Public Health Laboratories – Transcript and Audio
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Date of session: 07/22/20
Triona Henderson, MD, MPH
Centers for Disease Control and Prevention
Anthony Tran, DrPH, MPH
District of Columbia Public Health Laboratory
TRIONA HENDERSON: Good afternoon. My name is Triona Henderson. And I am a clinical pathologist and the facilitator of this ECHO Model™external icon pilot project. I extend a hot welcome from the Division of Laboratory Systems at the Centers for Disease Control and Prevention in Atlanta, Georgia. Thank you for joining us.
The topic for this interactive web discussion is Public Health Laboratories. Dr. Tony Tran will present today’s topic. Dr. Tran currently serves as the director of the District of Columbia’s Public Health Laboratory, which provides diagnostic testing services for health care providers in the district and surveillance and environmental testing for the DC Department of Health. He’s currently leading the district’s testing efforts for COVID-19 in addition to multiple national COVID-19 task forces, and also serves on the Association of Public Health Laboratory, APHL’s Board of Directors.
Also, today we have a two for one special, Dr. Tran’s colleague, Matthew McCarroll. Mr. McCarroll is the Chief of Laboratory Operations at the DC Public Health Laboratory. And his work is focused on informatics, interoperability between DC public health labs and epidemiologists. So here is some technical information before we get started. Before introductions, please use your videos. We’ve asked a couple of times. It’s really nice to see who we’re having a discussion with. It’s very helpful to put a name to a face.
Right now, Johanzynn has muted everybody’s microphone. So once we get to the discussion section, please announce yourself by name and organization if you are unable to get on to camera. If you’re experiencing technical difficulties during this session, please send a private chat message to Johanzynn Gatewood labeled as DLS ECHO Tech. She will do her best to respond to your issue, and she’s waving right now.
Finally, we design relevant sessions based on your evaluation responses. And thank you for those who’ve been doing them every single month. We would like to encourage you to complete the post-session evaluation. For those who require P.A.C.E.® credits there is an option for P.A.C.E.® credits when you do this evaluation. And for those who just want a certificate of participation, you can also fill out the evaluation and will receive that upon completion.
If you have additional comments, please send a private chat message directly to Johanzynn or email us directly at DLSECHO– so that’s D-L-S-E-C-H-O@CDC.gov. So here are how these sessions are different than your usual webinars or teleconferences. They’re really based around discussion of cases and information. So it should be very interactive, and that’s the main feature.
The subject matter experts will hope to share their work with you that will be translatable to all of you in your individual laboratories. These ECHO sessions will focus exclusively on clinical and public health laboratories in the United States and US territories. Once again, we value the discussion amongst all of you that ensues and want to encourage you to share your own experiences with these challenging topics.
So here’s an overview of the process. The subject matter expert will have a presentation; then, I will ask some clarifying questions to the SME, then we’ll open up for ideas and shared experiences and comments from the subject matter expert, then we will have closing comments and reminders and then adjourn. Today’s session is being recorded. If you do not wish to be recorded, please disconnect now. Closed captioning is also provided, and you can find the link in the Zoom chatbox.
The audio and transcript will be shared for this ECHO session on our ECHO website after the session. We will also be sending the slides and the presentations to all those registered or participants today. If some of you have registered based on a shared link, please email us, and we will send you the information with the links. So here is a biography of Dr. Tran. He received his BS in medical technology from the University of Maryland in Baltimore School of Medicine in 1998, his MPH from the University of Maryland College Park in 2001– go Terps– and his Doctor of Public Health from the University of California Berkeley in 2013.
He completed his ASM CPEP fellowship in medical and public health microbiology from the University of North Carolina Chapel Hill Health Care System in 2015, and is a diplomat of the American Board of Medical Microbiology. He has over 15 years of public health and clinical laboratory experience at national, state, and local levels. During the seven years prior to pursuing his doctorate, Tony worked at APHL, a national non-profit organization that represents states, territorial, and local public health laboratories in the United States.
During his time at APHL, he led the association’s efforts on domestic HIV, STD, TB, and viral hepatitis, and served on the global health team that closely works with ministries of health all over the world to develop core laboratory infrastructure and build capacity for a test of public health significance. Previously, as the Director of Policy and Operations at the New York City Department of Health and Mental Hygiene, Bureau of the Public Health Laboratory, Tony provided guidance and overall direction to all areas of the laboratory including scientific oversight of programs, quality assurance, and laboratory operations.
Now we’ll invite Dr. Tran to begin his presentation. While he’s doing so, please be thinking of similar situations that you’ve encountered on how you might apply Dr. Tran’s experiences to your institution. We expect this to be a robust discussion. Please offer your questions and feedback in the discussion period. Dr. Tran?
TONY TRAN: Thanks very much, Dr. Henderson. I’m going to go ahead and start sharing my presentation. Can everybody see my presentation? Is that up and running? Great. Thank you. I’d like to thank the Centers for Disease Control and Prevention for the opportunity to speak to you all today on a very, I know, thrilling topic of laboratory information management systems. It is– I’m being somewhat facetious, because obviously, it is truly, truly important to have a functional LAS or LIMS in your facility, especially for public health laboratories in this pandemic response, because I’m sure, as you know if you’re sending out those SARS-CoV-2 tests out to another outside laboratory for testing, getting that information back into your hands is critically important.
So as Dr. Henderson has indicated that I have my partner in crime here, Matt McCarroll, who’s also on the line as well, who is definitely more of the technical guru. And so if you all have any questions, feel free to go ahead and type it in the chatbox. He can actually answer in real-time, or try to at least, while I go through the presentation. But hopefully I can get through this pretty quickly and then at the end, obviously, will be questions and answers.
So here go. All right, so the Dark Ages. Why are we calling it the Dark Ages? Well, obviously this is a politically incorrect term. We don’t really use that anymore. However, it is important because it describes events, post-fall of the West Roman Empire from the 5th to the 10th century, and previously described as kind of a barbaric timing. You can see the photo that’s there, the depiction of it’s mayhem, it’s not a happy time, there was a lot of war and fighting, kind of this lack of cultural growth and enlightenment. Literature describes it as a desperate time that was dark.
So that’s kind of where we were a little bit just before I got to the Public Health Laboratory. I was kind of wrapping up my time in New York City, as Dr. Henderson has indicated, dealing with the last outbreak, big outbreak, which was Zika. So does anybody even remember Zika anymore? Zika, what? So yes, Zika, Zika virus. It was a kind of a dark and stormy day as I kind of walk through this with you.
Now, before I was here, but Matthew was actually here and had to go through a lot of this. So dark and stormy day, May of 2016, figuratively, maybe literally, I don’t remember, but DFS received a complaint from the health department in reference to missing Zika reports. What? Really? What happened? What’s going on here? Well, what we found was that– this was kind of the hands to the face moment really– so there were about 50 reports that had not yet been reported out to the health department.
And just for you all to understand, clinical tests from the Public Health Laboratory– excuse me– are reported both to the health care provider on record, IE, so if it was submitted by a hospital, or a clinic, or other health care facility, they would get the results, and then also back to the health department as well for epidemiological purposes, for surveillance purposes, for follow-up purposes. So nobody really understood what happened to these samples. So what happened to them? Why were they not tested in a timely manner?
Well, at that point in time, the laboratory was actually being kind of daily, on a daily basis, being overseen by our agency director. Just as a real quick aside, a little bit different here in the District of Columbia is that, you can see at the bottom of the slide set, it says Department of Forensic Science. The public health laboratory here in the district actually falls underneath a completely separate agency, it’s a sister agency to the health department, which is deemed DC Health here, or called, nicknamed, DC Health here.
And so it’s a completely separate laboratory-based and focused agency. So we’re sister agencies. And the Public Health Laboratory sits within DFS, not within DC Health. So a task force was actually developed on demand of the agency director to find out and investigate internally what was happening with these results, why were they not resulted in a timely manner? And so what the task force found was that the tests were actually– the reports– why they were not reported is because the tests were actually not run yet.
Now, kind of paling in comparison Zika to what is happening obviously with COVID-19 and SARS-CoV-2, the demand for testing, but it was quite a bit of testing request at that time as well if you can recall back in 2015, 2016. So what the task force discovered at that point in time is kind of a makeshift LIMS, and LIMS, I describe that as a Laboratory Information Management System, or some of you may describe it as an LIS, a Laboratory Information System. So we had one here in the district. And it’s called HORIZON, at that point it was ChemWare HORIZON, was the company, now it’s called HORIZON.
And it’s used mainly by public health laboratories, it’s not really used out in the clinical world, clinical diagnostic world either with commercial laboratories or hospital laboratories, but in the kind of pharma world, they use it as well. So kind of environmental testing. But what was happening was that even though we had the LIMS, the [INAUDIBLE] folks were logging things into the LIMS, and that was pretty much it. They were logging as– I was told they were logging it in because they were told to log it in, but that was pretty much it.
What ended up happening was that a large gigantic excel spreadsheet substituted for LIMS. And this is a snapshot of it there with patient information redacted. But you can kind of see the type of information of when the health department approved a test to be sent to the Public Health Laboratory for Zika testing where the state of residence, sex gender of the individual, their birthday, the facility that was sending it, so on and so forth. So some of these were sent out to the CDC, some of them were done internally here at the Public Health Laboratory.
So not only was there one spreadsheet, or what we call a log book, but there were two. So the first one that you just saw was actually just for logging in the samples. There were no kind of sample results or anything in there. But instead of kind of using the same line listing, if you will, the laboratory decided to develop a whole other spreadsheet, or logbook, for results. So there are two different sheets, or log books, that basically had to mate together manually, because as the next slide, you’ll see, this was the sample test report template at that point in time. This was basically a, quote, unquote, “mail merge” from the excel document into a template that was manually reported for every single result. What a nightmare?
We talk about Dark Ages. I mean, I think that’s pretty much The Dark Ages. And, really, the Public Health Laboratory in the District of Columbia, the Association of Public Health Laboratories, as Dr. Henderson has indicated, conducts an annual laboratory survey of testing services and capabilities. The Public Health Laboratory in the District of Columbia was the only public health laboratory that did not have the capability to both order– for health care providers to order electronically. It was all paper-based. You could download a form off our website, fill it out by hand, and then submit that to our lab for testing as our test request form.
But then also reporting was completely manual, because these reports had to be faxed. Each and every one had to be faxed. Who faxes nowadays? Our lab did. So if you can imagine, the issues were you fax it, sometimes the fax is not running on the other end, because who faxes anymore, but, yes, it wasn’t running, maybe they turned it off at the end of the night, maybe it ran out of ink, maybe there was a communication error. We don’t know. But things would go, they would get sent, so we thought, but then somebody wouldn’t receive the results.
And so for Zika virus, obviously, with implications for the soon to be mom, pregnant females, this was a big deal. This was a big deal, because clinical decisions were being made off of these test results. So this is about the time that I entered to the Public Health Laboratory. I’ve been here about four years. So I kind of think about this as one of my major things coming in is I said, well, we have a LIMS, we got to start using the LIMS, we got to go away from this Excel type of manual workflow. It just doesn’t make a lot of sense. We have the technology, we got to start using it.
So the Renaissance, the period immediately following this Dark Ages, or so-called Middle Ages, is kind of French for rebirth, and characterized by the surge of interest in classical scholarship and values, additionally it was part of this new discovery of exploration of new continents, discovering continents and growth of commerce and age of innovation– I love using that word innovation– such as paper– well, coincidentally, but, of course, we’re talking about times way long ago, about 1,000 years ago. But yes, they have a paper and printing and gunpowder, but yes, we’re still here using paper and printing 1,000 years later. So but, really, thinking about primarily a time for revival of the classical learning and wisdom after this long period of cultural decline and stagnation.
So you think about it here at Sistine Chapel, this was the time of da Vinci and Michelangelo and Raphael. So here we are so. The toughest part, I think, coming in was this culture change aspect. So the lab so long was, again, using this kind of what I call paper-based system. And Dr. Henderson has talked about some of my experiences overseas in sub-Saharan Africa working to build laboratory capacity, in mainly these PEPFAR countries, that’s the President’s Emergency Plan For AIDS Relief. So coming out from that, and really building labs from the ground up, mostly for HIV support and testing but also other related infectious diseases and disorders as well. But many of them were paper-based.
And this really kind of reminded me of those days, going in and everything is paper, everything is Excel, printed out, and you can probably imagine how much that is kind of ripe for human error, unintentional, but still human error. And that’s kind of what we want to avoid obviously in these laboratory information management systems, or LIMS. So that was the biggest thing, that we not only had to log in the samples, but we had to kind of build it where– and change the culture where people had to start thinking about, well, not only am I just logging them in and just leaving it over there, but I need to log it in, we’re going to track the results of the samples from beginning to end, pre-analytical, to analytical, to post-analytical analytical to ensure that our entire laboratory process is not only appropriate but efficient. And that was really, really difficult.
So this was kind of the process of this reimplementing of the LIMS. We had it, and they had used it. They had this LIMS for probably about a decade before I got here. So there was a lot of different upgrades that the LIMS was going to offer that, really, what we’re already paying for, we’re already paying for premium to the LIMS manufacturer to actually have the LIMS in place, but we just weren’t using it.
So this was really a no brainer for me. We have to upgrade from version 11 to version 12.5. And this was, really, the beginning of the Renaissance period for us with the informatics side of the house. So this basically, the version 12.5 greatly improved the graphic user interface, the ability to use what we call lab online, which we’ll talk about in a few moments, but it’s a web portal for actually reporting results. We couldn’t quite get past reporting results to external clients, IE, outside of the health department, or our medical examiner, or other city agencies because of firewall issues.
So we weren’t quite there yet, but we could at least report out electronically and didn’t have to fax results to the health department. So this was huge. And also with 12.5, actually met a lot of the district’s cyber security measures as well. So that was big. But it was a huge undertaking because we had to clear all of these manual backlogs, if you will. Everything was kind of sitting not really in the LIMS, but sitting in these Excel spreadsheets.
They had to come back in, they had to log everything in, they had to clear everything out, because we needed records of it, because the intention was to get rid of those spreadsheets. And then all the staff basically had to be retrained and understand how to use our LIMS. This really ended up being much more difficult than originally expected.
Now, you probably see Matt sitting on the screen there, but this is what he used to look like back then. He’s pulling his hair out. What are we going to do? How do we get this? How do we get folks to accept our new technology? And so this was a tough, tough process.
And it really took our senior management to buy into it. It took a lot of convincing for the staff to buy into it as well. It took a lot of handholding. It took a lot of the company actually having to come in and provide trainings and support in order for us to actually get into this LIMS 12.5, right? A lot of the other things you can kind of see where– our thought process of where we needed to go, but a lot of it took funding, which we really didn’t have a lot at that point in time, we had to beg for it, we had to plead for it, we had to put into federal cooperative agreements with the CDC to ask for it for these LIMS improvements, resources, staff to be able to have somebody actually internally watch over the process of the LIMS.
I’m sure in your hospitals and in your labs, I’m hoping that if you have an internal laboratory information management system, which I’m sure you do, that hopefully links into your electronic medical record, that you have administrators of that. We didn’t have any of that here. So a lot of this we had to basically farm out to the manufacturer, to the actual LIMS company, who then, of course, they couldn’t spend 24 hours a day, seven days a week supporting us either. And then for our stakeholders, I mean, they were kind of– even though it was a little bit arcane, in my opinion, they were so much used to, oh, where’s our fax, where’s our fax, where’s our fax. So we kind of had to move all of this and shift all of this, which was actually a Herculean task.
So kind of fast forward a few years to just about six months ago, and we were pretty much still kind of in the same boat. I mean, we had tried to– and so this is about almost 3 and 1/2 years in the making. So really three when we really kind of went into it, and said, OK, we’re transitioning over, so about six months after I started. So it’s been about three years. And we would have some gains, and then we took a step forward, then took a couple of steps back. We really needed to depend on our stakeholders, in this case, the Health Department, in order to get us, Department of Forensic Sciences, to link directly into the Health Department’s electronic medical record.
What we wanted when Matt and I had to kind of plan was to go through electronic laboratory reporting, or ELR, HL-7 messaging directly into their EMR, their Electronic Medical Records, so that they can receive, as soon as we report, they receive the results instead of having us and using our personal power to actually have to sit there and print out results and review them, make sure it’s correct, and then fax over, and then we didn’t receive your fax, well, let me try again, I don’t know why, it’s still not going. We’d fax over and over. It just takes so much time and effort. It was just– it was too much.
But here was the initial issue, we had– I talked about this previously– we need to get past the firewall. Well, it’s one of those things, and if you have met me and spent any time with me, and Matt knows, I don’t like to hear the word no or impossible, I like to hear the word, let’s be innovative, I like the other I word. And so I pushed Matt to say, hey, we are in a pandemic, we can’t accept the fact that we can’t get past the firewall, or we need a VPN, what can we do? And let’s get the chief technology officer, who we had her ear, so let’s get her in and figure out sitting together, and say, hey, this is a pandemic response issue and we cannot do what we need to do with our stakeholders.
And now it’s beyond DC Health, now it’s all the hospitals, it’s all the nursing homes, it’s all the clinics, it’s all the doctor’s office. Everybody wants a SARS-CoV-2 test. And so we needed to quickly figure out, and, of course, also all of the community-based testing, all the drive-through and walk-ups and all those sorts of things that we’ve been doing for folks out there in the community. So we needed a technology that was going to work.
And so we really developed and further developed the lab online model. So this is kind of our electronic web portal that is linked directly to our LIMS manufacturer, HORIZON. So this is something they have developed. Now, what we had originally had was, again, like I indicated, with our own stakeholders inside the agency– excuse me– inside the district government, we could send reports out electronically. We were doing that for our rabies testing, we were doing that with our medical examiners cases and things of that nature, but we hadn’t quite linked in with our health department on ELR, or Electronic Lab Reporting, directly into their medical record system.
And so it just took a pandemic, just took a, kind of, saying, resources, we’re good, that’s not going to be a barrier, now we have all of our stakeholders paying attention because we said we needed to get this done in order to get the results out as expeditiously as possible, and to reduce the turnaround time for results. And so we got it to work. We got it to work with help from OCTO, who’s our Office of the Chief Technology Officer. And now we have a lab online portal for our clients out in the district, in the jurisdiction, so they can actually log into the portal with their own credentials.
And this is a sample of the home page there. And they can look at the samples that they have and patients that they have to see the results. But what else they can obviously do, which is fantastic, is now online ordering through this web portal. So the terminology that’s out there is ETOR, it’s Electronic Test Ordering and Reporting. So we had kind of gotten the reporting portion down, but we really needed to get the electronic test ordering portion up.
Some of the complaints that we had was that, your process of paper, it’s too cumbersome. We don’t have time to sit there and fill out all this paperwork. Well, let’s try this, and at least for the long-term care facilities that we’re working with right now, these vulnerable populations, they love it. They love it.
So it’s really easy. They can log in. You can see right there that up on top, the top screen, you can see– you can look at your samples, your patients, you can order, and you can look at other reports. You can actually– other reports, you can download a line listing of all the test results in a certain date period. And then you can have that, and you can put that into your EMR or whatever the case may be– or into Excel and then do whatever kind of data analysis you need to do from that.
But here you can see you can order tests. So you can view your current orders, or orders that you currently have standing, but also order new tests. So you can see that on the screen there and what happens when you click down. And the next few slides are just kind of going to walk you through that. And so you can specifically order a test. It has the chain of custody that you would fill out. It tells you when the date and time of when that was ordered. And then what ends up happening here is this lab online test request form.
So now the test request form is printed directly from your printer. You don’t need anything special. You just need a printer that’s connected to the computer that you’re ordering it from, and it prints out all the information. You would then check the information, make sure it’s all appropriate and correct. And then that little bar code up at the upper right-hand corner, really, that test request form now will go with the samples– samples have to be appropriately labeled obviously as well– that goes to the lab, and all we have to do now is click and scan that in and it automatically accessions.
What we were doing previously is basically hand jamming these things in. We had to basically have double data entry. So we actually had somebody that was entering, inputting all that information into the laboratory information management system, and then we had to have another accessioning tech basically come through and double-check to make sure all of the data entry was correct. So that’s just common practice, obviously, when you’re doing it by hand. That would not only take human resources, but that would take a lot of time, and it was not an automated process.
So when we’re receiving now upwards of 1,000 to 1,200, 1,300 samples a day out from what we were getting prior to COVID-19, which was maybe on a light day several handfuls, on a heavy day maybe 100 or 200, I mean, we definitely needed a different system in order to handle the workload. So this was it. And it’s been working fantastic. So what you’ll see here is the lab online report.
So this is the portal that if you were to receive it from– or the test– and would be able to receive it from us, this is kind of what you see. You can run your queries, and you have all these queries, and then you can pull that line of listing down based on– excuse me– on the patient query. You can also download a PDF of the actual report and then link that into your medical record. But this was really meant, and in speaking to Matt about the vision for our LIMS vision, if you will, is that this would kind of only be a placeholder, because ideally what we would be doing with our hospital systems is going to direct interface.
So this would be similar and kind of seamless to what you all may see with your LabCorp and your Quest, or even if you– in your labs, if you’re doing a lot of in-house testing, then what you would have directly into EMRs, your labs into EMR whether that be EPIC or whatever other EMRs that you’re using. So here the LAS interface will obviously, and you can kind of see the schematic of what we’re envisioning here, it’s a cloud-based system that would link directly through HL-7 messaging bidirectional from the hospital, that will go into the cloud-based messaging broker, and then we could pull from that again, obviously, bidirectionally into our LIMS. We would pull from it, and then it would come, and we’d be able to scan in the test orders directly.
This would not– or I guess, this would kind of move the end-user, like the labs and the clinicians, health care providers within the hospitals to, again, direct interfacing with EMR. So you would just order it right from the EMR versus having to log into a web portal. So that’s kind of what we envisioned. This obviously would reduce the turnaround time, reduce the manual entry, reduce errors, reduce all of that, and hopefully increase the speed that we would be able to test.
Now, for larger states, and depending on where you’re from, you may have many hospitals. For us, which is really nice, we only have now eight hospitals within the district. And so we’re able to actually do this every single hospital, which is fantastic. And all of them are super excited about it.
So APHL out to the rescue. So we needed– obviously we couldn’t do this on our own– and APHL, through this lab web portal– they don’t really have a name for it, but it’s called the lab web portal– right now phase one of this is still kind of a web portal. So we have the lab online web portal and then we have the– which is run from our LIMS, HORIZON, and then we have the APHL’s laboratory web portal, or will be called the LWP.
So a lot of the barriers there– again, this laboratory data exchange, there’s an AMES platform which is the APHL informatics messaging services, that’s kind of what APHL and CDC are kind of moving into now for all public health laboratories to be able to send data back and forth through the CDC. But I think they’re also looking at it to work with, to integrate these laboratory information management systems into hospitals and other clients outside of just the public health world. And Matt can talk a lot more about that because he’s on our APHL informatics committee who’s been working very diligently on this.
But so this is kind of like– it’s a little bit of the future, but it’s kind of a little bit of right now. We’re in the pilot phase for this now on this phase one. And so what we’re doing here is you can kind of see. Now, this is the web portal home page, if you will, where it’s, like I said, again, it’s similar to [INAUDIBLE]. It’s a web portal, you still have to log in, you still have to get credentials, it kind of enhances this critical time timely communication between the laboratory staff, the FBs at the Health Department, and health care providers during response efforts by providing a secure centralized platform to submit test orders and share laboratory results.
It hopefully eventually will help support kind of this overall laboratory testing workflow, providing this customizable dashboard for all end users. So you would log in and you would actually see this dashboard of what’s– let me just see here– yeah, so you also can kind of be able to see and track your orders as well. So that’s something that the lab online portal can’t offer you. The one that we have with our own LIMS can, but this other one can’t.
And so you can kind of almost see, you’re tracking an Amazon package, where are we in the process? So it’s been collected, it’s been submitted, communicate, like I said, bidirectionally, our LIMS directly into the EMR, so you’ll know exactly, well, we’ve received it now, it is now in process, we’re testing it, the report is actually published, so it means you have a report sitting in your portal, go ahead and go take a look at it. And then it will tell you if somebody has actually looked at them and viewed the report already. So you can kind of tell between a published report and viewed report. Published mean it’s there, but you haven’t seen it as a health care provider, and the viewed report means that it’s been viewed by somebody, either you or your team.
And here you can see the test requisition form. It’s pretty similar to the lab online. That’s intentional. You’re able to actually design it any which way you want, and it has all the patient demographics, the submitter information, the specimen information on there. And we’ve even included some kind of clinical signs and symptoms. So we want to know whether or not somebody is asymptomatic or symptomatic that’s being submitted for SARS-CoV-2 testing, if they have symptoms, when was the onset, or date of onset of symptoms, and then a little bit of a checklist about which symptoms are there, because now there’s kind of the six signs and symptoms that you kind of worry about.
So it’s got a little bit of this epidemiological data collection tool right on there, which, again, some of the other ones we can’t have. So it’s kind of fantastic in that way. So this is my last slide. So kind of moving on to the next steps here right is continuing the use of this HORIZON lab online portal for ETOR, which is Electronic Test Ordering and Reporting, customizing the process with our stakeholders and ensuring that it works appropriately for them.
So right now what we’re doing is we’re looking at working with our long-term care facilities, our nursing homes to ensure that all of this kind of weekly testing, that we’re doing it for them, making sure that process works appropriately, all while that’s happening, we’re expanding this lab web portal, the LWP from APHL, phase one, implementation of it, we’re beta testing it now. And we’re going to start piloting that with some of the nursing homes as well to see how well that works while the other system is still in play. And then eventually phase two of the lab web portal is this complete integration with the hospital LIMS.
And I kind of throw this in there as well, is, potentially what we’ve seen, or what I have seen is with our LIMS, and with any LIMS manufacture that you have out there, it’s never a perfect system, because everybody wants, every lab wants its own customized system. And so I think this pandemic and the federal funding that has come down to us is giving us an opportunity potentially to kind of look at a new LIMS. And whether or not that’s going to be kind of an open system, an open access, open source type system where we develop it ourselves, and we customize it ourselves, or really look at potentially some sort of a clinical-based system, much like, maybe, what you’re running in your hospitals.
So there I’m going to close. But I am going to advertise, for next month as well, we have a clinical– well, I have to join. I know this, guys. And it’s a clinical micro discussion by Dr. Adams here from the VA Portland Health Care System. And that’s going to be August 19 from 1:00 to 2:15. And you can register right there. There’s the link. And with that, I will close, and happy to take any questions that you have. And, again, a reminder that Matt is also online as well, as he is our technical guru. So I appreciate your time. And should I stop the sharing, I’m assuming?
TRIONA HENDERSON: You can or you can leave this picture up. I love it.
TONY TRAN: That is our lab. Yes, exactly. I like to kind of– I was told once that you always need– we need to show off our lab whenever we can. So I said, OK, sure, I absolutely will. All right, thank you.
TRIONA HENDERSON: Thank you so much for that presentation– and so timely. All of us in the laboratory, who have been previously or currently in the laboratory, know how important it is to have a system that reduces manual entry. That’s also a pain. And streamlines the process and efficiency. That’s just one of my passions.
Have you received feedback? You said there are eight hospitals and systems that you cater to or you’re in collaboration with, have you received any feedback from them? What was their role in this process?
TONY TRAN: Yes, so the role thus far has been minimal, because it was basically just inching, inching along the past several years. What we’ve identified so far are some pilot sites that actually want to and we have good working relationships already, so they’re willing to basically say, hey, this is a great idea, let me be a pilot test site for you. With SARS-CoV-2 or COVID-19, I mean, the pandemic response has really kind of derailed that. And so we basically started accelerating our work directly with our health department, which was, supposedly, it was going to be kind of a hand-in-hand process.
So we’d work with our clinical stakeholders out in the hospitals at the same time we’re working with our health department, but because we’re working so closely and the information and data exchanged between the health department and us is so critical obviously for contact tracing purposes, we decided that that was kind of best to work with that first. So we’re kind of waiting for a little bit of a breather and then we’ll continue to work with the hospitals. So we have identified a hospital that that is willing to pilot with us, and that will kind of be part of that next step in phase one and phase two.
TRIONA HENDERSON: That’s awesome. I would love to throw out a question to the audience. I know we have presented quite a few on the line actually. How do your laboratories receive results from public health laboratories? I remember when I was a medical director in North Carolina last year, it was paper fax, yes. I know that people do still fax things. Would anybody like to speak up and share how they currently receive– or any transitions that have happened recently with COVID-19? And if you don’t want to speak up, you can type in the chatbox. Elsie, can I put you on the spot if you’re available to speak?
ELSIE: Did you just pick me?
TRIONA HENDERSON: Yes.
ELSIE: Just say how we transmit? I actually have a more fundamental question for Tony. So I was actually very surprised you don’t have the LIMB already set up previously, like you kind of alluded to, it’s 2020. Is there more background information that you can provide? Because especially for a government agency, I was kind of under the impression that this is, as a nation, we want to be electronic, and here you presented that it’s actually not as electronic as we thought, or is it a different challenge because you have so many other clients versus us small labs, we can use Beaker, some Quest, and all that, so is that why?
TONY TRAN: Yeah, so thank you for the question. Yes, so just to clarify, this was 2016, so not quite as bad as 2020, but yeah. So I agree with you, though. It’s way past the time when we should have had it. And to say that we didn’t, is– I don’t want to have it seem like we didn’t. Remember, we did have it, it just wasn’t being used. It was only actually being used to log in samples. Our LIMS was only being used to log in samples, but not actually to go through the entire testing process, which I agree with you. I didn’t understand either.
I don’t want to put Matt on the spot, but he was here and lived through that before I got here. And so there was a question about that. And maybe some of that potentially was the importance that was placed on that, some of it was maybe volume-based, maybe they weren’t seeing a lot of the volume at that point in time, they’re like, we don’t need one, I mean, we’re doing just fine with the way that we’re doing it. And so I think some of that is, if you kind of think into institutional memory, or institutional– the history behind things, you know what I mean? I think it may be some of that. I cannot explain it.
I don’t know. I was shocked myself when I came in, I said, wait, we have a LIMB, but we’re not using it, doesn’t make a lot of sense to me. So that was one of, like I said, one of the first things that I wanted to implement. And so the second thing is that once you start that uphill climb, and part of it is– maybe for my governmental colleagues, you can commiserate with me and sympathize and empathize, but it’s not easy– so some of that is staffing, some of that is funding. Once you have something, and that’s exactly right, I would love to go with a Beaker or a Cerner or something like that.
We used Sun Systems type of– when I was in the hospital in LAS. And so the differences between, I think, what I have seen in the public health world and in the clinical diagnostic world at hospitals is that it’s– the hospitals tend to be very patient-centric, which makes a lot of sense, whereas for us a lot of the public health LIMS tends to be very sample-centric, so it’s focused around the actual specimen or the sample itself and not so much the patient. And so for certain things, because we do do a lot of environmental testing, we do do a lot of testing for surveillance that are not clinical, not under that realm, so there is some of that where you need that system that fits all.
And so where some might have deficiencies on the clinical side, this system actually has very strong, or major strengths, on the environmental side. And so I think in choosing and picking a laboratory information management system, it’s really important to figure out kind of, obviously, what your current needs are, but what you see, envision down the line as well. So it’s all of those together that made the challenges what they are in the fact that we can’t interface much like in a hospital, you basically make the decision, and the hospital makes that decision independently, and either you go to Epic Beaker altogether, or you use EPIC in something else. And that decision is made for us.
Yes, we’re working with different hospital systems, we’re working with the health department. Even in our own health department there’s two different EMRs that they use. And then what about all the long-term care facilities and nursing homes? There’s so many other clients that we have and customers that we have versus one hospital. And so that’s– I think of us as very much like– the public health laboratories as very much like a small LabCorp request. But LabCorp request, millions upon millions of dollars that are built into just this, making your lives as easy as possible.
They have staff there at every facility to draw the blood, to do all the accessioning, to get all the paperwork, they got the couriers. I mean, that’s part of their livelihood. If they didn’t have that, you wouldn’t go to them. And so we just can’t– we don’t have those systems in place, and it’s going to be impossible to set up all of those systems much like that, but we can do something that hopefully is similar. So hopefully that answers your question, Elsie.
ELSIE: Yeah, you did. I just don’t understand, fully understand, the complexity of it. I’m sure funding come into place, like you mentioned.
TONY TRAN: Yes. Funding has a lot to do with it. Absolutely. Absolutely.
ELSIE: Yeah, so Triona, to answer, I think, your original questions, our settings is a lot simpler, it’s a multiple hospital system, patient-centric, and [INAUDIBLE] we can electronic transmit all those data to PADOH. So it’s actually a lot easier than back in the days, we have to fax them.
TRIONA HENDERSON: Perfect. Another question. Is Venita still on the line? She is our quality improvement guru at Yale New Haven Hospital. And I know she is very much into streamlining and laboratory efficiency and reporting and reducing diagnostic errors. And I don’t know if she has any comments, but I do have another question. Venita, are you here?
VENITA: I am here. I’m not sure that I have any specific question. So if I can help in any way and add to the discussion, I’m happy to. I don’t do a huge amount of lab medicine, and so I’m not entirely sure how all of this translates into AP other than the fact that AP, we’re still working on everything with paper. There is very little computerized entry. So we’re decades behind lab medicine and handling our specimens in most places.
TRIONA HENDERSON: Right. It’s true. And even with COVID-19, I know– I just came from deployment with the Infectious Disease Pathology branch, which is all tissue testing for COVID and exactly the complexities of accessioning samples of tissue and the paperwork that has to be filled in and clinical data abstraction. So we have a way to go.
TONY TRAN: So and if I can chime in real quick, because for our pathologists on the line I think you understand this as well, one of the hardest modules, if you will, to build was the microbiology module, because it’s not a binary response. You know what I mean? And so trying to build in from the clinical hospital, and at the time my [? micro ?] [? chief ?] also had come from a large hospital system as well, so both of us were kind of driving on that and building this system so that– what about all the worksheets that we had? I didn’t want the paper either.
I wanted all of that electronically. It needs to be captured electronically. We’re able to do at the hospital. So we’re trying to mimic that model, but a lot of it was basically, unfortunately, it was like fitting that square peg in the round hole because the system was really not built for that. And so they tried as best as they could, and so we’re still not quite there. You know what I mean? And that’s kind of the decision point I was talking about, is, if you have an opportunity, hopefully you do at some point in selecting that laboratory information management system, think about all the needs in all of the different areas, and not only for now but down the line in the future, because it is actually millions of dollars for you to actually have to switch these things out. It’s not an easy decision to make. But sometimes– you saw the one photo, it was pulling out your hair, because you’re just– you’re always trying to jam that square peg in the round hole doesn’t always quite work. So anyway, yeah.
VENITA: Yeah, I think one of the challenges that we face is that often decisions about what the LIS is going to be is part of the EMR process. And then that’s all directed primarily towards lab medicine, whereas anatomic pathology specimens, to my knowledge, lab specimens come as individual things, whereas anatomic pathology specimens come in parts. And that just messes everything up. Plus we are not numeric in our reporting processes to the extent that lab medicine is, and we need the history and background information from the clinicians.
So for instance, we have a sheet that prints out of Beaker– I’m sorry, out of Epic. And I have all the history about depression, and insomnia, and joint pain, but I won’t have the history that is pertinent to the current specimen because that does not have a CPT code because it doesn’t have a diagnosis yet– I’m sorry– ICD code. So we’re working around it. We’re very lucky. We have a homegrown system that interacts with Epic. But it’s tedious, it’s still tedious. And at some point, keeping it up is becoming a challenge.
TONY TRAN: Yeah, and I really appreciate you bringing that up, because that’s exactly my experiences when I was in the hospital. You could directly go in and look up as part of your workup the clinical history of the patient to have a much better understanding of what is happening, especially on the micro side I think it’s really, really important to understand what is potentially contamination or insignificant versus what’s growing that actually is and sometimes understanding the history you have that– we don’t have any of that here. We have no access, unfortunately, as a reference laboratory, no access to any EMRs. It has to come from our epidemiologists.
And it was coming at the beginning of SARS-CoV-2, but now it is not. They’re just completely inundated. They can’t– there’s no system for us to be able to share that sort of even clinical signs and symptoms, that sort of thing. And so patient history, age, I mean, we have a little bit of that because we can calculate it ourselves, but if we don’t capture the information, we have no depth of information about that sample. And so as laboratorians, I’m sure you all understand that the depth of information is incredibly important for us to actually be able to make that sort of determination of, well, is it too early in– is the result, let’s say, of an antibody test negative or non-reactive because maybe you collected it too early in the onset of signs and symptoms, or are they maybe truly non-responding, or are they just not exposed?
And every– what I always try to preach is every single test result is not just a binary test result, yes or no, pos, neg, there’s a lot that goes behind that, and a lot of understand that you need to have. And so our disclaimers are pretty intense. I mean, we have disclaimers in our reports that are pretty intense– I call them disclaimers, but they’re notes or comments and disclaimers, whatever it is, so that in hopes that the medical provider, the health care provider, will actually read that and understand some of these issues of timing of testing almost is very important, and what those results actually mean.
TRIONA HENDERSON: Right. I know the headaches. I built out Epic– not Epic– Beaker, before I started, so, yes, building out microbiology when AP and all the other parts take probably a week, and microbiology, we’re here four months and still building out every single test, every single report, every single comment, was painful.
TONY TRAN: Yeah, I mean, it’s one of those things you don’t even really think about until you build it. It’s like, for SARS-CoV-2 it’s so easy. I have a positive, a negative, and an invalid result. In microbiology I could have 15 plus 100 organisms that I want in there because I don’t want my folks having to spell out these very difficult to spell organisms in every report. And so it’s like these things that you kind of think about as well, or you don’t really think about it until you have to. But anyways–
TRIONA HENDERSON: Oh, the joy of micro. Any other questions? I can’t see– here. Jeffrey says, we’re still faxing our reports from CDC for diagnostic services as of 2018. So there you go, Tony, people are still faxing.
TONY TRAN: I smile, but that does not bring me joy. If we could get rid of fax machines, that would be great. I’d be so happy. Matt, you have anything to add? I’m sorry. I know you’re still there.
TRIONA HENDERSON: Please, Matt, share your thoughts.
MATTHEW MCCARROLL: I would just say that I know one of the large pushes over the next couple of years both by [? APHL ?] Informatics as well as CDC is this data modernization, so helping all the state public health laboratories, local public health laboratories, really modernize their informatics capabilities, and that includes both the epidemiology side with receiving reports through electronic laboratory reporting as well as the laboratory side with electronic test ordering and reporting. So really going to more of a electronic data exchange capabilities to automatically send results both to CDC as well as to the Department of Health to assist with monitoring diseases, outbreaks, helping with implementing prevention methods much, much faster.
TONY TRAN: And I think that kind of goes back to Elsie’s original question and thought process of kind of her surprise. And I think with the hospitals, I mean, you all are just so much more, honestly, advanced than that much of the governmental systems. And with APHL and CDC, they’re really trying to standardize the messaging, the messaging, IE, the HL-7 messaging. How we report to the mothership, if you will, because each– it still is, and hopefully will change, but many times each of the divisions, the branches, depending on the disease area, we have to report via a different mechanism.
And so there’s all the different ways that we can report, and I think that there’s no standardization at all– excuse me– which makes it very difficult for the public health laboratory, because the Public Health Laboratory, obviously, had, first and foremost, has to report back to the health care provider. That’s the most important thing on a clinical test, because you all have to make those clinical decisions, the health care providers have to make those clinical decisions. Then we have to report to the Health Department, because the Health Department needs to make their decisions based on our data on, in this case, whether or not are we going to go into phase one, phase two, phase three? Are we going to– are we shutting down? What are the recommendations with COVID? It’s extremely important to understand what the positivity is there.
And then, thirdly, CDC, obviously, is also interested in the data, and we have to report to the CDC as well. And so it’s just it’s a lot of different data exchange that actually has to happen, and none of them are actually the same. So it’s been a interesting process, let’s just say. But I do think it’s going to get better, as Matt’s indicating. There’s definitely initiatives that are being placed with this being very high up there.
TRIONA HENDERSON: Absolutely. Thank you, gentlemen, for that amazing presentation. And thank you, everyone, for participation. As Dr. Tran said, our next session is going to be August 19th, Wednesday from 1:00 to 2:15 PM in clinical microbiology. Dr. Adams from the VA Portland Health Care System in Portland, Oregon. Please visit the DLSECHO website to register for that session. Don’t forget to fill out the evaluation to receive your P.A.C.E.® credits.
Thank you for taking part today. We hope you found it very valuable and important in your work as you engage with your individual laboratories. We look forward to your participation in future sessions. And we’ll keep you posted on any changes that may occur. We will adjourn now. Thank you. And have a great day. Thanks, Tony and Matt. Bye, Venita.
Additional Resources and Related Publications
- Rajamani S, Kayser A, Emerson E, Solarz S. Evaluation of Data Exchange Process for Interoperability and Impact on Electronic Laboratory Reporting Quality to a State Public Health Agency. Online journal of public health informatics. 2018;10(2):e204.
- Hunter A, Dayalan S, De Souza D et al. MASTR-MS: a web-based collaborative laboratory information management system (LIMS) for metabolomics. Metabolomics : Official journal of the Metabolomic Society. 2017;13(2):14.
- Bendou H, Sizani L, Reid T et al. Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking. Biopreservation and biobanking. 2017;15(2):116-120.
- Henricks WH. Laboratory Information Systems. Clinics in laboratory medicine. 2016;36(1):1-11.
- Cucoranu IC. Laboratory Information Systems Management and Operations. Clinics in laboratory medicine. 2016;36(1):51-6.
- Cucoranu IC. Laboratory Information Systems Management and Operations. Surgical pathology clinics. 2015;8(2):153-7.
- Wilkerson ML, Henricks WH, Castellani WJ, Whitsitt MS, Sinard JH. Management of laboratory data and information exchange in the electronic health record. Archives of pathology & laboratory medicine. 2015;139(3):319-27.