SCCM Pod-443 How the Pneumonia Panel Aids in Antimicrobial Stewardship and in the Fight Against COVI

BioFire® FilmArray® is the latest in technologies for rapidly identifying pathogens that cause Lower Respiratory Tract Infections (LRTI). Host Pamela M. Peeke, MD, MPH, FACP, FACSM, is joined by Tufik Assad M.D., M.S.C.I. to discuss how this technology can be integrated into clinical care to improve patient outcomes, describe the benefits in diagnosing bacterial secondary infections in patients with COVID-19 and summarize the benefits of Pneumonia (PN) Panel in the fight against Antimicrobial Resistance. Dr. Assad is the Medical Director of the Lung Nodule Clinic at Williamson Medical Center. This podcast is sponsored by BioFire.

Tufik Assad M.D., M.S.C.I., is the Medical Director of the Lung Nodule Clinic at Williamson Medical Center. Dr. Assad is board certified in Pulmonary Medicine, Critical Care Medicine and Internal Medicine. He practices with Williamson Medical Group in Franklin and is a credentialed physician with Williamson Medical Center.

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The iCritical Care podcast is the copyrighted material of the Society of Critical Care Medicine and all rights are reserved. Statements of fact and opinions expressed in this podcast are those of authors and participants and do not imply an opinion or endorsement on the part of the Society of Critical Care Medicine, its officers, volunteers, or members, or that of the podcast commercial supporter.  

This podcast is sponsored by BioFire. High-acuity patients require time-sensitive, specialized care. As a critical care physician, you need rapid, reliable test results to make informed intervention decisions. The BioFire® FilmArray® System utilizes a syndromic approach—simultaneously testing for different pathogens that can cause similar symptoms—to deliver actionable results in about an hour.  

BioFire helps you quickly identify specific infectious agents, allowing you to begin targeted treatment sooner. Learn more about solutions from the leader in syndromic testing at biofiredx.com. 
 
Dr Pam Peeke: Hello and welcome to the Society of Critical Care Medicine's iCritical Care podcast. I'm your host, Dr. Pam Peeke. Today, we're going to be talking about how the pneumonia panel aids in anti-microbial stewardship and in the fight against COVID-19 
 
Today, I'm joined by Dr. Tufik Assad. He is the Medical Director of the Lung Nodule Clinic at Williamson Medical Center. Dr. Assad is board-certified in pulmonary medicine, critical care medicine and internal medicine. He practices with Williamson Medical Group in Franklin and is a credentialed physician with Williamson Medical Center. Welcome, Dr. Assaad. Before we start, do you have any disclosures to report? 
 
Dr Tufik Assad: Yes, Dr. Peeke. I am a consultant for BioFire Diagnostics, which is a subsidiary of bioMérieux. And they are a company that makes one of these pneumonia PCR panels. 
 
Dr Pam Peeke: Excellent. Very good. And for everyone out there and we'll all be learning about this together, I want to make sure you understand the learning objectives, which are to describe the benefits of the BioFire FilmArray Pneumonia Panel in diagnosing bacterial secondary infections in patients with COVID-19, to summarize the benefits of the BioFire FilmArray Pneumonia Panel in the fight against anti-microbial resistance and to also discuss the benefits of the BioFire. 
 
And why is this podcast needed? It's because we need to be made aware of the latest technologies for rapidly identifying pathogens that cause lower respiratory tract infections and how this technology can be integrated into clinical care to improve patient outcomes. And it's important to acknowledge the knowledge gaps that this podcast we'll address, which are, number one, learners will become more aware that the BioFire FilmArray Pneumonia Panel can rapidly identify the infectious etiology of primary or secondary lower respiratory tract infections, a powerful tool in patients with COVID-19, and to be more aware that this panel can serve as a vital tool in anti-microbial stewardship. 
 
All right. Now, let's just get right in here. This is really all about talking about your experience right off the bat, Dr. Assad, with bacterial pneumonia co-infection in patients with COVID-19. 
 
Dr Tufik Assad: So to get going, I mean, everything that is on the mind of a pulmonologist and a critical care physician over the past year and a half has been COVID-19. And so this talk is going to be focusing on that pandemic. But I also want to say this tool is a generalizable tool for all patients with lower respiratory tract infection. But starting to answer that question, bacterial secondary infections in patients with COVID-19, if we can kind of rewind back to December of 2019 through January, February of 2020, this was a brand new pandemic. Nobody knew what we were doing. There were reports coming out of Wuhan, China and the New York City and Italy, and then across the world. And we were stuck with this brand new respiratory illness that was leading to overwhelming respiratory failure, fevers, dramatic bilateral infiltrates, mechanical ventilation, everything. 
 
And so a lot of those early reports talked about empiric antibiotic use that was off the charts. And so it's kind of hard to remember back then, because it's been such a long year and a half, but just about everybody was getting placed on empiric antibiotics. So some of the reports that were coming out found that almost a 100% of patients on mechanical ventilation with what we now know is a viral respiratory illness, everybody's getting antibiotics. And so it's hard to know because some of the studies that looked at the actual rates of bacterial infections in these patients found that the reported incidence of true documented bacterial infections was kind of low. But the issue was everybody's getting antibiotics. And so, almost 100% of people were placed on them. And then when they tried to obtain sputum specimens and look into these and figure out how many people actually had bacterial infections, when you rely on sputum culture, it's greatly affected by empiric antibiotic use. 
 
And so it's really hard to know and tease out how many patients truly did have a bacterial secondary infection. But if you ask me based in my clinical practice, when we looked at a lot of our patients on mechanical ventilation, we found that a lot of them did have bacterial infection. And part of the way that we were able to identify that was through this pneumonia PCR panel, which is just a whole culture shift when you look at the way that we diagnose lower respiratory tract infections. It's not a culture. It doesn't rely on live viable organisms. Like everything else these days, it's the push to move towards molecular diagnosis. 
 
Dr Pam Peeke: All right. So tell us more about this panel. Clearly, people have used the classic bacterial culture, which takes quite a while to come back. Meanwhile, you're basically doing a guessing game, you know, what do you use? What do you think's going on, et cetera? So tell us more about the panel and why you think it's a game-changer. 
 
Dr Tufik Assad: Yeah, sure. Let me walk you through that because for those who haven't used it, you may not know exactly what we're talking about. So this panel is a multiplex PCR panel that is run on a lower respiratory tract specimen. So it can be an expectorated specimen, so somebody coughs into a cup and we can test it. It can be on an endotracheal aspirate for somebody on mechanical ventilation. It can be a bronchoalveolar lavage. 
 
So you start off with the lower respiratory tract specimen. And then this panel has a total of 33 different targets. It's got eight respiratory viruses. At the moment, COVID-19 is not on the panel, but that is something that obviously in the near future will be on the panel. It's got a total of 18 different bacteria on the panel, a few of the sort of atypical bacterial pathogens, like legionella, chlamydia mycoplasma, and then 15 of the more common, lower risk bacterial pathogens, like, you know, strep species, staph species, a whole bunch of Gram-negative rods. 
 
And then with those 15 common bacterial pathogen, not only does it tell you present or not present or detected or not detected, it gives you a semi-quantitative value. They call it a bin value, which is the relative amount of pathogen that is present in that specimen. Not quite the same as the CFU, colony forming units, that we're used to with culture, but a sort of correlate in the molecular world. And then finally it gives you a number of different anti-microbial resistance genes. So it detects the mecA/C and MREJ genes on staph, which is really what confers staphylococcal resistance to methicillin. So that tells you MRSA versus MSSA. It gives you the most common ESBL resistance gene, which is the CTX-M and then it gives you five different carbapenemase resistance genes, including the one that we think about the most, which is the KPC gene. 
 
And so you take a specimen from the lower respiratory tract. You put it in this little pouch. You have to insert the pouch into the BioFire panel, their FilmArray panel. And within one hour, you get a result that tells you if any of these viruses were detected, if any of the bacteria were detected and whether any of these anti-microbial resistance genes were noted. 
 
And so unlike, as you said, the conventional model that we're all pretty familiar with, where you get a sputum specimen, you wait a day until they identify something, you wait another day until they give you more info, and then another day until you get resistance info, you get a result within one hour. And in that way, I think it is totally game-changing. Within an hour of intubating somebody, let's say, with respiratory failure, you do a lavage of their endotracheal tube, you know if and what kind of bacterial or viral pathogens they have and some info on their resistance. 
 
Dr Pam Peeke: This is fantastic. Now, how long have you been using this? 
 
Dr Tufik Assad: We've had it for about three years now. So we had it well before COVID-19 and kind of right before, maybe about 6 to 12 months before COVID-19 hits. We were already trying to figure out how do we use this in our clinical practice. And then all of a sudden COVID hit and our number of patients with respiratory failure just skyrocketed. And we started to use it pretty consistently with every patient who could give us an expectorated specimen, who was not intubated and just about every patient who was on the ventilator. 
 
And like I said, unlike the reports that commented on a fairly low amount of bacterial secondary infections in patients with COVID-19, we were finding detection rates of 70% in some of our patients on mechanical ventilator, which was far higher than was reported. And I think it has a lot to do with the fact that this is an extremely sensitive test. Unlike sputum culture, it's not affected by empiric antibiotic use. And we were taking this information and changing clinical management. 
 
Dr Pam Peeke: How many pathogens are actually being identified by the panel? Because that could be another interesting challenge. So it's not just one, it could be up to three or more. 
 
Dr Tufik Assad: Yeah. There are times that we have a polymicrobial detection and that is something that we've seen a lot more post-COVID than pre-COVID. And so it's definitely more common in patients with chronic lung disease. So your patient with COPD or bronchiectasis or even interstitial lung diseases, we know that they are colonized with a variety of bacteria in their lower respiratory tract. And so in some of those situations, it is a bit of a challenge to identify which ones are pathogenic and which ones may be more of a colonizer. But we were kind of shocked in the COVID-19 pandemic how many patients without lung disease, respiratory failure on the ventilator had multiple pathogens identified. I think I told you about 70% of all of our patients on mechanical ventilation, where we found some bacterial pathogen and over half of the ones who had something identified, there was at least two different pathogens found. 
 
Dr Pam Peeke: Did you see a trending in the COVID-19 patients with one or two specific pathogens? Was there a particular trending toward that type of colonization? 
 
Dr Tufik Assad: We saw a ton of staph, a ton of staph and an interesting 50/50 split MRSA and MSSA. A lot of these people were, you know, in the hospital for several days or a week before going on the ventilator. So they have the opportunity to be colonized by healthcare-associated pathogens. Many of them were getting antibiotics at home, let's say, from their primary care doctor or an urgent care clinic. And so they were already getting some antibiotic exposure, which I think really did increase the chance that they were going to have more resistant pathogens found. 
 
We saw a bunch of Gram-negative species, a lot of Klebsiella, Enterobacter and E. coli, even a handful of pseudomonas. The pseudomonas tended to be found in patients with chronic lung disease or immunodeficiency. It was an amazing array of different pathogens, but tended to be a lot more of the resistant ones that we think of causing healthcare or ventilator-associated pneumonia. 
 
Dr Pam Peeke: And at the same time, you also deescalate, don't you? Or stop antibiotics? 
 
Dr Tufik Assad: Yeah. And so, for example, you know, if somebody comes in with COVID, bilateral infiltrates, you put them on the vent because they're in respiratory failure and you within an hour can identify if they have MSSA. And so we placed those patients on cefazolin right away. So instead of vanc-Zosyn or vanc-cefepime or vanc-meropenem, waiting a couple of days til the culture data comes back, within an hour of somebody going on the ventilator, if that's what they had, we put them on the appropriate tailored antibiotics. 
 
So for us, we have a pretty dedicated anti-microbial stewardship program in our facility, which is largely run by our pharmacists who were excellent. We have pretty good buy-in from our infectious disease doctors and hospitalists and critical care doctors as well. And so we just decided early on that we believe in this panel, we believe in anti-microbial stewardship. And as soon as there is a bacteria found that fits the clinical scenario, we would tailor antibiotics right away. 
 
Dr Pam Peeke: Address false positives. Do you believe that findings ever represent false positives? And how do you handle these situations? 
 
Dr Tufik Assad: That's a great question. And I do believe that occasionally there are false positives. So one thing that I will say is that there is a threshold that BioFire has placed to detect whether or not to call it infection or not and that is 10 to the 3.5 copies per milliliter. And so that means if a bacteria was found, but found at a threshold below that, they actually don't tell you anything about it and they say not detected. So there is a built-in mechanism to try to weed out some of the very low level bacterial pathogens identified. And if they do find a bacterial pathogen, one of the 15 that they call semi-quantitative, they give you a little bit of information on which bend they're in. 
 
And so it doesn't just tell you, you have MSSA. It tells you have MSSA at either 10 to the 4th, 10 to 5th, the 10 to the 6th or greater than or equal to 10 to the 7th copies per mL. And I've used that in my clinical practice as a sort of reflection on the relative bacterial burden. And so if I see somebody who has multiple pathogens and one of them is at 10 to the 4th and I'm just not convinced that it's pathogenic, there are times where we just ignore that information and maybe wait for the culture or just use our clinical intuition and judgment. But we found that when they're at the higher bin amount, that's greater than 10 to the 7th or 10 to the 6th, those are almost never colonization or contaminant. Those are almost always legitimate infection. But just like any test, you know, you've got to use your clinical judgment. And so there are times when you just have to weigh in all of the factors and all of the other data and make the best judgment for your patient. 
 
Dr Pam Peeke: Excellent. Fantastic. So who are these patients? In other words, how do you use it on which patients? Do they have to be on a vent, when they first come in and they are having difficulty breathing, but they're not on a vent yet? Just go through the patient selection algorithm. 
 
Dr Tufik Assad: So as we've become more comfortable with this panel and used it for the past couple of years, we have definitely liberalized who we're using this on. And so anybody that can expectorate a sputum specimen who has a concern for a lower respiratory tract infection is hospitalized, we tend to use this panel the same way that I would decide when to use a sputum culture. Essentially all of those patients, we use this panel. 
 
Now, sometimes and this is sort of institution by institution decision, what we decided to do was used the sputum Gram stain as a sort of gatekeeper on who we choose to use this panel on. As you know, many patients, we ask them to expectorate into a cup and they essentially just give us a couple of spit. 
 
If during the assessment of the sputum Gram stain, we find there's a bunch of epithelial cells, we use a Q score to kind of judge the quality of the sputum specimen, but there are other scoring systems. If we feel like it's an oral contaminant essentially, we don't run the pneumonia panel on it because this test is validated for lower respiratory tract specimens. And if you can't give it to us, then we can't run it. But if it's a good quality specimen and they have a pneumonia and we're considering to give them antibiotics and which one, we find the information to be extremely useful. And as you said, tailoring antibiotics and deescalating, or occasionally identifying a more resistant pathogen and escalating antibiotics. 
 
As for people on the ventilator, we essentially use it a hundred percent of the time if there is concern for lower respiratory tract infection. The specimens are high quality. You're getting it directly from their lower respiratory tract and it really guides our antibiotic decisions. 
 
Dr Pam Peeke: All right. So what if one of our brethren is listening to this out there and they really want to begin to utilize this? What is your recommendation about getting started? They've listened to this podcast and they said, "We'd like to try this out. What would they do?" 
 
Dr Tufik Assad: So they'd have to reach out to BioFire. So this is sort of a big capital purchase for your institution. And this is something that if you're interested, I would reach out to your lab director and have them reach out to BioFire. So what this is is you're buying the machine, the equipment, the FilmArray system that runs the panel. You're buying the pouches, which are the little mini test kits in which the specimen is placed in. And so you have to get buy-in from your institution and oftentimes buy-in from your laboratory directors to reach out and to get a demo and hear from the company. 
 
Dr Pam Peeke: Excellent. And how does the critical care team get educated about the utilization of this technology? 
 
Dr Tufik Assad: I think BioFire has a bunch of representatives and videos online. And they're coming out with publications now on the subject. And so if this is something that you think you could use, and honestly, I think this is just the way that medicine is heading, I think we're going further and further towards molecular rapid diagnostics, then I think you need to just speak up at your institution and the company would be more than happy to give you some examples and put you in touch with facilities that have used it and demos, et cetera. So I think you just have to speak up. 
 
Dr Pam Peeke: You yourself and your institution would be willing to help out if somebody listening to this podcast, wanting to reach out to you and ask you a few questions about your experience. 
 
Dr Tufik Assad: Yeah. I've made myself available to BioFire to sort of be the spokesperson based on our clinical experience. And so we've gotten on the phone before at institutions that have it and had questions about how we're handling things and what's our workflow. And I'm more than happy to speak to people about it because I really am a huge believer in it. And like I said, it's changed the way we practice. 
 
Dr Pam Peeke: Excellent. So you actually, as we're closing this podcast, you're a believer that you believe this is going to be integrated into critical care medicine in the near future that you're using it now, you're a believer, you've had it for two to three years, certainly with the advent of COVID-19, that it was quite timely to say the least, but in your expert opinion, you see this as being integrated into critical care practice. 
 
Dr Tufik Assad: Yeah, I think just like all rapid diagnostics and molecular diagnostics, this is the future. I'm not saying that culture is not going to be useful. I'm not saying that you're not going to occasionally have to rely on culture. There are certain bacterial pathogens and viral pathogens that won't be on this panel. But I think this is going to be the standard of care in the very near future. 
 
Dr Pam Peeke: Any idea when the COVID-19 virus itself will be part of the panel? 
 
Dr Tufik Assad: I do know that they make a number of different panels that we didn't speak about today. They make an upper respiratory panel, which is the nasopharyngeal swab. They make a meningitis panel on cerebral spinal fluid, a blood panel for blood cultures, a GI panel on stool specimens. And I know that the SARS-CoV-​2 is already on the upper respiratory panel. And so I don't know an exact timeline on when it's going to be on the pneumonia panel, but my assumption is it's only a matter of time, probably within a short few months or so, but I don't know that for sure. 
 
Dr Pam Peeke: Fantastic. This has been very, very helpful. And, you know, as we close this segment, Dr. Assad, do you have any words of wisdom out there for your fellow travelers in critical care as it relates to this technology? 
 
Dr Tufik Assad: I think it's imperative that practicing clinical providers speak up about what they want at their institution. I think all too often in the hospital, the laboratory makes decisions on what is or isn't a good test for a clinician. And I'm a big believer in having data and having information and having say in what tests that we order, because it's us, we're the ones interpreting them and taking care of patients. 
 
So I think if you believe in molecular diagnostics and rapid diagnostics like I do, you just need to speak up and be a voice of change in your institution because I can tell you waiting three days versus having results within one hour, it's a total game changer. So I'm a believer and I think you just need to speak up on behalf of your patients. 
 
Dr Pam Peeke: Excellent. Fantastic. So really what you're saying is proactivity on the part of the critical care team in really not only staying on top of this technology, but also voicing their interest in learning more about it and potentially purchasing and integrating the technology into medical practice. 
 
We've been speaking today with Dr. Tufik Assad, who is a Medical Director of the Lung Nodule Clinic at Williamson Medical Center. And the topic has been how the pneumonia panel aids in anti-microbial stewardship and in the fight against COVID-19. This concludes another edition of the iCritical Care Podcast. For the iCritical Care Podcast, I'm Dr. Pam Peeke. 
 
This podcast is sponsored by BioFire. High-acuity patients require time-sensitive, specialized care. As a critical care physician, you need rapid, reliable test results to make informed intervention decisions. The BioFire® FilmArray® System utilizes a syndromic approach—simultaneously testing for different pathogens that can cause similar symptoms—to deliver actionable results in about an hour.  

BioFire helps you quickly identify specific infectious agents, allowing you to begin targeted treatment sooner. Learn more about solutions from the leader in syndromic testing at biofiredx.com. 
 
Pamela M. Peeke, MD, MPH, FACP, FACSM is a nationally-renowned physician, scientist, expert and thought leader in the field of medicine. Dr. Peeke is a Pew Foundation scholar in Nutrition and Metabolism, Assistant Professor of Medicine at the University of Maryland, holds dual master's Degrees in Public Health and Policy, and is a fellow of both the American College of Physicians and the American College of Sports Medicine. 
 
Dr. Peeke has been named one of America's top physicians by the Consumer's Research Council of America. She is a regular in-studio medical commentator for the National Networks and an acclaimed TEDx presenter and national keynote speaker. Dr. Peeke is a three-time New York Times bestselling author and is a science and health advisor for Apple. 

The iCritical Care podcast is the copyrighted material of the Society of Critical Care Medicine and all rights are reserved. Statements of fact and opinions expressed in this podcast are those of authors and participants and do not imply an opinion or endorsement on the part of the Society of Critical Care Medicine, its officers, volunteers, or members, or that of the podcast commercial supporter.