Microbiology Transcriber: Ryan Blankenship
Slide 1: Primary Immunodeficiencies
Slide 2: T cells and B cells with the different molecules that go to through the password/ counter
password process of activation to produce an effective adaptive immune response. All the molecules
with the stars (only a partial list) on them can be defective in patients with significant immune
deficiencies. This shows only the adaptive immune system. There are also Immunodeficiencies in
Phagocytes, complement. Defensins are important in the defense of the skin and mentions that these
are important in the immune system but that they haven’t found any Immunodeficiencies associated
Slide 3: List of the defects associated with Immunodeficiencies. There are deficiencies that purely affect
the genes of the T Cell. If they are severe enough they will also effect B Cell function because you have
to have proper T Cell Helper function for the development of Ab from B Cells. By definition, severe T cell
deficiency causes what is called a Severe Combined Immunodeficiency (SCID).
We see SCID in childhood where there is a failure to grow properly, severe infections, failure to meet
developmental milestones, generally very sick infants that will die before they reach their second
birthday if not treated appropriately.
Milder Deficiencies of T and B cell functions are called Combined Immunodeficiencies.
There also Immunodeficiencies that affect the Phagocytic compartments of the innate immune system.
In this case the adaptive immune system is still functioning properly but the Neutrophils aren’t working.
Complement part of the innate immune system. When they are deficient you get terrible infections.
These are relatively rare. Infections are usually mild. Occasionally they don’t produce infections but
Slide 4: Clinically they look at the pattern of infections that the patient as been experiencing. 50% of
the time the patients in his clinic are referred because of recurring sinopulmonary, or GI infections.
They often look at B Cell function. If you are Ab deficient the biggest problem you are having recurrent
respiratory infection. Usually the worse the deficiency the worse the respiratory infection. Mild
deficiency has sinusitis, ear infection, bronchitis. Severe deficiencies have all that plus pneumonias.
T cell and Combined Immunodeficiencies can have all of the above of course but they also have a
tendency to have thrush, diarrhea, and a failure to thrive under infection. If you find Pneumosistis when
you do an bronchoalveolar lavage, a fungus that causes infection of AIDS patients, the patient has
abnormal T cell function.
Phagocyte deficiency can cause infection anywhere. They tend to show tissue and mucosal infections.
Swelling of the gingiva, perirectal abcesses, cellulites, osteomelitis.
Complement, part of the innate system. Similar to those of Phagocyte deficiency.
Microbiology: Immunodeficiency pg. 2
Slide 5: Syndromes associated with “Pure” T Cell Deficiencies. Zap 70 is actually an enzyme in T Cells
that is essential for the T Cell Receptor to work. If Zap 70 enzyme is not there then the T Cell Receptor
just sits on the surface but cannot function. It can’t generate any signals. Very Rare.
Slide 6: DiGeorge Syndrome is one you might see in practice. Fairly common. Associated with
Velocardiofacial syndrome. These patients tend to have cleft palate. They have a triad of usually very
severe congenital heart disease known as conotruncal cardiac malformation, hypoparathoidism, and
thymic hypoplasia. This is a developmental field defect not a hematopoetic problem at all. This is a
problem in the thymus. During fetal development it involves the migration of tissue from the third and
fourth branchial arches into the mediastinum. Lower jaw frequently abnormal, palate defects, typical
appearance to the face, and they have lots of defects in the mediastinum. The parathyroid epithelium
and thymus epithelium are affected. The thymus usually isn’t there. Fortunately there are small islands
of thymus cells that are found along the tract of migration so patients usually have some T cell function
and a mild immunodeficiency. The most common gene associated with this syndrome is on
chromosome 22 and the gene is called Tbx1. It is involved in the migration of embryologic cells. Many
times in the majority of cases there is a huge deletion in chromosome 22 that has taken out this site.
Slide 7: Picture of a patient with DiGeorge Syndrome. Small mandible, short filtrum, fish shaped mouth,
antimongiloid slant of the eyes, and malformed ears. This is the typical appearance. Unfortunately they
tend to have mild mental retardation or development delay and problems with speech development. It
is a dominant disorder. Only need one deletion. Cases where parent also had the syndrome, mild heart
disease, never had any immuno problems that anyone picked up. Had unusual shaped ears. Did fine in
life. Very variable.
Slide 8: Heart diseases tend to be pretty bad. Usually need big time Cardiovascular surgery.
Slide 9: Test used to find big deletion on a chromosome. Use a probe that binds to the region of
interest and label it with a fluorescent die. On this slide they have a probe that binds to the telomere of
chromosome 22 and also a probe that binds to the region of interest. This picture shows a cell in
metaphase and has been stained red to show all of the pairs of chromosomes. This patient is normal.
Slide 10: This picture is different. We can see the pair of chromosome 22. One of the chromosomes
appears smaller and only has a label on the telomeric end of the chromosome showing the deletion of
the region of interest. This is how the diagnosis is made. This is a syndrome so sometimes a patient will
not have the deletion of the Tbx1 gene on chromosome 22 but will still have the syndrome. On
chromosome 10 there is a gene associated with Charge Syndrome which is a more severe syndrome
with a lot more organ problems.
So again in this deficiency the thymus is missing and it is the WORST immunodeficiency that we see.
Because you can do a bone marrow transplant and it won’t have any effect because there are no T cells.
There is an immunologist that has perfected the transplant of thymic tissue. It has to be done very
carefully because you don’t want to transplant any T cells in with it. She transplants the epithelium of
the Thymus and it will produce mature T cells which go out into the periphery and work perfectly well.
It works as well because the patient doesn’t have any of there own T cells. They can also do parathyroid
Microbiology: Immunodeficiency pg. 3
transplants at the same time. The patients will often do well. Even a little bit of T cells will make a big
difference in the patient’s health. They won’t have the same broad ability to fight antigens but they
have enough to do pretty well.
Slide 11: SCID Syndromes are all rare. See maybe one or two a year. The most commom one is the X
linked one. This is due to a common subunit of cytokine receptors, particularly the IL 2 and IL 7
receptors. They have very low T cells and some B cells, but the B cells are dysfunctional. The patients
are little boys. 40% of the SCID patients have the X linked defect. There are a bunch of other genes that
are known that can cause this syndrome.
Slide 12: It is a syndrome that presents pretty early in infancy with a failure to thrive, there are early
onsets of infections because there is no functional adaptive immune system at all. They also have
opportunistic infections like pneumositis, chronic or recurrent thrush, and chronic rashes. The chronic
rashes maybe due to maternal T cells that were transfused at the time of birth and haven’t gone away
because the baby has no way to get rid of them on their own. This shows as chronic low grade graft
versus host disease in the skin, chronic or recurrent diarrhea which is usually viral. Once you get a virus
with one of these disorders, you have no way of getting rid of that virus. These patients will not have
any lymphoid tissue.
Slide 13: When you do labs on these patients we see very low Ab levels, low Ig levels and if they are 6 to
7 months old and they have had their first 3 set of vaccinations and we check their tetanus titer and
there is no Ab to tetanus that’s very abnormal. Tetanus is a strong Ag and most everybody makes Ab to
it within three immunizations to it. If you test the blood cells with things that make them proliferate
wildly, they don’t at all. There is no response to the mitogens. There are little if no T cells and often
there are low or absent B cells.
Question: What is a mitogen?
Answer: An old term for a plant protein that are lechtins that bind to carbohydrates that are on the cell
surface. They’ve been tested over the years and there are some that are particularly good at stimulating
T cells. The one we use the most for T cell identification is called phytohemogluten. It is a protein with
four binding sites that binds a carbohydrate that’s present on the T cell receptor or on other molecules
present on the T cell surface. These usually get enormous activation of T cells in even a new born infant.
Slide 14: Treatment is easy. They send stem cells units and they get a bone marrow transplant.
Because they can’t reject the transplant it goes over easily.
Gene Therapy is on the horizon. It is going to be a while before we can use it.
Slide 15: Picture of an infant with SCID that got chicken pox. His body is basically a culture medium for
this virus. You need some immune system to fight this. It is fatal for these infants or causes long lasting
neurologic and other organ system damage before you can get it under control.
T cell disorder are SCID and Selected T cells.
Microbiology: Immunodeficiency pg. 4
Slide 16: When a patient comes in with recurrent respiratory infections they usually look at the B cell
functions initially. If you don’t have good T cell function you won’t have good B cell function. There are
disorders that have selectively impaired B cell functions and have normal T cell function. Don’t need to
know the whole list just to give us an idea of the genes that have been found so far that when impaired
or deleted cause B cell deficiency. Again the most common one is X linked Agammaglobulinemia.
Because it is X linked it is seen in little boys, because they only have one X chromosome. If there is a
gene that is defective for the immune system in their X chromosome they have no back up. Usually the
gene is carried through the mother. The sons are affected. Children often die early in infancy or
childhood of recurrent pneumonia if they are not diagnosed. Most are diagnosed quickly though.
Number of other diseases that are a lot rarer, but are autosomal recessive with one other that is X
linked. They also cause decreased B cell function and variable degree Ab deficiency. Common Variable
Immunodeficiency (CVID) is one that you might see in adults. It frequently develops in adolescence and
young adults. A lot of work has been done on these disorders here at UAB.
Slide 17: There is a distinct connection between CVID and Selective IgA Deficiency and IgG subclass
Deficiency which are milder. IgA Deficiency don’t make IgA and often IgA and IgG Deficiencies are seen
together. Sometimes patients that have both IgA Deficiency and IgG Deficiency digress into CVID where
no Ig isotype is made at all. There is a linkage to the class 3 region. Often in kindred with CVID many
times there is a Mendelian inheritance of IgA Deficiency of their children. They are still trying to figure
out the main gene for CVID.
Slide 18: We do have four genes that can cause it. They are post stimulatory molecules. He refers back
to the second slide with the T cell/B cell signaling molecules. There were all these molecules that were
doing this handshaking that were important for co stimulating of the T cells and B cells. During this
process of B cell activation of T cells. It has been shown that these patients have normal B cell counts
but very low Ab counts. So something goes wrong with the maturation of the B cells into plasma cells
and memory cells. It is not present from birth. Maybe a little sickly but don’t develop this
Immunodeficiency until later.
Slide 19: Of the milder deficiencies such as IgG Subclass and IgA Deficiencies, IgA Deficiencies are very
common in Caucasians. Not as common in people of African or Asian heritage. Among people of
northern European heritage 1:400-600 have the IgA Deficiency. Large chance someone in our class has
it, doesn’t know it and just thinks they get a lot of colds. If the kid is around anyone with a cold they are
going to get. This is because IgA is the only Ig in the upper airway. Fortunately because the rest of the
immune system is there to back it up you don’t really develop any infections like pneumonia.
They do have problems with respiratory and GI allergies. There has been an increase in Celiac disease
which is a hypersensitivity to gluten the protein in wheat and causes diarrhea. Probably because you
don’t have IgA to protect mucosal surfaces.
Slide 20: There are a bunch of diseases that have a milder presentation but some are still quite severe
and difficult to deal with. They have a combined T cell and B cell Deficiency.
Microbiology: Immunodeficiency pg. 5
Wiskott-Aldrich Syndrome which is easy to diagnose because they have low platelet levels and the
platelets are small and don’t work well. They also have eczema and immunodeficiency.
Ataxia-Telanglectasia is a DNA repair disorder. They can’t recombine their receptors very well. Very
sensitive to Ionizing Radiation. You don’t want to do X-Rays on unless you have to. They develop
malignancies because they can’t repair DNA very well. They also can’t combine their antigen receptors
very well so the T cells receptors and the B cell receptors all require recombination that’s essential. If
you can’t repair these breaks in DNA you’ll have some kind of Immunodeficiency which will be mild.
Others he hasn’t mentioned where DNA repair is very disabling and the patients can even have a severe
Hyper IgM Syndrome is where isotype switching is broken and there is a variable degree of T cell
deficiency related to this as well. You are stuck in the IgM mode. It is a big molecule. It doesn’t get out
side the blood very well. It is good for controlling blood infections not so good for mucosal or tissue
X Linked Lymphoproliferative Disorder is a disease where the patients have particular trouble with the
Mono Virus. This is because it affects the B cells.
Chronic Mucocutaneous Candidiasis the patient have chronic oral thrush, and skin infections that deal
with fungus. They also have problems with autoimmunity.
A really severe problem is the Hyper IgE Syndrome. IgE is massively elevated and they have a tendency
to get bacterial and fungal infections. Uniquely the patients don’t shed their primary dentition. Their X-
Rays show a double row of teeth. The gene associated with this syndrome is STAT 3.
Slide 21: This Syndrome is caused by dominant negative mutations in STAT3 which is a cytokine
transcription factor that is activated after a number of different cytokine receptors. The interferon
receptors are all affected. They have an enormously elevated IgE and their antibody responses are not
advertly abnormal but they don’t respond to inflammation normally. You really need interferon and
other inflammatory cytokines like DAT to make good immune responses.
Slides 22 and 23: He skips the “Other Cellular Immunodeficiencies” and “Familial Hemophagocytic
Slide 24: There is a group of four genes that are known to cause Defect in the interferon-
gamma/Interleukin-12 pathway. These patients tend to get infections with innocuous microbacteria
such as TB. Things out in the environment that our body handles easily. It has been found that this
deficiency comes from problems with the interferon receptors on macrophages.
The picture shows a macrophage, a CD-8 T Cell and a NKC. The NKC and CD-8 T Cell are the main source
of IFNγ. IFNγ is very important for activating macrophages. So if the receptor is deficient or if the
feedback mechanism is deficient then macrophages will not work properly.
Microbiology: Immunodeficiency pg. 6
The feed back mechanism for macrophages is this: If you have an organism that can’t be digested
normally you are getting T cell activation, NKC activation, IFNγ production. The macrophages release
another inflammatory cytokine called IL 12 that feeds back on to the T cell and NKC to keep them
producing IFNγ. This is very important in generating granulomas. Balls of tissue that help you control
TB. If you can’t make granulomas those bacteria will have you for breakfast.
Slide 25: Patients with this syndrome get really bad infections with intracellular bacteria like a typical
microbacteria or salmonella; they have defects in the IFNγ receptor, in IL 12 itself or its receptor or in a
signaling molecule that is associated with the IFN receptors called STAT1. That is the typical pattern
seen, this overwhelming infection with a typical microbacteria.
Slide 26: Biopsy in a liver of a kid who got a bacterial immunization called BCG. BCG is a type of
attenuated TB. It’s used in the 3rd world. It is used as a vaccine for TB but not very good. Not used in
this country. If you get BCG and you can’t make granulomas then BCG will kill you. Lots of other
bacteria out there that will do the same thing.
Slide 27: Phagocyte Deficiencies. Neutrophils and Monocytes. The most common is an X Linked
disorder called Chronic Granulomatous Disease (CGD). There are four genes associated with CGD.
These patients get really terrible infections. Chronic grumbling infections that slowly gets larger and
Leukocyte adhesion defects (LAD) are associated with the molecules on the surface of the Monocytes
that are important to get out of the blood vessels. You have your Neutrophils searching for trouble and
when they find an area of inflammation the vasculature has expressed these molecules that are
adhesions that allow the Neutrophils to bind and move out into the tissue and migrate to the infection
and start killing. They have to be able to stop firmly to do that in order to get out because the blood is
moving very rapidly.
Granule Defects: Because they have all of these granules that are important in killing infections,
anything that affects the Neutrophils or Monocytes ability to do that causes big problems as well. There
are three major types of granule defects.
Lastly there are a group of patients who have chronically low numbers of Neutrophils. We know at least
one gene that can cause that. If their Neutrophil levels are low enough just because they can’t make
enough they can also get very bad infections. Lots of time those infections are oral. A classic sign is
gingivitis. The infection is very often seen orally or rectally.
Slide 28: Chronic Granulomatous Disease is a really interesting disorder due to an inability of the white
cells, Neutrophils and Monocytes, to make H2O2. It is due to a mutation in one of four proteins. One of
those is on the X chromosome so it is the most common Phagocyte disorder seen. They get really
severe infections, but only with bugs that contain the enzyme catalase. Because most bacteria and fungi
generate a little H2O2. But if they have catalase they destroy whatever H2O2 that is there. So there is
no H2O2 around. You need H2O2 to activate the cells and kill bacteria.
Microbiology: Immunodeficiency pg. 7
Slide 29: A really easy test that they use. Very diagnostic. The older one is called the Nitroblue
tetrazolium test (NBT). It detects the production of H2O2 inside the cells. Now they use the flow
cytometric test that uses fluorescent dyes to see if the cell is making H2O2.
Slide 30: This a slide that shows a NBT test on a child with Chronic Granulomatous Disease and his
parents. From left to right it is the child, the mother, and then the father. The dye NBT is added and it
precipitates on the cells that produce H2O2. For the father every cell is covered in blue, indicating the
production of H2O2. The mother some of the cells look normal while some don’t have the dye. Women
have two copies of the X chromosomes and only one of them is dominantly used. All of the mother’s
cells that are using the normal X chromosome in this slide stain blue but all of the cells coming from the
mutated X chromosome that has no NADPH Oxidase to make H2O2 and are not stained. The patient
had no cells that were able to make H2O2. This staining is also useful in identifying the carrier and
finding out whether or not this is a new mutation. The mother has a 50% chance of sending this to her
Slide 31: The DHR Flow Cytometric Assay. The cells are loaded with a fluorescent dye and they
fluoresce bright red on the x axis if they are activated normally. The number of cells is on the y axis. The
father has one peak that is very strong. The mother has two peaks just like the previous slide. The
abnormal cells use the broken X chromosome and the normal cells use the normal X chromosome. The
patient’s cells don’t fluoresce at all. Very useful test for carrier identification.
There are fewer patients that have an autosomal recessive version of the syndrome. In that case usually
the mother is normal.
Slide 32: A patient that had a skin infection due to Serratia. The doctor treated it for ten days with an
antibiotic for 10 days, forgot about it and after a while it came right back. It got bigger. After
subsequent treatment the infection continued to spread. Often patients present with multiple more
serious infections like Osteomalitis. If a patient presents with multi focal infections that is almost always
diagnostic of this disease.
Slide 33: Leukocyte Adhesion Deficiencies (LAD) are all rare. The one we usually see is LAD 1. All the
cases so far have been associated with the heavy chain of the Beta 2 integrin called CD11/CD18. They
lack the Velcro like molecules on the outside of the cells that allow them to leave the blood flow. After
an infection Leukocyte levels will rise to 100,000 but they can’t make any puss. They are trapped in the
Slide 34: Typical presentation of a patient with LAD 1. They don’t live long enough to get teeth if they
don’t get a transplant. Probably won’t see one of these patients that haven’t been diagnosed. This
patient got what is called umphilitis, which is an infection around the umbilical cord from the first
wound they ever got. This is a typical presentation. Unable to heal the cord.
Slide 35: Chediak-Higashi Syndrome and related are disorders of granule production. They not only
have problems in the hematopoetic system but they also have neurologic problems, because neurons
use granules too. They have funny hair with big blocky granules. The hair has a snowy sheen to it. You
Microbiology: Immunodeficiency pg. 8
can diagnose this disease with a hair because the fine pigment granules that are suppose to be there are
big blocky granules. You can diagnose it with a blood smear because the granules are abnormal and
Slide 36: Shows a slide of abnormal Neutrophils with large granules.
Slide 37: Complement deficiencies are pretty rare. One pathway not shown is the Mannose/Lechtin
pathway that activates Mannose binding protein and activates C4. Comes into the classical pathway at
the level of C4. C1 of course requires Ab for activation. The alternate pathway is activated by
appropriate surfaces. Doesn’t really need anything other than a bacterial pathway. They are all capable
of activating the terminal pathway of C5-9. Once is C5 is cleaved C5-9 is like molecular legos that
instantly assembles to for the Membrane Attack Complex. A pore like structure in bacterial or our own
There are recurrent neisserial infections in patients that have a defect in the terminal complement
pathway. People who are deficient in C5, 6, 7, or 8, they usually present with recurrent meningococcal
meningitis. That is the way 99% plus of them develop. This bacteria that causes the bacterial meningitis
has the tendency to occur in boot camps, college situations. The complements involved in the terminal
pathway are particularly important in controlling infection by this bacteria. It is a normal inhabitant of
the oropharynx. For some reason at some point it will move out in epidemic fashion and cause
devastating infection. Don’t really know why.
Deficiencies of the early classical pathway and the alternative pathway are really more associated with
pyogenic infections. Particularly with encapsulated organisms like pnuemococcus. There is a strong
tendency for patients with deficiencies in the classical pathway to develop autoimmunity particularly
Slide 38: There are two tests used to diagnose hereditary complement deficiencies. We also measure
the mannose binding lechtin in the blood, if you want to look at the third pathway. These assays test
the integrity of the whole pathway. If you have a defect anywhere from C1 up to C8, the CH50 will not
just be a little low but it will be very very low. You have to have all of the components to effectively
activate this test.
What’s done is they use sheep RBC and they are coated with Ab. You add solutions of the patient’s
serum and if there is complement activation of the Ab it will lyse the RBC. You can then titrate out the
patient’s complement to tell how much they have. Basically if you have a hereditary deficiency you
won’t be able to lyse the cells.
The alternate pathway deficiency test is run in a similar way. They use rabbit’s erythrocytes for the
activation of the alternate pathway, in the presence of magnesium. They add rabbit erythrocytes to the
patient’s serum with a little magnesium and you get hemolysis if the alternate pathway is working
correctly. If you run both tests and they are both abnormal this means the specimen is either handled
poorly or you have a terminal complement pathway component that is deficient. Anywhere these two
pathways come together they will be low in both of the assays. If only the CH50 is low you know that
Microbiology: Immunodeficiency pg. 9
you have an early classical pathway deficiency. If only the AH50 is low then you that you have an early
alternate pathway deficiency. It is not very hard to diagnose.
We are unable to fix them but appropriate Ab prophylaxis and immunization is what they usually do for