Latest / The SHEA Podcast / Stewardship of Metagenomic Sequencing
Transcript
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- 0:58SPEAKER_01: Joining me today is Dr.
- 1:00SPEAKER_01: Trevor Van Scoot, who is a professor of infectious diseases at the University of Nebraska Medical Center.
- 1:08SPEAKER_01: He's also the Associate Medical Director of Infection Control and Epidemiology and the Medical Director of Antimicrobial Stewardship, again, all at the University of Nebraska Medical Center.
- 1:19SPEAKER_01: We're both really excited to have this conversation today about the stewardship of metagenomic sequencing approaches, which is something I think is antimicrobial stewards, infectious diseases doctors, and infection control experts, we all have our stories and struggles with.
- 1:34SPEAKER_01: So to start off, I thought that it might be beneficial to just sort of describe the tests that we're talking about specifically and talk a little bit about exactly what is metagenomic sequencing.
- 1:44SPEAKER_01: So Trevor, maybe I'll kick that one over to you.
- 1:47SPEAKER_02: Yeah, yeah, that's a great question.
- 1:49SPEAKER_02: And I think this is an area where I had to do a lot of reading and uh digging to start to understand uh even the tests that we were ordering and what they involved.
- 1:58SPEAKER_02: So I think we're all familiar with whole genome sequencing as a technique for epidemiology.
- 2:03SPEAKER_02: It's a little different.
- 2:04SPEAKER_02: There's targeted next generation sequencing, which is generally done on tissue.
- 2:09SPEAKER_02: And when you talk about targeted, it's looking for specifically bacterial or fungal or mycobacterial pathogens.
- 2:16SPEAKER_02: And for example, the University of Washington does this.
- 2:19SPEAKER_02: There are other reference labs that provide these sorts of targeted assays.
- 2:23SPEAKER_02: And they're typically done on tissue specimens and can be requested on both fresh and even specimens that are uh already uh paraffin embedded.
- 2:31SPEAKER_02: It's a little different than uh metagenomic sequencing of uh plasma or CSF or other uh body fluids.
- 2:40SPEAKER_02: I think the probably the better known ones are Carius has one done at plasma, uh, Delve has one done at CSMF.
- 2:47SPEAKER_02: There are other uh more homegrown tests, and these are unique essays where they take all the DNA in a specimen, uh, amplify it all out, and throw out all the human stuff and just look for the pathogens.
- 2:58SPEAKER_02: These really are um, I think interesting and novel tools that are seeing increased use uh in the infectious disease world.
- 3:08SPEAKER_02: They're generating increased, I think, questions of what to do with them from a stewardship standpoint, from an infection control standpoint, and uh how do we engage with them as uh those who are involved in both as ID clinicians, but also as infection control and stewardship people.
- 3:24SPEAKER_02: So maybe I'll I'll ask you this one, Katie, if that's okay.
- 3:27SPEAKER_02: How sensitive or specific are these?
- 3:30SPEAKER_02: And how do we help people with like overinterpreting, misinterpreting?
- 3:34SPEAKER_02: There's I think a lot of maybe misconceptions sometimes with these tests.
- 3:38SPEAKER_02: Can you talk a little bit about that?
- 3:40SPEAKER_01: Absolutely.
- 3:41SPEAKER_01: I agree with you and um hear that a lot.
- 3:44SPEAKER_01: Like these are the game changer, these are the wave of the future.
- 3:46SPEAKER_01: Cultures are so out, they take so long to come back, and they're you know so inconvenient to wait for all of those susceptibility testing.
- 3:53SPEAKER_01: Why can't we just send the caryas and and you know, call it a day?
- 3:57SPEAKER_01: And and I can certainly understand the appeal of this, right?
- 4:00SPEAKER_01: I mean, we haven't had huge innovations in culture-based technology for many, many decades.
- 4:05SPEAKER_01: And so, in some ways, it does feel like we're using an antiquated method of ID diagnostics.
- 4:10SPEAKER_01: And so I can, you know, very much understand the appeal of something new.
- 4:15SPEAKER_01: I think the challenge, at least in the assays that I think are most often sent, at least, you know, at my institution and many other pediatric institutions, being the carious test or the microbial cell-free DNA test from plasma, is that, you know, unfortunately, they're not as reliable as they could be for routine use.
- 4:35SPEAKER_01: Um, we've got problems with false positives.
- 4:38SPEAKER_01: So in some initial validation work, at least for the carious test, about 20% of previously healthy, just normal people tested positive for things that are, you know, potentially pathogens.
- 4:49SPEAKER_01: And so you've got huge issues uh with false positives and overinterpretation, as you said.
- 4:56SPEAKER_01: And then we've also got the issue of missing things where you know patients are are later found to have true infections and the caryus was was not able to pick those those things up.
- 5:09SPEAKER_01: And so you've got this issue of sort of like the lab, you know, reliability characteristics, sensitivity, and specificity against a you know theoretical gold standard.
- 5:17SPEAKER_01: But because we know that so many infections lack a diagnostic gold standard, we sort of think about like, okay, well, what's the clinical utility of this test?
- 5:25SPEAKER_01: And how often does this produce you know clinically actionable information, you know, as as you said.
- 5:31SPEAKER_01: And you know, I think this is a tough question to answer, but at least in in the majority of studies that that have been done, you know, it it it's it's not always producing clinically actionable impact, sometimes less than 10% or so of the time, and and often actually generates some negative impact in the form of over-testing and over-treatment.
- 5:52SPEAKER_01: So I while I think this holds a lot of promise, I think there are a lot of pitfalls that that we still have to overcome in order to figure out exactly where these tests are most useful, at what time in the diagnostic evaluation they're most useful for, and and and when to target them and what what host to target them in.
- 6:12SPEAKER_01: And I think it's all of those questions that I think are unanswered at this point.
- 6:17SPEAKER_01: And so I think we hit the nail on the head in trying to understand a little bit better, like what are those situations and how do we steward them?
- 6:25SPEAKER_01: So I guess in your experience, what what's been some of the more or less successful ways you've done that or some of the more of the opportunities to do that better?
- 6:34SPEAKER_02: Yeah, that that's a great question.
- 6:36SPEAKER_02: How do you steward these tests?
- 6:37SPEAKER_02: I think one of the issues with these tests is if they cost uh 20 bucks, no one would care as much about stewarding them other than us antibiotic stewards who would say, Why are you treating all that stuff?
- 6:47SPEAKER_02: But there is a lot of interest, not just from I think infectious disease stewardship people in stewarding these tests because people treat what they detect on tests, but also from a lab standpoint, these are all very expensive tests.
- 7:01SPEAKER_02: And so the labs are always interested in their budgets and uh controlling their budgets, and so they want partners to help them in that.
- 7:08SPEAKER_02: And so so how do you do that?
- 7:09SPEAKER_02: Well, I think there's a variety of ways one can do that.
- 7:13SPEAKER_02: I mean, one way to do it is just to restrict it to infectious disease clinicians only.
- 7:17SPEAKER_02: Uh, and I know a lot of some a lot of places have done that, but there's advantages to that, but there's also disadvantages.
- 7:24SPEAKER_02: I mean, ID may not have to be involved in every single case, but at least at my facility, the challenge has been the non-ID clinicians don't necessarily understand the nuances of these tests and what a positive or even what a negative means.
- 7:43SPEAKER_02: And a negative, like you said, doesn't rule out infection.
- 7:46SPEAKER_02: And a positive doesn't mean we should treat what's detected.
- 7:50SPEAKER_02: And so it all, as you as you put very appropriately, it all really has to be put into clinical context of what's occurring with the patient, which I always think is an interesting thing.
- 7:59SPEAKER_02: I was just reflecting on this today.
- 8:01SPEAKER_02: When we say put the results in clinical context, what that means is that if I think it fits, I treat it, and if I think it doesn't, I ignore it.
- 8:10SPEAKER_02: Which I'm not sure how useful a test is that I use my.
- 8:14SPEAKER_02: I mean, I I guess that's what we do with radiography as well, but uh it's not usually how people think about tests.
- 8:20SPEAKER_02: Test people like to think about tests as black and white, positive, I have to do it, negative, I don't.
- 8:25SPEAKER_02: And so I think uh restricting to ID at least helps move it to people who are maybe a little more prepared to manage that uncertainty and understanding what to do with potential false positives uh and the sensitivity to the test.
- 8:40SPEAKER_02: Uh, there are other ways to do it, though.
- 8:41SPEAKER_02: That's not the only way to do it.
- 8:43SPEAKER_02: I think some labs have basically put it in the lab director's hands and said if the lab director says you can do it, you can do it.
- 8:51SPEAKER_02: Some lab directors feel confident and comfortable doing that.
- 8:55SPEAKER_02: Others um uh who maybe don't come from a clinical background or a physician background uh may feel less comfortable, although some do.
- 9:04SPEAKER_02: Uh and when a clinician comes up with a good reason for doing something, says yes.
- 9:09SPEAKER_02: And so I think uh lab directors like to have the support of um, say, stewardship programs or other ID clinicians to help give them advice.
- 9:18SPEAKER_02: Some centers actually have like a panel of people who look at these tests and say, yeah, we're not gonna, we don't think that's appropriate here, we do think that's appropriate here, or they pick which next generation sequencing test based on the clinical scenario.
- 9:34SPEAKER_02: Those are, I think, challenging to implement because of uh just the amount of time to sort through what's going on.
- 9:42SPEAKER_02: And so different centers sort of do it differently.
- 9:45SPEAKER_02: What we did was we had these unrestricted initially, mostly because we didn't know they were being ordered until our lab director said, Hey, you know, neurology's ordered uh 12 of these uh next generation sequences on CSF and they've all been negative.
- 10:00SPEAKER_02: What do you guys think?
- 10:02SPEAKER_02: And so we started looking at it and uh doing some more investigation, and we restricted them to ID only, which uh there's pluses and minuses.
- 10:12SPEAKER_02: Some ID clinicians are very enthusiastic about what's new and maybe uses use them more than they should, and others probably use them less.
- 10:20SPEAKER_02: So I don't know what do you guys do at your facility with these tests?
- 10:24SPEAKER_01: Yeah, I think those are all really great points.
- 10:27SPEAKER_01: At our facility, we don't have formal restrictions on this test or an approval system, so to speak, but generally speaking, it's generally ID that will ultimately recommend this test.
- 10:39SPEAKER_01: And I can say that we do it almost never because we've sort of put out the word that this is not a test right now that we quite know how to use.
- 10:46SPEAKER_01: And so I think most of our subspecialists don't send it very often because of because of that kind of internal consensus.
- 10:54SPEAKER_01: We have at times sent it in, you know, uh, for example, people with focal separative infections where we're looking for a specific uh diagnosis.
- 11:03SPEAKER_01: We've used it once or twice in the setting of possible endocarditis, which I think is one of the emerging areas where this may be of some utility, but we don't have a formal approval process or kind of system like that for this, although that is something that's probably very important and something that we should consider putting into place as these tests become more commonly used.
- 11:25SPEAKER_01: I think you made some really great points in general.
- 11:28SPEAKER_01: And one thing that I've tried to use with previous diagnostic stewardship efforts is the Shea Position paper that Valeria Fabre and others published a few years ago in infection control and hospital epidemiology, and you know, kind of steps through some of the you know things to do to establish a diagnostic stewardship intervention.
- 11:48SPEAKER_01: And you've outlined a lot of them really nicely.
- 11:50SPEAKER_01: For example, to define a clear goal of when the test, you know, should and should it be sent, identify the relevant stakeholders, in this case, including microbiology, stewardship, uh, end users, et cetera, um, ensure hospital support and define measures to track positive or negative impact of the intervention.
- 12:09SPEAKER_01: You know, I think for us, one thing that we really struggled with is that it was hard for us to actually define what that goal is.
- 12:15SPEAKER_01: And you alluded to this as well, just because of a lack of clear evidence of where this test is clearly beneficial and when this test in the course of the patient's you know presentation is beneficial, with most of the data really suggesting that most of these tests have really no impact whatsoever on clinical management.
- 12:32SPEAKER_01: It was really hard for us to kind of think of like, okay, how do we carve out this diagnostic stewardship, you know, niche?
- 12:39SPEAKER_01: And that's that's the reason that we essentially almost never send it here, is because we really don't know what that niche is right now.
- 12:48SPEAKER_02: Yeah, that's been our challenge too.
- 12:49SPEAKER_02: And I I agree with you.
- 12:50SPEAKER_02: I love that uh Shea Position paper.
- 12:53SPEAKER_02: And I think uh this sort of topic fits well into the CDC's diagnostic excellence framework where this sort of cuts even, you know, this cuts beyond uh, you know, the traditional areas where maybe we have thought of diagnostic stewardship.
- 13:09SPEAKER_02: And so I think uh there are real opportunities here to improve, like you said, improve the care of patients, because that's the goal, right?
- 13:16SPEAKER_02: I mean, that's the first goal of diagnostic stewardship is to improve the care.
- 13:20SPEAKER_02: And we want to use tests where they're really going to improve the care, uh, not maybe do it 24 hours earlier than traditional testing might.
- 13:28SPEAKER_02: Because I don't think in most cases that uh that really improves the care that much.
- 13:33SPEAKER_02: Maybe in a very rare one.
- 13:35SPEAKER_02: So that that's been our experience as well, as you mentioned, somewhere around 10 to 15 percent of results are meaningful and uh result in some positive outcome.
- 13:46SPEAKER_02: But you know, if you look at the literature, you know, up to two to five percent result in a negative outcome.
- 13:52SPEAKER_02: And so, you know, how many tests do we need to do to uh have a positive versus a negative outcome?
- 13:58SPEAKER_02: So one of the things that I just realized uh was that uh these non-culture-based tests are actually now included in the uh in the CLABSE definition.
- 14:08SPEAKER_02: And uh have you looked at uh the impact of these at all at your institution on uh any of your HAI measures?
- 14:17SPEAKER_01: We haven't, you know, to be very honest, we send it so infrequently that, at least as of now, knock on wood, um, that we really haven't had many occasions to um to go that route.
- 14:27SPEAKER_01: Um, although I think that's a really important thing to consider and that people may not be aware of that, in fact, you know, a positive one of these cell-free DNA or other NGS approaches can actually count uh towards uh a hospital onset infection, which you know, I think the probably the pros and cons of various surveillance definitions for hospital onset bacteremia and other things are beyond the scope of this discussion.
- 14:51SPEAKER_01: But I do think that that's something that people aren't aware of.
- 14:54SPEAKER_01: And given the you know, relatively high false positive rate, I think that's a really compelling argument for why investment in stewarding these tests becomes really important, particularly to hospital leaders.
- 15:05SPEAKER_01: Because the last thing I think probably the C-suite wants is to have even more CLABS to sort of explain and you know, kind of have, you know, potentially impact various metrics at the hospital when they're not, you know, deserved, because then you drive prevention efforts and other things towards, you know, uh systems and people and units and things like that that that probably don't need them or don't need them in some situations.
- 15:30SPEAKER_01: And so I think that really highlights the IPC, I think, uh, role for diagnostic test stewardship and if that is if we're not measuring an event accurately.
- 15:40SPEAKER_01: And I would argue that, you know, cell-free DNA, for example, is is probably not the most accurate way to diagnose a CLABSE.
- 15:47SPEAKER_01: We risk diverting prevention efforts away from where they're truly needed towards uh you know places where where they're not because of indiscriminate uh testing of a of a test that's really not designed for that purpose.
- 16:01SPEAKER_01: So I think it's a really important point and maybe something that our listeners may not always be aware of.
- 16:08SPEAKER_02: Yeah, I totally agree.
- 16:10SPEAKER_02: I think um we can debate the utility of including these in the CLABSE definition, but I think uh they're certainly things to be aware of um and uh they can have an impact beyond what you would expect if you're using them indiscriminately.
- 16:27SPEAKER_02: So uh yeah, I think a great opportunity to again engage uh stewards and infection control personnel and assisting the micro lab in managing these.
- 16:38SPEAKER_02: Any thoughts uh on where these tests are going to go in the future and what role stewardship could play in that?
- 16:47SPEAKER_01: Yeah, I think that's a really important thing.
- 16:49SPEAKER_01: And I think one, um, at least for me, one of the most important things to think about of these tests is the really the niches where they fit and how to fit them into existing algorithms.
- 17:00SPEAKER_01: So, you know, kind of thinking about a couple of manuscripts, and I'm I'm taking a little bit of the pediatrics lens because that's where my practice is, you know, folks have sent this in the setting of, for example, complicated pneumonia.
- 17:10SPEAKER_01: So children with parannemonic effusions, empyemas, necrotizing pneumonia, things like that, and have said, okay, well, most of those kids actually do have positive cell-free DNA sequencing tests.
- 17:21SPEAKER_01: Often these diagnose the things that you would expect for that clinical syndrome.
- 17:25SPEAKER_01: So, for example, pneumococcus, staph aureus, uh, strep uh strep pyogenies, um, etc.
- 17:31SPEAKER_01: And you know, they've touted that as a really powerful way to narrow antibiotics because maybe you get a microbiologic diagnosis, whereas you may not otherwise get a microbiologic diagnosis in a child with um with pneumonia.
- 17:45SPEAKER_01: And we love that from a stewardship perspective, right?
- 17:47SPEAKER_01: If we know the name of a bug, we can target it effectively.
- 17:50SPEAKER_01: I think we have to kind of pump the brakes a little bit on that conclusion, just because most of the pathogens that these these tests are identifying are pathogens that we're covering anyway, if we follow guideline recommendations for antibiotic choice and duration.
- 18:05SPEAKER_01: Most people are treating these complicated pneumonias, you know, for the example of like a paranemonic effusion or empyema, for about a week, maybe two weeks after the adequacy of source control is achieved.
- 18:17SPEAKER_01: Um, and in those situations, maybe saving, you know, a few days of amoxicillin, for example, an agent that covers many pneumococcus and group A strep, but not staph aureus, um, allowing you to transition a little earlier from something like a mox clav or ceftriaxone to amoxicillin.
- 18:33SPEAKER_01: I'm not sure that the financial trade-off is entirely worth it in that situation.
- 18:38SPEAKER_01: Now, if you're treating these patients for three, four, six weeks, you're probably not following the guidelines and the evidence-based in the first place, and that probably your stewardship efforts may be better invested in getting people to adhere to evidence-based guidelines rather than sending a bunch of expensive diagnostic tests.
- 18:56SPEAKER_01: Um, but I think that's the setting where, you know, there, there, there's a little bit of a tension and trade-off between just good antimicrobial stewardship versus the novel and greatest thing.
- 19:06SPEAKER_01: Similarly, you know, a lot of these cell-free DNA can't uh distinguish MRSA and MSSA the way that like a MRSA nasal swab can, for example.
- 19:15SPEAKER_01: And so probably your your the bang for your buck is probably better invested in getting people to actually obtain MERSA nasal swabs de-escalating off of MERSA anti-MRSA therapy rather than sending a you know test that's a few thousand dollars to tell you that maybe there's some staph warriors there, which you probably knew already based on the you know the clinical scenario.
- 19:35SPEAKER_01: So I'm going on a little bit of a of a rant with some of these, uh, some of these diagnostic tests and common pediatric conditions, but I do worry that the benefit is is overstated quite a bit.
- 19:46SPEAKER_01: And I think this gets to your point about like where do they fit in from a diagnostic stewardship perspective.
- 19:52SPEAKER_01: So I think like in these patients, getting a blood culture, getting a MERSA, you know, PCR, getting pleural fluid for culture and antimicrobial susceptibility, and if you have them in-house kind of PCR tests, probably is gonna do 99% of the work that any of these diagnostic tests could do on the best of days and do it in a more cost-effective fashion.
- 20:13SPEAKER_01: So I think it's a matter of incorporating these tests in the scheme of the other diagnostic tests you have available to you that's really important.
- 20:21SPEAKER_01: And another example of that might be endocarditis, right?
- 20:23SPEAKER_01: So I think we've seen some evidence that in these, you know, hard to culture organisms that that perhaps they have some benefit and some role, but the the trick is figuring out where in the scheme of things.
- 20:34SPEAKER_01: You don't want to send it two weeks into antibiotics when the sensitivity may be a little bit less, but you also don't want to send it on everybody.
- 20:40SPEAKER_01: So is there a role for some algorithmic approach where it's sort of drawn and held versus sent on everybody?
- 20:46SPEAKER_01: I think that's something that we need to explore.
- 20:48SPEAKER_01: And then finally, I feel like the data need to be there to show that these are generating clinically actionable information.
- 20:55SPEAKER_01: A lot of what we have so far has been industry funded, and not to say that that's not a great thing to have done, but you know, I think we need potentially unbiased uh trials that study the impact of what these could have done in the real world, not hypothetical, um, and and understand what the what the actual value is in caring for caring for real patients.
- 21:17SPEAKER_02: I agree with so many of your comments and have uh maybe some of the same rants to go on too.
- 21:23SPEAKER_02: I think um uh the need for uh systematic study and publication of these tests is great.
- 21:31SPEAKER_02: We mostly have uh we've tried it out, and here's what we found.
- 21:35SPEAKER_02: And that can be a bit of a self-fulfilling prophecy.
- 21:38SPEAKER_02: Uh you detect something, you treat it, is that good or bad?
- 21:41SPEAKER_02: And I think your points about de-escalation are exactly right.
- 21:44SPEAKER_02: Is the the bang worth a buck?
- 21:46SPEAKER_02: Yeah, we went from augmentin to moxicillin.
- 21:49SPEAKER_02: Okay, is that really worth the amount?
- 21:52SPEAKER_02: I don't it may be, it may not be.
- 21:53SPEAKER_02: I think those are the challenging questions to answer.
- 21:56SPEAKER_02: Uh, but I also agree there are places where I think it will have utility.
- 22:00SPEAKER_02: I think if an endovascular infection is a place, uh we've had a number of culture-negative endocarditis, particularly where people are starting in antibiotics early and have allowed us to identify pathogens and you know, get rid of BANCO that we would have given for four or six weeks.
- 22:16SPEAKER_02: And there it was a study that was just published in Itchy within the last couple of months.
- 22:20SPEAKER_02: It showed positive clinical impacts are associated with culture-negative endocarditis and then weird fastidious bugs, which is, I mean, those are kind of the areas where as ID clinicians said, boy, we really wish we had better tools in these areas.
- 22:32SPEAKER_02: And these are tools to add.
- 22:35SPEAKER_02: But like you said, I think they're tools to add after we've done our initial diagnostic testing because these aren't 100% sensitive assays.
- 22:43SPEAKER_02: I think of like the CSF assay.
- 22:45SPEAKER_02: There was another great paper that was just published on this where they looked at the utility of the CSF metagenomic assay diagnosing uh meningitis and cephalitis.
- 22:55SPEAKER_02: And they found uh 48 cases that were missed by traditional testing.
- 22:59SPEAKER_02: But they found another 80 cases that were detected by traditional testing that weren't detected by next generation sequencing.
- 23:05SPEAKER_02: And so I think we really need to build it into our diagnostic armamentarium after our initial workup, where we can thoughtfully deploy it at a time where it's going to have the most value.
- 23:16SPEAKER_02: So uh at our institution, we tried to put together a guideline for its use.
- 23:20SPEAKER_02: I don't know how successful it was.
- 23:22SPEAKER_02: I feel like some of the practices changed once we talked about, once we created the guideline, and that some people said, Oh, we have this test, we should use it more now that we know about it.
- 23:32SPEAKER_02: And so I think um, but I think we need more of that of unbiased study compared to gold standards, although the gold standards are challenging in this area, um, uh because it's uh it's really um a novel testing modality, and then really figuring out what syndromes is it most useful for and what syndromes should really should we not think about it.
- 23:55SPEAKER_02: So I think we'll probably close up our conversation there.
- 23:58SPEAKER_02: I just want to thank you, Dr.
- 23:59SPEAKER_02: Shotas, for a great conversation on a really interesting uh topic.
- 24:02SPEAKER_02: Uh it was great to hear your thoughts.
- 24:04SPEAKER_02: It was great to hear that they're very aligned with mine.
- 24:07SPEAKER_02: Uh, that's fabulous.
- 24:08SPEAKER_02: It's always great uh um hear that.
- 24:11SPEAKER_02: And uh, you know, I think it's a topic we need to think more about in the infection control stewardship world.
- 24:16SPEAKER_02: What can be our role to help shape uh the use of these tests?
- 24:20SPEAKER_02: I think ID clinicians in general are ideally uh positioned, and stewardship and infection control people particularly in helping to understand how to better deploy uh novel diagnostic testing assays and how to put them into practice so they most benefit patients.
- 24:37SPEAKER_02: Hope you have enjoyed this uh SHA podcast listeners, and this concludes our episode of the SHA podcast.
- 24:43SPEAKER_02: Thank you for tuning in.