxn – Norwalk-like virus selectively infx & disrupts
                   villus tip cells, leaving secr (crypt) cells intact
                         i. alters nl abs fluid balance & ↓brush-border digestive enz
       4. S. aureus: IP=1-8hrs; requires improper storate @rm temp (>freq in summer)
               a. Preformed toxin
               b. Nausea, vomiting, diarrhea, NO fever; assoc w/food handler
               c. Food: ↑salt/osmolality – ham, poultry, baked goods
       5. Bacillus cereus: IP=30min-6h; Freq assoc w/fried rice
               a. Preformed toxins
               b. Nausea, vomit &/or diarrhea
       6. V. cholerae: IP=1-3 days; Contam food & H2O; inoculum=108 - 1011; NON-invas
               a. *NONinvasive* (no fecal wbc)
               b. Enterotox: AB5 strx; activates ACase; causes intest secr h2o/elecltlumen
               c. Profuse watery diarrhea w/hypovolemia & shock;
               d. Antibiotics: shortner illness duration; Tetracylcline, quinolones
       7. Shigellosis: IP=1-2 days; Fecal-oral, may be food/water-bourne; ↓inocul (200 org)
               a. *Invasive* into mucosa + Fecal wbc
               b. Cytotoxin: AB5 strx—inhibits protein syn.
               c. fever, abd cramps, watery diarrhea followed by bloody, mucoid,
                   ―dysenteric‖ stools, tenesmus
               d. Antibiotics: quinolones, trimethoprim/sulfamethoxazole (if susceptible)
       8. Campylobacter: IP=1-7 days; worldwide zoonosis in animal GI; relaps=5-10%
               a. Toxins: cytosk-alt toxin, enterotoxin, cytotoxin (mech not well defined)
               b. poultry, sheep, cattle, raw milk, ground H2O; backpacker @risk (>giardia)
               c. C. jejeuni – GI illness; C. fetus – bacteremia in immunosprsd host
               d. Fever, abd cramps, diarrhea; non-spec inflm in jejunum, ileum, colon
               e. Antibiotics: Azithromycin, quinolones
       9. Salmonellosis: poultry, eggs, meat, dairy; person-2-person
               a. Acute gastroenteritis: IP=8-48h; *Invas* beyong mucsa; occas bacterem
                         i. *Invasive* + fecal wbc
                        ii. Prostaglandins & cNucleotides = mech of diarrhea
                                1. block Na abs & Cl secr into lumen
                       iii. Fever, nausea, vomit, abd cramps, h2o-y (bloody) diarrhea
                       iv. Antibiotics: quinolones=benefit (doesn’t prolong carrier state)
               b. Bacteremia: acute bacteremic illness, related to underlying gastroenteritis
                                             i. >common in neonates, elderly, lymporeticular disorders
                                            ii. recurrent in small%: underlying osteomyelitis, abscess, localized
                                                endothelial infxn (aneurysms)
                                           iii. Antibiotics: Ceftriazone, quinolones
                                    c. Localized dz: assoc w/osteomyelitis, esp w/sickle-cell anemia
                                             i. but most common cause of osteomyelitis kids w/HbSS=S. aureus
                                    d. Enteric Fever: Typhoid or Paratyphoid; Relapse=retx w/antibiotics
                                             i. sustained bacterm & prolonged fever w/out endovasc involvement
                                            ii. marked reticuloendothel hyperplas; multi organ dysfnx
                                           iii. Complicaiton: intest perfor @ peyer’s patches; intest hemrg; HUS1
                                           iv. Antibiotics: ceftriaxon, quinolones
                                    e. Asymptomatic carrier state: excr organism in stool for >1yr;
                                             i. not a cause of dz recurrence; Gallstones present (cholecystectomy)
                            10. E. coli:
                                    a. Enterotoxigenic (ETEC): Traveler’s diarrhea
                                             i. Toxins transmissible by plasmids (or phages)
                                            ii. ↓grade fever, myalgias, diarrhea
                                           iii. caused by cNT toxins (ie. cholera)
                                                    1. Heat labile (LT): ww; active ACase (~cholera, ↓tight bind)
                                                    2. Heat stable (ST): central amer; active GCase
                                           iv. usually self-lmtd, but course shortened by antibioticx; fxv prophlx
                                            v. similar toxins may found in Klebsiella, Citrobacter, Enterobacter
                                           vi. Antibiotics: quinolones
                                    b. Enterohemorrhagic (EHEC): E. coli O157:H7; IP=3-4days
                                             i. Shigella like toxins (SLT-1 & 2)
                                            ii. cramps, mild fever, watery diarrhea progressesbloody
                                           iii. rlnship w/ground beef, other foods
                                           iv. ID sorbitol (-) colonies or sorbital-MacConkey agar
                                            v. Complications: HUS (↑incidence assoc w/antibiotics);
                                                    1. Microangiopathic hemolytic anemia; Renal Failure;
                                                        Thrmobocytopenia; CNS sympt (seizures); Related to
                                                        Thrombotic Thrombocytopenic Purpura (adults)
      3. Diagnositic criteria that distinguish specific pathogens amg spectrum of enteric infxn

    Hemolytic uremic syndrome.
Pseudomonas aeruginosa ―crabgrass of bacteria‖
   1. Recog clinical features, VF, predisposing factors assoc w/Pseudomonas infxn
         a. Presdisposing factors:
                   i. prolonged hospitalization, esp. ICU; Trauma, surgery, burns; Immunosuppression , esp.
                      hematologic malignancies; Cystic fibrois
         b. Virulence Factors: (like other gram neg rods):
                   i. endotoxin, pili & flagella; Alginate (med attachment, blocks phagocytes); glycocalyx;
                      Exotoxin A; Exoenzyme S; Elastase; Alkaline Phosphatase; Hemolysins; Pyocyanin
                          1. Endotoxin A – most toxic!! (20K xs > endotox). target = EF-2; ADPR-transferase
   2. Recog clinical manifestations of Pseudomonas infxn
         a. Community-acquired clinical syndromes
                   i. Otitis externa—swimmer’s ear; humid climates; self-lmtd, rarely invades canal
                  ii. Malignant otitis externa—infxn of bone-cartilaginous jnx. Elderly &diabetics; ↑mortality
                          1. Pain, edema, tenderness of soft tis w/purulent discharge
                          2. Granulation tissue on floor of auditory canal;
                          3. maybe: parotid, TMJ, facial n, mastoid, skull (rarely other CN or cavernous sinus)
                iii. Chronic ear infxn
                 iv. ulcerative keratitis—extended wear contact lenses; trauma
                  v. Whirlpool folliculitis (P. a. O:11) – hot tubs. Pruritic maculopapular-vesicular lesions.
                      On trunk, under bathing suit. Apocrine sweat glands. Usually no therapy.
                          1. dilation of pores, evap of Cl; Incubation 48 h; 8h-5days
                 vi. ―sneaker‖ osteomyelitis. Osteomyelitis developing after puncture wound thru sneaker
                vii. Endocarditis in IV drug users (Detroit)
               viii. Pulmonary colonization/infection in Cystic Fibrosis
         b. Hospital –acquired clinical syndromes:
                   i. Pneumonia
                  ii. Bacteremia in immunosuppressed patients
                iii. UTIs (Asymptm bacteruria cystitis  acute pyelonephritis  chronic pyelonephritis)
                          1. Recurrences: Relapse (same strain); Reinfxn (diff strain)
                 iv. Typhilitis (GI) – necrotizing cecal infxn in neutropenic pt
                  v. Post-operative meningitis
                 vi. Soft-tissue infections
         c. Cutaneous Infxn: Paronychia (green-nail synd); toe web infxn; pyoderma; cellulites; Ecthyma
             gangrenosum; burn wound sepsis
         d. Bone & Joint Infxn: Hematogenous (IVDA, pelvic source; cartilag joints); Direct Inoc-sneaker
         e. GI Infxn: Perirectal absc (neutropenic pt); Diarrheal dz (kids); Shanghai fever (~enteric/typhoid)
         f. Tx issues: Difficulties in management (debilitated host; microbial VF; antibiotic resistance)
                   i. Clinical response related to degree of debilitation of host
                  ii. Multidrug resistance
                          1. inherently inactive against P. aeruginosa (anaerob don’t bind aminoglycosides)
                          2. Problem of induced/acquired resistance.
                                  a. environ: ↑β-lactamase syn in response to xposr to β-lactam antibiotic
**Pseudomonas infections are primarily a problem of debilitated host—not a super-virulent organism**
Urinary Tract Infxn
   1. Definitions:
          a. UTI – Infxn of kidneys +/ bladder; Dx est by quantitat cult (>105, 104 - 105? cfu/ml) of urine
                    i. Uncomplicated – strxly & neurologically nl UT
                   ii. Complicated – abn of urinary drainage
          b. Bacteruria – bact in urine; may be symptomatic or asympt
          c. Cystitis – bladder infxn w/dysuria, freq, urgency, suprapubic tenderness
          d. Pyelonephritis – Kidney infxn w/fever, chills, flank pain, dysuria, urgency, freq
          e. Recurrences
                    i. Relapse – same infecting organism. Due to persistence of organism in the urinary tract
                   ii. Reinfection – new microorganism. Often a predisposing condition.
   2. Epidemiology, Pathogenesis & Pathophysiology of UTIs
          a. Significant cause of morbidity & mortalitiy
                    i. Direct mortality 5-13% (community-acquired/hospital acquired)
                   ii. Leading cause of nosocomial infection;
                  iii. 10-30-fold more common in women; also in kids w/bacteriuria and in the elderly
          b. Predisposing Factors
                    i. Anatomic factors are major predisposing condition:
                          1. short urethra (♀); in non-preg, prevalence = 1-3% (in adult men = 0.1%)
                                  a. 10-20% of women have a UTI during their lifetime.
                          2. Children who develop bacteruria are more likely to have bacteruria as adults.
                   ii. Risk factors among non-pregnant women include:
                          1. Freq of intercourse/new partner; Diabetes; Hx-prior UTI (pt/mom); Urin incont
                  iii. Obstrxn of urine flow ↑UTI incidence
                          1. Extrarenal obstrxn: prostatic hypertrophy, preg, indwelling (foley) catheters,
                              calculi, extrinsic compression of the ureter
                          2. Intrarenal obstrxn–nephrocalcinosis, renal stone, polycyst kidney, sickle cell dz
                          3. Pregnancy –P of uterus on urethra ↑likelihood of infxn & P on ureters↑reflux
                          4. Sex
                  iv. Elderly Pt (10%♂; 20%♀)
                          1. ♂–prostatic obstrxn, loss of antibact prostat secr, neuromuscular dz, foley catheter
                          2. ♀ – vaginal muc atrophy w/↑bact coloniz, poor bladder empty (bc prolapse),
                              perineal soiling bc fecal incont, neurmusc dz, foley catheters
                   v. Nosocomial UTIs—40% of all nosocomial infections. Often related to catheterization
          c. Risk Factors: Sex (#partners, freq); Spermicide use; Hx UTI (self/mom); DM; urine incontinence
          d. Pathogenesis:
                    i. Host Resistance Factors:
                          1. Flushing mechanism
                          2. Antibact prop of urine: ↑ [C], ↓pH inhib bact growth, esp anaerobes & fastidious
                              bacteria found in the perineal flora.
                          3. Nl vaginal Flora & vagina acidity (protective??)
                          4. Antibacterial properties of prostatic fluid
                          5. Tamm-Horsfall prot (most abund prot in urine) binds to E. coli & prevents them
                              from attaching to mucosa
                          6. Bladder mucopolysaccharide that inhibits bacterial binding.
                          7. TLR11 (toll-like R) recog bact polysac of uropathogenic orgs;
                                  a. abundantly xprsd in bladder & kidney
                                  b. in absence of TLR11, the kidney is much more susceptible to infxn.
                                  c. Bladder infection, however, still occurs in the presence of TLR11.
                   ii. Route of Infection (note: NOT an immunologic dz; it is anatomic)
                          1. Ascending – common
        rectal flora perineal colonyvaginal colonyintroital colonyurethrabladder kidney
                               a. Colonization of vagina introitus & urethral meatas by fecal organisms
                                       i. introital c. ↓by ↓vag pH; Non-inflam; ↑clniz w/recent antibiotics
                                               1. esp. β-lactams
                               b. Migration up urethra bladder; Migration up ureter  kidney
                      2. Hematogenous – uncommon
                               a. bacteremia w/ or w/out endocarditis-usually S. aureus
                               b. C. albicans fungemia—prediliction for localization in the kidney.
      e. Microbiology – major uropathogens = aerobic gram (-); [anaerobes don’t cause UTI]
               i. Community acquired: E. coli, S. sparophyticus; other gram-neg bact
              ii. Hopital acquired: ↓E. coli; more other Gram Neg bact (ie. Pseudomonas)
             iii. Uropathogenic strains: Virulence factors:
                      1. Adhesins (2 types): Mannose-sensitive (bladder); Mannose-resistant (Kidney)
                               a. bladder (mann-sens)cystitis; Kidney  pyelonephritis
                      2. Serum resistance (compl); ↑K Ag (capsule); Presence of Aerobactin + strains;
                      3. Presence of Hemolysin + strains – aid in tissue invasion
      f. Immune Response:
               i. ↑er tract infxn, not ↓er tract, assoc w/strong system Ab rspns. anti-O, K, type1, P fimbriae
                      1. pre-existing Ab to infecting org isn’t protective
              ii. ↑levels of IgG to Lipid A correlate w/severity of dz
             iii. *no apparent ↑ in UTIs amg pt w/humoral immune deficiencies
             iv. Spec cell med immunity doesn’t seem to have big role
                      1. Nude (depressed-cell med immune) mice are not more susceptible than nl animal
                      2. no ↑incidence of UTI in pt w/CMI-deficiency.
3. Basic Principles of management of UTIs
      a. Diagnoisis
               i. Clinical Manifest: urgency, dysuria, fever. [kids<2: vomit, fever, fail-to-thrive)
                      1. Fever -↑er w/↑er tract infxn, flank pain more prominent
                      2. Cystitis (bladder infxn): dysuria, urgency, freq, suprapubic pain
                      3. Pyelonephritis: fever, dysuria, urgency, freq, flank pain
                      4. Elderly: fever, Δmental status
              ii. Micro Exam: Urinalysis & gram-stain of urine. wbc cast=dx of ↑er tract infxn
                      1. Seeing one organism per hpf on an unspun urine specimen suggests > 105 cfu/ml.
                      2. BUT, absence of pyuria argues against a UTI, even in pt w/signif bacteruria
                      3. presence of wbc casts indicates pyelonephritis (upper tract infection)
             iii. Biochem Tests – w/dipstick; ~2min (quick, but much less reliable)
                      1. Nitrate Reduction – when (+) suggests infxn w/Enterobacteriaceae
                      2. Leukocyte esterase – if (+) > 10 wbcs/hpf (abnormal);
             iv. Urine Culture:
                      1. Reliable Specimens vs Contamination
                               a. mid-stream specimen, catheterization, suprapubic aspirates
                               b. quantitative cultures  105 = gold standard (statistical)
                      2. < 105 organisms
                               a. Cystitis > 103 organisms (80% sensitivity, 90% specificity)
                                       i. most: E. coli; cult not neces in healthy women; short course (3d)
                               b. Pyelonephritis > 104 organisms (90% sensitivity, 95% specificity)
                                       i. E. coli, Klebsiella, Proteus; must cult; tx 10-14d;
                                      ii. Hospitalize for GI sympt, or severely debilitated
      b. Complications:
               i. Bacterermia – most common site from which gram (-) bacteremia arises
              ii. Perinephric abscess – abscess in kidney parenchyma;
                      1. most common predisposing factors = calculi & DM
             iii. Intrarenal abscess – (aka. carbuncle)—after hematogenous inection. U/A may be normal
              iv. Emphysematous pyelonephritis – Gas in renal parenchyma.
                       1. Usually due to facultative anaerobe, ie. E. coli, often in pt w/DM w/↑ serum [glc]
               v. Xanthogranulomatous pyelonephritis – focal/diffuse chronic infxn of parenchyma
                       1. renal tissue is replaced by granoulomatous inflammation.
                       2. Predisposing conditions = renal calculi, urinary or lymphatic obstruction,
              vi. Papillary necrosis – replacement of pyramid by wedge-shaped necrotic material
                       1. part of the papilla – may slough  ureteral obstruction.
             vii. Chronic Pyelonephritis? – ?It is likely that there is no such entity?
                       1. **Bacterial infxn don’t cause renal failure unless there is obstrxn**
            viii. Interstitial nephritis – variety causes incl: obstrxn, analgesics (NSAIDs), hyperuricemia.
      c. Management (sulfonamide, ampicillin, TMP/SMX, cephalosporin, quinolone, aminoglycoside)
                i. Who to Tx: (Symptomatic UTIs) & Asymptomatic bacteruria…
                       1. Asymp: Children, esp w/ reflux; Pregnant women; Prior to urologic procedure
                       2. Don’t tx asympt bacteriuria in adults (esp elderly); Tx assoc w/↑er mortality
               ii. Tx:
                       1. Urinary acidification – hard (impossible w/urease splitting organisms)
                       2. Analgesics – little role except in the acute setting
                       3. Antimicrobial therapy – Serum+urine [C]; agent choice; duratn; adjunct; followup
                               a. Choce of Agents: β-lactams, trimehoprim/sulfamethoxazole, quinolones
                               b. Duration of Tx: ↓er tract = 1-3days; ↑er tract = 10-14 days
                               c. Adjunctive measures: relieve obstrxn, stones, catheters
                               d. Follow-up cultures: children, pregnant women, (not neces in young ♀)
             iii. Reinfxn
                       1. Relapse: same org w/in short pd; suggests renal involvement (microabscess)
                               a. repeat 2 week course, follow by 4-6 week course
                               b. Strxl Abnormalities: stones, etc; Chronic bacterial prostatitis
                       2. Reinfxn: w/↓er tract infxn; tx each episode w/short-course
                               a. Prophylaxis: post-intercourse Antibiotic; Chronic prophylaxis
              iv. Pregnancy: ↑incidence bc physio obstrxn;
                       1. ↑incid asympt bacteriuriapyelonephritis; assoc btwn pyelonephrit & prematur
4. Prostatitis
      a. Pathogenesis: uncertain, but could involve…
                i. Hematogenous; Asc infxn from urethra; Reflux of infxd urine; Urethral instrument &
                   surgery; Prostatic secr of pt w/prostatitis =↓antibacterial prop compared w/nl ctrls
      b. Acute Bacterial Prostatitis: Preantibiotic era=N. gonorrhoeae; now = E. coli
                i. ↑fever, chills, perineal/back pain; UTI sympt: freq, urgency, dysuria;
               ii. Prostate = warm, swollen, very tender; Does NOT lead to chronic prostatitis
             iii. PMNs, microbial abscess=common; DON’T MASSAGE PROSTATE!
      c. Chronic Prostatitis: most freq non-bacterial (Chlamydia, ureaplasma, mycoplasma spp)
                i. occasionally: typical GNRs (E. coli); Doesn’t follow acute prostatitis
               ii. May be asymptomatic; some have perineal discomfort, low back pain, dysuria
             iii. Rectal exam may not be dx;
              iv. Prostatic massage w/>15 wbc/hpf = abnl & consistent w/prostatitis in voided specimen
                   after massage; Many pts have prostatic calculi
               v. Non-infectious—Reiter’s syndrome
      d. Treatment: difficulty=antibiotic penetration; Tx for 3+ weeks;
          1. Non-bacterial dz tx w/erythromycin, tetracycline or quinolone w/duratn based on clinic rspns.
Bacteremia [gram (+) & gram (-) bact – some diff, but clinically pretty much indisting]
   1. Pathophys of sepsis & septic shock
         a. Bacteremia: in ½ - ⅔ of cases can id 1o focus of infxn.
                  i. ie. 1o source of bacterem of pt w/pneumococ pneumonia and pneumococ bacterem =lung.
                 ii. Tx implications: harder to tx site of infxn than the bacteria in the blood stream.
                          1. IV infusn antibioticssterilize blood stream fast, BUT lung infxn linger bc cant
                              get as much antibiotic into the lung as we can into the blood stream.
         b. Definitions:
                  i. Bacteremia – bact in blood (symptomatic or asymptomatic)
                 ii. Systemic Inflam Response Syndr (SIRS) – clinical manifest of sepsis/septic shock, but no
                     evidence of microbial infection. Ie. severe pancreatitis. Dx req 2 of following:
                          1. Fever or hypothermia (T > 38.0 or < 36.0)
                          2. Tachycardia (heart rate > 90)
                          3. Tachypnea (RR > 20 or PaCO, < 32 or mechanical ventilation)
                          4. WBC > 12,000 or < 4000 or > 10% immmature forms.
                iii. Sepsis – Infxn w/signs of systemic response; infxn w/SIRS—fever, tachycard, tachypnea
                iv. Severe Sepsis – Sepsis w/hypoTN/evidence of altered organ perfusion
                 v. Septic Shock – Sepsis syndrome w/hypoTN despite fluid resuscitation
                vi. Multi Organ Dysfnx (MOSF)– evidence of altered organ fnx in acutely ill pt
                          1. homeostasis cant be maintained w/out intervention
         c. Predisposing Factors:
                  i. Violate mechan barriers – IV & intraarterial catheters, Foley cath, surg/invas procedure
                 ii. Obstrxn of viscus – Prolif of bact prox to obstrxn w/escape of bacteria into blood stream
                iii. Impaired host defense mech – cytotox chemotherapy. Immunodeficiencies
                iv. Prior antibiotic therapy – Δing microbial flora
         d. Microbio
                  i. Gram (+) bacteremia (Staph most common spp) more common > Gram (-) bacterem.
                          1. Coagulase (-) Staph thought as cause of bacterem in pt w/indwelling iv catheters
                 ii. Amg Gram (-): E. coli most common > (other enterobact: klebsiel, enterobacter, serratia)
                          1. Pseudomonas & Acinetobacter & ↑ly resistant Enterobac spp = nosocomial infxns
                iii. Site of Infxn: most freq site where bacteremia arises=urinary tract,
                          1. BUT lung =most freq id site of severe infxn followed by intraabdominal source.
                iv. In terms of septic shock: approx ⅓ pt w/gram (-) bacterem have hemodyn Δ
                          1. if these hemodynamic Δs are severe enough, the pt is said to be in septic shock.
   2. Role of exogenous & endogenous mediators in the pathogenesis of septic shock
         a. Hemydynamic Fx of Endotoxemia – charactereistic feature of septic shock = ↓systemic vasc R
                  i. Septic Shock: ↓SVR↑CO (anaphylaxis is hemodynamically simil to septic shock)
                          1. even if ↑CO, endotoxin has dir depressant fx on myocard contractility
                          2. ↓SVR + myocard deprs fx =profound so that BP can’t be maintainedshock
                 ii. Cardiogenic/Hypovolemic shock: ↑SVR & ↓CO
         b. Endotoxin (LPS) – component of cell-wall of gram (-) bact that results in septic shock syndr
                  i. O-polysac – hydrophilic end of molec which is Agic determinant; >100Agic diff E.coli
                 ii. Core polysac – Agicly simil for many gram (-) organisms.
                iii. Lipid A – hydrophobic portion of molecule which is most bio active portion of molecule.
         c. Biologic Activities of Endotoxin
                  i. Humoral fx
                          1. Compl Cascade – O-polysac activate compl in absence of Ab via alt compl pthwy
                                 a.   Lipid A can activate the classical pathway.
                         2. Hageman factor – activated dir by endotox or thru TNF damaged endothelial cells
                                 a.   coagulation cascade
                                 b.   fibrinolytic system (thru activation of plasmin).
                                            i. Fibrionlysis + Coag combo disseminated intravascular coagultn
                                 c.   kallikrein/kinin system w/BK (most potent vasodepressor) prodxn
                    ii. Cellular fx (cytokines)
                            1. Mφ & Monocytes – *IL-1*2, IL-6, IL-12, TNF
                            2. Lymphocytes – IL-2, IL-4, IL-6, IL-10, -IFN
                            3. Neutrophils—Prostaglandins, Leukotrienes, Superoxide
                            4. Endothelial cells—IL-6, *TNF*, NO
             d. Endogenous Mediators (bio fx of endotox not due to dir fx, but due to host med/cytokines)
                     i. TNF Mediator Experiments
                            1. Bone marrow transplants btwn endotoxin-sens & endotoxin-resist mice
                                    a. Δendotoxin sensitivity;
                                    b. i.e. endotoxin-sens mice made endotoxin resist by bone marrow transplant
                            2. Reticuloendothelial hyperplasia  ↑ endotox sensitivity
                            3. Supernatan from bone marrow cult obtained from endotoxin-sens mice  shock
                               in endotoxin-sensitive and endotoxin-resistant mice
                            4. Injxn of TNS  septic shock in animals
                            5. TNF produced by Mφ in bone marrow
                    ii. Pathogen-Assoc Molec Patterns (PAMPS)
                            1. Mech for recog of pathogens and presentation to cells.
                            2. LPS, teichoic acid or other conserved microbial molecules act as ligands
                            3. LPS binds to Lipopolysac binding prot which binds to CD14 on phagocytic cells.
                            4. CD14 passes LPS to TLR4 signal transduction and cytokine synthesis.
                            5. w/Gram (+)-staph/strep- produce toxin (ie Toxic-shock staphylococcal toxin)
                               act as ―superAg‖ & dir bind w/lymphocytes rel of inflammatory cytokines.
                   iii. Other Proximal mediators
                            1. IL-1  hypoTN (in experimental animals)
                            2. IL-6 (Activ few hours after IL-1 & TNF)  acts as cell SOS signal
                            3. May promote syn of antiinflammary cytokines.
                   iv. Activities of Proximal Mediators
                            1. Stim pro-inflam & anti-inflam cytokine syn & rel – acute phase response
                            2. Activate endothelial cells which xprs adhesion molecules
                            3. ↑vasc perm
                    v. Complement Activation
                            1. Classical & alternative pathway may be activated
                            2. Rel of C5a  ↑wbc agglut, prodxn of O2 rad & lysosomal enz rel
                            3. Damage to caps – adult respire distress syndrome
             e. IL-6 (controversial role; ?dir rel to severity of sepsis?)
                     i. Hypothesis: IL-6 is major contrib to acute phase rspns & this rspns is 1o pro-inflam.
                    ii. New data doesn’t agree: IL-6 is responding to severity of sepsis & predom activity of
                        acute phase response is anti-inflammatory—turning off the systemic immune response.
                   iii. In severe sepsis & septic shock, host can become immunosuppressed as a result of the
                        profound anti-inflammatory stimulus.
                   iv. Components of the acute phase response include:
                            1. Anti-infxv – syn & rel of compl factors, patter recog molec (TPRs, LPS-BP);
                                    a. Fe sequestration
                            2. Anti-inflam – cytokind antag, steroids, anti-ox, protease inhib
                            3. Procoag – walls of infxn
                            4. Metabolic – mobilize FAs, maintain normal glucose
                            5. dose fx w/many med:
                                    a. Cortisol @ nl [C] is permissive for syn of acute-phase proinflam proteins.
                                             i. @↑er [C] = suppress these prot & stim anti-inflam prot like IL-10
                                                     1. ↑-reg IL-1, IL-6, TNF and -interferon

 IL-1 & TNF are two of host’s earliest mediators activated (bio fx of endotoxin not due to dir axn, but due to these med)
      f. Adult Respiratory Distress Syndrome (ARDS)
               i. Pulm complication of severe sepsis or septic shock
              ii. #of med may contrib. to devel of this syndr
             iii. TNF  ↑cap perm & stim xprsn of adhesion molec (ICAM-1) on pulm enodthel
                      1. also promotes nphil sequest thru CD18 binding
             iv. Adhesion molec (active by TNF, IL-1, IL-8) prom nphils
              v. Sticking to pulm endothel cells
             vi. Activ compl (C5a)  nphils clump & rel toxic nphil enz  damage endothelial cells
      g. Tx of Severe Sepsis – hx of unsuccessful clinical trials:
               i. IL-1 R antag; Monoclonal Ab to TNF; Tumor Necrosis R prot
      h. Sepsis in immunosuppressive dz
               i. Overprodxn of pro-inflam cytokines  immunosuppressed state
              ii. Many therapies which were designed to ↓inflam are also immunosupprsv (maybe infxv?)
             iii. Survival in sepsis may be fnx of ability of host to achieve ―nl‖ immune responsivenss
             iv. Evidence for immunosuppression in sepsis:
                      1. In later stages of sepsis: shift from proinflam (Th1)  anti-inflam (Th2) response
                      2. Sepsisi  state of anergy
                      3. loss of B-cells, follicular dendritic cells & CD4 cells in spleen
                      4. Sepsis promotes apoptosis  induces anti-inflam response (not necrosis)
                         enhances antimicrobial defenses
      i. Disseminated Intravascular Coagulation (DIC) – assoc w/marked ↑mortality
               i. Predom procoag fx w/microvasc thrombosis  organ ischemia & infarction
              ii. ↓natural anticoag – antithromb III & activated Prot C
             iii. Tx w/Prot C  improvement in DIC & ↓mortality
      j. Clinical Manifestations of Sepsis
               i. CV – besides ↓SVR, thre is myocard dysfnx w/↓myocard contractility
              ii. Respir – acute lung injury w/tachypnea & respire alk  ARDS bc alveolar cell injury
             iii. Renal – acute tubular necrosis 2o to hypoTN
             iv. GI cell injury w/apoptosis of mucosal cells—may  bacterial translocation
              v. Hepatic dysfnx, as cholestasis w/↓bilirubin excr
                      1. if severe shock  hepatocell cell necr & liver fail
             vi. Hematologic – Leukocytosis is common, but leukopenia represents more severe infxn
                      1. Thrombocytopenia may occur  DIC or dir via IgG med mech
                      2. DIC w/prolong bleeding times  consumption of clotting factors
            vii. Metabolic Δ – Gluconeogenesis  ↑plasma glc; Hypoglycemia is rare
                      1. ↓Serum LDL & HDL bc ↓chol syn; ↑VLDL & TAG bc TNF inhib lipoprot lipase
                      2. ↑serum lactate  ↓tissue perfusion & acidosis
3. Sepsis Summary:
      a. Sepsis is a dz of microcirc dysfnx & endothel cell activation
      b. Triggers for dysfnx incl endotoxin and the exotoxins of gram-(+) bacteria
      c. dysfnx med thru variety of humoral substances incl TNFα, cytokines, compl proteins, kinins, etc.
      d. DIC = poor prognostic sign, although ↑DIC mortality mechanism is not known.
      e. natural anticoagulant, activated Protein C, improves mortality.
               i. BUT, no patho findings indicating that its activ is med thru inhib of microvasc thrombos
      f. Sepsis in an immunosuppressive condition.
Epidemio feat, modes of transmisn, clinical presentation & dx of relapsing fever, lyme dz, leptospirosis
Diff & simil in clinical presentation of non-venereal treponemal dz: 2 lineages…
    1. Spirochaetaceae Family (Treponema & Borrelia)
           a. Treponema Genus (non-venereal trepano dz dx by dark-field microscopy & seriologic tests)
                     i. Treponema pallidum subsp. pallidum  venereal syphilis (talk about later)
                    ii. Non-venereal = contag dz in rural areas, transmitted by direct contact; unhygienic
                            1. morph indisting; clncl dz; self-lmtd 1o/2o phases; latent dz free pd; destxv 3o phase
                   iii. *Treponema pallidum subsp. pertenue: yaws
                            1. warm, humid-Africa, S. Amer, SE Asia; skin contact, usually in kids.
                            2. Blood stream infxninvolve bone, lymphatics and distant skin sites.
                            3. 1o lesions: papules on extremities, enlarge, erode and then spontaneously heal.
                            4. 2o phase (mos later): simil lesions w/multiple exacerbations and remissions
                                    a. Osteitis of the fingers, long bones and para-nasal maxillae can also occur.
                            5. Late phase: cutan plaques, nodules, gummat les w/hyperkeratotic palms and soles
                   iv. *Treponema pallidum subsp. endemicum: bejel (endemic syphilis)
                            1. Africa & W. Asia; skin contact & sharing eating & drinking utensils.
                            2. 1o lesion: oral mucosal lesion-rarely seen.
                            3. 2o phase: Mucous patches, periostitis and adenopathy
                            4. Late phase: gummatous lesions occur.
                    v. *Treponema carateum: pinta
                            1. Arid regions of mexico, central America, Colombia; skin contact
                            2. organisms multiply locally & spread via blood & lymphatics
                            3. 1o lesions: small pruritic, erythematous papules on face, neck, extremities or chest
                                    a. can persist for years.
                            4. 2o Phase: (mos later) scaly papules-may develop into pigmented lesions.
                            5. Late Phase: characterized by depigmented lesions on wrists, elbows and ankles.
           b. Borrelia (all are anthropod-bourne; differ in host, vector, spp they infect & dz they cause)
                     i. Relapsing Fever (louse-bourne or tick-bourne)
                            1. Louse-bourne (B. recurrentis); trans vaia body louse; crushed lice rel orgs-
                               penetrate skin. Endemic: E Africa, S America; epidemics after catastrophy
                            2. Tick-Bourne (15 diff subspp): world-wide; rodents=reservoirs
                                    a. trans: saliva/excrement rel by tick while feeding
                            3. Pathophys: both types – org in blood when febrile, disappears when fever resolves
                               and returns during the subsequent fever; when afebrile pd – org hide in internal
                               organs and then re-emerge Ag-ically different.
                                    a. cyclic proc of Agic variation & specific Ab formrelapsing nature of dz
                            4. Clinical Manifest: both–fever/chills/headache/myalgia/arthralgia/truncal rash.
                                    a. Exam: conjunctival suffusions, petechia, hepatomegally. Neuro findings.
                                    b. Causes of death, usually: myocarditis, CNS hemorrhage and liver failure.
                                    c. sympt intensity usual ↓w/each relapse. Louse-borne dz usually=1 relapse.
                            5. Diagnosis: demonstrate org in perihp of febrile pt.
                                    a. Dark-field microscopy & Giemsa or Wright stained thin & thick smears
                            6. Tx: significantly ↓mortality (from 40% to 5%)
                                    a. Louse-bourne: 1 dose of tetracycline or erythromycin
                                    b. Tick-bourne: longer course is required due to higher rates of relapse
                    ii. Borrelia Burgdorferi (Lyme Dz)
                            1. Vector of Transmission:
                                    a. Ixodes scapularis in NE: larvae, nymphs feed on rodent, adults on deer
                                    b. Ixodes pacificus in west; Ixodes ricinus in Europe
                            2. Epidemiology: 3 regions in US: NE, MidW & Wcoast. Onset mainly in summer
                            3. Pathogenesis: Introdxn to hostspreads via blood and lymphatics.
                              a. Specif IgM response peaks @3-6 weeks, & IgG follows grad over mo’s
                      4. Clinical Manifestaitons
                              a. Stages:
                                       i. (1): erythema chronicum migrans (ECM-bullseye rash)
                                      ii. (2): disseminated infection (follows stage 1 by days or weeks)
                                     iii. (3): persist infxn, mo-yrs after 1st infxn, maybe after long latent pd
                              b. Cutaneous: ECM @ tick-bite site. 3-30 days after the bite.
                                       i. ECM=lesion w/outer red borders & ctrl clearing, but may be atypcl
                                      ii. often assoc w/systemic sympt: fatigue, fever, adenopathy.
                                     iii. pt may have meningeal signs, hepatitis or splenomegally.
                                     iv. annular 2o lesions-50% after ECM by several days;
                                              1. smaller, multiple and can appear and fade.
                                      v. ECM and secondary lesions usually fade in 3-4 weeks.
                              c. MSK: Up to 80% of untx pt; sympt w/in 2wks-yrs after infxn.
                                       i. sympt range: joint pain - intermit arthritis – chron erosive synovitis
                                      ii. early: migratory pain in joints, tendons and bursa are common
                                     iii. Arthritis can be severe w/marked swelling & mostly fx large joints.
                                     iv. Attacks may last from wks - months and sep by pds of remission.
                                      v. minority of pts can develop chronic arthritis, with sympt for >1yr.
                              d. Neuro: early, pt have sympt: meningeal irritation but NO CSF abn/deficits
                                       i. 15% of untx pt will have neuro sympt in late dz:
                                              1. meningitis, encephalitis, chorea, cranial neuritis/CN paslsy
                                                  (CN VII: Bell’s Palsy); myelitis/motor/sensory radiculitis.
                                              2. pt = fluctuating meningitis and CN or periph neuropathy.
                                      ii. W/meningitis = lymphocytic pleocytosis and ↑CSF protein.
                                     iii. Pts can develop chronic cognitive deficits: memory loss or mood,
                                          sleep and language disturbances.
                              e. Cardio: 5% untx pt w/in several weeks of infxn.
                                       i. Pt = diff deg of <3 block, EKG Δ, L-vent dysfxn, myopericarditis.
                                      ii. Duration of symptoms is usually brief.
                      5. Dx: clinically +/ serologically
                              a. Early: serolog tests = less useful, only 30-40% of pts are + (IgM).
                              b. up to 70% will have + serol 2-4 wks later.
                              c. 90% have + IgG Ab 4-6 wks after infxn. Ab titers ↓grad post tx
                              d. the longer duration of infxn b4 tx  the longer it takes for Ab titers to fall.
                      6. Tx: oral antibiotics (doxycycline or amoxicillin) unless neuro/cardio symptoms
                              a. Cardio/neuro symptoms require intravenous therapy (ceftriaxone).
2. Leptospiraceae Family (Leptospira)
      a. Epidemiology & Transmission: (Leptospira interrogans) zoonosis;world-wide distribution.
               i. Trans: H20/soil contam w/infxd animal urine; wild animals=reservoir, infect domestic ani
              ii. Occupational/recreational xposr common during summer/fall.
      b. Pathophys: after skin penetration, org enter blood & dissem. Jaundice from hepatocell damage.
               i. Immune-med renal fail & meningitis. Org can persist in aqueous humor chron uveitis.
      c. Clinical Manifestations: dz=Sub-clinical; 90%pt w/sympt have milder anicteric form;
               i. Biphasic dz w/initial flu-like phase when Leptospira can be isolated from most tissues,
                      1. followed by an ―immune‖ phase when meningitis, uveitis and rash occur
              ii. Anicteric: fever, headache, severe muscle pains.
                      1. 2nd Stage: may be absent, but can have severe headache and myalgias, meningitis,
                          N/V and abdominal pain, splenomegally, rash and pulmonary infiltrates.
             iii. Icteric: (Weil’s dz): impair renal/hepat fnx, hemrg, circ collapse (shock), mortal: 5-10%.
      d. Diagnosis: Isolation requires special lab technique; Serological tests (ELISA) also available
      e. Tx: Intravenous penicillin/ampicillin in severely ill patients, oral therapy in all others.
Bordetella, Haemophilus and Legionella Infxns
*Clinical Syndr assoc w/bordetella, Haemophilus, Legionella spp
*Bact pathogenesis & host immunity in devel of dz & to be able to recog important epidem feat
*Laboratory dx, tx, prevention
    Overview of Bordetella, Haemophilus and Legionella Infections
         1. Share following characteristics
                 a. Aerobic gram negative rods
                 b. Cause respire dz (↓er tract dz=pneumon & ↑er tract infxn=otit media, sinusit, epiglottitis),
                            i. but can cause a wide variety of clinical illnesses
         2. Clinical infections:
              a. Bordetella pertussis, cause of pertussis or ―whooping cough‖
              b. Haemophilus sp., cause of respiratory and genital tract diseases
              c. Legionella pneumpohila, cause of pneumonia ―Legionnaires Disease‖
    1. Bordetella spp that infx humans: non motile, aerobic gram (-) rod or cocco-bacillus.
          d. Bordetella pertussis
                       i. 1st recorded descrip of ―whooping‖ cough in middle ages; aka. ―cough of 100 days‖
                      ii. Isolated in 1906 w/devel of special media (Bordet-Gengou); Slow grow colon (3-7days)
             e. Epidemiology
                    i. Exclusv human patho, reservoir in: younger adult w/mild URI sympt; older adult w/chronic bronchit
                   ii. Spread by aerosolized droplets (cough from infxd person!); ↑attack rate (50-100%) – close contact
                  iii. DPT vaccine  ↓rates of pertussis in children 1-5 yo; Waning post-vaccine immunity –
                           1. adults/adolescents @ risk for disease
                  iv. 20-30% of adults w/prolonged cough may have pertussis
                   v. Pertussis vaccination (DPT) has changed the epidemiology of disease
                               1.  Pre-vaccine era disease
                                       a. Pertus in age 1-5 years old; < 20% cases in kids <1 yo; Adult women surviving infxn
                                           would pass maternal immunity (antibodies) to children
                              2. Post-vaccine era
                                       a. Immunity wanes after 12 years, no boosters given; Adult women dont pass protective Ab
                                       b. >50% are under 1 yo (pre-vaccination); least protected and at greatest risk!
                      vi. In developing world Bordetella infxns=endemic and account for >90% of cases in world
                              1. 60 million cases a year and contributing to over 300,000 deaths a year.
             f. Pathogenesis
                    i. xposr thru inhalation of aerosolized bacteria (infected human reservoir)
                   ii. Bordetella attaches to ciliated epithelial cells of bronchial tree and proliferates
                  iii. VF Localized tissue damage & Systemic toxicity: VF include:
                          1. Filamentous hemagglutinin – block nphil phagocytosis, helps bind to respir cilia
                          2. *Pertussis toxin* (one of several exotoxins)
                                        a. Locally - toxins ↑ mucus secr; Systemically – promotes leukocytosis, encephalopathy
                                        b. Subunits of toxin responsible for various modes of avoiding neutrophil host defenses, etc.
                          3.        Bacterial pili and pertactin– attachment of bacteria to respiratory epithelium
             g. Clinical Manifestations – 4 stages of dz**
                          1. IP (7-21 days), asympt; Bacteria attach & proliferate on ciliated epithelial cells
                          2. Catarrhal stage (1-2 weeks), most contagious!
                                        a.   Sx: rhinorrheae, malaise, ↓-grade fever, sneez, anorex; Leukocytosis on periph smear
                                        b.   Peak bacteria produced, disease is not recognized
                               3. Paroxysmal stage (2-4 weeks)  40-50 paroxysms/ day!
                                        a.   Sx: repet cough w/whooping (expir cough w/inspiratory gasp), vomiting, exhaustion
                                        b.   Extruded ciliated epithel cells impair mucus clearance & leads to mucus plugs in airways
                               4. Convalescent stage (≥3-4 weeks), improved paroxysmal cough
                                        a.   Devel 2o sx/complicatn incl pneumon (main cause of mortality), seizures, encephalopathy
                                        b. Complications
                                                  i. Rare encephalopathy and seizures
                                                 ii. Paroxysmal cough↑ intra-thoracic & intra-abd P, cause of: subconjunctiv
                                                     hemrg, truncal hemrg, epistaxis (nose bleed), pneumothorax and rectal prolapse
                                                         1. Frenal ulcer - traumatic ulcer bc tongue protrude against sharp teeth
                                           iii. Pnemonia Complications: Main cause of mortality
                                                     1.   Pneumon from: aspiratn during whooping/vomiting/impaired secr clear
                                                     2.   Radiographs may show lung collapse from mucus plug of
                                                      smaller bronchi and bronchioles
         h. Diagnosis (lab dx is hard b/c org burden ↓ as sympt↑; dx clue=cough 2weeks (in hx)
                i. Sputum culture: Bordet-Gengou media (up to 2-7 d)
               ii. Sputum stain: direct fluorescent antibody (DFA) only positive in 50%
              iii. Serology with a significant rise between acute and convalescent sera
          Tx & Prevention
               i. Supportive therapy includes supplemental O2, freq suctioning of secr, apnea monitoring
              ii. Tx: Antibiotics; Consider vaccination. ↑ly contag dz: isolate & erythromycin for prophylax close contacts
2.   Haemophilus imp: H. influenzae and H. ducreyi; other spp in human dz listed, but not mentioned here
         a. Haemophilus influenzae – requires **X factor (hemin) & V factor (NAD)** for aerobic growth!!
                  i. ―blood loving;‖ only H. flu needs both factors, available in blood-enriched media.
                         1. Heating media rel V factor from cells; lab clue=satellite colonies of Haemophilus around
                              hemolytic org (which cause rel V factor), ie. S. aureus.
                         2. In CO2-rich atm, bact grow on heated blood = ―chocolate‖ agar.
                         3. gram stain shows small, pleomorphic, pale-staining gram-negative bacilli.
                         4. 6 Agic distinct capsular types A to F; HIB vaccine made against type B capsule producing strains.
                                  a. This strain assoc w/most invasive infxns; If strain has no capsule, it is called nontypeable.
                 ii. Epidemiology: transmission thru contacts w/*secr or airborne droplets*
                          1.   Humans=only natural host; 80% of healthy ppl =carriers of nonencapsulated H. influenzae
                          2.   Introduced conj type B vaccine in 198795% ↓incidence of systemic dz in children < 5 yo
                                    b. ↑er respire carriage rates ↓ w/vaccine (2-4% <1% after HIB vaccine),
                                             i. direct association to frequency of disease
                        3. Since advent of widespread vaccin, H. influenzae infxns most likely to occur
                               c. Non-encapsulated strains, other types (A-C, F)
                               d. Type B infxns if non-immune children or elderly with waning immunity
                        4. Risk factors: HIV/AIDS, Sickle cell dz, Splenectomy, Chronic lung dz
                               e. Also smoking, malignancy, pregnancy and alcoholism
                iii. Pathogenesis
                        1. VF:
                               a. Capsule – Inhibit opsonization & intracellular killing
                               b. Lipo-oligosaccharides (LPSs) – endotox like activity, tissue damage;
                                             i. Facilitate survival on mucosal surfaces (nasopharynx), initiate invasive disease
                                   c. Outer membrane proteins (OMPs)
                                             i. contribute to iron scavenging and binding required for organism survival
                                d. Fimbriae–in both typeable & non-typeable; on bact surf help enhance adher to muc surf
                          2. Host immunity important in defense
                                a. Humoral immunity
                                            i. kids @risk when they lose passive acq mom imm & devel active humoral imm
                                           ii. Protective Ab opsonize bact to facil clearance;
                                          iii. Increase risk if functional asplenia (sickle cell disease) or splenectomy
                                   b.   Complement: ↑susceptibility with C2, C3 deficiency
                 iv. Clinical Syndromes
                         1. Meningitis
                                   a.   b4 HIB vaccine, it was most common etiologic agent of pediatric meningitis
                                   b.   after bacteremic spread of org from nasopharynx
                                              i. (more likley if type B capsule producing strain)
                                   c.   Occurs after 1- to 3-days of mild upper respiratory tract infection
                                   d.   May be associated with trauma, neurosurgery, CSF leak or paranasal            sinusitis
                                   e.   With prompt therapy mortality < 10%
                          2. Epiglotitis
                                a. life-threatening ER w/cellulitis and swelling of the supraglottic tissues
                                   b.   Pre-vaccine era, peak incidence 2-4 yo
                               c. Presentation: pharyngitis, fever  drooling, difficulty swallowing and
                                   breathing (patient often leaning forward, chin thrust out)
                                        i. may progress rapidly to complete airway obstrxnn & death
                                       ii. Lat neck radiograph: large round epiglottis w/distention of pharynx by air
                                           and the ―thumbprint sign‖ (swollen epiglottis); Cherry red color of epiglottis
                        3. Otitis/Sinusitis & Pneumonia
                                 a.   Nonencapsulated strains common cause of acute purulent sinusitis in adults and children
                                 b. most common cause of otit media in young kids (90% nontypeable H. flu)
                                 c. Immunocompromised, chronic lung disease
                                       i. Exacerbation of bronchitis
                                      ii. Pneumonia – community-acquired or hospital-acquired
                                                   1.   Lobar consolidation, effusions/empyema
                     4. Arthritis – b4 HIB-#1 cause of arthritis >2 yo; rare in older kids/adults
                            a. Bacteremic spread to single large joints
                            b. mostly immunocompromised or with previously damaged joints
               v. Diagnosis
                     1. Blood cultures for meningitis, epiglottitis, cellulitis, arthritis or pneumonia
                     2. H. influenzae needs supplemented media (X and V factor, Chocolate agar)
                        3.   Antigen detection ELISA (urine, CSF)
               vi. Treatment
                        1.   Serious infxn req I.V. tx: Epiglotitis/Meningitis – 100% fatal w/o tx;
                                 a. 3rd gen. cephalosporins: IV cefotaxime or ceftriaxone
                        2.   Given ↑ing resist by B-lactamase prodxn ampicillin should not be used for empiric therapy
                        3.   Resistance ↑ to macrolides and chlorampheicol
                        4.   Infants >2 mos with type B meningitis: dexamethasone ↓neuro sequelae if added to antibiotics
              vii. Prevention
                      1. HIB vaccine = ↓↓↓incidence of H. influenzae infxn (~ 98% fxv in prevent dz)
                                a. ↓ in nasal carriage of type B; Potential ↓neuro complications from childhood meninigitis
                                b. Prevention in light of increasing antibiotic resistance
                       2. Chemoprophylaxis with Rifampin
                                a. Household contacts w/child < 48 mos. whose immunization is incomplete
                                b. If >2 cases w/in 60 days in daycare w/@risk kid (unvacc/incomp vacc)give prophylax
       b. H.   ducreyi, the causative agent of Chancroid. – sex trans dz -most commonly diagnosed in men
                i. Cause of genital ulcers in Asia and Africa (major contrib. to trans of HIV); IP=5-7 days
                ii. Tender papule with erythematous base on the genital or perianal area
               iii. Lesion ulcerates and is painful with suppurative inguinal lymphadenopathy
               iv. Diagnosis clinical, most (85%) culture swab of base or margin of ulcer have no growth
3. Legionella pneumophila – slender, pleomorphic, obligately aerobic gram-negative bacilli.
      a. causes 90% of human dz (serogroup 1 most common);
      b. nutritionally fastid & req special media, charcoal yeast enriched media (CYE) for optimal growth
      c. Epidemiology: most epidemic cases in the summer and fall
               i. WW distrib, Fresh water (lakes, streams). Grows up to 46°C, Cl-tolerant; human=accidental host
                ii. Optimal growth in symbiotic microorg (amebas and ciliated protozoan); in US > 1,000 cases/yr reported
             iii. Environmental spread thru water distribution systems:
                     3. Showers, Humidifiers, respir therapy equipment, Evaporative cooling towers of
                          AC systems, Micro-aspiration during or after ingestion of contaminated water/ice
       d. Pathogenesis: human/host defns rspns (cell & humoral imm)-bact survive intracell & evade human imm defenses
               i. Pulm alveolar macrophages engulf the Legionella bacteria (phagocytosis)
              ii. No intracellular killing (evades the host defense system!)
             iii. multiplies within a specialized endosome and produces toxic cytokines
             iv. Macrophage is killed and new bacteria released and infect other macrophages
       e. Clinical manifestations: Pontiac Fever (self-lmtd illness); ―Typical‖ form of Legionellosis…
              a. Febrile systemic illness with pneumonia; Pulm sx initially mild w/non-product/purulent cough
               b.   Prodromal illness: malaise, ↓-grade fever, anorex; Myalgia, fatigue, ↑fever, abd pain, nausea, vomit, diarrha
         c. Pulmonary infiltrates: Rapid progrsn of alveolar infiltrates with multi-lobar consolidation
                  i. Begins with limited or minimal with interstitial infiltrates, pleural effusion on x-ray
      d. Respiratory deterioration, multi-system failure and DIC
      e. Overall mortality 15-20%– ↑er if immunocompromised – such as renal or cardiac transplants
      f. Path: intense inflam Δ in alveoli, aveolar ducts, bronchioles and alveolar septa
      g. Complic: pleuritis, plerual empyema, pericarditits and cavitary lung dz/abscesses
      h. Extrapulmonary legionellosis: Immunocompromised hosts, by bacteremic spread
             i. cellult, sinust, perirect absc, pericardt, pyelonephrt, peritont, pancreat, endocardit
f. Diagnosis
       i. High clinical suspicion required!
         ii. Gram stain: abundant neutrophils, rare bacteria
      iii. Culture on enriched media (you need to inform micro lab!)
              1. Buffered CYE agar – must ask for this to be done (not routine for respir workup).
      iv. Urine antigen - enzyme immunoassay detects serogroup 1 antigen
       v. DFA microscopy (secretions)
       vi. Serum antibody – acute and convalescent sera with 4-fold increase in titer
g. Treatment
          i. In vitro susceptibility testing not standardized
         ii. Antibiotics need to have ↑ intracellular concentrations to be effective against Legionella
        iii. Classic antibiotic treatment = Erythromycin
                 1. Newer macrolides – azithromycin are better tolerated
                 2. Also used: Quinolones – such as levofloxacin or ciprofloxacin
         iv. No activity with penicillins, cephalosporins and aminoglycosides
          v. Need high clinical suspicion for disease!
h.   Prevention and Surveillance
          i. CDC and other sources recommend
                 1. Routine environmental cult of hospital environ sources only on discovery of cases
                    or if performing organ and bone marrow transplants
                 2. Not contagious – isolation precautions not required
         ii. Ionization units and UV light for water distribution systems are highly effective to disinfect reservoirs
Gram Positive Rods (GPRs)
Epidemiology, pathogenesis and recognize clinical syndr assoc w/infxns caused by GPRs.
1. GPRs of clinical Importance
   a. Bacillus sp.                                                       e. Clostridia sp.
      i. B. anthracis                                                         i. C. tetani (tetanus)
      ii. B. cereus                                                           ii. C. botulinum (botulism)
   b. Corynebacteria sp.                                                      iii. C. perfringens (gas gangrene)
      i. C. diptheriae                                                        iv. C. difficle (diarrhea in patients on
      ii. C. jeikeium                                                              antibiotics)
      iii. Rhodococcus (C. equi)                                         f. Occasional GPR pathogens (don’t memorize
      iv. Archanobacterium haemolyticum                                       these)
   c. Listeria monocytogenes                                                  i. Lactobacillus
   d. Erysipelothrix rhusiopathiae                                            ii. Propionibacterium
   g. Classification based on spore forming (Bacillius and Clostridia sp); motile (Listeria); non-sporeforming
2. Bacillus =ubiquitous (soil, H20).; aerobes/facultative anaerobes; form spores (w/stand hrs of boiling)
   a.   common as non-patho skin flora & occas contaminants of blood cult. *opportunistic infxns cause dz in immunocompr pt*
   b.   Bacillus anthracis –―anthracis‖ (Greek for coal) bc black eschar/ulcer produced in skin infxn. Bioterrorism
        i.     Spores found WW & infect herbivores in contact w/spores/bacteria in the soil. can persist mo-yrs
        ii.    Dz of herbivorous ANIMALS (sheep, goats, cattle) & HUMANS (contact w/animal, hides or wool).
        iii.   3 Forms of Dz in humans: Cutaneous (95% of natural infections), Respriratory & GI
        iv.    Epidemiology (Epidemic = widespread in animals; Endemic = reg fx animals)
               (1) Naturally occurring infection – ALL three types of disease
                     (a) herbivores 1o reservoir w/humans incidental host.
                     (b) human dz from dir contact w/infxd wild/domesticated animals developing countries, endemic dz some countries
                     (c) w/contact w/imported infxd animal products; agricult/indust manufact w/tainted materials (hides, furs)
               (2)   Biologic Warfare Agent - INHALATIONAL is goal, but have seen CUTANEOUS
                     (a) Spores potent – lethal inhalational dose 1 millionth of a gram
        v. Pathogenesis
            (1) Spores deposited in skin, respire, GI mucosa; Spores germinate in tissues
            (2) Bacteria multiply, produce toxins
                (a) Lethal toxin is dominant virulence factor
                (b) Edema toxin
                (c) Capsule blocks phagocytosis, toxin inhib nphil fnx (oxidatv burst) & induce cytotoxic fxtissue necrosis
            (3) Bact Dissem (bloodstream, lymphatics)systemic toxicity (more w/non-cutaneous forms) death w/out tx
        vi. Clinical Syndr w/corresponding clinical manifestations
            (1) Cutaneous Anthrax
                (a) Xpsd skin areas (arms, hands, neck and face); Pruritic/―itchy‖ papule (confused w/insect bite)
                (b) Enlarge several days ulcer +/- surrounding vesicles. Lesion center=black/necrotic (eschar)
                (c) Important finding: *edema* surrounds lesion; Often painLESS, regional lymphadenopathy
                     (d) After 7-14 days, eschar heals and scar develops; Few systemic sympt: malaise, headache, low grade fevers
               (2) Respiratory Anthrax
                   (a) Inhal spores (very few needed  tissue destrxn); Germinatn/transport lymphatics to hilar/mediastinal ln
                   (b) Toxins: necrosis and hemorrhage in mediastinum
                       (i) Chest Xray shows widening of mediastinum; CT scan may show necrotic ln
                       (ii) Sx =substernal pain and cough; Signs = stridor on exam and neck/mediastinal edema
                   (c) xtnsn of necrosis to pleura leads to pleural effusions (upon examination of pleural fluid, found to be bloody)
                   (d) Hematogenous spread  gastric/bowel lesions, meningitis and bacteremia with shock/sepsis
                   (e) Two phases to disease
                       (i) Initial phase, 1-3 days: Malaise, fever, dry cough, sub-sternal pressure
                       (ii) Secondary phase: Sudden onset, rapid progression to death in 1-2 days
                            1. Sx: dyspnea, stridor, high fever, diaphoresis; GI bleeding (melena, gross blood)
                            2. Mental status Δ, meningitis(<5%); ↑Mortality, over 90% (difficult to diagnose!)
                            3. Dx: CXR w/wide mediast, bloody pleural tap; cult blood, pleural fluid, CSF for GPRs
           (3) GI Anthrax
               (a) Meat from infxd animal consumed in times of hardship; inspector bribe -social breakdown/corruption.
               (b) Ingested spores germinate in intestinal mucosa, incubate ~ one week
               (c) Presents in one of two forms:
                   (i) Oropharnyngeal Anthrax (hard palate, post pharynx)
                         1.   Cervical edema, necrosis. Often fatal, death from bacteremic spread
                     (ii) Abdominal Anthrax (large bowel, cecal lesions)
                         1.   Fever, nausea and vomit. 2-5 days stools become bloody, tissue invasn  bacteremic spread and death
       vii. Diagnosis
            (1) recog clinical syndromes; ↑ clinical suspicion in right setting crucial to dx/therapy due to high mortality
           (2) Cultures + GPR (skin/vesicles, sputum, pleura, CSF, blood); Toxin assays (ELISA)
       viii. Treatment/Prophylaxis
            (1) Treat IV PCN G, doxycycline, ciprofloxacin. Prophylaxis doxycycline or cipro, up to 6 wks
           (2) Immunization (US, sterile filtrate avirulent nonencapsulated strain)
               (a) >90% effective, 3 doses and annual booster. Vets, exposed animal handlers, military or laboratory workers
           (3) Control natural dz: Controlling animal disease controls natural human disease
   c. Bacillus cereus – aerobic spore forming GPR most common assoc w/food poisoning-inadeq food reheat
      i. Epidemiology
           (1) Normal flora, potential culture contaminant. Contaminant of drug paraphernalia/heroin
           (2) Immunocompromised (HIV, corticosteroids, HbSS) host or IVDU- risk of serious infxn (bacteremia, meningitis)
           (3) Immunocompetent hosts, usually contaminant (wounds, cultures) but can see associated
              (a) FOOD POISONING
       ii. Pathogenesis
           (1) 3 types of extracellular products contribute to the manifestations of clinical disease
               (a) Enzymes (collagenase, hemolysin, protease, phospholipase) contribute to tissue destruction
               (b) Toxins (enterotoxins) lead to diarrhea/emesis
               (c) Antimicrobial agents produced by bacteria (examples: polymyxin, bacitracin) help bacteria to compete
       iii. 2 main Clinical Syndromes
            (1) Bacillus cereus Food Poisoning: Rice contam w/bact cooked; cooled & spores germinate after reheat
                (a) 2 Types of Food poisoning
                    (i) EMETIC form (vomiting predominate feature):
                         1. IP <6 H; Similar to S. aureus food poisoning; *Fried Rice*
                    (ii) DIARRHEAL form (cramps, nausea, watery stools)
                         1. IP=10-12h, improv in 24h; Simil to C. perfringens food poisoning; Contam meats-turkey, vegs
                (b) Due to enterotoxin production
                (c) Diagnosis: Clinical syndrome; Culture the *food*!
                 (d) Self-limited, NO antibiotic therapy needed
                 (e) Prevention – avoid cooling foods at RT (keep <10°C) and must be properly reheated to destroy spores (>60°C)
           (2)   Bacillus Ocular Infxns – caused predomin by B. cereus, but can see with other Bacillus species.
                 (a) Assoc w/trauma (soil xposr) +/ foreign body (dust partic, soil or metal shrapnel).
                     (i) Also common in IVDA.
                 (b) Serious infections, including panophthalmitis and ocular abscess
                     (i) EC enz destroy eye tis  rapid destrxn (12-48 H) w/main complaints: pain, redness, visualΔ
                 (c) Early dx key to save eye; req surgical therapy & antibiotics (IV, intra-vitreal); IV Clindamycin, Vancomycin
3. Corynebacteria - aerobic, club shaped bact, ―dipthroids‖.
   a. C. diptheriae – nonspore forming GPR; causes DIPTHERIA;
      i. produce potent exotoxin (VF)–inhib prot syn & responsible for tenacious tonsilar/pharyngeal exudat
      ii. Epidemiology: Humans = reservoir; transmitted by infxd pt/carrier contacts susceptible host
           (1) Asympt carrier state (< 5%) on skin and in pharynx; Immuniz ↓carrier state
           (2) Transmission through bacteria in airborne droplets or contact with secretions/exudate
           (3) COLDER months, temperate climates, crowded conditions
           (4) endemic in developing countries but rare dz due to widespread immunization (DPT) in developed world
           (5) Resurgence in times of unrest/political/social breakdown (immuniz programs affected); epidemics have occurred
            (6) Those at risk today:
                (a) Children < 15 yo if unvaccinated;
                (b) Unimmunized/unboosted adolescents/adults (urban poor, no access to health care, IVDU)
       iii. Clinical Manifestations: Respiratory tract (local dz) incubates 2-3d
            (1) Toxin inflam, dense necr exudate in pharynx/trachea = necrotic collection of cells, fibrin, dead
                respiratory epithelial cells, RBCs, WBCs and bacteria. Its removal promotes bleeding of submucosa
            (2) Exudate is tough and leathery, grey. Extends and can occlude airway obstruction
            (3) Soft tissues of the neck can swell, ―bull neck.‖ Death aspiration of the membrane
            (4) Fever, sore throat and membrane development (tonsils, posterior pharynx). Cervical ln common
            (5) Once toxin abs, can see systemic effects on tissues at distant sites (risk ↑ w/severity of dz)
                (a) Cardiac Toxicity (Myocarditis)
                   (i) 1-2 wks after illness; up to 10-15% infected. Lead to arrhythmia, heart block, heart failure if progresses
               (b) Neurologic Toxicity
                   (i) Up to several months later. Cranial neuropathies to wide range of presentations
       iv. Diagnosis/Treatment
           (1) Use clinical clues to prompt early therapy
               (a) Tonsillitis/pharyngitis w/assoc membr w/febrile/toxic appearance
               (b) Cervical adenopathy, cervical swelling (―bull neck‖)
               (c) Paralysis of palate, hoarseness or stridor
           (2) Immunofluorescent staining (several hours)
           (3) Cult from pt show GPRs & grow w/characteristic colony morphology/media requirements
           (4) Therapy:
               (a) Antitoxin (hyperimmune horse antiserum) – available europe
               (b) Antibiotics: PCN G, Clnida, Erythromycin, Rifampin, Tetracycline
               (c) Respir & contact Isolation. Supportive, monitor for cardiac/neurologic complications
   b. Clinically important species: (other than diptheriae)
       i. C. jeikeium (Group JK) – cause of bacteremia in immunocompromised pt/neutropenia,
            (1) hospital acquired infections (IV catheters); Resistant to most antibiotics, usually sens. to vancomycin
       ii. Arcanobacterium haemolyticum – cause of pharyngitis associated with diffuse erythematous rash
       iii. Rhodococcus equi – pulm infxns in immunocompromised hosts (HIV+); Animal/manure xposr; vancomycin
4. Listeria monocytogenes – small GPR (cocci, diplococi).
   a. Tumbling motility at 25°C; unique intracell pathogenesis. Rare cause of dz, but w/select @risk pop
   b. Epidemiology: Vertical transmission (momkid), no other human-human
       i. Zoonosis, ubiquitous in nature (soil, decaying vegetable matter, feces).
       ii. Up to 70% raw vegetables; raw milk, fish, meats (including processed meats), poultry
       iii. FOODS: coleslaw, unpasturized soft cheeses, ready-to-eat products/meats, smoked fish
       iv. Most @risk: Neonates, elderly (extreme age), preg ♀, impaired cell med immunity, immunosupprsn
            (steroids, transplant recipients); HIV + (100x > HIV-), ↓incidence bc prophylx antibiotics
   c. Pathogenesis: IP = 11-70 days; Infxn most likely begins w/contaminated food ingestion (possible maternal-fetal)
       i. Gastric surgery or H2 blockers promote infection (stomach pH increased)
       ii. Xs GI mucosa, if evades cell med immunity  dissem hematogenously; likes CNS (meningitis) and placenta
       iii. Binds epithelial cells, able to escape INTRACELLULAR killing and survives/divides
            (1) Filopods (bact push against membr) to allow passage to adj cells, avoid xpos to immune system
   d. Clinical Manifestations/Syndromes
       i. Meningitits (important to recognize!) – in top 5 causes of meningitis, ↑mortality ~20%!!
            (1) Bacterial tropism for brain, brain stem and meninges (can form abscesses)
            (2) >60 yo and neonates; patients on steroids/chemotherapy
            (3) More likely seizures, 30% CSF samples have monocyte predominance
       ii. Bacteremia (seen in immunocompromised host)
       iii. Gastroenteritis: Relatively rarely dx food borne illness; IP ~20H w/fever, diarrhea, cramps lasting 24-48H
       iv. Neonatal infxn
            (1) Infxn in-utero (placenta)Granulomatosis Infantiseptica –immed spontan abortion/neonatal death
            (2) Infxn @parturition - meningitis 2wk post-birth or immediate sepsis after delivery
        v.    Listeriosis during pregnancy: By 30 weeks major decline in cell mediated immunity and woman at risk
              (1) Infections in last trimester cause premature labor, infant death; early infection may cause spontaneous abortion
   e. Diagnosis/Treatment
      i. Clinical setting w/approp host imp to recog!
         (1) Empiric therapy for Listeria meningitis and to tx maternal infxn to prevent neonatal death.
        ii.   Standard bacterial identification. Treatment : Ampicillin and if PCN allergic – SMP/TMX (Bactrim)
5. Erysipelothrix rhusiopathiae – thin, nonsporulating GPR; WW. dz in animals (zoonosis).
      i. Occupational and/or recreational xposrs imp in dz. In humans  skin infection called erysipeloid.
   a. Epidemiology: Human infection occurs through direct cutaneous contact …(―crab finger,‖ ―whale finger‖)
          (1) Occupational exposures: fishermen, butchers, veterinarians
   b.   Pathogenesis: Abrasion or puncture wounds, enzymatic virulence factor (hyaluronidase)
   c. Clinical Manifestations/ 3 Clinical Syndromes assoc w/infxn
          (1) ERYSIPELOID skin lesion - local cellulitis (fingers)
              (a) Violaceous, raised and well defined lesion; lymphadenopathy common
                (b) Incubation 2-7days, severe pain is major patient complaint. Resolves w/out tx in 3-4 weeks
            (2) DIFFUSE SKIN RASH/SYSTEMIC sx: Cutan lesion spreads, (-) blood cult; Fever/arthralgias-several weeks
            (3) ENDOCARDITIS: Uncommon, (+) Blood cult for org. Mortality twice other causes (~40%) of endocarditis
   d.   Diagnosis/Treatment: Know exposure history to be able to distinguish erysipeloid from routine cellulitis
        i. Routine microbiologic testing (specimen culture or blood)
        ii. Tx: Highly susceptible to PCN, cephalosporin, clindamycin, quinolones; Resistant to vancomycin
Mycoplasma, Ureaplasma & Chlamydia
Epidemiology, pathogensis & recognize clinical syndromes assoc w/infxn caused by org
1. Mycoplasmataceae (Mycoplasma, Ureaplasma spp) lack a cell wall (pleomorphic shapes, flask-like),
   a. have fastidious growth requirements; commensal (don’t  dz) +/ pathos (active/chronic dz) in ppl
   b. smallest self-replic life form;. respnsbl for diverse dz collxn
   c. Clinically important species: M. pneumoniae; M. hominis; M. genitalium; Ureaplasma urealyticum
   d. Pathogenesis
      i. Particular affinity for epithelium: respire & urogenital tract;
      ii. After inoculation, ↓ciliary axn; Desquamation/loss of cilia contrib to manifest of dz (cough/infertility)
   e. Diagnosis
      i. Lack cell wall – not visible by gram staining; Slow growing! (3-4weeks);Fastidious-req sterols to grow
      ii. Unusual appearance on agar (―Fried egg‖ appearance); except -M. pneumoniae - spherical ―mulberry‖ colonies
   f. Epidemiology: 2 categories of clnical dz; commensals & pathogens. Ubiq in nature
       i.   Common cell-culture contaminant (able to pass through biologic filters)
       ii. RESPIRATORY INFETIONS: M. pneumoniae (tracheobronchitis, pneumonia-―atypical/walking‖)
           (1) Epidemiology: ↑est attack rate=5-20yo; IP=2-3 weeks (diff from viral illness-usually only 1-3 days)
               (a) spread by aerosolized droplets, contact w/infected individual (young children often the index case)
               (b) 2 million respiratory infections/yr in the US; Worldwide, no seasonal variation
               (c) Single cases or ―mini‖ epidemics (families, military recruits, colleges, prisons, day care facilities)
               (d) Partic risk of serious infxn/complication/mortality: Sickle cell dz, hemaglobinopathies
           (2) Pathogenesis
               (a) Adhere to epithelial lining:
                      (i) Polar/flask-like–slip btwn cilia; P1=adherence prot localizes to bact tips, binds to glycoprot on host cell
                (b)   Anti-ciliary axn; suppress nl clearance mech of resp tract
                (c)   Immunopathogenesis (cytokines increase inflammation; host immune cells are activated)
                (d)   make Toxic prod (damage host, H2O2); Cilia inhib; exfoliatn/inflam (cough/exudates/bronch plug)
            (3) Clinical Features
                (a) Tracheobronchitis, 70% of infections and 30% progress to pneumonia
                (b) Pneumonia: 1 of many ―atypical‖ pneumonias
                         1. Culture negative; Gram stain negative; Do not respond to beta-lactam antibiotics
                    (ii) Mild symptoms (―walking‖ pneumonia); rarely fatal, self-limited in most cases
                    (iii)Insidious onset (malaise, fevers, headache); Clinical symptoms and xrays are slow to resolve
                    (iv) Prolonged symptomology (2-3 weeks); characteristic prolonged dry, hacking cough
                    (v) Chest X-ray shows bilateral infiltrates, even prior to symptoms
                      (vi) Assoc clinical features that may help differentiate from other atypical/viral pneumonia:
                          1. Bullous myringitis (rare); Clinical symptoms worse than the pulmonary exam
                          2.   GI complaints (nausea or diarrhea) and myalgia uncommon
                    (vii) Extrapulmonary involvement
                         1. Derm (~10%) - various exanthems; assoc w/Stevens-Johnson syndr (erythema multiforme)
                         2. Cardiac (~10% may have arrhythmia/conduction defects)
                         3. Raynaud’s phenomenon (transient reversible vasospasm)
                         4. Neurologic (aseptic meningitis, meningoencephalitis, myelitis)
            (4) Diagnosis is generally clinical, evaluation includes:
                (a) Sputum:
                    (i) Gram-stain (inflam Δ, elim other pathogens); Cult (2-3 wks, special media, unique colonies)
                (b) Serologic
                    (i) M. pneumoniae specific complement fixing Abs; After 2-3 weeks titers ↑, 6 wks look for 4 fold↑
                    (ii) Cold agglutinins 40-70% but nonspecific—Can be found at time of presentation (early)
            (5) Treatment: Recognize the clinical presentation
                (a) ↑er respir tract infxns: usually self-limited; Pneumonia is usually mild, therapy often empiric
                      (i) Antibiotics reduce symptoms; CXR lags behind clinical resolution (wks)
                      (ii) Chose antibacterial tx not active @ cell wall-bc don’t have it (Macrolides, Tetracyclines, Quinolones)
                           1. one of major reasons why drugs are added to empiric tx of ―CAP‖
         iii. GENITAL INFECTIONS: genital mycoplasms also lack cell wall
                  (a) M. hominis (pyelonephritis, PID=pelvic inflammatory disease)
                  (b) Ureaplasma urealyticum (urethritis)
                  (c) M. genitalium (urethritis, PID)
              (1) Epidemiology – Opportunists!!
                  (a) Normal flora of the urogenital tract of ♀/♂(40% sexually active ♀+ M. hominis from cervix)
                  (b) Extra-genital manifestations rare (wound/STI infections, joint infections)
                                                                                      or vertical (mother to child)
                  (c) Transmission is direct genital-genital contact (sexually transmitted)
             (2) Clinical presentation: Most infections lmtd to GU tract
                 (a) Rare to have dissemination outside GU tract; may occur in immunocompromised
                 (b) Urethritis (non-gonococcal or non-GC)
                     (i) Sympt persist post-GC tx (bc of inapprop tx– nb:GC tx w/penicillin/β-lactams=no act against org)
                     (ii) ~ 20% associated with M. genitalium or ureaplasma (30%+ are Chlamydia)
             (3) Diagnosis
                  (a) No routine serologic testing available (reference labs/research setting)
                  (b) Culture: special media-takes days-wks; ―fried egg‖ appearance colonies
                      (i) Since commensal, use cult + clinical suspicion (Urine/swabs of urethra/cervix etc—for culture)
                  (c) PCR/molecular techniques (reference/research)
            (4)   Therapy: Most is empiric, based on clinical suspicion; Tetracyclines, macrolides, quinolones
2.   Chlamydiaceae (Chlamydia spp.) – gram (-); w/tropism to columnar epithel (respir, UG)
     a. obligate intracell bact w/unique, biphasic life-cycle; also respnsbl diverse dz collxn in ppl
     b. Clinically important species: C. trachomatis; C. psittaci; C. pneumoniae;
     c. Pathogenesis
        i. Elementary bodies (EB) = ―infxs‖ form; EC; resist environ cond, bind to rcptrinitiate infxn (epithel cell, Mφ).
        ii. Reticulate bodies (RB)=―non-infxs;‖ IC- fragile (suscep to environ condi). metab active, replic form of org.
         iii. Developmental cycle: EB binds to rcptr on suscep cell Internalized (phagocyte/endocyt)in ―inclusn‖ ves (protected, membrane
              bound) in host cell Inhib fusion w/lysosomes (evades host defense)RBs replicate/reorg into EBsInclusn have 100-500 new org
                  (a) Cells LYSE in the case of C. psittaci; EXTRUDE new organisms without lysis in C. pneumoniae, C. trachomatis

Chlamydia species         Serovars    Tissue tropism                        Infection
C. trachomatis            A-C         Conjunctiva                 Conjuctivitis,                        Blindness
C. trachomatis            D-K         Anogenital mucosa, urethra, Non-GC urethritis,                    PID, Ecotpic pregnancy,
                                      cervix                      cervicitis                            Infertility, Reactive arthritis
C. trachomatis            L1,L2,L3    Genital mucosa, lymphocytes Genital ulcers, LAN                   Granulomatous ulcerations,
                                                                  (LGV)                                 Elephantiasis
C. pneumoniae                         Respiratory epithelium      ↑er Resp. tract infxns                Atherosclerosis?
                                                                  and Pneumonia
C. psittaci          (many)                                       Pneumonia          Hepatitis
    d. Chlamydia trachomatis
         i. Pathogenesis –Infx non-ciliated columnar epithel cells; No long-lasting immunity; Reinfxn common
             (1) Inflam/tissue destrxn mech poorly understood – PMNs infiltrate area, others follow; Cell destrxn w/scarring/fibrosis
             (2) Responsible for blindness/infertility (scarring). Infxn assoc w/post-infectious complications
         ii. Epidemiology
             (1) Ocular infection (Trachoma)
                 (a) Worldwide, usually in areas of poverty/overcrowding; 500 million infxns, ~10 million cases of blindness
                 (b) Transmission: droplet, person-person, contaminated clothing, flies and vertical (mother-child)
                 (c) Clinical presentation
                     (i) Trachoma – 1st infxn <2 years old in endemic areas; resolve spontan; cornl opacificatnblindness
                         1. Repeated infxn: inflam and scarring; 2 bact infxn thru blockage of tears (antibacterial activity)
                         2. Tx: Ocular Trachoma (WHO-‖SAFE‖ strategy)
                            a. Antibiot fxv (complianc poor, contraind in kids); mass tx (comm) w/Azithromycn
                            b. Surg (lid deform); Face wash (get clean h20); Environ ctrls (hygiene, fly control)
                 (ii) Neonat Conjunctiv: Postnat trans (hand-eye); 20-40% w/infxd mom devel infxn; 5-12d post partum
                 (iii) Infant Pneumonitis: 10% with infected mothers develop infection; Protracted sympt if untx
                       1. 4-11 wks post part: ↓grade fever/afebrile; Nasal congest, cough; Occurs w/or w/out conjunctivitis
                 (iv) TX: conjunctiv/Pneumonitis in kids: systemic antibiotics, prenat mom screen
         (2) Genital infection
             (a) Urethritis/cervicitis – 5 - 15% men/women < 25 are infected
                   (i) Common STD in the US (4 million NEW cases/yr); 90 million worldwide
                   (ii) Annual screening, sexually active women of childbearing age (preventable disease)
               (b) MEN (urethritis, epididymitis, prostatitis, proctitis); 75% asymptomatic
               (c) WOMEN (cervicitis, urethritis, salpingitis, proctitis); 80% asymptomatic
                   (i) 40% ♀progrs to PID; 50%  infertile if untxd;
                   (ii) Other complications: ectopic preg, premature delivery, post-partum fevers, chronic pelvic pain
               (d) Non-GC urethritis: Dysuria, urethral discharge (minimal); can also have conjunctiv; 30-50% = C. trachomat
               (e) Post-GC urethritis (co-infxn w/N. gonorrhoeae) – Symptoms can occur after therapy for GC
                   (i) Incubation longer (7-14 days) vs 4 days for GC; Dual infxn w/GC not uncommon (>50%)
               (f) Reactive arthritis (post-infectious, Reiter’s syndrome); immune-mediated inflammatory response
               (g) Tx: Genital Dz –if non-GC or post-GC suspected = must tx empirically; tx partners of infxd ppl
                   (i) Antibiotics Tetracyclines, macrolides, quinolones
                   (ii) Screen: ↑risk pop: All sex activ♀<25yrs; All preg ♀; Any older ―↑risk‖ ♀; now=insuff evid for ♂ screen
                   (iii)Screen: HIV and other blood-borne pathogens; Screen: HPV (cervical cancers) in women
         (3)   Lymphogranuloma venerum (LGV) –Africa/Asia/S. Amer; US: reservoir is MSM with ~300 cases/year
               (a) 1o lesion small painless, vesicular-pustular lesion @ inoculation site (genitals)
               (b) Days-weeks later, systemic symptoms (fever, malaise, headache, myalgia) + lymphadenopathy (LAN)
               (c) Progresses to involve local lymph nodes (enlarged, unilateral, painful) ―buboes‖
                       1. Groove sign (LAN above and below ing. ligament)
                       2. Eventual rupture and drainage of the lymphnodes
                       3.   Chronic ulceration, elephantiasis may result
              (d) Tx: LGV: Antibiotics, prolonged courses; surgery for draining buboes
     iii. Diagnostics difficult (intracellular) – Nucleic acid amplification (swabs) ** used clinically
          (1) Culture – limited (Cell culture); Serologies, limited – LGV, Psittacosis; Cytology (inclusion bodies)
          (2) Special stains: DFA, Iodine staining of inclusion bodies, genomic probes
e.   Chlamydia psittaci = Psittacosis (―parrot‖ fever, ornithosis)
     i. Epidemiology: ~50-100 cases/year in the US
         (1) Birds are the natural reservoir C. psittaci – xposr to feathers, feces from sympt/asympt birds
         (2) Those at risk: bird owners, veterinarians, zoo/pet shop workers, poultry industry
     ii. Clinical presentation: Incubation 7-14 days; asymptomatic infection common
          (1) Sympt infxn, pneumonitis (5% mortality): prolong sympt (4-6 wks); exam + splenomegaly, rash
                  (i) systemic symptoms: fever, chills, headache, mild cough. assoc hepatitis; endocarditis, encephalitis–are rare
     iii. Dx: Serologic dx (acute and convalescent titers), >4 fold rise. Tx=Tetracyclines
f. Chlamydia pneumoniae (one of the causes ―atypical‖ pneumonia)
   i. Epidemiology – Young adults (crowding conditions), person-person transmission
         (1) 300,000 cases/year; 50% adults + evidence of past infection; reinfection common
     ii. Clinical presentation (similar to M. pneumoniae)
          (1) Most infxns asymptomatic/mild; ↑er (bronchitis, pharyngitis) & ↓er(pneumonia) respiratory tract
     iii. Dx: Acute/convalescent titers. Tx: Tetracyclines, Macrolides and Quinolones
Recognize the epidemiology and clinical features of community-acquired and nosocomial pneumonia
1. Pneumonia = most common cause of infxn-rel death; caused by many microb; dz of all ages, esp elderly
   a. Acute Community-acquired pneumonia
   b. Atypical pneumonia
   c. Aspiration Pneumonia
   d. Hospital-acquired pneumonia
   e. Pneumonia in the immunosuppressed host
   f. Pulmonary infiltrate with eosinophilia
   g. Chronic pneumonia
2. Most from aspiration of oropharyngeal bact w/resultant fail of pulm host defense to prevent estab of 1o infxn
3. Recurrent Pneumonias:
   a. Anatomic abnormalities – bronchiectasis, tumor, compressed bronchus, pulm sequestration
   b. Ig Deficiencies; Depressed nphil fnx
   c. Abnormal ciliar activity – immotile cilia syndr; Kartagener’s syndr, Cystic fibrosis
4. Dx Considerations:
   a. Sputum specimens – contam by mouth flora often makes interpretation of cult results difficult
   b. Sputume gram-stains – careful exam by trained individ, can be very useful in providing dx direction
   c. Reliable Speicmens – (in terms of cult) blood, empyema fluid, percutan needle aspiration, bronchoscopy
      w/protected brush, transtracheal aspiration. (not practical in most pt admitted w/simple pneumonia)
   d. Sputum cultures – notoriously unreliable!!!
5. Pneumonia Syndromes
   a. CAP
      i. Pneumococcal – most common cause of routine bacterial pneumonia (↑mortal w/HbSS etc)
           (1) Single Shaking chill, pleuritic pain and rusty sputum more common in younger patients.
           (2) Penicllin resist—↑ing; med by alter in penicillin binding proteins. Assoc w/MDR
                 (a) Ceftriaxone is acceptable for intermediate level resistance; Vancomycin is used for high-level resistance
           (3) Vaccine—contains 23 of the more common serotypes.
               (a) Give to pt @↑risk: >65yo?, w/impaired host defense mechanisms. Every 5-7 years.
               (b) Conjugate vaccine (pneumococ polysac conj w/prot-tetanus toxoid).
                   (i) Better immune response in children < 2 years of age.
       ii. Hemophilus influenzae – often seen w/COPD; Encaps strains=more virulent, assoc w/invasive dz
           (1) Resistance due to β-lactamase prodxn; Cant routinely use: amoxicillin
                 (a) 2nd-gen cephalosporins (ceftriaxone)=useful. Respir fluoroquinolone (moxifloxacin)=IV/oral
            (2) Hib. Vaccine w/type b polysac – has reduced incidence of invasive dz among children.
       iii. Klebsiella pneumoniae – elderly, alcoholic, cancer, debilitated patients. Esp nursing home patients
            (1) Isolate from sputum: cultures freq show coloniz of oropharynx, not etiologic agent of pneumonia
            (2) May cause a necrotizing pneumonia
           (3) Second-generation cephalosporin (e.g., ceftriaxone), quinolones or tmp/smx are useful agents.
       iv. S. aureas – ↑in flu season (less common <pneumococ); 2o to hematog spread w/multi pulm nodules
           (1) MRSA – prob for hospital-acq pneumonia, also assoc w/comm-acq infxn.
               (a) Many isolates have enzyme, the Panton-Valentine leukocidin that destroys tissues.
               (b) Ppl w/this type of pneumonia freq have abscesses or lung cavities.
               (c) For MRSA pneumonia, linezolid has replaced vancomycin bc better penetration in lung
           (2) For MSensS – nafcillin = drug of choice
       v. Anaerobic bacteria (Prevotella melaninogenicus & peptosterptococci)
          (1) Aspir pneumonia in pt w/impaired cough/gag reflex.
          (2) Predispose factors: CNS dz, alcohol accomp by severe periodontal dz
          (3) Newer cephalosporins, penicillins or carbapenems w/activity against anaerobes often selected.
           (4) Clindamycin =drug of choice for abscesses.
           (5) Metronidazole shouldnt be used despite excellent anerobic activity bc less fxv in lung infections.
       vi. Atypical Pneumonia – acute, usually comm-acq pneum; Pulse-temp dissoc =common
           (1) org not seen on routine stains/grown on routine cult media.
           (2) Mycoplasma pneumoniae – most common cause of ↓er respire tract infxn in young adults
               (a) Sx: Sore throat, nonproductive cough, headache; X-rays appear worse than clinical findings.
               (b) Extrapulm manifest: rash (rarely Stevens-Johnson), DIC, hemolysis, meningoencephalitis,
                   myocarditis, hepatitis.
               (c) Dx: clinically and confirmed by serology or culture. Tx: Macrolides or quinolones are effective
           (3) Chlamyophila pneumoniae – college students, ~½ as common as mycoplasma.
               (a) Sx: Hoarsenes. Tx: Macrolides or quinolones.
           (4) Legionella pneumophilia – No pathognomonic clinical or lab feature; lots spp can’t be differen
               (a) incidence very variable: dep on degree of contam in aquatic reservoirs.
               (b) Dx: serology, DNA probe, special stains of bronchial specimens or culture (CYE).
               (c) Macrolides or quinolones.
           (5) Chlamydophila psittaci –psittacosis. Assoc w/psittacine/bird xposr, incl turkeys
           (6) Coxiella burnetti – Q-fever. assoc w/sheep/goat/cattle; endocard, hepatit, osteomyelit, meningit
           (7) Franciscella tularensis – Tularemia--xposr to infxd tis of mammal/rabbit or from infxd tick bite.
               (a) Requires cysteine-enriched media for growth.
      vii. Viral Pneumonias – immunocompetent adults flu & adenovirus (recruits/dorms)
           (1) Outbreak of severe pandemic influenza due to H5N1 (bird-flu) strain is a topic of great concern.
           (2) Other viruses that occas cause pneumon in adults: parainfluenzae, RSV and VZV.
               (a) Human metapneumovirus has been identified as a new viral agent of pneumonia in children.
   b. Nosocomial Pneumonia – 3rd most freq nosocomial infxn (after UTI/wound), ↑est mortality
      i. Pathogenesis: colonization of oropharynx w/pathogenic org (gram – bacilli), followed by aspiration.
           (1) Major risk factors for colonization based on degree of debilitation (>debil  coloniz)
               (a) majority of ICU pts will be colonized w/in 72h of admission to the unit.
           (2) Microbio – difficult to define based on sputum bc most pts colonized w/variety of patho spp.
               (a) gram (–) bacilli (Klebsiella, Enterobacter, Serratia, Pseudomonas) = ~¾ nosocomial pneum
               (b) large portion of remainder is due to S. aureus. Anaerobic bacteria are rarely implicated.
           (3) Tx: vs aerobic gram (–) bacilli/staph.
               (a) 3rd gen cephalosporin, w/aminoglycoside/quinolone = usual choice for pts w/GNB infections.
               (b) Linezolid =drug of choice for tx of hospital-acq MRSA pneumonia.
Understand the host defense mechanisms and pathogenesis of pneumonia
1. ↑er resp tract – major host defense mech = nl swallow reflex, w/epiglot close respir tract & cough reflex
2. Host Defense Mech in Respiratory Tract:
   a. Aerodynamic Filt – turbinates & branching bronchial tree result in partic matter settling on muc surf
   b. Cough and epiglottic reflex
   c. Mucociliary Clear – muc trap bact + concerted ciliar axndirect flow of bact out of respiratory tree.
       i. Impaired w/alcohol & cigarette smoke.
   d. Fibronectin – glycoprotein covering cell receptors and preventing microbial adherence.
   e. Lysozyme – prot found in pulm secretions that is bactericidal for gram(+) bacteria.
   f. Surfactant – ↑ macrophage microbicidal activity
   g. Lactoferrin – prot found in pulmonary secretions that is bacteriostatic for gram-negative bacteria.
   h. Ig/Compl – opsonization & phagocytosis of bact (IgG & IgM w/complement). IgA blocks adherence.
   i. Phagocytic cells – alveolar Mphages (impaired by cigarette smoke)=resident phagocytes of lung.
       i. When neutrophils are called in it represents pneumonia.
3. Impairment of Pulmonary Host Defenses
   a. Alterations in consciousness—stroke, overdose, alcohol  ↓epiglottic reflex, ↓cough
   b. Cigarette Smoke  ↓mucociliary function, ↓macrophage activity
   c. Alcohol  ↓epiglottic reflex, cough, mucociliary clearance. ↓neutrophil mobilization, chemotaxis.
       i. Abnormal phagocyte oxidative metabolism, ↑colonization with aerobic gram(–) bacilli.
   d. Viral URIs – destroy resp epithel  ↑adher of patho bact. Disrupt nl ciliary act so that clear of muc &
       bact from lung is impaired. Nphil & alveolar Mphage activity may also be impaired by viruses.

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