Lecturio Live – Session 2: Microbiology with Dr. Sean Elliott

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    00:00 Okay so lots of school destinations. You know, let's see what we learned about microbiology, about COVID today, coronaviruses. Maybe at some point I can come visit you all, but let's see. So alright, as we are still getting started, we're going to introduce ourselves in a second, but first I would like to know who are you. So we are going to have a poll pop-up.

    00:34 If you are on a computer, it should be coming up on the right side. If you are on your phone, it should either come up at the bottom, you might have to scroll up. Or there's like a little dot at the bottom that has poll so you can just click on your answer just so we can get an idea of who is joining us today so I know if we're covering a lot of the globe, it looks like we're covering a lot of medical school. For those of you who are not students or other, can you maybe write in the chat who you are or what you do and what brought you here today. We've got biotech, we've got a postdoctorate surgery in public health. Alright.

    01:27 Biomedical, GHS, pharmacist, highschool senior. Are you thinking of going to medical school? Alright so BSN, taking micro now. That's a medical education faculty and so for those who are faculty we do also Lecturio, those of us hosting. We do also have lots of partnerships and opportunities for institutions as well so at the end we can put some contact information in there in case you are interested. Alright, let's go to the next question. How familiar are you with Lecturio? So, Lecturio is an e-learning company. We, you know, specialize in medical and nursing content and we are hosting this med today with one of our educators. So, we have another poll up. Yup, it seems to be working.

    02:26 Let us know if you've used the platform before. You know, if you have a premium membership, happy to have you on the community. If you're using the free version, we're seeing a lot of many people are new to Lecturio as well which is fantastic. Alright. So let people keep answering, right down staying pretty much the same now. And oh Sarah just signed up for premium after a 10-minute pharmacology session yesterday. Well, we are so glad to hear that. Yeah, we do a bunch of different free events. Some of them within medical, some of them with the nursing, some of course content can overlap a little bit and yeah but we have a lot of different opportunities for you to act with us so we're very very happy to have you all here. Those of you who are premium members or who used the free version, welcome back. Those who are new to Lecturio, welcome. And my last question and then we can really get started, it's "Have you been at one of our previous events? So I just mentioned that we do a bunch of different events, maybe just tell us in the chat if you've been to another one. We have someone who is in our pharmacology review last night or yesterday, it's depending on your time zone. Alright, so we have a mix of people who have been here and who haven't. Excellent. alright, someone who is in physical examination that was our event last month. Yes, this is a free session. The physical examination session because since you missed it, we did record it and that is in our platform as well. So when you get the link later to this event, it will be right there with it. So, alright. Well, thank you all so much for joining us. I'm so excited to, you know, get us started and introduce you to Dr. Sean Elliott. He is a professor at the University of Arizona and he is one of our wonderful educators and he's going to be talking to you today about microbiology. So, I will get off the stage and Dr. Elliott please take it away. Alright, thank you everybody and good morning, good afternoon, good evening, or good night depending on where you're coming from. As noted, I am a specialist in pediatric infectious diseases and have had the joy of working with Lecturio in the past. Today, we're going to be doing a short presentation about 3 separate microbes that being 2 viruses; the filoviridae, the coronavirus, a very timely topic. And then a bacteria, Klebsiella pneumonia, which as we'll find out is probably more significant and some give it a credit for. We will start with the filoviridae and these are probably better known to you as Ebola virus and Marburg virus, but there's a whole family of these viruses which are likely to cause hemorrhagic disease.

    05:27 They are mid-sized, the filament is an enveloped so typically encapsulated with some sort of a protein and a lipoid structure. They contain, and this is important, a linear single strand negative-sensed RNA genome which means that unless they were to carry, which they do, an RNA dependent RNA polymerase, the RDRP see listed there on the slide. They would not be able to transcribe themselves, alright, to create new virus. So, after this virus attaches to its target cell which most often is endothelial cells, so cells lining blood vessels, it then fuses into the membrane, inserts its genome and along with that has this RNA polymerase which transcribes that negative sense RNA into a positive RNA strand or messenger RNA.

    06:20 Then that messenger RNA just like normal in the other parts of the human body could be translated into protein structure. So, as noted that the 2 principal viruses we talked about here are the Ebola and the Marburg virus. A lot of what we are talking about is based on Ebola virus and it didn't see anybody currently in the Democratic Republic at the Congo but if you are I'm so sorry that DRC as many know is currently having yet another outbreak, 5 new cases reported last night. So medicines on frontier doctors that order is on seeing trying to limit that vaccines and care. So, transmission. This is sort of a classic cycle for the hemorrhagic viruses as well as for other bacteria-borne infections.

    07:06 Most often, the viruses translate and transfer between a primate such as chimpanzee, monkey, gorilla, etc. and another animal which many times is a bat or sometimes as in the case of Ebola virus, the duiker which is a sort of an antelope species. Typically it cycles there without exiting until humans become infected as an accidental host and this can be via ingesting infected meat such as bush meat as occurs in some parts of Africa or by being exposed to body fluids or droppings from the bat. There is now a thought that the very terrible outbreak of Ebola virus in West Africa beginning in 2013 may have been patient zero, a young hunter at night basically resting underneath the tree and being exposed to bat droppings. So, in any event, for humans to become infected with Ebola or Marburg is an accidental process. Once there unfortunately, it becomes quite contagious between humans. So as mentioned before, target cells for these viruses are endothelial cells.

    08:19 So the cells lining blood vessels large and small and then secondarily phagocytes which consume or ingest infected particles of those cells and then ultimately into the hepatocytes.

    08:33 The binding target is via a viral glycoprotein which as with any other microbe you have to have an antigen recognition site to attach to a specific target on the endothelial cells.

    08:46 Once that occurs, of course, it stands the tissues can be affected because of course all tissues in the body are perfused with blood and therefore endothelial cells. So one gets an extensive tropism or are targeting tissues throughout the body with these viruses. The major damage, however, is not just you know local damage of a specific endothelial cell but the fact that it initiates the cytokines storm. So as always, we are victims of our own very successful immune systems which release phacogytes and release pro-inflammatory cytokines. All of which cause secondary destruction which you might think of as an innocent bystander reactions. So a very wide blast of anti-inflammatory reaction which takes out all the healthy stuff along with the infected cell itself. What do these diseases look like? So incubation period is under 21 days, that's important to remember, and the clinical manifestations are an abrupt onset of flu-like illness. Unfortunately, a lot of the super nasty infections in our world all start just like the flu which is not helpful at all. And then, there is development over the next several days of pronounced nausea, vomiting, diarrhea, some patients have a maculopapular rash, many have high fevers, many have the myalgias, all of which we assume are associated with the flu-like illness. And then in those patients who are going to progress into that cytokine storm, they will then develop the extensive hemorrhage which became associated with the filoviruses, the hemorrhagic viruses.

    10:23 And this can be everywhere. So, especially the GI tract will have disseminated intravascular coagulopathy, DIC, followed by vascular leak and then because the leaking of the fluids and the blood products hypovolemic shock and then death on average in 80% of the cases with the range of 50-90%. So, diagnosis now is by RTPCR. It in the past has been via antibodies and enzyme immunoassays but currently we were able to do a reverse transcriptase PCR to detect this RNA virus. And treatment is of course the best that we can do, supportive care, blood products for those that are able to, absolutely strict isolation and as much support as is possible. So, we'll just forward here we go. We have a poll now just to test your knowledge which the following answers corresponds to that typical incubation period of the viruses we just talked about. And go ahead and click on your answer and what we'll see how it comes up. Up to 21 days, 35 days, up to 7 days, up to 28 days, or up to 14 days. Alrighty. Yes, don't be shy. You can answer this. We just talked about it. Excellent. Good. Yup, it looks like pretty much everybody is hitting answer A which is up to 21 days and that is correct. Now that is the outer limit of incubation period and that's important because when we had concern for cases transmitted to other parts of the world from West Africa's outbreak, the incubation period that we screen for was a 3-week or a 21-day period. If you look, however, patients who are suffering from especially Ebola virus, most often their incubation period was around 10 to 14 days. So, for those of you who did answer 14 days, clinically you're actually accurate as well but the range is up to 21 days. Alright, let's go on to our next topic. Again, we want to leave plenty of time at the end. So the next, the coronaviruses. I'm assuming that everybody has heard just a little bit about the coronaviruses and that of course SARS coronavirus 2 is the source of the current COVID-19 pandemic and is a huge source of major angst and morbidity and mortality. So these viruses are big and of course probably everyone is seeing pictures of these even in the media. They're big, they appear sort of circular or spherical. They also are an enveloped virus, an intracellular membrane and have a helical capsid versus the linear capsid we just talked about for the filoviruses. Here again is a single stranded, positive-sensed RNA. So it functions like messenger RNA. So this virus does not have to have an RNA polymerase for it to be able to transcribe itself into an active genome and allow new viruses to be created. What are the clinically relevant species that there are at minimum at least 7 species that are known to have human pathogenicity although that number will continue to increase upwards as we get yet new pandemics and new infections associated. Of those 7, 4 are disordered that the minor common colds. See we think of something similar to a rhinovirus. So, low-grade fevers, upper respiratory tract infections, minimal pathology, minimal morbidity, and certainly minimal mortality are cause of death.

    14:05 However, we now know of 3 that have far more severe associations with that disease.

    14:11 Starting in 2002-2003, the first of the severe acute respiratory syndrome coronaviruses, the SARS coronavirus 1, which had a thankfully somewhat limited outbreak for the world but there are still over 1000 cases and 774 deaths. So a mortality rate reported, keep in mind, we didn't catch every patient, but a reported mortality rate of over 9 percent followed then by the Middle East Respiratory Syndrome coronavirus, the MERS coronavirus which as the name suggest was associated with countries especially surrounding the Arabian peninsula. So Middle East and this one has been associated, if you're looking for a buzz berg remember with exposure to camels. So especially camel secretions, those who are camel herders, camel sellers, even those who ride on camels as a mode of transportation in their country where the ones most at risk. However, this virus also is quite contagious and so there were secondary and tertiary cases reported in other countries especially related to travel in South Korea was one of those so affected. So, the initial outbreak of MERS coronavirus started or was first described in 2012 and there continued to be potential cases at last count just over 2500 total, but a much higher mortality rate. So 885 deaths because this also cause a severe respiratory syndrome. And then of course SARS coronavirus 2 which is the current debuckle in the world causing COVID-19. Actually the number is of course, this size is a bit older, but the numbers are close to 300, 400 million cases reported worldwide, 7 million deaths, and incredibly increased numbers as new variants come through. So, this virus of course has been an eye opener in terms of the pathogenicity of coronaviruses. So, what does the virus itself look like? So, as noted it's fairly large, about 125 nanometers in diameter. The genome is also quite large, you see it written there, over 2600 kilobytes, which is the largest of the RNA viruses that we know of.

    16:37 That genome encodes 4 structural proteins, 3 of which constitute or involve with creation of that viral envelope. So, despite protein which importantly is the point of attachment of the virus to its target cells binded to angiotensin converting enzyme 2, so ACE 2 receptor. And also the E, N, M proteins, the envelope in membrane proteins which together constitute the viral envelope. This in association with the lipid membrane is or constitutes that capsule that we talked about for this very large virus. The 4th protein encoded by the genome is the nucleocapsid protein, the N protein, which is necessary to do complex with that RNA genome and regulate synthesis. So together it's a relatively simple virus but it has a whole bunch of pathogenicity. Transmission primarily is through large respiratory droplets. So those droplets which are expressed by coughing perhaps by singing or shouting and they travel no further than 2 meters, so the classic, you know 3-6 feet, you know, for those of us on the English system comes from the thought of respiratory droplets. However, we now know that there is airborne spread as well. So much smaller particles which contained active virus and can travel far further. So, I think in this model of tuberculosis, unfortunately or varicella as a viral example which can travel for easily well past 6-10 meters and remain airborne for quite long. So, it is because of this mechanism to travel just so successful that we have extensive outbreaks of this virus elsewhere. Other transmission can occur. So less common routes would be fecal oral. So crossing into the "it" factor, there has been virus detected in bathrooms in which urine was the fluid of target but also unfortunately explosive diarrhea can aerosolize just like with respiratory aerosols the virus itself. Vertical - mother to child, initially that the first variance beginning with the alpha variant and the beta variant were not felt to be a major risk of transmitting vertically certainly not transplacentally so any transmission from mother to child was post delivery while mother was cuddling and bonding with her baby then there was a typical respiratory transmission. However, with the current delta variant which is the big one in the world, the one that 617 subvariant 2 delta variant is felt potentially to be a cause of transplacental spread and we are now seeing babies, I'm managing one right now, as it turns out in hospital. Babies who are infected at delivery, so they come out whether it's a Cesarean section delivery or vaginal delivery, they come out already infected. So that could only be a transplacental spread. And of course, via contaminated surfaces, similar to another respiratory virus which is big during the winter months for many countries and that would be respiratory syncytial virus, RSV, which comes out in large droplets deposits on horizontal surfaces and remains active for transmission for a very prolonged period of time. So, what is the pathogenesis? So we've had acquisition of the virus typically via some respiratory route, large droplet, or aerosol droplet and then we inhale or acquire virus into the lungs. So again, it starts as an upper respiratory tract infection with 2 times viral load of what eventually translates down into the lower respiratory tract. And that's important in terms of antibody protection against either. But early infection is that the first replication of that virus it binds to its ACE-2 receptor and we'll show a picture of how that binds within respiratory tissue of the lungs in just a second but then replicates with the cell causes local cell death as that cell is consumed by a viral replication and that would account for the early illness symptoms reported in COVID-19 patients. However, the bigger pathology comes from delayed infection which is driven by that hyperimmune process or as you see in this slide an exaggerated immune inflammatory response and that again precipitates immune disease or immune cause disease in innocent bystander destruction. Two mechanisms for the cell to enter and this is continuing to be flushed out in the labs right now, one is via normal membrane fusion. So, the spike protein, the S1 component of the spike protein of the virus binds to the ACE-2 receptor, it's a very tight binding, and then the virus fuses its membrane with that of its target cell injects the genome and replication commences. But endocytosis is now also felt to occur and this will typically be in cells that are able to do so such as phagocytes and certainly antigen presenting cells so you have not just target respiratory cells, but also macrophages. What happens next? In this picture is a beautiful summary of a normal adaptive immune response.

    22:08 Starting in the left side of the slide, you see there antigen presenting cells, macrophage dendritic cell even some epithelial cells that have this ability that are exposed to endocytose the virus and then in the case of SARS coronavirus 2 they ingest the messenger RNA, this positive-sensed RNA, translate that into among other things the spike protein and then presents the spike protein antigen at their cell surface to both T lymphocytes and B lymphocytes and that's what you see in the middle of this slide. So a very normal triggering of the adaptive response. And again, this triggering occurs in the context of MHC class I and II. So that is a specific response recognizing a human base antigen presenting cell.

    23:01 So, the activated T lymphocytes again come in 2 flavors, CD4 positive or you may know that is the T helper lymphocytes, and CD8 positive which are the cytotoxic T lymphocytes which in in of themselves can conduct a cell-mediated immune response to other infected cells with coronavirus, the SARS coronavirus. The activated CD4 T lymphocytes then interact via cytokines with the activated B lymphocyte of the same antigen epitope and then creates the production of activated B cells to release antibody specifically to the SARS coronavirus 2 and most often to all 4 of those antigenic, those proteins that we talked about. So it triggers a robust immune response which then harnesses other phagocytes, other cytokines, and the whole thing turns into an uncontrollable hyperimmune response. Here's the picture I promised in terms of the local targeting and what you see here is how the virus actually affects and infects pulmonary tissue. So again, we inhale the virus, it goes down into the ultimately lower part of the lungs as you see in the left part of the slide and then deposits within the alveoli complex especially targeting type 2 pneumocytes which I preferred target as well as macrophages and those 2 cells together that precipitate immune reaction which we just discussed and one gets inflammatory burst cytotoxic effect meaning cell's death then leakage of fluids. If that also affects the blood vessel supplying that alveolus, then one gets a hemorrhagic component and that is a known part of COVID-19. So altogether, the majority of the severe lower respiratory disease the failure comes from this hyperimmune burst which basically floods the lungs with inflammatory stuff. Clinically, how does this look? Incubation period for COVID-19, the infection related, the SARS coronavirus 2 is from 2-14 days. On average, it is 4-5 days, 80% of the cases are mild or even asymptomatic thankfully. 15% are more severe, so those patients may require hospitalization certainly require oxygen therapy and then 5% of patients have a very severe, meaning critical disease, in which they need either non-invasive or even invasive ventilation in an intensive care unit. Wow, what gets involved in COVID-19? Common symptoms of course are the upper respiratory ones, the flu-like illness. Once again, there is a flu-like infection, but severe symptoms as you see in the lower part of the slide will include that dyspnea, that shortness of breath, that chest tightness which absolutely correlates with flooding of the lungs with inflammatory base fluids. Patients will have chest pain. If there is a hemorrhagic component as noted before, they may have hemoptysis coughing up blood, they certainly on physical exam will have crackles, fine and coarse crackles, and of course they'll demonstrate evidence of respiratory insufficiency with a need for oxygen delivery typically a peripheral oxygenation level of well less than 93% and typically even in the mid 80s or so.

    26:28 Complications of COVID-19 you see listed on the right side of the slide are pretty much anything and everything. Of course, a focal to multifocal pneumonia accounting for that ground glass appearance which many have seen on chest x-ray and CT scan going all the way to fulminate acute respiratory distress syndrome with absolute respiratory failure.

    26:49 Cardiac injury including myocardial dysfunction, congestive heart failure, and dysrhythmias are quite common as well all the way up to septic shock with multi-organ involvement.

    27:01 So, name your organs that can be, has been, and could be so yet infected with and affected by SARS coronavirus 2 and that hyperimmune burst. So, again, let's test our knowledge retention. So another poll for you all. This time what structure on the coronavirus 2 virus is responsible for that receptor binding infusion with the host cell membrane and you have your choices listed there, the N protein, the spike S protein, the membrane M protein, the envelope E protein, or the lipid membrane. Go ahead and fire your answers away there. Yup, we're looking pretty good so I think everybody's figuring it out. This is the spike protein, the S protein which as noted is the target or the binding site for the virus to the ACE-2 receptor. Interesting because that specific protein is so critical to the whole cascade of infection to cause COVID-19 that it is the preferred target for all the vaccine products which are available in the world. So, excellent. Alright, so I think we will continue on then to our next topic and this is the underrecognized bacteria, Klebsiella pneumoniae.

    28:22 Why do I say unrecognized? Well, because Klebsiella is actually highly associated with pneumonia when we think of pneumonia knowing that that pretty much every type of microbe reported in the world can cause pneumonia. So certainly fungi, bacteria, viruses, we know that. But if you look at 100 patients around the world with pneumonia, most of them will have a viral pneumonia. Certainly in the United States and certainly right now where we're having a flood of other respiratory viruses, most pneumonia is caused by virus. The aforementioned respiratory syncytial virus, RSV influenza is already showing its evil head in other parts of the world, it is starting to be in sporadic spread in the states thankfully not severe yet but everyone anticipates a bad year this year because we have nothing last year and then of course SARS coronavirus 2. So, beautiful examples of viral pneumonias. When we think of bacterial pneumonia, however, most of us think of Streptococcus pneumoniae or pneumococcus for short. However, Klebsiella pneumoniae is also a cause of bacterial pneumonia affecting especially a specific population as we'll see in just a second. So, this bacteria has fairly clear characteristic growth patterns. It is gram negative, it is non-motile, meaning when you look at the organism under the microscope it does not have any mobility across the microscope side. It grows aerobically and it is a bacillus, not a coccus, a bacillus meaning that it has a rod-like shape. Even more when one looks this organism under the microscope, it is a big juicy, gram-negative rod. It looks kind of like a box car, very similar to what is reported for E. coli and in fact both of these E. coli and Klebsiella pneumoniae also can cause urinary tract infections. So, Klebsiella, however, is a respiratory pathogen in addition because it does have virulence-promoting polysaccharide capsule. So very typical for a gram-negative capsule which includes lipopolysaccharide and is a fabulous trigger also for pro-inflammatory cytokines especially TNF alpha. But it also inhibits the activity of phagocytes, the cell-eating cell-mediated component of viral and human immune system. When this grows in culture, it creates large mucoid colonies which are pinkish to even purplish. You see a picture of that on the right side of the screen. They lack those positive oxidase negative and can grow on specialized culture media such as a MacConkey plate and then also the eosin methylene blue agar. So, transmission and risk factors. Klebsiella really behaves as an opportunistic organism, meaning that most of us who have healthy immune systems have no underlying medical disease or concerns are not as likely to get severe disease certainly pneumonia from Klebsiella, but in those who are at risk, so a catheterized meaning a urinary catheterized patient are at high risk to develop urinary tract infection from Klebsiella. Patients who suffer from alcohol use disorder, alcoholic patients who are likely to have aspiration events especially aspiration of gastrointestinal material are at high, high, high risk for pneumonia from Klebsiella. Certainly those with compromised pulmonary function and those who are diabetic because patients with diabetes have a negative effect under immune system and its ability to recognize other infectious pathogens such as Klebsiella. So, the mechanism is again largely related to that gram-negative capsule which hinders the exocytosis and allows the organism to target its cells and then cause, in this case, primary lobar pneumonia. So, especially aspirated Klebsiella not as much in a respiratory inhalation with an aspiration of Klebsiella especially from gastrointestinal fluids into the lungs is the principal cause of pneumonia in patients. The diseases as mentioned that are caused by Klebsiella pneumonia especially as an opportunistic pathogen and most especially in nursing homes. Why is that? Well if you imagine people who typically are living in nursing homes; A are older, B will have compromised immune systems because of their age, C may have decreased swallow and protection mechanisms of their lungs and so they will be at high risk to aspirate and less able to respond to that. As noted before, patients especially who have indwelling urinary catheters are at high risk for urinary tract infections and then of course patients with both of those illnesses can develop bacteremia to sepsis. Patients who have Klebsiella as a cause of their pneumonia, many times will cough up bloody sputum which looks like currant jelly and for those of you who like I when I was in training did not know what currant jelly was. It's a black jelly or a blackberry which looks a very, very dark purple. So it's a striking picture when it comes out of somebody's mouth in sputum.

    33:46 Growth pattern. So the organism itself grows in a typical bacterial way so by replication and the slide here is actually looking more typically a transfer of pathogenic features via a plasmid from a donor bacteria to a recipient bacteria. So, at the top of the slide you see 2 conjoined bacteria which may be one bacteria which is now replicating itself or potentially Klebsiella in a promiscuous way binding to another gram-negative organism potentially like an E. coli believe it or not. But in that conjoined bridge, you can see a plasmid transferring from one organism on the left, the donor bacteria, the Klebsiella to the recipient bacteria and then one has a successful then translation of that plasmid and the new bacteria, the recipient, has the same genome with pathogenetic factors as did the donor. So, this largely occurs in Klebsiella but also in E. coli and is a hallmark of how easily virulence factors can translate and transmit between bacteria. Treatment. So the cephalosporins are especially successful against Klebsiella as our beta-lactam antibiotics which are stabilized with a beta-lactamase inhibitor. So the BL-BLI. However, Klebsiella as notable for is very successful and promiscuous at sharing genomes via plasmid transfer and along with that it can transfer and share resistance mechanisms. So Klebsiella is one of the gram-negative bacteria out in the world which is known to have acquired and to share multi-drug resistance mechanisms. So one can actually come in to a very difficult to treat organism because of that mechanism. So, we now have another poll question for you to test your knowledge about Klebsiella. So which group of persons are most at risk of developing pneumonia due to Klebsiella pneumoniae? If your answer is there, elderly persons living in a nursing home, zoo visitors, teenagers who purchase food thru drive thrus, and then people who work in factories. And yes, I would hopefully would all get this answer correct.

    36:08 I'm just trying to think of zoo visitors. Heaven knows what one might be at risk for but hopefully having a good time and supporting animal husbandry and safety. So, alright.

    36:19 Great. And let's see, we have. Yeah, there you go. So the answer of course elderly persons living in a nursing home as stated before. Again, due to their risk for aspiration pneumonias and also their compromised immune system. And then another question related to this new poll. Which type of disease is caused by Klebsiella pneumoniae? In this case urinary catheterized patients kind of gives it away. Yup, I would hope we will all get this one correctly. You can choose gastritis, Crohn's disease, ulcerative colitis so 2 types of inflammatory bowel disease, urinary tract infection, or duodenal ulcers. And yes, this is kind of give me question so yehey. We're all choosing appropriately urinary tract infections. Good. Okay, so that is the end of the presentation. Now we'll see if we want to go to questions first or back to the Lecturio concept. Hi everyone. I'm back again. Okay.

    37:25 So, before we go on to Q&A, I want to give you guys the chance to write your questions in the chat, the questions you've been asking throughout the event. We've marked some of them for Dr. Elliott to answer. But I just wanted to bring to your attention just something really cool that we have a Lecturio that can also help to answer a lot of your questions.

    37:45 And these are our concept pages. So, they are all high-yield, up-to-date comprehensive, you know concept pages. The tables they have illustrations, they are linked to video lectures and all of the information that you possibly need about, you know, certain things such as the coronavirus or Klebsiella which we've talked about today. So we will link those as well, but please write your questions in the chat because now we have some time for Dr. Elliott to answer them and as you can also see one of our team members and med students is also a big fan of the concept pages there as well but we just want to let you know that we've got this so that you can use them. But why don't we jump into some of the Q&A so I will pop a question on screen, Dr. Elliott, and then you can just go ahead and answer it live. Perfect. Let me grab, let's just start with this one. Okay, so "Is there a prolonged partial immunity to all the COVID viruses including those expected in the future and do we need an annual shot of COVID vaccine?" Well, boy, I wish I was able to be, to predict the future in terms of viruses out coming. There is partial immunity to the spike protein because that is similar between SARS coronavirus 1 and SARS coronavirus 2 and in fact the initial vaccine discovery which allowed us to have a protected COVID vaccine right now was initially tested with SARS coronavirus 1 and even the MERS coronavirus.

    39:30 But unfortunately especially the coronavirus we're experiencing now is adapting rapidly, mean that mutations are occurring. Many times several mutations within the code for the spike protein itself and that is starting to affect the ability of current vaccines to protect us and then create protected antibody response. So, prolonged partial immunity, yes, especially if it is related to vaccine. Those who are infected with COVID-19, I think we all are aware, are at risk for secondary and even 3rd infections with the SARS coronavirus 2.

    40:10 So, it's only partial protection, not complete protection. Vaccine protection is far more robust against spike protein, but whether or not we'll need annual COVID vaccines after getting boosters really depends on what happens in terms of new variants coming down the pipeline. So, I don't have a specific answer for you I'm sorry, but that at least is some of the background for the science. Alright and I have another one that is also related to some of the safety protocols and how that might change. So maybe this kind of ties to it. Excellent, okay. So, if the airborne spread not just droplet route, of COVID is now proven doesn't mean that our current safety protocols, i.e. wearing of masks, are no longer effective and should be updated in the cell but the only solution now will be vaccination or lockdowns.

    41:01 So, yeah, this gets into how protective is a typical mask, meaning a cloth mask or a surgical paper mask that the loop mask which you all wear, how good is that against airborne transmission. Those are all fine against droplet absolutely, but to have true protection against airborne one needs an N95. However, if everyone is wearing a surgical loop mask that the normal mask that actually does a fairly robust job, 60-70% of preventing airborne transmission from the index patient. So, it really is a question of how successful can we be at having everyone wear masks? There is population data and it states for sure in other parts of the world that are found that areas, environments for example classrooms and school in which everyone is wearing a mask have remote risks of transmission compared to those parts of the same class or school that don't wear masks. So there is something we said for routine masks. Ideally of course the way to get over this pandemic is to vaccinate everyone and remove that active viral load in which nature is able to create just normal spontaneous mutations. So, SARS coronavirus 2 is behaving much as influenza behaves in that it has multiple spontaneous mutations, some of which are successful and create new variants and only by vaccinating everyone can we finally reduce the virus to a low level where it will no longer do that. Masks are a very safe, effective temporary fix.

    42:43 Oh, there you go. Thank you. Yeah. Let's talk about one of the other viruses you are just presenting on. Okay. There is other question. Alright. So what's the treatment for Klebsiella pneumoniae that does have an extended spectrum beta-lactamase, an ESBL, and also a carbapenemase producer? Have I encountered cases? Yes. Sadly I have. So to start off with the ESBL producers, most of those organisms, the Klebsiellas and even others like acinetobacter, for example, are still susceptible to carbapenems. So very advanced beta-lactam antibiotics that had very complex side chains and remain effective and so sadly the organism is driving poor antibiotic stewardship. We are forced to use our big guns, our most powerful antibiotics, to treat what should be a simple urinary tract infection or pneumonia. However, the carbapenemase-producing organisms are very complicated and many times we have to use drugs which have higher toxicity such as aminoglycosides, fluoroquinolones which at least in my role in pediatric infectious diseases are limited by how well the child can tolerate those. Ultimately, there are some antibiotics which are close to being untreatable even with the brand new advanced beta-lactam antibiotics and in those we end up using products which are historic. So going back to things like nalidixic acid to going to glorify detergents. So, there are options out there but there are several gram negatives including Klebsiella pneumoniae that are bordering untreatable because of the emergence of those resistance mechanisms. And another somewhat similar question, or related at least. Oh yeah, okay so "If one has an asthmatic patient with Klebsiella pneumoniae causing a pneumonia, do we stop the steroids in the treatment regimen?" So of course typically an asthmatic patient with an exacerbation which may be triggered by Klebsiella pneumonia is going to need steroids to address that hyperreactive process within their lungs. Ideally, we would not have steroids to inhibit the immune response for treating a bacterial pneumonia or even a viral pneumonia, but actually it's been shown that the impact on the systemic steroids for an asthmatic in terms of successfully treating Klebsiella pneumonia is quite limited. As far worse, to stop the steroids because a major part of that asthmatic patient's pathogenesis is from their reactive lung disease. So we have to have the steroids and thus we typically continue the steroid burst as we call it in treating that asthmatic while we also use antibiotics to treat the Klebsiella. Alright. Here's another question. Okay. "What implications does endocytosis have to development of disease or complications?" Yeah, this is a very interesting scientific question because a large amount of vaccine discovery, the use of monoclonal antibodies in treating SARS coronavirus 2, for example, are focusing on that fusion aspect. So despite protein attaching to the ACE2 receptor and then the fusion component. If one interrupt that binding step through fusion via vaccine or monoclonal antibodies, then one can interrupt disease pathogenesis. But the endocytosis is sort of an end-run around that and unfortunately it's an end-run around that affecting a component of the immune system. So, I think that there is significant clinical implications but fortunately they don't yet appear to have significant clinical significance meaning that the patients who are vaccine protected and/or received a monoclonal antibody treatment in their early stage of disease still have significant clinical benefits. So far milder disease, far lower risk of ICU stay, far lower risk of death. So the endocytosis component of disease pathogenesis is probably a very minor component of the overall binding of the virus thankfully. I hope it stays that way.

    47:21 You do. Yes. Alright. Okay. With MRNA vaccines were for all RNA viruses? Whoa, it's a great question I hope it's a prescient question that the MRNA vaccine concept which has been around for quite sometime and has finally achieved a world stage in which to demonstrate success, i.e. via its action against SARS coronavirus 2 that science should be successful against many different types of infections and not just RNA viruses but certainly it is being used now to look at the filoviruses so Ebola and Marburg viruses against HIV, human immunodeficiency virus. So, theoretically and scientifically yes, the science of MRNA vaccine research should work for all RNA viruses, the challenge then comes in finding a target within that RNA virus which is clinically significant. As we just talked about with SARS coronavirus 2, we're lucky. We're able to target the S1 component of the spike protein which is the active binding site for the ACE2 receptor. That's a very clinically important target. That target may not be quite as accessible or as easy to find in other RNA viruses, but theoretically the short answer to a fabulous question is yes, hopefully they were.

    48:52 Alright. Okay. What is RT-PCR? So, reverse transcriptase PCR. So, the concept of PCR or polymerase chain reaction, is to use primers which bind to DNA, it was the original one, and allow enzymatic activity to first transcribe and then translate a specific gene within that DNA into a protein structure. Reverse transcriptase PCR is an additional step because it is going to harness and amplify RNA. So it reverse transcribes that RNA, typically a positive-sensed RNA, into a detectable strand of MRNA which then can create a protein structure. So reverse transcriptase simply means adding EN, an additional enzymatic step to take an RNA product into a protein structure and allow that to be detected. Alright and let's take one more question so we can wrap up on time. Here's a really good one.

    50:09 Okay. "Any tips on studying microbiology?" Hahahahaha. Fabulous question. As you are all probably quite aware, a lot of microbiology is wrote memorization. For me and I think one of the benefits of platforms certainly like Lecturio provides is the ability to translate that memorization into a clinical scenario. And there are many different ways to do that, some people create songs, some people create pictures. I prefer to think of it as looking at the diseases first because I see patients with those diseases and it sticks in my head.

    50:49 It's a case report basically or a case scenario. And then having sort of fixed the clinical part of the disease in my head, then I can understand more about the organism which causes it. Kind of how we talked about for Klebsiella. Okay, so I know that Klebsiella can cause pneumonia but what about the organism allows to cause that pneumonia as an opportunistic pathogen. Oh, the fact that it has a gram-negative outer membrane which limits or inhibits phagocytes or it downregulates immune system function and then triggers pro-inflammatory cytokines to cause more innocent bystandard damage. So a sort of like, for me, clinical scenario first then go into the organism to apply it. You might think of that as translational learning or applicational learning basically putting that memorized pathogen into context. So, goodluck with that and thank you all so much for your participation in today's session. Yes, thank you all so much. So one resource that you of course just mentioned is Lecturio. Just so those of you who have not already been part of Lecturio which is about third of the people who are here, Lecturio is an all-in-one study resource for medical school. It's a companion to your studies so you can learn using our short high-yield video lectures. We have an adaptive spaced repetition algorithm that feed to quiz questions about the videos you've watched and that information and then feeds the questions back to you at the opportune time to help with that memorization and that long-term memory and encoding that into your long-term memory. And then of course we got a lot of clinical case questions so Q bank questions and our Q bank actually mirrors the USMLE for those of you who are going to take that at some point. So just to let you all know what Lecturio is and then as I mentioned before we do have these concept pages and I think Dr. Elliott you worked on some of these. Right? Yes, I did and enjoyed it too.

    52:57 For me, just even creating the concept pages that same translational component. So greatly to harness all the information together. Alright, yeah. So these again we've linked on in the chat. We'll link them again but as one last little thing for all of you who are not yet premium subscribers, we would love for you to join us and obviously in many parts of the world Halloween is coming up this weekend so there's no tricks, it's just a treat.

    53:25 We are currently running a Halloween sale with 50% off all of our plans. So you can check out Lecturio, try the premium version. We do have a lot of our content that is free so you know if you saw in the first poll there were some people who are using the free version.

    53:39 This just means that they have access to a bit less content and not all of the features, but the premium plan, you know, has it all in there. So, this is something we want to give to you as, you know, those of you who are coming to our event and just to remind you that this does end this weekend on the 31st. So just a couple more days for this. But with it you get everything. You have the concept pages, all of the related videos. There are actually Q bank tests that are made out of the content from the concept pages so you are able to then really test your knowledge and your clinical application of these different concepts and then of course you know all of the videos, all of the quiz questions, all of the Q bank questions, study planner, a lot more. So this is just something for you and we just want to say as well thank you all so much for joining us today. This has been a wonderful session. Thank you so much Dr. Elliott for taking time out of your day to also prepare with us and to, yeah, just to present and yeah if you want to watch the rest of Dr. Elliott's microbiology lectures they're on Lecturio so go check it out and yeah. So that is all I've got for today. If we were not able to get to your question, you can always email us at, one of my colleagues will post that in the chat. If you have any follow-up questions, we will do our best to get back to you with a good answer and yeah thank you all so much and have a wonderful day wherever you are. Great. Thanks everyone. Everyone be well.

    About the Lecture

    The lecture Lecturio Live – Session 2: Microbiology with Dr. Sean Elliott by Lecturio Online Courses is from the course Lecturio’s Free Student Events On-Demand.

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