Note - Responses in red are official corrections that correct the record from material presented in lecture or elsewhere in the course.  You are responsible for noting this corrected material.
Other questions and comments are clarifications from student questions.  These responses do not correct erroneous material, but you likely will find them useful.

Q9.  I was refreshing my memory on type III secreted proteins by looking at the notes from last section and you have written down "non-professional phagocytes (epithelial cells, endothelial cells, hepatocytes, etc.) by bacterial mediated endocytosis resulting in a phagosome/endosome (can involve type III secreted proteins - injected into host cell affecting actin polymerization)" (page 25 of unit 2 notes). Then in the notes for this section you talk about type III secretions and actin polymerization separately to describe separate organisms (ie S enteritidis vs Shigella)[page 11 and 9 respectively]. Could you explain to me the difference between the two types of spread.

A9.  First, realize that type 3 is a method for bacteria injecting proteins (toxins directly into host cells).  There as many functions for the toxins as there are other exotoxins.  Some of them induce uptake of bacteria into host cells (Shigella and Salmonella), other prevent uptake of bacteria by macrophages (Yersinia).  Salmonella has a second one that prevents phagosome-lysosome fusion of macrophages.  Others cause the attaching-effacing cellular lesion (EPEC and EHEC).  Pseudomonas uses one to inject cytotoxic toxins.

   For Salmonella and Shigella, completely different things happen after these bacteria get into the host cell.  Shigella breaks out of the vacuole and replicates in the cytoplasm, using host actin polymerization to push it around until it finally punches through to an adjacent cell.  It will also kill the initial cell.  Salmonella directs its vacuole to dump it out on the basal side.  Since Salmonella doesn't get into the cytoplasm where the actin is, it can't use actin for propulsion.

    So it is complicated.  You should be familiar with the E. coli, Shigella, Salmonella, and Yersinia stories.

Q8.  In Dr. Forsmark's lecture, he mentioned that C. diff is also invasive while your notes say that it is inflammatory.  Just would like clarification.

A8.  Dr. Forsmark did not list C. diff. as invasive.  He listed it under exudative.  It is true that Shigella and other invasive organisms tend to cause exudative diarrhea.  See page 232 of Schaecter.  It clearly states that C. diff. is not invasive (to tell you the truth I had to check this myself!).  So why does it cause exudative diarrhea?  Because its two toxins destroy the mucosal epithelium with an end result similar to Shigella leading to ulceration and even pseudomembrane formation.  Remember that the pseudomembrane is a combination of necrosed epithelium and WBCs.  Hence, the stool will have the appearance and the symptoms could follow exudative diarrhea.  However, note that there is a wide range of symptoms with C. diff. diarrhea.  It is your first choice in a hospitalized patient with diarrhea.

Q7.  In regards to your meningitis lecture, why is it important to use a special culture medium for lumbar puncture/CSF cultures.  CSF is normally sterile.  In ID book and online it keeps saying to use a special media, but no reasoning.

A7.  CSF will always be plated on blood - the standard medium.  Listeria, Pneumococcus, and many other common agents will grow on this.  However, Haemophilus (and possibly Neisseria - I'm not sure) will not.  The nutrients locked in the RBCs are not accessible to this fastidious organism.  Therefore, chocolate agar, which is blood agar with the RBCs lysed by heat (hence the brown color) is used.  Neisseria will grow on chocolate agar, too.  If you suspect more exotic organisms, you might have to request special media.  The fact that CSF (and blood) are normally sterile means that you don't have to use a selective medium to suppress the normal flora that would make identification of the pathogen difficult.  You would use a selective medium for stool, urine, etc. (for example Thayer-Martin for Neisseria would be used on a urethral exudates for gonorrhea, but not on CSF for meningitidis).  It would be extremely rare for an obligate anaerobe to cause meningitis unless there was some form of abscess to create a localized anaerobic environment.

Q6.  I was going through the salmonella interactive program & was wondering why CTL is seperated from CMI.  I thought I was missing an immunology concept, but my roommate agreed that we were taught in Path that they are one in the same.  How should I think of this from an immunolgy stand point.  Here is what I know:  You are distinguishing them based on ability to inhibit phagosome/lysosome fusion therefore Salmonella is CMI/Th1 not CTL/Th1-- so then is CTL/Th1 true intracellular and CMI merely for those bugs that stay hidden in the pahgosome and are thus truly in an extracelluar environment.

A6.  I strongly suggest that you and your colleagues check out pages 107 and 108 of Schaecter.  Th1-CMI (also known as delayed type hypersensitivity when it goes too far) is very different from CTLs.  Th1-CMI is mediated by CD4+ T cells secreting mainly IFN-gamma to stimulate macrophages to kill intracellular pathogens (usually those that remain within vacuoles).  CTLs are CD8+ T cells that kill infected cells by contact and stimulating a death response by various methods that we did not discuss in detail.  This is usually used against pathogens that infect non-phagocytes and get into the cytoplasm.  I am very, very sure that your roommate is confused about what was said in pathology, because my pathology colleagues are immunology experts who know this system to very great detail.  There is no way that they would say that CTL and Th1-CMI are the same.  As the text shows, the effector cells, themselves are completely different.  It is possible that CTLs get some help from Th1 cells (which might be the same Th1 that also secrete IFN-gamma - but I am not sure about this), but that is about as far as any similarities go.  Notice how I do not use the term CTL/Th1 too foten, because the CTL is the effector cell, not the Th1 that might help activate it.  However, when I write Th1 CMI, I am referring specifically to the CD4+ T cell that is secreting IFN-gamma.  Note also, as the book points out, that Th1 CMI is based on antigen presentation in the context of MHC class 2, while CTLs are based on MHC class 1.  This is intimately tied to their cellular function, and if you understand their cellular function (Th1 CMI helping macrophages, while CTL killing non-phagocytic cells) this would make sense.  So, don't focus on the regulatory T cell - focus on the effector T cell.

    Phagosome-lysosome fusion really has nothing to do with it.  For Th1-CMI it is of the organism infects macrophages and (usually) stays in a vacuole.  For CTL it is if the organism gets into the cytoplasm of any cell, including macrophages, I believe.  It is possible that Th1 could help macrophages kill organisms that get into their cytoplasm as well, but I tried to paint the world in a little simpler context.

    Neither of these forms of CMI is for organisms that stay extracellular.  That is what antibodies are for.

    Salmonella stays in the phagosome (prevents phagosome-lysosome fusion), so it is intracellular.  Listeria gets into the cytoplasm and is intracellular.  S. pneumoniae has an antiphagocytic capsule and is extracellular.

Q5.  I was confused about the differences between the salmonella strains that cause typhoid fever and gastroenteritis after it has passed through the guy epithelium.  According to the book, salmonella often enters the bloodstream and causes at least a temporary bacteremia. The logic the book uses for the differences between the typhoid fever type and the gastroenteritis type (p. 211) is that the typhoid fever type is more resistant to destruction once taken up by host macrophages. Its within these macrophages that the typhi salmonella can grow up until a point where a second bacteremia is caused that signals the beginning of the clinical illness of typhoid fever. However in the notes it states the increased growth rate within macrophages under the gastroenteritis type of salmonella. This is continued with the next section on page 11 of the notes c. bacteremia and metastatic infection which states that the pathogenesis is similar to gastroenteritis. How can this be if gastroenteritis causes diarrheal symptoms while the typhi type is the one that causes the systemic effects? Could you please clarify this for me because it has caused extreme confusion with trying to understand the differences between these organisms.

A5.  Salmonella is one of the most complicated organisms that we teach because it has so many forms (serovars) and such a wide array of diseases.  Typhi is pretty clear in that it causes only typhoid fever.  It replicates in macrophages using means other than those encoded on the virulence plasmid of some non-Typhi serovars.

    Typhimurium and Enteritidis (and other non-Typhi serovars) are the complicated cases.  They have virulence plasmids that enable them to replicate in macrophages.  However, these serovars are not as virulent as Typhi, and, in fact, it is primarily in immunocompromised patients that these non-Typhi serovars with the plasmid cause systemic disease.  I think that I might have failed to mention this in my lecture and/or notes.  That doesn’t mean that Typhimurium and Enteritidis never cause bacteremia or systemic infection in otherwise healthy people.  We are dealing with propensities here, not black and white.  Most of the time, these non-Typhi serovars are held at the intestinal lamina propria by our defenses, in spite of plasmids.

    When I said that bacteremia and focal infections have pathogenesis similar to gastroenteritis, I meant that they adhered to and invaded through the gut the same, and resisted complement and macrophages using the same methods.  They are also primarily inflammatory damage.  They just settled elsewhere than the intestines as their ultimate home.  I believe that the focal infection and bacteremia are usually preceded by gastroenteritis.  It’s a matter that the infection wasn’t stopped at the intestines.

4.  Comment from Dr. Gulig - I am going through the BUGS cases looking for areas where there are needed corrections (rare), updates (some), and deletions of extraneous information.  I started with Endocarditis and have worked my way through Sick Baby (meningitis).  There are significant change to meningitis, so if you've already done this case, you should go back and take a look starting at questions 5-7, and 15.  The case deals with Haemophilus influenzae type b, which is very rare.  Some of the previous questions were based on old data before the vaccine became widely used.  You'll find that the revised questions are much more aligned and confirming of what you heard from Dr. Southwick and me.  I apologize for this situation, but there's nothing I can do about it right now but try to work on these as best as I can with the limited time I have available.

Q3.  I just have a quick question about EHEC.  In your lecture, you had said that EHEC is technically NOT an invasive bacteria because it attacks the endothelium, not the epithelium.  Therefore, you may get bloody diarrhea but not necessarily dysentery.  In Dr. Forsmark lecture today, he has EHEC listed under exudative and infectious, invasive organisms.  I'm just a little confused as to what we are supposed to understand about EHEC.  Anyways, if you could clear that up, that would be great!  I know we've already asked so many questions about this, but I really am confused.

A3.  Dr. Forsmark gave a great lecture today that complemented very nicely what I had taught you already taught in my previous three lectures.  I noted that he had EHEC under "invasive" organisms, whereas I told you that it is not invasive.  In fact, it is not invasive - see Schaecter page 207.  Because it causes bloody diarrhea (kind of like dysentery but not exactly), it is easy to assign it to this group (along with Shigella which belongs there).  Dr. Forsmark's predecessor did the same thing.  But that doesn't make EHEC invasive.  I will ask Dr. Forsmark to change his PowerPoint for next year to avoid further confusion.  So please note this FOR THE RECORD.  If there is ever a question about EHEC being invasive, you will not be allowed to quote Dr. Forsmark's lecture to say that it is invasive. 

2.  Comment from Dr. Gulig - I have spoken with a couple of you recently about improving performance by improved studying for the course.  Here is the advice that I have given:

     1)    Focusing on the notes and lecture is of prime importance.  I take notes on all of the lectures just like you should.  I look at what was added during lecture and what was not covered.  I use this information to write appropriate questions (including the added material, avoiding that which was not covered).  That means that there are going to be questions on material not in the handouts or PowerPoints.  If you’re not attending class – beware!

     2)    Use the assigned texts as supplemental/confirmatory resources, unless you are instructed to self study in a directed way (note that I have not done this for my own material, but I am getting ready to give you some focused self studying on a couple of organisms not covered in lecture due to time constraints).  I love Schaecter because I used it years ago to model my view and teaching on pathogenesis.  It does not have much extraneous material.  It should follow and flow with my outlines very easily.  It should be an easy read.  Reading someone else’s style may resonate with some of you better than my lecture and presentation style.

     3)    Dr. Southwick is using ID30 heavily for CMCs (warm-ups and small groups) and his lectures.  You should use it appropriately for those purposes. 

     4)    A common comment from the students with whom I have spoken is the time commitment to the BUGS cases.  Here is what I told them.  I am writing about 5 questions total from the cases for each exam.  Of those 5 questions, likely only 2 or 3 are derived exclusively from the cases.  I realize that a lot of material is covered redundantly (BUGS, basic lecture, clinical lecture, CMC), and so when I write an exam question from BUGS (or any other single course element), I often have the intention of reinforcing this material.  I understand how the “testable” material in the BUGS cases is difficult to test.  I am looking for material that is in alignment with what is being taught in other parts of the course.  I am editing the cases, deleting and updating material that is either out of date or not in alignment (e.g., antibiotics used when there is no general principle being applied).  Therefore, you should closely monitor the amount of time that you are devoting to these cases.  I know that they are fun, but they are not going to constitute a huge portion of the exam in themselves.  However, they should be good reinforcement for other material.

1.  Comment from Dr. Gulig - Some of the CMC faculty have asked me to pass on to you that your answers for the warm-ups should demonstrate your understanding of the material.  Some of the faculty are concerned that it appears that some of you are more interested in brevity than thoroughness.  I have to say that in relaying this information to you, I realize that there could be an overreaction of books being written, so please consider some balance.  Your answers should consist of a few sentences each, rather than a few words.  Please note also, that, as Dr. Southwick pointed out, cutting and pasting from the book does not demonstrate understanding.  I am asking the CMC leaders to communicate to each student some indication of how your responses have been graded so far, so that you have the opportunity to make appropriate changes, if needed, in the final two warm-ups.  Please keep in mind that your warm-ups count for half of your CMC competency grade, the other half being your attendance/participation.