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The Utility of Whole Genome Sequencing: Academic and/or Clinically Pragmatic? · The SHEA Podcast

• 0:05
  SPEAKER_01: Welcome to our podcast series, Digital and Electronic Innovations in Hospital Epidemiology and Antimicrobial Stewardship, brought to you by the Society for Healthcare Epidemiology of America, SHA, promoting the prevention of healthcare associated infections and antibiotic resistance, and seeking to advance the field of healthcare epidemiology and antibiotic stewardship.
• 0:23
  SPEAKER_01: This series will identify new or emerging technologies that can be leveraged to improve patient safety, data quality, and efficiency, describe the advantages and disadvantages of recent innovations and recognize strategies to demonstrate success or lack thereof and substantiate implementation of new technology.
• 0:39
  SPEAKER_01: I am Chad Nix, a third-year medical student at Oregon Health and Science University, and I will be your podcast moderator today.
• 0:44
  SPEAKER_01: Shay is excited to launch this episode of the podcast series, which is entitled The Utility of Whole Genome Sequencing, Academic andor Clinically Pragmatic.
• 0:52
  SPEAKER_01: This podcast will explore the utility of whole genome sequencing in the context of hospital epidemiology of infection prevention, including recent evidence showcasing success in identifying and/or determining the nidis of a cluster or outbreak.
• 1:04
  SPEAKER_01: The speakers will explain how they are or are planning to use whole genome sequencing and the interplay between those performing or studying whole genome sequencing and clinicians and effect prevention staff.
• 1:14
  SPEAKER_01: Advantages, challenges, limitations, and research gaps will be addressed as well as what the speakers envision for the future.
• 1:20
  SPEAKER_01: I'm happy to introduce our two speakers for today.
• 1:22
  SPEAKER_01: First, we have Dr.
• 1:23
  SPEAKER_01: Dina Altman, Associate Professor at Icon School of Medicine at Mao Sin in New York City, and Dr.
• 1:28
  SPEAKER_01: Alex Sunderman, assistant professor at the University of Pittsburgh.
• 1:32
  SPEAKER_01: Thank you both for joining us today.
• 1:33
  SPEAKER_02: Thank you so much for having us today.
• 1:35
  SPEAKER_01: Thanks, Chad.
• 1:36
  SPEAKER_01: Happy to be here.
• 1:37
  SPEAKER_01: First, can both of you provide our audience with your background, Dr.
• 1:40
  SPEAKER_01: Altman?
• 1:41
  SPEAKER_02: Yes, I'm an infectious diseases doctor, uh physicist and scientist.
• 1:46
  SPEAKER_02: I work on pathogen genomics, primarily the pathogen staph aureus, but other clinically relevant pathogens.
• 1:54
  SPEAKER_02: I'm interested in how genomics can be used to define inter-intra-host transmission dynamics, define novel virulence and resistance genes.
• 2:04
  SPEAKER_02: At the moment, I'm pretty evenly divided between clinical duties, infectious diseases inpatient consultation, HIV outpatient clinics, and my research.
• 2:14
  SPEAKER_01: Thank you for that information, Dr.
• 2:15
  SPEAKER_01: Altman.
• 2:15
  SPEAKER_01: And Dr.
• 2:16
  SPEAKER_01: Alex Sunderman.
• 2:17
  SPEAKER_00: Yes, currently I'm an assistant professor of infectious diseases at University of Pittsburgh and our Center for Genomic Epidemiology.
• 2:23
  SPEAKER_00: By background, I have a master's in public health and infectious diseases in microbiology.
• 2:27
  SPEAKER_00: After getting that degree out of an MPH, I worked in infection prevention for a few years at our hospital at the University of Pittsburgh Medical Center.
• 2:35
  SPEAKER_00: While I was doing that, I started my doctorate of public health and epidemiology, where my research and uh work was focused on outbreak detection and investigation using uh pathogen genomics and the application to that to the infection preventionist.
• 2:49
  SPEAKER_00: When I finished that degree recently, that's one of our adjoined faculty at the University of Pittsburgh, where I'm continuing my research and using genomic sequencing for looking into outbreaks.
• 2:58
  SPEAKER_00: Great.
• 2:58
  SPEAKER_01: Thank you, Dr.
• 2:59
  SPEAKER_01: Sunderman.
• 3:00
  SPEAKER_01: So to ensure the audience has the appropriate background information, can you all begin by defining whole genome sequencing, the equipment, expertise necessary to employ such techniques?
• 3:08
  SPEAKER_02: Yes.
• 3:08
  SPEAKER_02: So whole genome sequencing is basically looking at the pathogens, viral, bacterial, fungal at the DNA level, and to define relationships between pathogens at the very deep DNA level in order to describe relationships between pathogens or non-relationships between pathogens.
• 3:30
  SPEAKER_02: Yeah, the equipment is essentially a pipeline that involves bacterial or viral extraction and processing the sequences into DNA, then sequencing them on uh whole genome sequencing machines that produce a set of DNA sequences that are later analyzed in these very elaborate bioinformatic pipelines.
• 3:56
  SPEAKER_01: Great.
• 3:56
  SPEAKER_01: Thank you, Dr.
• 3:57
  SPEAKER_01: Altman.
• 3:58
  SPEAKER_01: How long does it take from the sample receipt through the final analytical stages?
• 4:02
  SPEAKER_00: So it depends on the amount of infrastructure that you have when whenever a patient actually has a culture for an infection versus whenever, like Dr.
• 4:10
  SPEAKER_00: Altman just said, you have that bioinformatics analysis at the end.
• 4:14
  SPEAKER_00: At our institution, we're performing real-time sequencing from a time that a patient has a culture to the time that we analyze it.
• 4:21
  SPEAKER_00: We're looking at about two weeks of gathering that isolate, uh, breaking it down through our machines, and then that final analysis.
• 4:28
  SPEAKER_00: It varies depending on different institutions and the resources dedicated to it, though.
• 4:33
  SPEAKER_02: Yeah, I would add that it depends on how fast your bacteria, fungi, or whatever you are sequencing grows in order to prepare the DNA as well.
• 4:44
  SPEAKER_02: So that's a factor.
• 4:45
  SPEAKER_02: Some things are very slow growing, like mycobacteria, and other things grow really fast, like my pathogens, Staph aureus.
• 4:52
  SPEAKER_02: And so it can depend on also just obtaining the DNA from the sample, depending on how fast it grows for you to do that.
• 5:00
  SPEAKER_02: And it absolutely depends on what you have, what pipelines you have in place, the workforce you have around it.
• 5:06
  SPEAKER_02: But it could be shorter if you have, you know, weekends, nights, and processing of samples.
• 5:13
  SPEAKER_02: Great.
• 5:13
  SPEAKER_02: Thank you for that information.
• 5:15
  SPEAKER_01: How has whole genome sequencing historically been used in the context of hospital epidemiology?
• 5:20
  SPEAKER_00: So we say that whole genome sequencing in the past has been primarily what we call reactive whole genome sequencing.
• 5:26
  SPEAKER_00: So often when hospital epidemiology or an infection preventionist suspects that they have an ongoing outbreak, traditionally that outbreak's been going on for a while that it's been noticed.
• 5:37
  SPEAKER_00: So typically, then once an investigation has already been performed, they'll perform whole genome sequencing to confirm or refute that presence of an outbreak.
• 5:45
  SPEAKER_00: So that's what the traditional method has been, primarily to date.
• 5:49
  SPEAKER_00: Some institutions are switching to doing it prospectively, so performing surveillance on a large sample of the isolates in a hospital rather than waiting for an outbreak.
• 5:59
  SPEAKER_02: Yeah, I would add uh traditional epidemiologic investigation, looking at time and space overlaps in an epi investigation really prompts in the reactive sense, as Dr.
• 6:11
  SPEAKER_02: Sunderman was stating, the investigation of whole genome sequencing when certain features of an outbreak or potential outbreak seem to fit a potential outbreak than historically infection prevention has worked and with at the genomics group affiliated to sequence isolates.
• 6:29
  SPEAKER_02: But I think the future is going more in a proactive manner.
• 6:33
  SPEAKER_01: How can these data be paired with that from the electronic medical record or EHR to identify transmission events?
• 6:39
  SPEAKER_01: Dr.
• 6:39
  SPEAKER_01: Altman?
• 6:40
  SPEAKER_02: We can develop certain visualization tools by taking the EMR data, basically the ward location or specific location to the bed level of patients and overlap that with the date of their hospital stay.
• 6:57
  SPEAKER_02: And then you potentially visualize that.
• 6:59
  SPEAKER_02: And we've actually done that in our Pathospot manuscript we published in 2020, where we overlay genetic information of the isolates with the spatiotemporal information of an outbreak.
• 7:13
  SPEAKER_02: But these tools are, you know, not readily available.
• 7:16
  SPEAKER_02: To me, seem very homegrown.
• 7:20
  SPEAKER_02: And so it takes time to generate them.
• 7:23
  SPEAKER_02: There are some other commercial tools available, but not that incorporate internal sequencing that may be done in an academic setting.
• 7:32
  SPEAKER_00: I wholeheartedly agree with Dr.
• 7:34
  SPEAKER_00: Altman.
• 7:34
  SPEAKER_00: A lot of these tools that are out there currently are often made in-house at a hospital's own institution.
• 7:40
  SPEAKER_00: If they are made from a commercial setting, they really do have to be adapted to the hospital setting.
• 7:45
  SPEAKER_00: From our perspective, we built a tool that uses charge codes because hospitals bill for everything.
• 7:50
  SPEAKER_00: So procedures, medications, like Dr.
• 7:53
  SPEAKER_00: Altman said your bed location, that those are billed.
• 7:56
  SPEAKER_00: So from our tool, we extract those charge codes and merge them with their genetic data and essentially do an analysis that way to show us where the transmission may be happening.
• 8:05
  SPEAKER_01: Interesting.
• 8:06
  SPEAKER_01: Dr.
• 8:06
  SPEAKER_01: Sunderman, in your study in clinical infectious diseases in 2021 titled Whole Genome Sequencing, Surveillance, and Machine Learning of Electronic Medical Record for Enhanced Healthcare Outbreak Detection, what kinds of transmission events were you able to identify that those using traditional infection prevention methods were not able to?
• 8:22
  SPEAKER_00: Yeah, so in that article, we did sequencing surveillance for two years and we gave it a big lag time.
• 8:29
  SPEAKER_00: So we didn't want infection prevention to essentially intervene with any outbreaks we detected during that time.
• 8:35
  SPEAKER_00: And we gathered isolates of major bacterial pathogens that were potentially healthcare associated.
• 8:40
  SPEAKER_00: And we detected many outbreaks over the course of those two years, 99 outbreaks of almost 300 patients.
• 8:46
  SPEAKER_00: Two of the biggest outbreaks we detected were an outbreak of encomyosin-resistant enter cocci-invasive infections that we trace back to the use of interventional radiology with contrast injection.
• 8:58
  SPEAKER_00: We found that the contrast was being prepared in an unsterile fashion and being injected into all these patients that uh developed a VRE infection.
• 9:07
  SPEAKER_00: We worked with the manufacturer of that device to address those issues and stop its outbreak.
• 9:12
  SPEAKER_00: And another outbreak that was pretty notable was a Pseudomonas reginosa outbreak that we traced back to a single contaminated gastroscope that was used on multiple patients.
• 9:21
  SPEAKER_00: And it was interesting that both of these outbreaks that I just talked about, traditionally, when we think of outbreaks in infection prevention, we think in the same time or the same space, same unit, but almost all these patients were on different units in the hospital and occurred over many months.
• 9:37
  SPEAKER_00: So most of these outbreaks were actually not detected by traditional infection prevention.
• 9:42
  SPEAKER_00: And that's what genomic sequencing can do is really uh find these outbreaks that aren't often found by our traditional methods.
• 9:49
  SPEAKER_01: Thank you, Dr.
• 9:50
  SPEAKER_01: Sunderman.
• 9:50
  SPEAKER_01: So how is whole genome sequencing currently being used at your institutions and in which department does it live, Dr.
• 9:56
  SPEAKER_01: Altman?
• 9:57
  SPEAKER_02: Whole genome sequencing at our institution was really started out in the genomics department at Mouseamai Hospital.
• 10:05
  SPEAKER_02: And it is a collaboration between the clinical microbiology, infection prevention, and genomics group.
• 10:11
  SPEAKER_02: I think ideally it moves into a clinical microbiology setting so that the speed at which we need to be proactive can be there if it's done as part of the standard clinical workup.
• 10:25
  SPEAKER_02: That's an ideal situation.
• 10:27
  SPEAKER_02: And I think that the COVID pandemic really helped streamline this in our institution.
• 10:32
  SPEAKER_02: The technology is constantly getting faster and cheaper.
• 10:34
  SPEAKER_02: But I do think that although it may start in outside of the microbiology lab, it should be done right during the workup in microbiology in order for it to be most efficient.
• 10:45
  SPEAKER_00: Dr.
• 10:46
  SPEAKER_01: Sunderman?
• 10:46
  SPEAKER_00: Yeah, so at the University of Pittsburgh Medical Center, we have a lot of hospitals and they're all associated with the University of Pittsburgh.
• 10:52
  SPEAKER_00: And all of our hospitals have access to reactive sequencing through our lab if they suspect an outbreak.
• 10:58
  SPEAKER_00: But our at our flagship hospital at UPMC Presbyterian, we do whole genome sequencing surveillance weekly.
• 11:05
  SPEAKER_00: So if a patient had been in the hospital for more than two days and developed a bacterial infection, we'll gather that isolate and sequence it.
• 11:12
  SPEAKER_00: Or if they've had recent healthcare exposure in the past month, we also gather that bacterial isolate for certain pathogens and sequence that as well.
• 11:21
  SPEAKER_00: We do this weekly through our research lab and then feed it back to our infection prevention department if we actually find outbreaks.
• 11:28
  SPEAKER_01: Are there plans to broaden its use, Dr.
• 11:30
  SPEAKER_01: Sunderman?
• 11:31
  SPEAKER_00: Yeah, so right now, like I said, we're performing sequencing in real time at one hospital.
• 11:36
  SPEAKER_00: Our prior study that I just referred to before was retrospective in nature.
• 11:40
  SPEAKER_00: So before we expand its use to additional hospitals, we actually want to make sure that it's working at our one, our biggest hospital right now.
• 11:48
  SPEAKER_00: So we're sequencing for about a year in real time and we're intervening as we go.
• 11:53
  SPEAKER_00: We're going to perform an analysis after that's done to see how well it's working, what can we do better?
• 11:59
  SPEAKER_00: And if it's working well, we definitely want to expand it to other hospitals and share that data with everybody else.
• 12:04
  SPEAKER_00: Dr.
• 12:04
  SPEAKER_00: Altman?
• 12:05
  SPEAKER_02: Yes, at this point, we have a centralized microbiology lab.
• 12:08
  SPEAKER_02: So the whole Mount Sinai Health System runs its specimens through our microbiology lab that's on site, one of the main hospitals here, which is convenient so that our genomics group and our technology is all in the same location as the centralized microlab.
• 12:24
  SPEAKER_02: So I think that expansion to the New York City area is something we are always trying to obtain funding for, which is of course a major factor into how much we can do.
• 12:36
  SPEAKER_02: But I think there is a lot of interest in the data that we produce.
• 12:40
  SPEAKER_02: So I hopefully we can continue to broaden our use of it.
• 12:43
  SPEAKER_02: Thank you.
• 12:44
  SPEAKER_01: What kind of institutional support or funding did you or others have to pursue to employ whole genome sequencing, Dr.
• 12:50
  SPEAKER_01: Altman?
• 12:51
  SPEAKER_02: So initially our funding came from internal funding from the genomics department in order to place initial infrastructure.
• 13:00
  SPEAKER_02: And then we were able to obtain R01 funding from NIH.
• 13:04
  SPEAKER_02: And our hospital now values our work and is providing support as well.
• 13:08
  SPEAKER_00: Dr.
• 13:09
  SPEAKER_00: Sunderman?
• 13:09
  SPEAKER_00: Yeah, so our reactive sequencing, our hospital system supports that as well.
• 13:14
  SPEAKER_00: And we have great support from our leadership to actually find these outbreaks.
• 13:18
  SPEAKER_00: It's rare that you find a hospital that wants to find the outbreaks, but they represent opportunities to intervene and stop.
• 13:25
  SPEAKER_00: From a surveillance perspective, we're funded primarily through the NIH.
• 13:30
  SPEAKER_00: And we continue to fund ourselves through that route to do that large amount of sequencing at our hospital.
• 13:35
  SPEAKER_01: Thank you.
• 13:36
  SPEAKER_01: And this has been touched upon briefly, but how is it or can it be used to intervene from a practical perspective, Dr.
• 13:42
  SPEAKER_01: Sunderman?
• 13:43
  SPEAKER_00: So it for me, a genomic surveillance program has to be quick and efficient.
• 13:49
  SPEAKER_00: Because if you're waiting on the results of sequencing for months on end, that there lies opportunity for the outbreak or transmission to keep spreading while you're waiting for that data.
• 14:00
  SPEAKER_00: So that's why we try to reduce our turnaround time from the time that a patient has an infection to the time that we sequence and then subsequently intervene.
• 14:08
  SPEAKER_00: Because if we can reduce that amount of time, that's less opportunity for that outbreak to spread.
• 14:14
  SPEAKER_00: So having a really well-versed infection prevention department that understands the genomic basis of what we're doing and having that infrastructure have sufficient investment to be quick is really key.
• 14:25
  SPEAKER_00: Dr.
• 14:26
  SPEAKER_00: Altman?
• 14:26
  SPEAKER_02: Yes, I agree with everything.
• 14:28
  SPEAKER_02: Outbreaks, as was mentioned by Dr.
• 14:29
  SPEAKER_02: Sunderman, are are happening whether we know about them or not.
• 14:33
  SPEAKER_02: And so the idea is to identify them and to STEM them as quick as possible and to intervene in terms of staff education, I think is a major component.
• 14:44
  SPEAKER_02: And having a very well-engaged infection prevention department who understand the basics of whole genome sequencing and what it can and cannot provide is really important.
• 14:54
  SPEAKER_02: And then educating the house staff and the nursing staff, as Dr.
• 14:58
  SPEAKER_02: Sunderman mentioned, the manufacturers of certain appliances that can be contaminated.
• 15:05
  SPEAKER_02: This is all very important, but again, has to be really fast and require a lot of education to identify the source of the outbreak.
• 15:12
  SPEAKER_02: If there is one, as mentioned, sometimes we are unable to find or pinpoint the actual route of outbreaks because they happen over either not in the hospital or over long periods of time.
• 15:25
  SPEAKER_01: Thank you, both.
• 15:26
  SPEAKER_01: That was very insightful.
• 15:27
  SPEAKER_01: If using whole genome sequencing for the purposes of identifying transmission events, is there automated data transmission to infection prevention control?
• 15:35
  SPEAKER_01: And if not, how are possible or confirmed transmission events communicated, Dr.
• 15:39
  SPEAKER_01: Allman?
• 15:40
  SPEAKER_02: At this point, we are having weekly meetings with infection prevention to report on our findings.
• 15:46
  SPEAKER_02: And we previously had a secure email report that was going out.
• 15:51
  SPEAKER_02: Things have shifted slightly recently due to our pandemic response, but we hope to get back and do more real-time sequencing and send reports to our infection prevention staff.
• 16:02
  SPEAKER_00: Dr.
• 16:02
  SPEAKER_00: Sunderman?
• 16:03
  SPEAKER_00: Yeah, so whenever we detect an outbreak each week, I myself review them and create a summary for the ARP infection prevention department.
• 16:10
  SPEAKER_00: And we share that through a secure email similar to what Dr.
• 16:13
  SPEAKER_00: Altman just said to communicate those findings.
• 16:16
  SPEAKER_00: To make it more automated, we're trying to develop a user interface where infection preventionists can kind of log on, get alerts of new outbreaks coming in, and then where we can really merge it with that EHR data to have a really rapid review of that outbreak.
• 16:30
  SPEAKER_00: So the infection preventionists and myself don't actually have to spend a lot of time reviewing the outbreak, where it's the data is just provided for you to better review.
• 16:39
  SPEAKER_01: For professionals and infection prevention control, what kind of training or support is required to make the best use of the data, Dr.
• 16:45
  SPEAKER_01: Sunderman?
• 16:46
  SPEAKER_00: I think having a really multidisciplinary infection prevention department that has backgrounds in different areas is really helpful.
• 16:53
  SPEAKER_00: And having the manager support for infection preventionists to learn this type of approach and this type of data, because it really is an emerging technology.
• 17:01
  SPEAKER_00: So an infection preventionists or infection prevention department that wants to stay up to date should really put investment into training IPs into this type of technology is really key.
• 17:12
  SPEAKER_00: Dr.
• 17:13
  SPEAKER_00: Alman?
• 17:14
  SPEAKER_02: I would agree with that.
• 17:15
  SPEAKER_02: I think that that getting the basics of what the whole genome sequencing data is providing is suffice.
• 17:21
  SPEAKER_02: So I think that giving informational sessions to all the staff involved and so that they understand what we are learning from the genomics is important to do.
• 17:32
  SPEAKER_02: And I think they are interested in this because it is a novel technology and is the future.
• 17:37
  SPEAKER_02: So it's important to do educational sessions and to break it down into more basic terms so that it's very easy to absorb for all staff involved in these results so that we can maximize education.
• 17:52
  SPEAKER_02: But I think that it is a future and it'll probably be more of our language in the years to come.
• 17:58
  SPEAKER_02: And so it's definitely a good investment to educate people involved in these results.
• 18:03
  SPEAKER_00: To add on to my other answer as well, I think when we look at the infrastructure is really key.
• 18:09
  SPEAKER_00: There's some different strategies that I've seen where people like us are using our academic resources to perform sequencing.
• 18:16
  SPEAKER_00: Some people rely off of the public health departments to perform their sequencing.
• 18:20
  SPEAKER_00: And then some people partner with industry companies that perform mass levels of sequencing.
• 18:25
  SPEAKER_00: And then some hospitals are switching to having the sequencing performed in-house in a hospital setting.
• 18:31
  SPEAKER_00: I think going forward, we're going to see which strategy works best.
• 18:35
  SPEAKER_00: And that's just something we're going to have to figure out.
• 18:37
  SPEAKER_01: How can the cost savings of using such methods be quantified?
• 18:41
  SPEAKER_00: Dr.
• 18:41
  SPEAKER_01: Sunderman?
• 18:42
  SPEAKER_00: So that's one of the key things that we wanted to do in our CID paper from 2021, because calculating cost savings from infection prevention research is a really difficult topic to try to figure out.
• 18:54
  SPEAKER_00: And that's also why we didn't let infection prevention interfere with the outbreaks that we found for the two years and did this retrospectively.
• 19:01
  SPEAKER_00: We essentially wanted to say if we ran a surveillance program in real time, when would we have intervened?
• 19:08
  SPEAKER_00: And about what is the efficacy of the proposed interventions at preventing the subsequent infections that shared that same route in that outbreak.
• 19:17
  SPEAKER_00: And the long story short is that we found if you implemented a real-time sequencing program that uses some EHR analysis, it would offset the costs by preventing those subsequent infections.
• 19:29
  SPEAKER_00: And that's because infections are expensive.
• 19:32
  SPEAKER_00: And saving an infection, when you look at the cost of sequencing in isolate, is about$80 to$90.
• 19:38
  SPEAKER_00: So it's relatively cheap versus an infection treating it as$20,000 or more.
• 19:43
  SPEAKER_00: So from our perspective, having investment into sequencing surveillance will actually save the hospital costs in the end.
• 19:51
  SPEAKER_01: What are the limitations of whole genome sequencing in the context of infection prevention control, Dr.
• 19:56
  SPEAKER_01: Altman?
• 19:57
  SPEAKER_02: Thank you.
• 19:57
  SPEAKER_02: So yes, there are a lot of these transmissions that we detect in the hospital are not necessarily occurring at our hospital.
• 20:04
  SPEAKER_02: So I think that having centralized EMR would really help the communication of transmission events occurring at the hospital.
• 20:14
  SPEAKER_02: We get a lot of people being transferred from hospital to hospital, from nursing homes, from LTACs.
• 20:21
  SPEAKER_02: And so these transmission events might actually occur elsewhere and then be identified at our hospital.
• 20:26
  SPEAKER_02: I think that's one of the limitations to combat, like where are these events occurring?
• 20:31
  SPEAKER_02: They could be very well happening at the person's gym or at their home.
• 20:35
  SPEAKER_02: And so, at least for hospital systems in the region, you know, we're not in a silo.
• 20:40
  SPEAKER_02: Getting a centralized EMR would really help.
• 20:43
  SPEAKER_02: And communication between facilities would really assist tracking down transmission events and make the whole genome sequencing more effective.
• 20:52
  unknown: Dr.
• 20:52
  SPEAKER_00: Sunderman.
• 20:53
  SPEAKER_00: Yeah, I really agree with Dr.
• 20:54
  SPEAKER_00: Altman.
• 20:54
  SPEAKER_00: A huge problem we run into is what do you do if you find isolates that are genetically related, but you have no epidemiologic commonalities between them?
• 21:03
  SPEAKER_00: How do you actually handle that?
• 21:05
  SPEAKER_00: And a lot of that might be due to under-sampling.
• 21:08
  SPEAKER_00: You don't have all the isolates that you've sequenced, or there might be some colonized patients or healthcare workers that you haven't really cultured and sequenced.
• 21:17
  SPEAKER_00: So just because you have genetic relatedness between two isolates, there's still a lot of work that you need to do to investigate that and make sense of it.
• 21:25
  SPEAKER_01: Great.
• 21:25
  SPEAKER_01: Thank you.
• 21:26
  SPEAKER_01: What are the future directions of whole genome sequencing as it applies to hospital epidemiology?
• 21:30
  SPEAKER_01: Dr.
• 21:30
  SPEAKER_01: Sunderman?
• 21:31
  SPEAKER_00: Yeah, Dr.
• 21:32
  SPEAKER_00: Rellman and I really said this a lot during the podcast is we think this is going to be commonplace in the future.
• 21:37
  SPEAKER_00: It's going to be a routine thing that most hospitals are going to do that really highlights the outbreaks and transmission that are going on.
• 21:45
  SPEAKER_00: For me, I hope that it becomes commonplace that, you know, a single outbreak is no longer acceptable anymore.
• 21:51
  SPEAKER_00: Where we find outbreaks early, we can intervene and actually stop them from growing.
• 21:56
  SPEAKER_00: I truly think that's going to be the future of infection prevention.
• 21:58
  SPEAKER_00: And hospital epidemiologists and infection preventionists are going to be at the forefront of driving that change.
• 22:04
  SPEAKER_00: Dr.
• 22:04
  SPEAKER_00: Altman?
• 22:05
  SPEAKER_02: Agree completely with what you said, Dr.
• 22:07
  SPEAKER_02: Sunderman.
• 22:08
  SPEAKER_02: Incorporation of real-time, I mean, with whole genome sequencing for clinical microbiology, I think that detection of resistance mechanisms, how those relate to transmission events, as well as virulence features of the pathogen, to really understand more about why certain people are getting certain infections or how they're responding to them, and incorporating that into like a clinical picture of a host pathogen response.
• 22:34
  SPEAKER_02: Also, that incorporates into outcomes, patient outcomes as well.
• 22:39
  SPEAKER_02: And of course, diagnostics that's down the road or in process.
• 22:43
  SPEAKER_01: Thank you, Dr.
• 22:43
  SPEAKER_01: Allman and Dr.
• 22:44
  SPEAKER_01: Sunderman, for such a fantastic conversation.
• 22:47
  SPEAKER_01: We appreciate you joining us today.
• 22:48
  SPEAKER_02: Our pleasure.
• 22:49
  SPEAKER_00: Yeah, thank you, Chen, for having us.
• 22:51
  SPEAKER_01: You can find more educational content like this podcast on Shay's Online Education Center, Learning CE, at www.learningce.shay hyphenonline.org.
• 23:02
  SPEAKER_01: This concludes today's episode of the Digital Electronic Innovation Hospital Epidemiology and Stimicrobial Stewardship Series.
• 23:08
  SPEAKER_01: Thank you for tuning in.