Lead BMS Histopathology
Colchester Hospital University NHS Foundation Trust
Infectious diseases caused by non-
What types of organisms?
7. Helminths (worms)
Infectious diseases caused by non-
What do we mean by non-culturable?
They cannot be grown (cultured) in the laboratory…
…for the purposes of diagnosis or it is very difficult to do
Why are some organisms non-culturable?
1. Obligate intracellular organisms
2. Slow growth rates
3. Complex growth requirements
Infectious diseases caused by non-
What is an infectious disease and which ones are we
An infectious disease is a clinically evident illness
resulting from the presence of pathogenic
microbial agents (pathogens)
These pathogens are able to cause disease in humans
Infectious pathologies are also called communicable
diseases or transmissible diseases due to their potential
of transmission from one person or species to another by
a replicating agent (as opposed to a toxin)
“Why should I care about infectious diseases? This is the
21st century, haven’t we got vaccinations?! Shouldn’t we
be investigating cancer, heart disease and dementia?”
1. Only one infectious disease, smallpox, has been
eradicated by human effort in all of human history
2. Infections are responsible for ¼ of deaths worldwide
Time to exercise the brain…
Working in pairs
1. How many infectious diseases (of humans) can you
2. Can you also name the infective agents?
3. How many infectious diseases (of humans) do you
think there are?
You have 10 minutes
Acinetobacter infections Acinetobacter baumannii Actinomycosis Actinomyces israelii, Actinomyces gerencseriae and Propionibacterium propionicus Adenovirus infection Adenoviridae family African
sleeping sickness (African trypanosomiasis) Trypanosoma brucei AIDS (Acquired immune deficiency syndrome) HIV (Human immunodeficiency virus) Amebiasis Entamoeba histolytica Anaplasmosis
Ana plasma genus Anthrax Bacillus anthraces Arcanobacterium haemolyticum infection Arcanobacterium haemolyticum Argentine hemorrhagic fever Junin virus Ascariasis Ascaris lumbricoides
Aspergillosis Aspergillus genus Astrovirus infection Astroviridae family Babesiosis Babesia genus Bacillus cereus infection Bacillus cereus Bacterial pneumonia multiple bacteria Bacterial vaginosis (BV)
multiple bacteria Bacteroides infection Bacteroides genus Balantidiasis Balantidium coli Baylisascaris infection Baylisascaris genus BK virus infection BK virus Black piedra Piedraia hortae Blastocystis
hominis infection Blastocystis hominis Blastomycosis Blastomyces dermatitidis Bolivian hemorrhagic fever Machupo virus Borrelia infection Borrelia genus Botulism (and Infant botulism) Clostridium
botulinum; Note: Botulism is not an infection by Clostridium botulinum but caused by the intake of botulinum toxin. Brazilian hemorrhagic fever Sabia Brucellosis Brucella genus Burkholderia infection
usually Burkholderia cepacia and other Burkholderia species Calicivirus infection (Norovirus and Sapovirus) Caliciviridae family Campylobacteriosis Campylobacter genus Candidiasis (Moniliasis; Thrush)
usually Candida albicans and other Candida species Cat-scratch disease Bartonella henselae Cellulitis usually Group A Streptococcus and Staphylococcus Chagas Disease (American trypanosomiasis)
Trypanosoma cruzi Chancroid Haemophilus ducreyi Chickenpox Varicella zoster virus (VZV) Chlamydia Chlamydia trachomatis Chlamydophila pneumoniae infection Chlamydophila pneumoniae
Cholera Vibrio cholerae Chromoblastomycosis usually Fonsecaea pedrosoi Clonorchiasis Clonorchis sinensis Clostridium difficile infection Clostridium difficile Coccidioidomycosis Coccidioides
immitis and Coccidioides posadasii Colorado tick fever (CTF) Colorado tick fever virus (CTFV) Common cold (Acute viral rhinopharyngitis; Acute coryza) usually rhinoviruses and coronaviruses.
Creutzfeldt-Jakob disease (CJD) CJD prion Crimean-Congo hemorrhagic fever (CCHF) Crimean-Congo hemorrhagic fever virus Cryptococcosis Cryptococcus neoformans Cryptosporidiosis
Cryptosporidium genus Cutaneous larva migrans (CLM) usually Ancylostoma braziliense; multiple other parasites Cyclosporiasis Cyclospora cayetanensis Cysticercosis Taenia solium
Cytomegalovirus infection Cytomegalovirus Dengue fever Dengue viruses (DEN-1, DEN-2, DEN-3 and DEN-4) – Flaviviruses Dientamoebiasis Dientamoeba fragilis Diphtheria Corynebacterium
diphtheriae Diphyllobothriasis Diphyllobothrium Dracunculiasis Dracunculus medinensis Ebola hemorrhagic fever Ebolavirus (EBOV) Echinococcosis Echinococcus genus Ehrlichiosis Ehrlichia genus
Enterobiasis (Pinworm infection) Enterobius vermicularis Enterococcus infection Enterococcus genus Enterovirus infection Enterovirus genus Epidemic typhus Rickettsia prowazekii Erythema
infectiosum (Fifth disease) Parvovirus B19 Exanthem subitum Human herpesvirus 6 (HHV-6) and Human herpesvirus 7 (HHV-7) Fasciolopsiasis Fasciolopsis buski Fasciolosis Fasciola
hepatica and Fasciola gigantica Fatal familial insomnia (FFI) FFI prion Filariasis Filarioidea superfamily Food poisoning by Clostridium perfringens Clostridium perfringens Free-living amoebic infection
multiple Fusobacterium infection Fusobacterium genus Gas gangrene (Clostridial myonecrosis) usually Clostridium perfringens; other Clostridium species Geotrichosis Geotrichum candidum Gerstmann-
Sträussler-Scheinker syndrome (GSS) GSS prion Giardiasis Giardia intestinalis Glanders Burkholderia mallei Gnathostomiasis Gnathostoma spinigerum and Gnathostoma hispidum Gonorrhea Neisseria
gonorrhoeae Granuloma inguinale (Donovanosis) Klebsiella granulomatis Group A streptococcal infection Streptococcus pyogenes Group B streptococcal infection Streptococcus agalactiae Haemophilus
influenzae infection Haemophilus influenzae Hand, foot and mouth disease (HFMD) Enteroviruses, mainly Coxsackie A virus and Enterovirus 71 (EV71) Hantavirus Pulmonary Syndrome (HPS) Sin
Nombre virus Helicobacter pylori infection Helicobacter pylori Hemolytic-uremic syndrome (HUS) Escherichia coli O157:H7 Hemorrhagic fever with renal syndrome (HFRS) Bunyaviridae family
Hepatitis A Hepatitis A Virus Hepatitis B Hepatitis B Virus Hepatitis C Hepatitis C Virus Hepatitis D Hepatitis D Virus Hepatitis E Hepatitis E Virus Herpes simplex Herpes simplex virus 1 and 2 (HSV-1
and HSV-2) Histoplasmosis Histoplasma capsulatum Hookworm infection Ancylostoma duodenale and Necator americanus Human bocavirus infection Human bocavirus (HBoV) Human ewingii
ehrlichiosis Ehrlichia ewingii Human granulocytic anaplasmosis (HGA) Anaplasma phagocytophilum Human metapneumovirus infection Human metapneumovirus (hMPV) Human monocytic
ehrlichiosis Ehrlichia chaffeensis Human papillomavirus (HPV) infection Human papillomavirus (HPV) Human parainfluenza virus infection Human parainfluenza viruses (HPIV) Hymenolepiasis
Hymenolepis nana and Hymenolepis diminuta Epstein-Barr Virus Infectious Mononucleosis (Mono) Epstein-Barr Virus (EBV) Influenza (flu) Orthomyxoviridae family Isosporiasis Isospora belli Kawasaki
disease unknown; evidence supports that it is infectious Keratitis multiple Kingella kingae infection Kingella kingae Kuru Kuru prion Lassa fever Lassa virus Legionellosis (Legionnaires' disease)
Legionella pneumophila Legionellosis (Pontiac fever) Legionella pneumophila Leishmaniasis Leishmania genus Leprosy Mycobacterium leprae and Mycobacterium lepromatosis Leptospirosis
Leptospira genus Listeriosis Listeria monocytogenes Lyme disease (Lyme borreliosis) usually Borrelia burgdorferi and other Borrelia species Lymphatic filariasis (Elephantiasis) Wuchereria
bancrofti and Brugia malayi Lymphocytic choriomeningitis Lymphocytic choriomeningitis virus (LCMV) Malaria Plasmodium genus Marburg hemorrhagic fever (MHF) Marburg virus Measles Measles
virus Melioidosis (Whitmore's disease) Burkholderia pseudomallei Meningitis multiple Meningococcal disease Neisseria meningitidis Metagonimiasis usually Metagonimus yokagawai Microsporidiosis
Microsporidia phylum Molluscum contagiosum (MC) Molluscum contagiosum virus (MCV) Mumps Mumps virus Murine typhus (Endemic typhus) Rickettsia typhi Mycoplasma pneumonia Mycoplasma
pneumoniae Mycetoma numerous species of bacteria (Actinomycetoma) and fungi (Eumycetoma) Myiasis parasitic dipterous fly larvae Neonatal conjunctivitis (Ophthalmia neonatorum) most
commonly Chlamydia trachomatis and Neisseria gonorrhoeae (New) Variant Creutzfeldt-Jakob disease (vCJD, vCJD) vCJD prion Nocardiosis usually Nocardia asteroides and other Nocardia species
Onchocerciasis (River blindness) Onchocerca volvulus Paracoccidioidomycosis (South American blastomycosis) Paracoccidioides brasiliensis Paragonimiasis usually Paragonimus westermani and
other Paragonimus species Pasteurellosis Pasteurella genus Pediculosis capitis (Head lice) Pediculus humanus capitis Pediculosis corporis (Body lice) Onchocerca volvulus Pediculosis pubis (Pubic lice,
Crab lice) Phthirus pubis Pelvic inflammatory disease (PID) multiple Pertussis (Whooping cough) Bordetella pertussis Plague Yersinia pestis Pneumococcal infection Streptococcus pneumoniae
Pneumocystis pneumonia (PCP) Pneumocystis jirovecii Pneumonia multiple Poliomyelitis Poliovirus Prevotella infection Prevotella genus Primary amoebic meningoencephalitis (PAM) usually Naegleria
fowleri Progressive multifocal leukoencephalopathy JC virus Psittacosis Chlamydophila psittaci Q fever Coxiella burnetii Rabies Rabies virus Rat-bite fever Streptobacillus moniliformis and Spirillum
minus Respiratory syncytial virus infection Respiratory syncytial virus (RSV) Rhinosporidiosis Rhinosporidium seeberi Rhinovirus infection Rhinovirus Rickettsial infection Rickettsia genus Rickettsialpox
Rickettsia akari Rift Valley fever (RVF) Rift Valley fever virus Rocky mountain spotted fever (RMSF) Rickettsia rickettsii Rotavirus infection Rotavirus Rubella Rubella virus Salmonellosis Salmonella genus
SARS (Severe Acute Respiratory Syndrome) SARS coronavirus Scabies Sarcoptes scabiei Schistosomiasis Schistosoma genus Sepsis multiple Shigellosis (Bacillary dysentery) Shigella genus Shingles
(Herpes zoster) Varicella zoster virus (VZV) Smallpox (Variola) Variola major or Variola minor Sporotrichosis Sporothrix schenckii Staphylococcal food poisoning Staphylococcus genus Staphylococcal
infection Staphylococcus genus Strongyloidiasis Strongyloides stercoralis Syphilis Treponema pallidum Taeniasis Taenia genus Tetanus (Lockjaw) Clostridium tetani Tinea barbae (Barber's itch)
usually Trichophyton genus Tinea capitis (Ringworm of the Scalp) usually Trichophyton tonsurans Tinea corporis (Ringworm of the Body) usually Trichophyton genus Tinea cruris (Jock itch)
usually Epidermophyton floccosum, Trichophyton rubrum, and Trichophyton mentagrophytes Tinea manuum (Ringworm of the Hand) Trichophyton rubrum Tinea nigra usually Hortaea werneckii Tinea
pedis (Athlete’s foot) usually Trichophyton genus Tinea unguium (Onychomycosis) usually Trichophyton genus Tinea versicolor (Pityriasis versicolor) Malassezia genus Toxocariasis (Ocular Larva
Migrans (OLM)) Toxocara canis or Toxocara cati Toxocariasis (Visceral Larva Migrans (VLM)) Toxocara canis or Toxocara cati Toxoplasmosis Toxoplasma gondii Trichinellosis Trichinella spiralis
Trichomoniasis Trichomonas vaginalis Trichuriasis (Whipworm infection) Trichuris trichiura Tuberculosis usually Mycobacterium tuberculosis Tularemia Francisella tularensis Ureaplasma
urealyticum infection Ureaplasma urealyticum Venezuelan equine encephalitis Venezuelan equine encephalitis virus Venezuelan hemorrhagic fever Guanarito virus Viral pneumonia multiple viruses
West Nile Fever West Nile virus White piedra (Tinea blanca) Trichosporon beigelii Yersinia pseudotuberculosis infection Yersinia pseudotuberculosis Yersiniosis Yersinia enterocolitica Yellow fever
Yellow fever virus Zygomycosis Mucorales order (Mucormycosis) and Entomophthorales order (Entomophthoramycosis)
Diagnosis of infectious diseases
Diagnosis of infectious diseases may be presumptive or
History, clinical symptoms, physical examination, imaging,
laboratory findings (e.g. blood count)
Culture, serology, morphology (cytology/histology), PCR etc.
There are more bacteria on and in the human body than
there are cells of the human body. So why don’t we get
sick all of the time?
1. Most bacteria don’t cause us any harm, some are even
beneficial to us.
2. Otherwise healthy people don’t readily succumb to
3. Adaptive immunity
Obligate Intracellular Bacterial
2. Rickettsia species
4. Mycobacterium species
Chlamydia – Aetiology
Genital Chlamydia is caused by Chlamydia trachomatis
C. trachomatis (Ct) is a non-motile, gram-negative bacterial pathogen with
a two phase life cycle. Unable to synthesize its own adenosine triphosphate
(ATP), C. trachomatis requires an exogenous (host) source.
In females, the initial site of infection is usually the endocervical columnar
epithelia. Adolescents with columnar epithelial cells on the ectocervix and
oral contraceptive pill (OCP) users are highly susceptible to infection.
Cervical infections may resolve spontaneously or continue as a low-grade
chronic infection with minimal signs of inflammation. Infections can
ascend through the upper genital tract to involve the endometrium and
fallopian tubes. The severity and the chronicity of C. trachomatis
infections appear to be highly variable.
In males, infections usually remain localized to the urethra but can spread
to cause epididymitis or prostatitis. Infections may resolve spontaneously
but the natural course of untreated infection in men is not well known.
Genital chlamydia is the most common bacterial
sexually transmitted infection (STI) in the UK, being
most common in men and women under 25
The infection can be passed through vaginal, anal, or
C. trachomatis may be treated with any of several
antibiotics: zithromax/azithromycin, erythromycin or
Chlamydia is known as the ‘silent’ infection due to its lack of noticeable
symptoms. However, 25 per cent of women and 50 per cent of men do develop
Vaginal discharge (fluor); Dysuria; Vague lower abdominal pain; Fever; Intermenstrual
or postcoital bleeding; Dyspareunia
Classical urethritis with dysuria and urethral discharge; Epididymo-orchitis presenting
as unilateral testicular pain ± swelling; Fever
Proctitis with mucopurulent discharge (rectal chlamydia)
Definitive Diagnosis – Women (endocervical swab preferred. First-void urine
sample or self-administered vaginal swab may also be used); Men (urine
Transcription mediated amplification (TMA) – Aptima Combo 2
Strand displacement amplification (SDA) – BD Probetec
Real Time PCR (alternative to above methods)
Not generally a cellular pathology diagnosis but can be diagnosed by cervical
screening or biopsy.
Chlamydial cervicitis in a
female patient characterized
by mucopurulent cervical
discharge, erythema, and
A friable, inflamed cervix,
sometimes with a follicular or
Male patients may develop a
white, cloudy or watery
discharge (shown) from the
tip of the penis
Human pap smear (+Hx)
showing chlamydia in the
infection in women is
suggested by inflammatory
changes in their cervical
cytology or histology report
and this may require follow-
Cervical smear from a 29 y-o
female discharging fluor
metaplastic cell on the left
contains a nevular inclusion
body in the cytoplasm
Restaining of the same
cytology specimen with
immunostaining for C.
Demonstration of C.
trachomatis antigen in the
nevular inclusion body is
confirmative of the diagnosis
of chlamydial infection.
Not utilised diagnostically at
present, other sensitive
nucleic acid amplification
tests mean it probably won’t
R. prowazekii (Epidemic, recrudescent and sporadic typhus)
R. typhi (Murine (endemic) typhus)
Spotted Fever Group
R. rickettsii (Rocky Mountain spotted fever)
R. akari (Rickettsialpox)
R. conorii (Boutonneuse fever)
R. siberica (Siberian tick typhus)
R. australis (Australian tick typhus)
R. japonica (Oriental spotted fever)
R. africae (African tick bite fever)
Rickettsiae are obligate intracellular bacteria transmitted to
man via an arthropod host (tick). R. prowazekii causes
epidemic typhus and is spread by the human body louse
(Pediculus corporis). R. prowazekii is not transmitted directly
by bites, but by contamination of the bite site with infected
louse faeces which are then inoculated by human excoriation.
They then parasitise the endothelial cells of blood vessels,
causing a multisystem vasculitis.
causes endemic or murine typhus and is transmitted by fleas
Epidemic typhus fever mainly occurs in cooler regions of Africa, South America
and Asia. During the 1990s, there were outbreaks in Burundi, Russia and Peru.
Outbreaks occur where poverty, homelessness, close human contact and lack
of opportunity for washing and laundry co-exist, favouring the person-to-
person spread of the human body louse. Tick-associated reservoirs of R.
prowazekii have been described in Ethiopia, Mexico and Brazil.
Sylvatic typhus (due to R. prowazekii) is found in the USA and associated with
bites from the fleas of a flying squirrel.
The incubation period of epidemic typhus is 10-14 days.
Recrudescent typhus (Brill-Zinsser disease) occurs when latent infection
reactivates and is found in about 15% of cases (even where previously treated).
It may trigger new epidemics through infection of a new generation of lice.
Endemic or murine typhus is a milder form of disease compared to epidemic
typhus. It occurs globally - in temperate climates usually during the summer
months and, in tropical countries, throughout the year. Active foci of endemic
typhus are known in the Andes' regions of South America and in Burundi and
R. prowazekii vasculitis:
Prodromal malaise lasting 1-3 days before abrupt onset of severe headache and fever (39-40°C).
There may be myalgia (sufferers may adopt a crouching posture), photophobia and neurological
abnormalities (seizures, confusion, drowsiness, coma and hearing loss).
Initially, a non-confluent, erythematous, blanching rash commencing centrally (axilla, trunk) and
spreading centrifugally to the extremities (this pattern is the opposite of rashes associated with the
spotted fever group of rickettsial infections). The rash does not involve the face, palms and soles and
there are no eschars.
The rash becomes petechial and unblanching within 1–2 days of appearing. Purpura occur in a third of
Cough, wheeze, nausea and abdominal pain are common.
Severe vascular compromise may cause peripheral gangrene and necrosis.
Recrudescent typhus (Brill-Zinsser disease) is clinically milder than the epidemic form.
R. typhi (murine typhus):
Maculopapular or petechial rash in 80% fair-skinned and 20% dark-skinned people.
Nausea and vomiting in approximately half of cases.
Abdominal pain and diarrhoea in around a quarter.
Cough in about a third.
A small proportion suffer confusion, stupor and hallucinations.
Approximately 10% of those admitted to hospital have acute renal failure, respiratory failure or severe
neurological disorders including seizures.
Diagnosis is usually made clinically on the basis of characteristic onset and progression
Investigations are used mainly to confirm clinical suspicions and to assess severity.
Where the condition is suspected then antimicrobial therapy should be given whilst
waiting for confirmatory serological tests, which can take up to a week to complete.
Full blood count (FBC) can show leucopenia ± thrombocytopenia, but white cell count
(WCC) can be elevated or normal; atypical lymphocytes may be seen in blood film.
Urea & Electrolytes (U&E) may reveal hyponatraemia or raised creatinine/urea.
Liver function tests (LFTs) may show mild elevation of transaminases and low albumin
Prothrombin time is usually normal.
Serology shows rising IgM titre in acute infection and rising IgG titre in recrudescent
Polymerase chain reaction (PCR) amplification and analysis of rickettsial DNA from
serum or skin biopsy specimens can be used to diagnose the condition.
Complement fixation (CF) test may be used to detect the specific rickettsial organism
causing the illness, via detection of specific antibodies.
Adult male Paralysis tick,
An eschar on a patient with
Q Fever Aetiology
Caused by Coxiella burnettii infection
Humans usually become infected from domestic animals:
This is through inhaling the organism, although occasionally
by ingesting raw milk.
The incubation period is approximately 2 weeks (2-29 days)
Q fever is an highly infectious zoonosis where the main
reservoir are either arthropods (mainly ticks) or farm
animals e.g. cattle, sheep, goats; although pets (dogs,
rabbits and particularly cats) may be the reservoir in urban
areas, and wild rats have been shown to be a potential
reservoir in the UK.
Q Fever Epidemiology
Occupational disease of slaughterhouse, animal
husbandry, and animal research workers.
Q fever is endemic in every part of the world except New
Zealand. Cases of Q fever have been reported in 45
countries on 5 continents and is a significant problem in
In June 2006, the United Kingdom experienced its largest
outbreak of Q fever with 138 cases associated with a
slaughterhouse near Stirling in Scotland. The
slaughterhouse had been processing post-parturition ewes,
that were thought to be the likely source.
Vaccination of those whose occupation places them at high
risk is indicated.
Q Fever Presentation
Up to 50% of cases may be asymptomatic
Acute Q Fever
Most commonly a self-limiting flu-like illness:
Lasts for 1-3 weeks
Sudden onset high fever, headache, fatigue, and muscle aches
Usually mild, with dry cough, fever, and minimal chest signs
Very occasionally can present with acute respiratory distress or pleural effusion
CXR changes are usually non-specific
Symptoms usually last 10-90 days
Mortality rate 0.5-1.5%
May be clinically asymptomatic
Alternatively presents similarly to infective hepatitis with hepatomegaly and (rarely) jaundice
Or as a chronic FUO (fever of unknown origin) with granulomas on liver biopsy
Q fever in pregnancy can cause miscarriage, premature deliveries, and stillbirths.
Chronic Q Fever
Appears as culture-negative endocarditis, almost exclusively affecting patients with abnormal or prosthetic heart valves.
Hepatomegaly ±splenomegaly (50%)
Clubbing of digits (~30%)
Purpuric rash (vasculitic) is found in 20% cases
Q Fever Diagnostic Overview
In the acute phase:
WCC raised in 1/3 cases
Liver enzymes raised at 2-3x normal; alkaline phosphatase raised in 70% of cases
Plasma sodium reduced in 28% cases
Reactive thrombocytosis and microscopic haematuria are common
Hyperglobulinaemia of up to 60g/l is commonly found and a useful diagnostic sign
Serology - paired acute and convalescent phase show >4x changes in IgG or IgM
Elevated antibody response to C. burnetii phase I or II antigens (phase-II antigen > phase-I antigen in
acute Q fever, converse in chronic Q fever)
Significant titres may take 3 to 4 weeks to appear.
Treatment should be started as soon as a clinician suspects the disease to be present.
Only 40% of people presenting with Q fever are positive on their first test.
Other techniques include polymerase chain reaction or immunohistochemical staining:
The sensitivity of serum PCR has been disappointing.
Of 100 patients with Q fever, only 18 were PCR positive.
There is also on-going controversy over PCR methods, with some tests branded insensitive and claims that
others produce false positives through cross-contamination.
Plain X-ray shows typical signs of bacterial pneumonia but rounded opacities are suggestive of Q fever.
Chronic Q fever cases may test positive for rheumatoid factor, anti-smooth muscle, antinuclear or
antimitochondrial antibodies, or circulating anticoagulant antibodies.
Normal Q fever pneumonia
A. Chronic inflammatory infiltrate (yellow arrowhead),
fibrosis (black arrowhead), and ill-formed
B. B. Closer view of the ill-formed granuloma (arrow).
About 100 species
Tuberculosis (TB) group
M. bovis (M. bovis BCG)
Caused by M. tuberculosis and others
When M. tuberculosis is first encountered (primary infection), host macrophages in the
lung engulf the organisms and carry them to hilar lymph nodes in an attempt to control
infection. Some organisms may disseminate via the lymphatics or bloodstream to distant
sites. Small granulomas (tubercles) are formed around the body to contain the
mycobacteria. The tubercles may heal spontaneously or calcify and persist in an
otherwise healthy individual.
Only a small proportion of patients develop overt TB or further disease. Miliary TB occurs
when primary infection is not adequately contained and invades the bloodstream
resulting in severe disease. Secondary TB is due to subsequent reactivation of semi-
dormant M. tuberculosis and is usually precipitated by impaired immune function such
as malnutrition, AIDS or immunosuppressive therapy. Reactivation usually occurs in the
apex of the lungs and can spread locally or to distant sites.
Close contact of TB patient: a patient with untreated, infectious pulmonary TB will infect
a further 10-15 people each year. The risk of infection is related to the nature and duration
of exposure, with household members of a TB index case having a 1 in 3 chance of
contracting the infection. Risk also extends to healthcare workers.
Only pulmonary tuberculosis is infectious.
Worldwide, approximately one third of the population is infected with TB and, from this pool, about 9 million cases of
active TB emerge every year.
These active cases resulted in approximately 1.7 million deaths in 2004. TB now causes nearly 2 million deaths each year.
It is the 2nd leading cause of death from an infectious disease (after HIV) and the leading cause of death among curable
The disease is responsible for more than a quarter of all avoidable adult deaths in the developing world.
Most new cases appear in the most populated nations - India and China, but the highest rates are seen in sub-Saharan
Africa, Indonesia, the Philippines, Afghanistan, Bolivia and Peru. Rates in these regions exceed 300 cases per 100,000 per
Incidence in eastern Europe (mostly countries of the former Soviet Union) increased in the 1990s but has fallen since
peaking in 2001.
The United Kingdom
A decline in incidence throughout the latter half of the 20th century occurred in the UK as in North America and western
However, over the last 10 years the number of reported cases of TB is rising again in the UK:
There were approximately 7,000 cases in the UK in 2004 after falling to a low of 5,086 in 1987.
There were 8,497 TB cases in the UK in 2006 with a rate of 14 per 100,000 population and 8417 cases in 2007 with a rate of 13.8 per
100,000 population. The numbers and rates have remained stable since 2005.
This has been ascribed to immigration, HIV/AIDS and the neglect of TB control programmes.
92% of cases were reported in England. London accounted for the largest proportion (39% of UK cases) and the highest
regional rate (43.2 per 100,000 population).
Infection occurs predominately in urban areas, due to immigration from developing countries with higher TB prevalence,
high population densities or larger numbers of patients in the high-risk groups.
Migration within Europe, particularly from former Eastern-bloc countries, should not be forgotten, as many European
countries are classed as having a high incidence of TB.
The onset of TB is insidious. Primary infection is usually asymptomatic. The presentation of
secondary infection is variable and often non-specific. A high index of suspicion in patients from
particular risk groups is essential to make a diagnosis. TB can affect all organs and body systems.
Extra-pulmonary TB is more common in children or in the immunosuppressed.
General symptoms: fatigue, malaise, fever, weight loss, anorexia, failure to thrive and fever of
unknown origin (FUO).
Pulmonary: respiratory TB accounts for 60% of cases in the UK. Symptoms include chronic,
productive cough with purulent ± bloodstained sputum. May result in lobar collapse, bronchiectasis,
pleural effusion and pneumonia.
Genitourinary: the most common site outside the lungs often presents with 'sterile' pyuria. There may
be kidney lesions, salpingitis, abscesses and infertility in females and swelling of the epididymis in
Musculoskeletal: arthritis, osteomyelitis and abscess formation, particularly in the spine (Pott's
Central nervous system: tuberculous meningitis and tuberculomas.
Gastrointestinal: mainly ileocaecal lesions but occasional peritoneal spread causes ascites
Lymph nodes: hilar, paratracheal or superficial node involvement. Palpable nodes may be initially
tender, firm and discrete but later matted and suppurative with discharging sinuses.
Skin: erythema nodosum (represents an early immunological response to infection), erythema
Chest x-ray (CXR) is essential even in non-pulmonary disease, as there may have been
Primary TB usually appears as a central apical portion with a left lower-lobe infiltrate or
Reactivated TB - there is no pleural effusion and lesions are apical in position.
Severe disease with poor immune response can produce a picture like millet seeds over the
CXR. Hence the name miliary tuberculosis
Pulmonary TB is unlikely with a normal CXR.
Even patients with non-pulmonary disease may have CXR findings due to initial lung
infection. Typical appearances include:
Patchy or nodular shadows in the upper zones, loss of volume, fibrosis ± cavitation
Uniform 1-10 mm shadows throughout the lung in miliary TB
Firm diagnosis rests on isolating the infecting organism, and subsequent sensitivity
testing can be used to guide antibiotic therapy. Isolation of the organism can be difficult.
Possible specimens include:
Early morning urine
An anteroposterior X-ray of a
patient diagnosed with
pulmonary tuberculosis. This
AP X-ray of the chest reveals
the presence of bilateral
pulmonary infiltrate (white
triangles), and “caving
formation” (black arrows)
present in the right apical
region. The diagnosis is far-
This is a close-up of a
culture revealing this
morphology. Note the
colourless rough surface,
which are typical
seen in M. tuberculosis
colonial growth. Macroscopic
examination of colonial
growth patterns is still one of
the ways micro-organisms
are often identified.
Microscopy using concentrated sputum smears is much more
sensitive than with unconcentrated sputum.
If sputum cannot be expectorated or repeated specimens are
negative, bronchoscopy and bronchial washings should be
Samples are analysed by:
Staining with Ziehl-Neelsen (ZN) stain and rapid direct microscopy
for acid/alcohol-fast bacilli.
Culture on a Lowenstein-Jensen slope which takes 4-8 weeks due to
slow bacterial growth.
Antibiotic sensitivity cultures take a further 3-4 weeks. Rapid
detection of rifampicin resistance from cultured M. tuberculosis is
now possible using molecular techniques. Results are fairly accurate
and allow appropriate treatment to begin more promptly; however,
results must still be confirmed with conventional techniques.
Anatomic pathology involves examining tissue for signs of TB. Tissue
samples may be obtained either by biopsy from a patient or at autopsy.
Histology consists of macroscopic examination of lesions that suggest the
presence of tuberculosis if the pathologist has access to all or a large part of
the affected organ (lymph node or kidney), and microscopic examination
of a sample.
Multiplication of tubercle bacilli in any site of the human body causes a
specific type of inflammation, with formation of a characteristic
granuloma. Multinucleate giant cells are also seen.
Histology is an aid to diagnosis when bacteriological techniques cannot be
It is especially useful for extrapulmonary tuberculosis.
It is helpful to consider histological examination and bacteriological
techniques as complementary.
Carbol-fuchsin methods (ZN or Kinyoun) can be used to positively identify
M. tuberculosis bacteria.
(stained red; ZN) in
The definitive diagnosis is
simple when the patient has
large numbers of bacilli in
the sputum (more than 5000
bacilli/ml), as these can be
seen on microscopic
examination of a sputum
smear; these patients are
Under the microscope
multinucleate giant cells and
granulomatosis are seen
Caseous necrosis and
The follicle is surrounded by
a crown of lymphocytes; in
the centre are two giant cells
and acluster of epithelioid
bacteria using acid-
The acid-fast stains depend
on the ability of
mycobacteria to retain dye
when treated with mineral
acid or an acid-alcohol
solution such as the Ziehl-
Neelsen, or the Kinyoun
stains that are carbol fuchsin
methods specific for M.
Caused by M. leprae and more rarely by M.
An obligate intracellular bacterium due to the loss of
genes necessary for independent growth
Infects schwann cells causing damage to myelin and
Not highly infectious
Transmission is by prolonged close contact with
untreated infected persons (10% of untreated are
infectious) by droplets from the nose and mouth
Predominantly occurs in poor populations (Africa,
Infection may spontaneously resolve in otherwise
Residence or visit to high risk area/proximity to affected persons in
the last 2-20 years (slow growth, average incubation 7 years)
Observation of hypopigmented/erythematous lesions with reduced
sensation on touch test (light touch with cotton bud, subject with
Swollen peripheral nerves
Skin biopsy, scraping or slit smear; Wade-Fite (modified ZN)
staining shows red rod-shaped organisms (usually against blue
Phenolic glycolipid-1 (PGL-1) ELISA
Fluorescent leprosy antibody absorption test (FLA-ABS)
Paucibacillary (Tuberculoid form)
single or only a few hypopigmented skin lesions with
reduced sensation, may be macular or plaque-like
Multibacillary: (Lepromatous form)
multiple (>5) hypopigmented and reduced sensation or
erythematous skin lesions (sometimes poorly defined)
which may be nodular.
Lesions most commonly arise in “cool” areas of the body
(face, ears, arms, knees, buttocks)
Active cell-mediated immune
response to infection, single
or only a few hypopigmented
skin lesions with reduced
sensation, may be macular or
no effective cell-mediated
response to infection,
multiple (>5) hypopigmented
and reduced sensation or
erythematous skin lesions
(sometimes poorly defined)
which may be nodular
Nodular type lesions
Leprosy Microscopic Appearance
H&E – histiocytic granulomas (non-caseous) with a heavy surrounding lymphocytic
infiltrate throughout dermis, particularly in relation to small nerves
Langhans giant cells often present – fused macrophages with peripheral nuclei
Wade Fite – bacteria not seen
Gram – negative
H&E – subcutaneous deposits of macrophages filled with lipid and bacilli (foamy)
Langhans giant cells
band of Unna – acellular band below epidermis
Lymphocytes few or absent
Nerves typically show lamination – onion peel appearance
Globi are often seen – Brown bodies thought to be degenerate forms of macrophages in
which the organisms are no longer viable and have become granular or amorphous).
Wade Fite – red stained bacilli seen throughout (rod-shaped bacilli and granular
elements); within macrophages, surrounding nerves (sheath and intraneurally)
Gram – negative
Inflammation of the erector
Indeterminate leprosy. There
is a superficial and deep
infiltrate of lymphocytes with
Epithelioid cells are present
deep infiltrate of
Tuberculoid leprosy. Non-
caseating granulomas extend
throughout the dermis
Tuberculoid leprosy. A deep
cutaneous nerve contains a
Lepromatous leprosy with
masses of organisms (globi)
in the cytoplasm of
Numerous acid-fast bacilli
(red) are present within
macrophages and lying free
in the dermis
M. leprae (red)
Other non-culturable bacterial
Treponema pallidum subspecies
Does culture contribute to a quick and early diagnosis?
Unfortunately, leptospires grow slowly so that, by the time they can
be identified in the culture, the patient will already have antibodies
detectable by serology. For this reason, culture does not contribute to
a rapid diagnosis in the early phase of the disease. It is also a
relatively insensitive diagnostic method. However, culture may be a
useful method of diagnosing leptospirosis in patients who die soon
after the onset of symptoms and before antibodies can be detected.
Biopsies should not be done purely to identify H.
pylori (HP); there are equally good alternative and
much cheaper tests. (RCPath)
Immunohistochemical staining H. pylori colonized on the
of H. pylori from a gastric biopsy surface of regenerative
Treponema pallidum subspecies
T. pallidum endemicum (Bejel)
T. pallidum carateum (Pinta)
T. pallidum pertenue (Yaws)
T. pallidum pallidum (Syphilis)
Infection caused by the spirochete Treponema pallidum
pallidum; can be primary, secondary or tertiary.
T. pallidum pallidum enters via abraded skin or intact mucous
membrane and distributes via the blood stream and
lymphatics after an incubation period of around 3 weeks
(range 2-6 weeks).
In 2003, there were 1,580 cases diagnosed in STD clinics in
England, Wales and Northern Ireland. The highest rates of
syphilis are seen in women aged 20-24 and men aged 25-34
The tertiary stage is now rarely seen in the UK, possibly
because those affected many years ago have received
antibiotics for other infections in the intervening time.
Primary lesion develops at the site of infection, which heals in 2-6
Small, painless papule that rapidly forms an ulcer (the chancre). The
chancre is usually single, round or oval, painless, surrounded by a
bright red margin and indurated with a clean base, and discharging
Chancres may be atypical, e.g. multiple, painful, purulent, destructive
and may be extra-genital.
Usually found in heterosexual men on the glans and inner surface of
the prepuce but may appear on the shaft and beyond. In homosexual
men, usually found in the anal canal and less frequently in the mouth
and genitalia. In women, found on the vulva, labia and much less
frequently on the cervix.
Extra-genital sites are the lips, mouth, buttocks and fingers.
Enlarged regional lymph nodes that are painless, discrete, firm and not
fixed to surrounding tissues.
Secondary syphilis often appears 6 weeks after the beginning of the primary
lesion but may overlap or not appear for several months.
Multisystem involvement occurs within the first two years of infection.
Systemic symptoms are mild or absent, but include night time headaches,
malaise, slight fever and aches.
A generalised polymorphic rash often affects the palms, soles and face. The rash
is classically non-itchy but may be itchy, especially in dark-skinned patients. It
is associated with generalised painless lymphadenopathy.
Papules enlarge into condylomata lata (pink or grey discs) in moist warm areas.
Papule lesions disappear spontaneously.
There may also be mucocutaneous lesions.
Less common presentations include patchy alopecia, anterior uveitis,
meningitis, cranial nerve palsies, hepatitis, splenomegaly, periostitis and
In 80% of cases, patients enter the latent asymptomatic stage which for over
half of them persists for life. In about 20% of patients, an infectious relapse
occurs during the next year.
This consists of three major clinical manifestations, which may co-exist:
Asymptomatic neurosyphilis: late syphilis with abnormal CSF examination but with no associated
neurological symptoms or signs.
Symptomatic neurosyphilis: the most common presentations are dorsal column loss (tabes dorsalis),
dementia (general paralysis of the insane) and meningovascular involvement.
Characterised by an aortitis, which usually involves the aortic root but may affect other parts of the
aorta usually spreading distally from the aortic root.
The most frequent clinical manifestations are aortic regurgitation, aortic aneurysm and angina.
Inflammatory fibrous nodules or plaques, which may be locally destructive.
Can occur in any organ but most commonly affect bone and skin.
Characterised by positive serological tests for syphilis with no clinical evidence of
treponemal infection within the first two years of infection.
Treponemal tests (the TPHA test and the TPPA test are generally used for screening):
T. pallidum particle agglutination assay (TPPA): incubation period 4-6 weeks (incubation period is the
usual time after infection that the test becomes positive).
T. pallidum haemagglutination assay (TPHA): incubation period is 4-6 weeks.
Enzyme immunosorbant assay (EIA) IgG/IgM: incubation period is 3 weeks.
Fluorescent treponemal antibody absorption (FTA-ABS) test; is reactive in 85% of primary cases, in 99-
100% of secondary cases, and in 95% of latent or late cases. It should be used as a confirmatory test for
positive VDRL or RPR test findings (see below).
Non-treponemal tests; give a titre that acts as measure of disease activity, i.e. the titre is reduced with
treatment and raised with reinfection. False positives occur with other acute and chronic infections
and autoimmune diseases.
Rapid plasma reagin (RPR): incubation period is 4 weeks.
Venereal Disease Reference Laboratory (VDRL): incubation period is 4 weeks.
Serological tests cannot differentiate from other treponemal infections, e.g. yaws (caused by the non-
sexually transmitted organism T. pertenue).
Demonstration of T. pallidum:
From lesions or infected lymph nodes in early syphilis
Dark field microscopy
Direct fluorescent antibody (DFA) test
Polymerase chain reaction (PCR)
Secondary syphilis. The
perivascular infiltrate of
inflammatory cells includes
some plasma cells.
Secondary syphilis. There is a
superficial and deep
perivascular infiltrate in the
Late secondary syphilis. A
granuloma is present in the
Warthin & Starry also used
Pathogenic species cause Leptospirosis (Weil’s disease)
Leptospirosis is an infection of worldwide distribution
caused by spirochetes of the genus Leptospira, which infect
many species of both wild and domestic animals.
The principal source of human infection is the rat but other
sources include dogs, livestock and other wild animals.
Disease is acquired through contact with contaminated
water or soil, or through contact with urine or tissues of
The spirochetes are shed from the urine and can survive in
the environment for several months in moist, warm
They enter the bloodstream through abraded skin or the
mucosa from contaminated water or soil.
Reported to be the most widespread zoonosis in the world
(having an incidence greater in warm-climate areas than in
A large proportion of the population is antibody positive in
areas such as rural Belize and Vietnam. Leptospirosis is a
significant human disease in eastern and southern Europe,
Australia and New Zealand.
Most often affects teenagers and adults and is more
common in men.
Risk factors include sewage workers, travellers (e.g.
swimming in contaminated water), farmers, veterinarians,
abattoir workers, rodent control workers, and other
occupations with animals.
Incubation period is usually 7-14 days but can range from 2 to 25 days. Onset is usually abrupt.
Many infections are mild with fever, headache, myalgia, anorexia, nausea and vomiting, dry cough
and lethargy. Affected patients may not seek medical attention.
The anicteric form may cause pneumonitis, arthritis, orchiditis, cholecystitis, myocarditis, coronary
arteritis, aortitis, aseptic meningitis and uveitis.
Approximately 10% of those infected become jaundiced (with hepatocellular necrosis) and have a
severe and rapidly progressive form of the disease with liver failure and renal failure.
The jaundice appears during days 5-9 of illness and is most intense 4-5 days later, continuing for
about 1 month.
The degree of jaundice itself is not indicative of prognosis but leptospirosis without jaundice is very
Purpura, petechia, epistaxis, minor haemoptysis and other signs of bleeding are common.
Other symptoms include fever, vomiting, abdominal pain, skin rashes, conjunctival haemorrhage,
uveitis. There is often a severe headache, retro-orbital pain, and photophobia. A severe myalgia (lower
back, and legs) is common. Leptospirosis may present as aseptic meningitis.
Pulmonary symptoms vary from cough, dyspnoea, and haemoptysis to adult respiratory distress
syndrome and massive pulmonary haemorrhage.
Hepatomegaly: hepatic percussion tenderness is a useful indicator of continuing disease activity.
Kidney dysfunction (Leptospiral nephropathy) is usual, sometimes with life threatening renal failure
with signs of uraemia and disturbance of consciousness.
Liver function tests: increased serum bilirubin, transaminases
Prolonged prothrombin time
Full blood count: thrombocytopenia, leucocytosis and anaemia
Renal function and electrolytes (renal failure); serum amylase levels
are raised in acute renal failure
Raised creatine kinase (muscle involvement, rhabdomyolysis)
Mid-stream urine (MSU) usually shows sediment and proteinuria
CXR may be normal or show patchy shadowing in alveolar
Diagnosis is based on serology (paired), either using microscopic
slide agglutination test or new rapid sero-diagnostic kits
Enzyme-linked immunosorbent assay (ELISA); has greater
sensitivity and comparable specificity to microscopic slide
Silver staining: Steiner or Warthin-Starry
Direct immunofluorescence staining using rabbit
(Sheldon, 1953) or fluorescein-labelled mouse
monoclonal antibodies (Stevens et al., 1985; Zaki &
Immunoperoxidase staining (Tripathy & Hanson,
In situ hybridization using DNA probes (Terpstra et
Generally not used in diagnosis
Skin rashes are a common
Although this technique is
described in textbooks as a
useful method of
demonstrating leptospires in
fluids, it has sometimes proved
to be of doubtful value even in
the hands of very experienced
Serum protein and fibrin
strands and other cell debris in
blood resemble leptospires,
while the concentration of
organisms in the urine of
humans and animals is
frequently too low to be
detectable by this method. Care
and great experience are
therefore necessary to avoid
mistaking artefacts for
Photomicrograph of kidney
tissue, using a silver staining
technique, revealing the
presence of Leptospira
Lyme disease group
Lyme disease Aetiology
The spirochete responsible is transmitted from host to host by Ixodes species or deer
ticks. Understanding the life cycle of these organisms gives better understanding of the
epidemiology and other clinical aspects of Lyme disease and prevention of Lyme disease.
The Ixodes tick:
Is made up of different species, found in different areas of the world. For example:
Ixodes persulcatus and Ixodes ricinus (European ticks), Ixodes scapularis, Ixodes
Emerges in a larval form in the summer and feeds just once on a host animal (often a
In the spring the larva becomes a nymph and feeds, again only once, from similar animal
host. Humans can be victims in the nymph stage (85% of tick bites in humans occur at
this time in spring and early summer).
In the autumn the adult tick finally emerges to feed on deer, again just once. Humans can
be hosts at this stage (15% of tick bites in humans are at this stage and occur in the
The spirochete responsible:
Is transmitted by the tick. The tick must have fed on a host significantly infected with spirochete
to pass on the infection to man.
Once it infects the tick has to go through a particular cycle of multiplication and dissemination
to salivary glands within the tick before it can be passed on to the animal victim. Hence a tick
must be attached for 2-3 days to a person before infection can be passed on.
In the UK, areas where infection is acquired include: Exmoor, The New Forest, The South Downs,
Parts of Wiltshire and Berkshire, Thetford Forest, The Lake District, The Yorkshire moors and The
About 20% of confirmed cases are reported to have been acquired abroad (The United States, France,
Germany, Austria, Scandinavia, Eastern Europe)
Laboratory-confirmed reports of Lyme borreliosis have risen steadily since reporting began in 1986.
Several factors have contributed to the observed increase, including increased awareness of the
disease, access to diagnostic facilities, more sensitive diagnostic methods, the enhanced surveillance
scheme (introduced in 1996) and since 2000, more complete reporting of cases.
Other possible factors producing a real increase include changes in the geographical ranges of I.
ricinus both in the UK and Europe (successive mild winters), more recreational travel to high
endemic areas and the increasing popularity of activity holidays (walking, trekking and mountain
Over 3,000 reports of Lyme borreliosis have been received since 1986, almost 2,800 of which have
been reported since the introduction of enhanced surveillance in 1997.
Mean annual incidence rates for laboratory-confirmed cases have risen from 0.06 per 100,000 total
population for the period 1986 to 1992, to 0.64 cases per 100,000 total population in 2002, to 1.1 cases
per 100,000 total population in 2005. The highest rates in the United States are 69.9 cases per 100,000
persons in Connecticut.
Lyme disease occurs in temperate regions of North America, Europe, and Asia.
In some of Europe, the incidence of Lyme disease has been estimated to be over 100 per 100,000
people a year.
Lyme disease infection has occurred in northern forested regions of Russia, in China, and in Japan.
It has not been found in tropical areas or in the southern hemisphere.
Some infected people will have no symptoms. Up to 64% of patients with Lyme disease do not remember being bitten.
Early Lyme Disease (Stage 1 or localised disease):
The characteristic manifestation is erythema migrans: A circular rash at the site of the infectious tick attachment that
radiates from the bite, within 2 - 40 days. It expands over a period of days to weeks in 80-90% of people with Lyme
Fever, arthritis, musculoskeletal symptoms and local lymphadenopathy may occur in about two thirds of patients but one
third of patients will develop no further symptoms.
Disseminated Lyme disease (or stage 2 disease ). This disseminated stage is still considered to be early infection and
occurs weeks to months later, with:
Flu-like illness, oligoarthralgia (60%). Typically with myalgia, multiple erythema migrans and sometimes systemic upset.
Malaise and fatigue are very marked
Intermittent inflammatory arthritis
Central nervous system disorders (15%):
Cardiovascular problems (10%):
Occasionally hepatitis, orchiditis, uveitis and panophthalmitis.
Late manifestations of Lyme disease (or stage 3 disease):
These late manifestations typically include prolonged arthritis, polyneuropathy, encephalopathy and symptoms consistent
Chronic lyme arthritis - a chronic erosive arthropathy typically involving knees.
Acrodermatitis chronica atrophicans . This is a blueish discolouration (usually lower leg over extensor surfaces) signifying
epidermal atrophy usually with mild sensory neuropathy and myalgia.
Chronic neurological syndromes
There is currently no definitive test. Lyme disease is a clinical diagnosis and tests
should be used to support clinical judgement. The most useful tests are antibody
detection tests. The only national guidelines for testing come from the US Centers for
Disease Control and Prevention (CDC). They recommend a 2 step testing process:
1. Lyme disease symptoms (other than erythema migrans) - antibody titre (total or IgG
2. Confirm positive titres with a Western blot.
Antibody testing in patients with erythema migrans is unhelpful because the rash
develops before the antibodies.
Serology may help in cases of endemic exposure who have clinical features suggestive of
Serology (ELISA) remains negative for several weeks in the initial phase, but is usually
positive in serum and CSF in disseminated stage. False positives may occur with other
Polymerase chain reaction (PCR) may identify very small numbers of spirochetes in
samples, and may influence decisions about whether to treat asymptomatic
individuals with positive serology. Usually however PCR techniques are not helpful
because of the uncertain correlation between positive results and the presence of live
organisms in biological fluids.
A circular rash at the site of
the infectious tick
attachment that radiates
from the bite, within 2 - 40
days. It expands over a period
of days to weeks in 80-90% of
people with Lyme disease.
Spirochetes, or “corkscrew-
shaped” bacteria Borrelia
burgdorferi, which is the
pathogen responsible for
causing Lyme disease.
Borrelia burgdorferi are
helical shaped bacteria, and
are about 10-25µm long
Viruses – Traditional Methods
Phloxine-tartrazine for viral inclusions
Selectivity of this method relies on the removal of the
red stain (phloxine) from other tissue elements. Keratin
can retain the dye and mimic the appearance of viral
Shikata’s orcein for hepatitis B surface antigen
Method can be capricious. Depends on freshly prepared
solutions and has poor selectivity.
There are multiple antibodies available including those
against adenovirus, CMV, hepatitis B, HIV, HPV, and
In situ hybridisation
Many probes becoming available including Epstein-Barr
Virus, CMV and human herpesvirus-8
Hodgkin lymphoma (FFPE)
stained with Anti-Epstein-
Human condyloma (FFPE)
stained with Anti-HPV
cervical cytology specimen,
LSIL, stained with
GenPoint™ HPV, Biotinylated
DNA Probe Cocktail
Visualization of SARS
coronavirus in Lung tissue
of infected C57BL6 mice by
In Situ Hybridization
using a Digoxigenin
labeled probe. (research)
Creutzfeldt-Jakob disease (CJD) is the best known of
the human prion diseases
Fatal familial insomnia (sFI) and Kuru
Caused by misfolding of normal prion protein (PrPC)
to the disease type (PrPSc) and aggregation in amyloid
The causative agents are believed to be misfolded
The prion can be transmitted by ingestion, after which it multiplies in the
lymphoreticular system, usually spleen and lymph nodes, from where it enters
the spinal cord and it spreads to the brain. There seems to be a genetic
predisposition by being methionine homozygous at codon 129 of the prion
protein gene (PRNP).
Proposed mechanism of prion propagation
It has been recognized that prion diseases can arise in three different ways:
acquired, familial, or sporadic. It is often assumed that the diseased form
directly interacts with the normal form to make it rearrange its structure. One
idea, the "Protein X" hypothesis, is that an as-yet unidentified cellular protein
(Protein X) enables the conversion of PrPC to PrPSc by bringing a molecule of
each of the two together into a complex.
Current research suggests that the primary method of infection in animals is
through ingestion. It is thought that prions may be deposited in the
environment through the remains of dead animals and via urine, saliva, and
other body fluids. They may then linger in the soil by binding to clay and other
There is a National CJD Surveillance Unit (NCJDSU) based at the Western
General Infirmary in Edinburgh, which brings together a team of clinical
neurologists, neuropathologists and scientists specialising in the investigation
of this disease. Between 1990 and 2011 the number of recorded deaths in the
UK from the various forms, based on NCJDSU information were:
Sporadic - 1289
Familial - 92
vCJD - 176
Total - 1670 (includes 45 cases of GSS syndrome)
Press coverage of this issue gave the impression that the streets would be
littered with the dead of vCJD and many people were very concerned about the
possibility of catching the disease. This was based on the assumption of wide
exposure to BSE infection in cattle, producing estimates of eventual total
numbers of cases of vCJD in the UK in excess of 100,000. In 2004 it was
estimated that the total number of cases would not exceed 2,000. In the rest of
the world there have been 49 cases including 25 in France, 5 in Spain, 4 in
Ireland, 3 in USA and Netherlands, 2 in Italy and Portugal, and 1 in Saudi
Arabia, Japan and Taiwan. Incidence in the UK peaked in 2000 when there
were 28 cases of vCJD.
Sporadic CJD usually affects middle-aged or older people, whilst vCJD affects young adults; however,
there are overlaps. The oldest case of vCJD was aged 74 and sporadic and hereditary cases have
affected those in their teens and twenties. Why vCJD should have a predilection for young people is
The duration of illness is not a rigid guide but usually cases of vCJD have durations of a year or more.
The duration of sporadic CJD is typically a few months, and, in a few cases, a few weeks.
The symptoms of sporadic and vCJD tend to be different. Sporadic CJD usually presents with a clearly
neurological illness that is very rapidly progressive. In vCJD, the initial presentation is often with
psychiatric or behavioural changes and it may not be clear that there is neurological illness until
several months after the onset. An experienced neurologist can normally distinguish the clinical
patterns of sporadic and vCJD but there is some overlap in the symptoms of the two forms, and, on
occasions, it may be difficult to be certain as to the classification of the type of CJD if this were based
on the clinical symptoms alone.
Neurological features include progressive ataxia, dementia and involuntary movements that may be
choreiform or dystonic, often changing into myoclonus
In the hereditary form, clinical features differ between families and the disease lasts longer than in
the sporadic form
In the iatrogenic form, clinical features and the course of the disease depend upon route of
transmission. Where there is implantation into the CNS, most cases present with progressive
dementia similar to the sporadic form. With peripheral transmission, as with injections of pituitary
hormones, it presents with progressive cerebellar ataxia with cognitive impairment appearing later.
With inoculation into the CNS, symptoms can appear after around 18 months but, with other routes,
it is around 12 years and may be up to 30 years.
Brain biopsy is only considered if there is a good chance of another diagnosis.
Tonsil biopsy in vCJD can support diagnosis.
EEG shows periodic wave complexes in sporadic CJD but not vCJD. Further
biochemical markers in the CSF namely, 14-3-3 may be useful in sporadic CJD
where the clinical manifestations have been present for under 2 years it is
MRI can help distinguish between sporadic CJD and vCJD. In vCJD there is
changes including high signal in the posterior thalamus (has high sensitivity
and specificity). On the other hand in sporadic CJD there is increased intensity
in the caudate nucleus and putamen.
The neuropathological features of sporadic CJD and vCJD are quite distinct and
this is the only definitive way to distinguish between the two. Therefore, if
there has been neither a brain biopsy in life, nor at post mortem, then the
diagnosis cannot be made with absolute certainty. However, where a diagnosis
of probable sporadic CJD has been made in life, it has been correct in 95% of
cases and at post mortem the in vivo diagnosis of probable vCJD is yet to be
Transverse FLAIR MRI
showing bilateral anterior
basal ganglia high signal of
Transverse FLAIR MRI
showing bilateral and
symmetrical high signal in
the pulvinar nuclei of the
thalamus - the 'pulvinar
sign' of variant CJD
Microscopic "holes" are
characteristic in prion-
affected tissue sections,
causing the tissue to develop
a "spongy" architecture
Examination of brain tissue
reveals florid plaques of
agglomerated prions and
Tonsil biopsy in vCJD.
Malaria is a parasitic disease caused by infection by species of the genus
Plasmodium falciparum Responsible for severe disease and malaria related
Plasmodium vivax Causes benign tertian malaria – fever every 3rd day
Plasmodium ovale Relapsing course as with P. vivax
Plasmodium malariae Causes benign quartan malaria - fever every 4th day
A fifth species causing malaria in humans, Plasmodium knowlesi, has recently
emerged. It is distributed across South East Asia and is often misdiagnosed by
microscopy as P. malariae but infection has a potentially more serious and
even life-threatening course.
Humans acquire malaria after being bitten by an infected mosquito. The
sporozoites in the mosquito saliva then travel via the bloodstream to the liver
where they mature or, in certain species, may lie dormant (when they are
known as hypnozoites). The mature organisms then rupture to release further
organisms (merozoites) into the blood, where they invade red blood cells and
undergo asexual reproduction. Feeding mosquitoes ingest these in a blood
meal, and in the mosquito gut they undergo sexual reproduction to produce
thousands of infective sporozoites, and the cycle continues.
Malaria occurs almost exclusively in the tropics and subtropics, and approximately 40% of the world's
population, mostly those living in the world's poorest countries, are at risk of malaria. Every year,
more than 500 million people become severely ill with malaria - most cases and deaths occur within
The groups most at risk of developing severe disease are:
The poor (60% of deaths from malaria worldwide occur in the poorest 20% of the population due to lack of
access to effective treatment)
Young children and infants
Pregnant women (especially primigravidae)
Nonimmune people (e.g. travellers, foreign workers)
Malaria is the most common imported tropical disease to the UK with 1,500-2,000 cases reported
Risk of contracting malaria in travellers to these areas is proportional to the number of potentially
infectious mosquito bites they receive. Risk factors for malaria in travellers, therefore, include:
Travel to areas of high humidity and ambient temperature between 20-30°C (there is no malarial transmission
<16°C or at altitudes >200 m above sea level)
Travel at times of high seasonal rainfall
Visits to rural locations (risk of contracting malaria in African villages is eight times that in its urban areas)
Staying in cheap backpacker accommodation
Being outdoors between dusk and dawn
Longer durations of travel
In view of the life-cycle of the malaria parasite, symptoms may occur from 6
days of naturally acquired infection to many months later. Most patients with
P. falciparum infection present in the first month or within the first six months
of infection. P. vivax or P. ovale infections commonly present later than 6
months after exposure, and sometimes after years.
There are no specific symptoms of malaria - so it is critical to consider the
possibility of the diagnosis. Most missed malarial infections are wrongly
diagnosed as nonspecific viral infections, influenza, gastroenteritis or
hepatitis. Children, in particular, are more likely to present with nonspecific
symptoms (fever, lethargy, malaise, somnolence) and to have gastrointestinal
Fever, often recurring; Chills; Headache; Cough; Myalgia; Gastrointestinal upset
Fever; Splenomegaly; Hepatomegaly; Jaundice; +/- abdominal tenderness
Signs of severe disease (usually P. falciparum)
Impaired consciousness; Shortness of breath; Bleeding; Fits; Hypovolaemia;
Hypoglycaemia; Renal failure; Nephrotic syndrome; Acute respiratory distress
syndrome (during treatment)
Thick and thin blood smears stained with Giemsa stain remain the 'gold standard'. Advantages
include low cost and high sensitivity and specificity when used by well-trained staff. Where
there is suspicion of malaria, a venous blood specimen in an EDTA tube should be sent to the
lab in under an hour. If there is potential for delay, refer the patient to hospital for testing.
Where the blood film is negative, at least 2 further films should be obtained over the next 48
hours, before excluding the diagnosis. Be aware that an individual can have malaria
despite a negative film. This is particularly the case in pregnancy where parasite biomass can
be sequestered in the placenta - seek expert help early if concerned. See separate article Malaria
Rapid diagnostic tests (or 'dipstick' tests) which detect parasite antigens are available and are
easier to use for staff without microscopy training, have less waiting time and indirect costs but
have been relatively more expensive. These tests may have uses in remote areas without formal
medical facilities but there is a risk that travellers use them incorrectly and delay treatment as a
PCR is becoming available, but remains expensive and requires specialist equipment.
Other investigations frequently performed include:
Full blood count - typically reveals thrombocytopenia and anaemia. Leukocytosis is rarely seen
but is an indicator of a poor prognosis when present.
G6PD activity - prior to giving primaquine.
Liver function tests - often abnormal.
Urea and electrolytes - may show lowered Na+ and increased creatinine.
Low blood glucose may be present in severe disease.
P. falciparum. Several red
blood cells have ring stages
inside them. Close to the
centre there is a schizont and
on the upper left a
The liver tissue at autopsy
exhibits stasis of red cells
containing coarse malaria
pigment in the sinusoid,
and activation of Kupffer
cells, phagocytizing the
infected red cells (Giemsa).
In case of falciparum
malaria, the red cells
infected by trophozoites
and schizonts are trapped
to the endothelial cells via
CD36 and ICAM-I, so that
these cells are not seen in
the peripheral blood.
The spleen is soft,
swollen and black in
color (gross findings).
Histologically, the red
pulp is filled with
pigments. The cause of
death was coma due to
Other Protozoan Diseases
Trypanosomiasis “Chagas disease”
Pathophysiology Cryptosporidial oocysts when ingested are immediately
infectious at quite low doses (10 to 1,000 oocysts required to produce human
disease). Oocysts attach to cells of the small bowel and invade the cells of the
intestine. They become intracellular but extracytoplasmic and are resistant to
treatment. The life cycle is completed in the host and large numbers of oocytes are
then excreted with the potential to spread the infection.
Transmission is: From personal contact with infected individuals Waterborne.
Foodborne (salads, meat products, unpasteurised dairy products and milk). From
infected patients in hospital.
Presentation Mild fever (59% of consulting patients). General malaise progressing
rapidly to further symptoms. Sudden onset of watery diarrhoea (often green and
offensive, sometimes with blood) accompanied by abdominal cramps, nausea and
anorexia (96% of consulting patients). Symptoms are prolonged and last on average
for two weeks but can persist for up to one month.
Investigations Stool microscopy for oocysts. Special tests and staining can be used,
including immunofluorescent assays, enzyme-linked immunosorbent assay (ELISA)
and the most sensitive polymerase chain reaction (PCR) assays. Stool culture
(negative). Urea and electrolytes; liver function tests may be necessary in more
Ileal biopsy. A small number of tiny basophilic particles seen on
the surface of the enterocytes (HE)
Acid-fast cysts in diarrheal stool (Ziehl-Neelsen)
Transmission: Giardia is transmitted via the faeco-oral route.
Transmission is usually via contaminated drinking water. Other
possible sources are ingested food, contaminated swimming pools, and
direct contact with infected people, animals or contaminated objects.
In the UK, many cases are associated with recent foreign travel.
Symptoms: Acute or chronic diarrhoea. Malabsorption, weight loss.
Abdominal pain, anorexia, flatulence, bloating, and nausea.
Signs: No physical signs
Stool microscopy is the usual test: About 60% of giardial infections are
identified using a single sample, and >90% are identified after three stool
Other tests for giardiasis are: Stool antigen tests are available and may be
the best test.
DNA probes for Giardia species are available.
Other tests: duodenal samples for microscopy can be obtained by biopsy
Duodenal biopsy (abdominal discomfort and mild diarrhoea)
Chronic active duodenitis with lymphoid follicle formation (HE)
Trophozoites of G. lamblia seen in the lumen of the duodenal
mucosa (HE, high power)
Trophozoites of Giardia lamblia seen in bile. Flagellated and
binucleated giardial trophozoites are co-infected with bacteria in the
Distribution of CD3-positive T-cells in the duodenal mucosa showing
marked increase of intraepithelial lymphocytes (IHC).
CD79a-positive B-cells are seen in the lymphoid follicle, in association
with focal intraepithelial clustering (IHC).
Transmission: Human domestic cats are the main source of infection.
Infectious oocysts are excreted by the cat for up to two weeks after the
initial infection and can survive in warm, moist soil for more than 1
year. Humans acquire infection from cats or from eating raw or
undercooked meat from another intermediate host. Human to human
transfer only occurs via the maternal-foetal route but is being seen with
increasing frequency in patients whose immunity is compromised by
Epidemiology: T. gondii is worldwide in distribution but the disease
occurs less frequently in areas where the environment is unfavorable
for the oocysts, such as higher altitudes and extremes of temperature.
Acquired Infection: These are usually mild and commonly present as
asymptomatic lymphadenopathy, often localised to the neck, but
sometimes more generalised. The condition usually resolves within one
to three months, but can last up to a year. A generalised non-pruritic
skin rash may occur; usually transient and most pronounced on the
trunk and proximal extremities.
Lab Studies - The immunoglobulin M (IgM) immunofluorescent antibody test
(IgM-IFA) is used as standard for the diagnosis of acute toxoplasmosis. An IgM-IFA
titre of 1:160 or greater or an IgM-enzyme-linked immunosorbent assay (IgM-
ELISA) titre of 1:256 or greater is considered diagnostic of recently acquired
infection. In cases of diagnostic difficulty, T. gondii-specific IgG and polymerase
chain reaction (PCR) tests have been used.
Imaging Studies - MRI is considered the best diagnostic imaging technique for
toxoplasmic encephalitis and may detect lesions not visualised on CT scan.
Ultrasound screening throughout pregnancy in pregnant women known to be
infected helps to identify infected foetuses.
Other Tests - Cerebrospinal fluid may show elevated protein, normal glucose and
mononuclear pleocytosis. The presence of tissue cysts is diagnostic for
toxoplasmosis but does not distinguish between acute and chronic infection.
Indirect latex agglutination test and enzyme-linked immunosorbent assays may be
The presence of tachyzoites or toxoplasmal antigens in tissue or smears may be
contributory in confirming acute infection.
Brain biopsy may reveal the presence of tachyzoites and may be required for
patients with suspected toxoplasmic encephalitis who have negative serology or
who fail to respond to two week's empirical treatment. This investigation is being
supplanted by less invasive methods in many cases.
Trophozoites (High power) Giemsa stain
Multifocal interstitial lung lesions. Alveolar pneumocytes are
infected by Toxoplasma gondii, presenting tachyzoite-filled
terminal colonies (HE).
Toxoplasma gondii antigens are demonstrated in a good number
of stromal cells in the fibrotic lesion (IHC using a research pab).
Multifocal necrotizing brain lesions. The tachyzoites within the
pseudocysts are stained black with Grocott's silver. PAS reactivity
is also noted.
Transmission: by contamination with infected faeces of reduviid bugs (known as kissing,
assassin, or cone-nosed bugs) when they drop faeces and urine onto the host during or shortly
after feeding. These then enter the body when rubbed into abrasions, mucosa, or conjunctiva.
It can also be acquired via blood transfusion and congenitally.
Epidemiology: It is found in South America and the South and Southwestern USA. It is
estimated that 16 to 18 million people in South and Central America are infected with
Trypanosoma cruzi and that 50,000 die of the disease each year. In some communities, over
70% of the population are seropositive with an estimated 300,000 new infections occurring in
Latin America every year.
Acute phase features:
Fever, headache and myalgia
Generalised lymphadenopathy occurs in 60%
Facial or generalised oedema
Hepatosplenomegaly, particularly in children
Diarrhoea, vomiting and anorexia
Other classical features include:
Unilateral conjunctivitis and swelling around the eye, called Romana's sign, occurs if
infection was via the eye. This is a characteristic sign of infection and occurs in 20 to 50% of
Where the skin is the portal of infection, an indurated, oedematous skin lesion called a
chagoma is seen. There may be multiple chagomas.
Acute phase visual detection
Microscopy of wet blood preparations requires inspection of at least 100
fields. Motile trypomastigotes may be seen but this is very unreliable.
Concentration methods can improve the detection rate. They include
centrifuging separated serum, examination of buffy coat layer or Giemsa-
stained thick films or of sediment after lysis of red blood cells.
Indirect methods of multiplying the parasite in vector or haemoculture give
results only after 1 to 6 months and are used only in specialist centres and
CXR may reveal cardiomegaly
In the latent and chronic phases, serology is required.
PCR, ELISA, haemagglutination inhibition, complement fixation,
immunofluoresence and other tests for IgG are available.
It is important to use at least 2 tests as many false positives occur.
These advanced tests may not be readily available in areas of high
Cardiomegaly on CXR
Hemilateral swelling of the face and eye lid and
lymphadenopathy (Romana's sign)
Peripheral blood smear. C-shaped trypomastigotes of T. cruzi are
seen in the peripheral blood (parasitemia).
Trypanosoma gambiense in mouse blood (Giemsa)
Trypanosoma cruzi in cultured HeLa cells (Giemsa). Within the
infected cells, it is difficult to distinguish Trypanosoma from
Giemsa-stained Trypanosoma cruzi
It is possible to grow many of these in vitro but there is
no diagnostic use for this
They can be seen with the naked eye or
They can usually be seen in blood, urine, stool or
Anisakiasis – Anisakis species
Anisakiasis is caused by the accidental ingestion of larvae of the Anisakis
simplex and Pseudoterranova decipiens.
There is a higher incidence in areas where raw fish is eaten (e.g., Japan,
Pacific coast of South America, the Netherlands)
After ingestion, the anisakid larvae penetrate the gastric and intestinal
mucosa, causing the symptoms of anisakiasis.
Within hours after ingestion of infected larvae, violent abdominal pain,
nausea, and vomiting may occur.
If the larvae pass into the bowel, a severe eosinophilic granulomatous
response may also occur 1 to 2 weeks after infection.
Gastroscopy: 2 cm larvae are seen and can be removed.
Histology of tissue removed at biopsy or during surgery.
A 13 mm-long white helminth is stuck in the highly edematous
and hyperemic jejunum (gross findings). (Anisakiasis is most
commonly seen in the stomach).
A 1 cm-long Necator americanus stuck in the duodenal mucosa
is red-colored, because of blood sucking (endoscopic findings).
The Anisakis larva is histologically characterized by a pair of
clover-shaped lateral chords, eosinophilic Renett cells
(exocretory organ), and the gut consisting of high columnar
A 100 mm-wide small nematode larva reveals a pair of swollen
clover-shaped lateral chords and the gut (HE).
Trichinosis - Trichinella spiralis
Trichinosis is a parasitic disease caused by eating raw or undercooked pork and wild game products infected with
the larvae of a species of Trichinella spiralis.
Trichinosis is endemic in central and eastern Europe, the whole of the Americas, parts of Africa and Asia.
Usually asymptomatic but in heavy infection causes gastrointestinal symptoms, fever, tachycardia and
hypersensitivity reactions during the migration phase.
Within 1-2 days of infection, nausea, heartburn, dyspepsia, and diarrhoea may occur, the severity depending on
the number of worms ingested.
Later other manifestations may occur, e.g. headache, fever, chills, cough, eye swelling, joint pain, muscle pain,
petechiae, and itching.
Worms may enter the central nervous system, causing serious neurological deficits, e.g. ataxia or respiratory
paralysis, and even death. Infestation of the heart may also lead to death.
However most symptoms subside within a few months.
Full blood count shows eosinophilia in virtually all patients.
Creatine kinase is elevated in most patients.
Parasite-specific indirect immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA) titres and anti-
newborn larvae antibodies: recommended but may not be positive initially and there is some cross-reactivity with
other parasitic disorders and so specificity is less when results are weakly positive.
Stool studies can identify adult worms, with females being about 3 mm long and males about half that size.
A muscle biopsy is the definitive diagnostic test.
Other tests may be indicated depending on presentation, e.g. CT scan for suspected central nervous system
Striated muscle cells contain 1 mm-sized, encapsulated foci with
a coiled larva (HE). Inflammatory change is hardly observed.
The esophagus of the larva shows the stichosome, a chain of
basophilic globular or columnar cells (HE).