October 28, 2021 Supply Chain Lessons Learned and Q&A
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Date of session: 10/28/2021
CHELSEA PARSONS: All right, we can go ahead and get going. My name is Chelsea Parsons, and I’m a consultant with Guidehouse supporting the CDC OneLab Initiative. A couple of notes about the webinar before we dive in. If you’re having any technical issues throughout, feel free to email the OneLab inbox, and we’ll help you get that sorted, and that’s email@example.com. And that’s firstname.lastname@example.org.
If you have any questions throughout the session, we really want to encourage you to put them in the Q&A. You’ll see in the bottom banner of this Zoom meeting, there’s a Q&A function. If any questions arise throughout the entirety of the presentation, please put them in there. We’re going to have a Q&A session at the end of the presentation, where we’ll try and address as many questions as possible.
Note that Daveed has posted the link to the live captions in the chat. If you need the live captions throughout the presentation, you’ll just need to keep this Zoom page open as well as the live captions page open. And you can follow along as they go throughout.
So let’s go ahead and jump into the agenda. I’ll close out these polls here. All right.
So we’re going to start by going through a little introduction of today’s presenters. We’ll talk about some new and featured OneLab resources, some of them being supply chain oriented, so that should be really helpful for this presentation. We’ll do a couple of Mentimeter activities, and Triona will give you more instructions once we get there.
We’ll get into our main presentation part 1, have a little break in between there before we go into part 2, and then we’ll have that Q&A session that I mentioned earlier. We’ll close out the event, just letting you know about our next OneLab event. So thank you again for joining us today. We’re really excited to get started. And with that, I will go ahead and introduce you to today’s speakers.
So I’m really excited to welcome Dr. Matthew Pettengill. He’s the Scientific Director of Clinical Microbiology at Thomas Jefferson University Hospital in Philadelphia, Pennsylvania, and he’s also a Diplomate of the American Board of Medical Microbiology. His research interests include developing alternative blood culture methods, and rapid blood culture isolate identification assays. Thanks for joining us today, Dr. Pettengill.
Secondly, we’ll be hearing from Dr. Joe Saad today. He’s the Vice Chair of the College of American Pathologists Council on Professional and Government Affairs, and the past Chair of the College of American Pathologists Federal and Staff Affairs Committee. He’s also serving his first term on the Board of Governors. He is Chief of Pathology for the Methodist Health Systems in Dallas, President-elect of the medical staff, and Adjunct Associate Professor of Pathology at the University of Texas Southwestern Medical Center.
Dr. Saad received his medical degree from the American University of Beirut. After a research fellowship and internship in general surgery, he completed an Anatomic and Clinical Pathology residency at the University of Texas Medical Branch, and a fellowship in cytopathology at Baylor College of Medicine. He has been in private practice at Methodist for 29 years.
He is the past president of the Texas Society of Pathologists, and has served as a Texas delegate to the College of American Pathologists House of Delegates for many years. He chaired the Texas Society of Pathologists Council on Legislation for five years, is a board member of the Dallas County Medical Society, where he serves on the Legislative Council, and he is a delegate to the Texas Medical Association. Dr. Saad, thank you so much for joining us today. I’m now going to pass it over to Dr. Triona Henderson-Samuel from CDC’s Division of Laboratory Systems.
TRIONA HENDERSON-SAMUEL: Thank you so much, Chelsea. And before we get into the main presentation, I’d like to take a moment to orient you to some new resources that we have here at CDC. Next slide, please.
So the Introduction to Laboratory Risk Management– this basic level e-learning course provides information on applying risk management principles, and briefly describes related processes to emphasize the importance of risk management in laboratory settings. Our next training, Personal Protective Equipment– PPE– a lab training virtual reality. So this is a basic level course designed to enhance laboratory scientists’ ability to identify how PPE can help reduce the risk of exposure to hazardous materials, prevent transmission of infectious agents, and demonstrate how to don and doff PPE in the correct order to minimize contamination and potential exposures.
This course empowers learners to apply knowledge, and practice selecting the appropriate PPE, and properly donning and doffing it in a virtual museum. It concludes with a final exam in the virtual laboratory. All OneLab Network members will receive information about this course in their inbox tomorrow morning.
Our next set of resources are CDC self-testing videos. CDC has released two short animated videos. The first one, How to Use a Self-test, and How to Interpret Self-test Results. The videos help individuals use the self-test if they have COVID-19 symptoms, or if they may have been exposed to someone with COVID-19. The videos also explain the basics of COVID-19 self-test, and what to do after performing such tests.
The first video, How to Use a Self-test, explains the basics of COVID-19 self-test, and instructs consumers how to purchase a test, collect a specimen, perform the test, and properly dispose of the test. The second video, How to Interpret Self-test Results, instructs consumers what to do if their test result is positive, their test result is negative, their test shows an invalid result or a test error, or if they think their test result is a false positive or false negative.
Now I would like to orient you all to some existing resources related specifically to today’s topic on supply chains. CDC’s Division of Laboratory Systems convenes regular calls with clinical laboratories, to discuss the nation’s clinical laboratory response to the coronavirus disease. These calls listed on the slide, contain messaging, updates, and tips regarding the supply chain challenges that clinical labs are facing due to the current state of COVID-19 pandemic. You can access the transcripts, the slides, and audio recordings of these sessions on the Quicker Call CDC webpage.
The Summary of Health Facilities Strategies for Optimizing the Supply of PPE During Shortages is a quick reference which summarizes CDC strategies to optimize personal protective equipment, or PPE supplies, in healthcare settings, and provides links to CDC’s full guidance documents on optimizing supplies, which provide additional strategies and details. These strategies offer a continuum of options, using the framework of surge capacity when PPE supplies are stressed, running low, or absent.
The Supply Chain Disaster Preparedness Manual is designed to help supply chain managers become more familiar with the hazard scenarios likely to impact their facilities or systems and their communities. This manual indicated on the slide was developed with significant input from subject matter experts. To that end, its purpose is to help supply chain managers become more familiar with the hazard scenarios likely to impact their facilities or system, as well as their community, to develop supply chain related plans to help respond to these scenarios, and to develop an all-hazard cache of medical supplies to ensure a hospital or healthcare system is prepared for these hazard scenarios.
In addition, we’ve developed a personal protective equipment, or PPE, burn rate calculator, which is a spreadsheet based model that will help healthcare facilities plan and optimize the use of PPE for response to COVID-19. The tool will calculate the average consumption rates, as referred to as a burn rate, for each type of PPE entered in the spreadsheet. This information can then be used to estimate how long the remaining supply of PPE will last, based on the average consumption rate. Using the calculator can help your facility make order projections for future needs.
And then finally, I would like to make you all aware of some resources that we will be launching very soon. The first one– CDC will offer a training of trainers, unpacking and shipping category B infectious substances and dry ice, on Dec. 6th through the 17th. A training of trainers is intended to engage lead trainers in coaching new trainers that are less experienced with a particular topic or skill, or with training overall.
This workshop will build a pool of competent instructors who can then teach the material to other people. Instead of having just one trainer who teaches a course for a long time, there are multiple trainers teaching the same course at the same time in this model. This means a new participant typically gets to watch an experienced trainer teach, completes the exercises, and then practices teaching segments to other participants. The lead trainer and trainer participants should use the CDC Professional Development best practices.
This workshop will be held live via Zoom. Full details will be available on our OneLab webpage in the next few weeks. In the meantime, you’re welcome to email Isaiah Hurtado at email@example.com to learn more. We’ll paste this email address into the chat right now. There are 15 spots available for clinical and public health laboratory professionals, who train other laboratory professionals as a regular part of their job responsibilities.
OneLab is developing a laboratory communications toolkit to help laboratories develop plain language communication strategies. And if you remember, we had a session two months ago on this. The laboratory communications toolkit will be released later this year.
OneLab is also developing a sensitivity and specificity job aid, to help public and clinical laboratory professionals understand how specificity and sensitivity performance characteristics affect test result interpretation. The job aid will be released later this year. Now before our main presenters begin, we want to have a quick interactive exercise that we’d like everyone to participate in.
So please open up a tab in your browser, and go to www.menti– that’s M-E-N-T-I– .com. And use the code at the top of the screen, 48774703. The link is also being posted for you in the chat box in order to interact with our session.
You’ll see the statement on the screen that reads, “my organization faced major supply chain issues throughout the COVID-19 pandemic.” Please indicate if you agree with the statement by selecting Yes, do you not agree with this statement by selecting No, or if you aren’t sure by selecting Not Sure. And we’ll give everybody a couple of seconds to get logged in and enter their responses.
Perfect. 100% is yes. A couple, not sure. Awesome.
The next statement that you will see on the screen is, “my organization is still facing major supply chain issues.” Please indicate if you agree with this statement by selecting Yes, do not agree with the statement by selecting No, or if you are not sure, by selecting Not Sure. It seems like– we’re still entering.
Thank you so much. And our final statement is going to be, “I worry about future supply chain issues.” Please indicate if you agree with this statement by selecting Yes, do not agree with this statement by selecting No, or if you are not sure, by selecting Not Sure. Thank you so much.
For everyone who’s participated in this interactive activity, we will be using Mentimeter a few more times throughout this presentation. But now, I’ll be turning it over to Dr. Matthew Pettengill, representing the American Society of Microbiology, who will be speaking about his COVID-19 experience of clinical microbiology at the Thomas Jefferson University Hospital. Dr. Pettengill.
MATTHEW PETTENGILL: Well, just a sound check where you can hear me well?
CHELSEA PARSONS: Yes, we can.
MATTHEW PETTENGILL: All right. Thank you, Chelsea and Dr. Henderson-Samuel for the introduction. So I’m just going to talk, focusing a bit on our individual experience here at our clinical lab, at an academic medical center in Philadelphia. But you can go to the next slide, just an outline of some of the things I’m going to cover.
So I’ll talk about our experience early in the pandemic, developing a COVID assay, and the other impact on our normal clinical lab functions. Supply chain shortages of reagents, both data that the American Society for Microbiology collected from more than 100 clinical labs, but also our individual experience here. And then also shortages of personnel from a study from ASCP, and also comments on our experience with that. But then also touching on, that advocacy matters. That our organizations, and we as individuals, can reach out to government agencies, et cetera, to try to make a difference both now and for future preparedness, and impacts on supply chain of future events. Next slide.
So just going back to March of 2020, was a very hectic time in labs in general. So you know, we’re basically in January and early February of 2020, watching this on the news like anybody else, and not sure what the impact was going to be on clinical labs. Whether this was going to be something of the scale of the original SARS coronavirus, or MERS or something like that, where North American labs had really limited impact, limited need to test. Or what the scope of this would be.
As we approached the end of February, it was pretty clear this was going to be something that we needed to provide testing for, in individual labs. And that the volumes might be quite high. We all learned during this process about the emergency use authorization mechanism at the FDA, which was in place before COVID, but unless you were in a lab who had previously made or considered testing– for something like the Zika virus– not something that you had probably had personal experience with. But now we all do. We’ve all been through the EUA.
And these are just a collection of pictures of some of our experience in March, of trying to find the equipment to be able to run the CDC assay, or something approximately close to it. Or any other way that we could get an LBT off the ground. And there’s also, over on the far right, popping up collection sites, trying to get enough PPE, eventually trying to get enough collection devices. I’ll talk about that later.
And then also the people in the lab. So in the lower right hand corner there, one of our lead technologists, [? Sara ?] [? Goss, ?] working– it was the second day of COVID testing at our facility, running a modified version of the CDC assay. Go to the next slide.
So just a little snippet from our lab developed test, modification of the CDC assay. So this was something that we spent an enormous amount of time on. So trying to acquire nucleic acid from the virus.
Trying to, as I mentioned, trying to find the equipment, trying to get the materials in place, and train for an assay that we had not run before. In a lab actually, as microbiology techs, running it over in a separate molecular pathology lab. And wrote up the validation.
This was in middle to late March that we submitted this to the FDA and began testing. Actually began testing the day we submitted our notification to the FDA, and eventually submitted our EUA. Although by the time we heard back from them, they said it was close enough to the CDC assay that we fell under their EUA. Anyway, been just a very interesting experience going through this whole lab develop assay, and trying to build up the personnel training to be able to make this happen on a large scale.
And eventually we started getting in some commercial assays. You can go to the next slide. So vendors started to have materials available, on all of these tests that are approved under emergency use authorization.
And so labs needed some guidance on, how do we– from a regulatory perspective– how do we verify or validate these assays? How do we implement them in our labs? What are the QC requirements? There was a lot of assistance along the way from organizations, that helped to provide feedback to labs. This was a publication by the American Society for Microbiology’s Clinical and Public Health Microbiology and Clinical Practice subcommittee, on guidance for labs and how to implement these EUA assays as they became available.
And we, like most labs, brought in a significant number of tests. We didn’t end up implementing all of them. But I think we’ve had at least eight or nine different tests that we’ve used clinically at some point during the pandemic. And go to the next slide.
We also spent a fair amount of time– and I know a lot of labs did this, too– on evaluating serologic or antibody testing for SARS-CoV-2. And in our microlab we evaluated two, and signed off a validation for one antibody test. And it was considered at the time that there was going to be a very high demand for these tests.
I’m showing here a couple of advertisements that I saw on Twitter from one of the manufacturers of a COVID antibody test. Which you can see, in the one on the left saying, should I get tested? Should everyone get tested?
It turns out as more evaluation of these tests, and how they could be interpreted and used, came about, that maybe a better question was, should anyone get tested? Ended up being more of a test of curiosity, although there are some clinical situations in which they’re helpful, such as multi-system inflammatory syndrome in children, or somebody’s presenting [INAUDIBLE]. Potentially useful, but it is something we spent a lot of time on in the lab, ramped up for. And the demand for it never really materialized.
Still actually pretty low volumes, although now with vaccines available, they are used sometimes. Still more of a test of curiosity, but evaluating somebody’s sort of response to vaccination. But demand relatively low, although we wouldn’t have known that in the early summer of 2020 when we sort of brought these in. Next slide.
We also did some things along the way, that we would never have considered really in the peace times. So we started running out of all kinds of things. This is sort of a talk focused on supply chain.
We could not get enough nasopharyngeal swabs or viral transport media from commercial sources, and a lot of institutions struggled with this. Our Health Design lab, under the directorship of Rob Pugliese, partnered with the University of South Florida and Northwell, and started using their 3D printers to manufacture a nasopharyngeal swab of sorts, which we evaluated on about 300 patients. Using one traditional nasopharyngeal, through one nostril, and the 3D printed swab through the other one.
Clinically, it worked quite well. They also polled the volunteers– patients who were showing up for COVID testing at that tent that I showed earlier. Basically polled them as to their experience with a traditional flocked nasopharyngeal swab versus this 3D printed swab, and their responses actually indicated that it wasn’t particularly less pleasant than a regular nasopharyngeal swab.
Having had both, I would say I kind of prefer the flocked nasopharyngeal swab. I did use a 3D swab on myself, and I’ve had the regular swab. But clinically, it worked well. And we couldn’t get enough material for the commercially available ones.
And so I think we ended up using– I think they manufactured about 20,000 swabs. I think we ended up using 4,000 or 5,000 of these for patient testing. [INAUDIBLE] an extensive validation. You can go to the next slide.
We also couldn’t get viral transport media, to pair with these three dimensional swabs. And then eventually, when we were able to get individually packaged commercial nasopharyngeal swabs, but were not able to get them paired with commercial viral transport media. Our Thomas Jefferson University Biotechnology program, under the directorship of Dr. [INAUDIBLE] and his team of 10 or 12 students, however many they had working on this.
Actually ended up manufacturing about 30,000 viral transport media collection kits, most of which were paired with commercial nasopharyngeal swabs. But we actually did use quite a bit of this. We didn’t validate that media on every commercial assay that we had, just to sort of limit the extent of validation. So we did limit that testing to certain platforms, just to reduce the number of validations. You can go to the next slide.
We also played around with other ways to reduce the reagents that were required to perform the testing. So we, as well as several other institutions, looked at methods using– skipping the extraction step. Basically going straight into the PCR after a heat lysis [INAUDIBLE] portion of the assay. And that had pretty good results, at least for specimens below a CT of about 35 to 37, the sensitivity was, performed well in that range. And we go to the next slide.
So it wasn’t just COVID testing that we had issues as far as supply chain, as any of you affiliated with the clinical labs and public health labs know. The American Society for Microbiology Clinical and Public Health Committee did a fair amount of work surveying labs, to make data available– both to the labs, to see generally, if they’re having the same experience as others. But also to use this information to try to improve supply chain issues and advocate for labs. So they were surveying labs. More than 100– I want to say 150 to 200– labs were responding weekly with their shortages of a variety of different reagents and test equipment as well.
So you can advance to the next slide. It’s just the next figure. So this– and I can’t see the numbers. But the red bars are the COVID related kits and consumables consumables, the number of labs that were short of reagents.
And then also the blue [INAUDIBLE] instruments for performing the testing, and the light blue, quality control materials. So you can see it’s upwards of 60% to 80% that were short of consumables. And this is over the time frame of sort of fall of 2020 to winter of 2021.
Next slide or next figure. It was not restricted to COVID related testing. So you can see that labs ran out of a variety of things, including agar media. Glass slides has recently been an issue. So we were not able to perform all of our routine testing for bacteria, fungi– you know, microbacteriology, parasitology.
There was a shortage of sexually transmitted infection testing reagents, for chlamydia and gonorrhea specifically, for actually most of the pandemic. That’s kind of eased up recently. But it was not just COVID supplies. We can go to the next slide.
So our lab manager put together this list. I won’t go through with them individually, but we ran out of a lot of the things that everybody else did. And so it was always a scramble from week to week.
You know, what are we out of this week? And how do we try to replace that? And when we can’t replace it, putting out disclaimers in our lab results, to indicate that testing was not optimal. That we’re unable to get– you know, various things that may impact interpretation of the test results. You can see that last note there. One of the things we were short of was people. So we can go to the next slide.
I’ll just briefly go through this. You can look up the paper yourself. So it’s American Society of Clinical Pathology Survey in 2018. Next slide.
Vacancy in clinical labs– so you can see here, various clinical labs have fairly high vacancy rates for the number of positions approved for those lab sections. How many of them open at a given time? So for microbiology, close to 11% of positions were vacant. And also in [INAUDIBLE] for supervisor, 7% of labs did not have a supervisor at that time. And this was representative of 200 labs in the United States.
The next slide. It’s also the sort of expected retirement rate over five years from 2018 and we’ve experienced some of this as well. You can see, ranging from 10 to 27%, microbiology at 17%, of all positions expected to retire during that timeframe. Next slide.
Also mentioned in the outline, advocacy matters. So I mean, we can see what our problems are locally. But if we want something to change we– individually, or the organizations that represent us or that we serve with– can advocate to government agencies, to try to make a change. So you can see this is actually something that was– a bill submitted in the House of Representatives just over a week ago, by Representatives Lori Trahan and David McKinley, titled The Biopreparedness and Infectious Diseases Workforce Loan Repayment Program. Next slide.
So this is obviously not approved yet, so nothing finalized about this. It was brought up for discussion in the House this Tuesday. So this is very fresh, and I know they’re trying to find representation in the Senate to pick this up as well. But basically trying to advocate for the infectious diseases testing and clinical workforce, through trying to provide loan repayment for training programs, for medical lab science programs, and so forth.
And you see on the next slide, that includes a variety of different professions related to infectious diseases, but includes– you can see down there in M an N– people that have a Bachelor of Science in Medical Technology, or certification in medical technology, or as a medical lab scientist. So it could impact our field, trying to provide some loan repayment if you meet certain qualifications.
And obviously not finalized, but just wanted to mention– you can go to the next slide– that this is something that our organizations can help advocate for. The American Society for Microbiology has been active in having their Capitol Hill Day, and having representation meet with members of Congress to try to advocate for the medical technology field and supply chain issues. And this is a letter written to the Representatives, Lori Trahan and David McKinley, that helped submit that bill in the House last week.
And it’s from ASM, helping to advocate– and actually helped lead to certain changes in the bill, that they thought would better serve medical technologists generally. You can go to the next slide. Signed off by– Melissa Miller is the Chair of the Clinical and Public Health Microbiology Committee, and Stacy Schultz, chaired as well.
I’m going to go to the next slide. Just briefly go– I’m not going to name all the people. But obviously, a lot of the work done in the lab. And a lot of you saw the New York Times special, said nobody sees us.
So a lot of this work is done behind the scenes in a clinical lab, and don’t get a lot of acknowledgment. Our medical technologists always step up when we have issues, we need overtime, putting in the extra time. And so just a big thank you to all that they’ve done for our response here at Jefferson. And I know medical technologists around the country have really stepped up during this pandemic in the last year and a half.
So thank you again. I know we’ll take questions at the end. Let me try to send it over to Dr. Saad.
TRIONA HENDERSON-SAMUEL: Thank you so much, Dr. Pettengill, for your presentation. And in the interest of time, we’re just going to go directly into Dr. Saad’s presentation, who will be presenting on behalf of the College of American Pathologists regarding surveys conducted with laboratory’s accreditation to evaluate the impact of the pandemic on pathologists and laboratories. Dr. Saad?
JOE SAAD: Thank you, and thank you, OneLab Network, for the opportunity to speak on behalf of the College of American Pathologists. I’m Vice Chair of the CAP Council on Government and Professional Affairs. Also, I’m a practicing pathologist and a laboratory medical director. Like many or all of you listening today, I’ve been on the front lines of COVID testing since early March of last year. Next slide, please.
So very early on in the pandemic, starting in the early part of March, the CAP began to hear from their members about shortages in laboratory supplies. So the CAP decided to survey the laboratories it accredits to evaluate the impact of the pandemic on pathologists and laboratories. A series of surveys were conducted over the course of a year.
I’m going to present data from April 2020, June 2020, and February of 2021. The data that follow are taken from these surveys, and focus on the issue of laboratory shortages specifically. These data have helped to inform and educate our members, as well as inform the CAP’s advocacy and engagement with Congress and the administration. Next slide, please.
So this slide is taken from the survey conducted in February of 2021, COVID Impact Survey, and recorded the percentages of CLIA laboratory directors and pathologists who perform various testing activities in their laboratories. And I just want to backtrack a tiny bit, and kind of put this in context. In our first COVID survey, going back to April of 2020, about 59% of labs were performing on-site PCR testing. By June, that number had reached 76%, and that has held steady since then over the past year. Somewhere between 75% and 80% of the labs that were surveyed have been conducting on-site COVID-19 PCR testing.
In this table here, we can see that percentage of labs and CLIA directors and all respondents that were doing high throughput testing. I’ll focus on the left-hand columns. Of all respondents, about 52% high throughput, 53% pretty similar, non-high throughput, 37% antigen testing. For whatever it’s worth, about 49% or so antibody testing. Obviously, several labs were doing many of these, and that’s why the numbers add up to well over 100%. Next slide, please.
Again, this is data from our February 2021 survey, and there’s a lot of information on this, so I’m just going to highlight a few things. Academic medical centers are more likely to offer high throughput PCR testing, almost 72%. If we look at the nonacademic hospitals, the majority of them– about 2/3 or so, 64.7%– are offering non-high throughput testing. I think this is an important point that I’ll get back to in a second.
Independent laboratories, the N is much smaller, and these laboratories are across the board. You can see from this table that almost half of them didn’t do any COVID testing at all. But only about 41% were doing high throughput testing, and about 28% non-high throughput testing.
Another important thing I want to point out is in red here. Depending on practice size, the likelihood of doing COVID testing, we can see that practices with less than six pathologists [INAUDIBLE]. Only about 25% of them were doing high throughput, but over 50% were doing non-high throughput. And fairly consistently across the board, a large number of the bigger practices were doing high throughput testing. I can’t explain why [INAUDIBLE] drops off so dramatically. And over 50% of them were also doing non-high throughput testing.
Now I think there’s a couple of important things I need to point out in this table. The fact that community hospitals are more likely to offer non-high throughput COVID testing is very important. Because, although we want to rely on the large national chains and the large regional hospitals as being the backbone for testing, it’s very important to support the community hospitals. Because these hospitals and these practices can offer testing close to the patient, and are an essential part of a rapid response in a public health emergency. Next slide, please.
Again, data from the February 2021 survey. One finding from our surveys was that laboratories had to maintain more than one kind of platform. We asked laboratory directors about the number of unique PCR testing platforms that their laboratories were using, first of all, and then by type of platform, either high throughput or non-high throughput.
On this slide, you can see that more than 80% of practices use two or more platforms, and just over half of practices were using three or more platforms. Now the reasons, I think, are pretty obvious, but I have to state them. Number one, to handle the high volume. Number two, and very importantly, different platforms were necessary because of the availability of those platforms, and of course very importantly, the availability of reagents and supplies to run the platforms.
I’m sure that all of you have experienced being able to get reagents for one platform one week, and then running out of reagents and having to use another platform the next week. And so that was fairly consistent across the board in our surveys. Next slide, please.
Also from the February 2021 data, this slide shows that many laboratories have multiple versions of the same type of testing platform. In blue, we see the high throughput, and in red, we see the non-high throughput testing. For example, about 45% of respondents who do COVID-19 PCR testing, stated that their lab has more than one platform for high throughput testing. Nearly 60% stated that their laboratory had more than one unique platform for non-high throughput testing. Next slide, please.
This slide shows that the laboratory directors reported problems acquiring reagents across the board. And while it suggests that there’s been an apparent easing over time, if we look at April 2020, for example, and compare to February 2021, you can see that even in February 2021, there were still severe shortages in some areas. 45% of laboratory directors reported it was either difficult or very difficult to obtain reagents for platforms, or testing supplies. 30% stated that it was very difficult or difficult to obtain pipette tips.
And the reason we don’t have data for that from June and April, is because we didn’t ask that question until February of 2021. So we have no other data to provide. But anecdotally, I’m sure all of you have heard and experienced the fact that anything plastics was in short supply for the duration of the pandemic. And we currently are still in a pandemic now, but we’re still experiencing severe shortages in some plastics.
We heard earlier that there were issues in the clinical microbiology lab, with sexually transmitted disease infection reagents testing. Certainly that’s been a consistent message we’ve heard from our members. Early this year, there were severe shortages in blue top tubes. More recently, pink top, green top, and even purple top tubes. And while some of those have eased somewhat, we’re still experiencing severe shortages in blue top tubes.
Again, if you look down this table, you can see instruments, severe– very difficult to obtain in April, 42%, down to 19% in February. Viral transport media, 62% down to 17%. And again, many labs including ours, resorted to making our own VTM. Personal protective equipment from 42% to 16%, et cetera.
More recently, in June of this year, the CAP fielded a practice leader survey, which found that the difficulty was actually much lower in many areas. But the data were collected prior to the emergence of the Delta variant and the widespread Delta variant in the country. And so anecdotally, we’ve heard since then with the Delta surge, that there were spot shortages of many of these supplies listed here. Next slide, please.
Again from the February 2021 survey, we asked the laboratory directors to identify which staffing difficulties, related to COVID-19 testing, their laboratories had faced in the prior three months, that limited their ability to provide COVID-19 testing. Nearly 60% of respondents that provided COVID-19 testing reported that they faced some kind of staffing difficulty. The most frequent difficulty was testing personnel, and that was cited by 43.4%.
Over one third of these laboratory directors cited difficulties in obtaining adequate personnel for specimen collection. And nearly one fourth of those that responded cited problems in obtaining adequate numbers of accessioners. All these can lead to backlogs and difficulty in testing, obviously.
And as was mentioned by Matthew about staffing problems, I can tell you these have only gotten worse over the course of this pandemic across the laboratory workforce. We’ve seen higher burnout. We’ve seen early retirements. We’ve seen laboratory professionals just quitting or taking other jobs. We need to focus on the wellness and resilience of our workforce in the laboratory. Next slide, please.
So what are some of the lessons we’ve learned over the course of this pandemic? Testing supplies will be strained as laboratories ramp up capacity, and try to meet demands for testing in their communities during a healthcare crisis. Our healthcare system needs a reliable source for testing materials during pandemics. It has become obvious that laboratories will compete for the same resources, maybe even hoard some of those resources. Although I must admit, in our community, there was great collaboration and cooperation between the laboratories and North Texas.
Supplies need to be targeted to hot spots, and they need to be targeted effectively and transparently. We can and must improve the monitoring and communication of shortages of testing supplies when they occur. We definitely need to address the workforce pipeline for laboratory professionals– critical level before the pandemic, now at an even more critical level. We must have testing available close to the patient, although the network of large laboratories and regional laboratories is important. Certainly the ability to test in our communities is essential as well. Next slide, please.
So the CAP has engaged with Congress and the administration to support various efforts to mitigate supply shortages. In our engagement with Congress, the CAP for example, has supported strengthening the strategic national stockpile. The CAP further supports establishing state stockpiles for medical products and supplies needed during a public health emergency.
The FDA’s fiscal year 2022 budget includes $21.6 million for a new resilient supply chain and shortage prevention program, to be housed in the Center for Devices and Radiological Health. This fund will provide, for the first time, resources to establish a permanent program for US supply chain resilience for medical devices. The funding will help stand up this program, which will build on the work done to implement the CARES Act during the COVID-19 public health emergency, and will focus on strengthening the domestic supply chain through investments and preventive measures, identifying potential medical product supply shortfalls, continuing surveillance, and rapid intervention.
The program will enhance the FDA’s ability to enable rapid intervention, to prevent and mitigate supply chain interruptions, through proactive regulatory measures and partnerships with industry, healthcare providers, patients, and others, development and application of state-of-the-art supply chain intelligence for predictive modeling, early signal detection and continuous surveillance, and fostering a more resilient domestic supply chain through investments and preventive measures, that can help prevent shortages before they occur. The CAP stands ready, able, and willing to serve as a resource for federal agencies by providing them with additional information and expertise. So thank you very much. And with that, I’ll turn it back over to [? Jay Z ?] and Triona.
TRIONA HENDERSON-SAMUEL: Thank you so much, Dr. Saad, for your presentation. And so for our members, we have some time about, 10 minutes, for questions– or about eight minutes for some questions. So let’s start off with our final Mentimeter question. So if you’re having an issue seeing this question, please refresh your screen.
But the question will read, “what questions do you still have concerning the supply chain issues?” Oops, we have a different one on the screen. So, “what were your most challenging supply chain issues?” And so your answer [INAUDIBLE] are yes. No questions at the time. How to coordinate– yes. OK, [INAUDIBLE] specific. Perfect.
CHELSEA PARSONS: Yeah, these are some answers that we’ve already gotten in.
TRIONA HENDERSON-SAMUEL: OK, perfect, thanks. And just a reminder, it’s the same number, 48774703. You can either refresh your screen or re-enter it at www.menti– M-E-N-T-I .com. Perfect. Do you want to go on to the last one, Chelsea?
CHELSEA PARSONS: [INAUDIBLE]
TRIONA HENDERSON-SAMUEL: There are more questions coming in. [? Jay Z, ?] are you on screen?
INTERVIEWER: Hi, are we starting the Q&A now?
TRIONA HENDERSON-SAMUEL: Yes, so we can start with some of the questions that you have, that we’ve already received. And there are actually some questions that are entered. So two options, you guys can either use the Q&A function in Zoom, or as you are currently doing, entering some of the questions. Thank you, Chelsea for scrolling through the Mentimeter.
INTERVIEWER: All right, awesome. So we’re going to spend the next couple of minutes answering some of your questions. And thanks in advance for putting them in the Q&A. If we don’t get to them today, please send us an email, even if you have questions after today’s meeting.
So I’m going to start with our first question. “Should my lab outsource non-essential testing?” And I think Dr. Pettengill and Dr. Saad could both answer this, so I’m just going to start with Dr. Pettengill and see what he wants to say first.
MATTHEW PETTENGILL: You know, I mean, I suppose– it depends on what you mean by non-essential testing, and what the staffing issues are for that particular lab. I know some labs have had to outsource testing that they otherwise would never do. But they’ve had so many departures of medical technologists during COVID. One hospital lab that I’m familiar with has 50 FTEs and has 18 openings.
And so they’re having to send out testing, just because they cannot possibly perform all of the work. So it’s something that the lab director would have to consider carefully, what’s acceptable for turnaround time, and what kind of testing could be sent to reference laboratories– something kind of, you’d have to weigh each situation separately.
INTERVIEWER: Great, thank you. Dr. Saad, do you want to add to that?
JOE SAAD: Yeah, I would add to that. I agree with Matthew. Just as a last resort in our laboratory, I mean sometimes you have to. We don’t want to.
But for example, with the sexually transmitted infections, we couldn’t get supplies for almost a year. I don’t know if you consider that nonessential. I certainly wouldn’t. But we were forced to outsource for about a year, our gonorrhea and chlamydia testing. So I would say in general, as a last resort, if you’re unable to do the testing, either because of lack of personnel or lack of supplies, you may have to. Obviously the preference is not to outsource, if you can do it in-house.
INTERVIEWER: Great, thank you both. All right. So, “how will supply chains improve for small clinical laboratories, or even [INAUDIBLE] laboratories?”
JOE SAAD: I’m sorry, can you repeat the question? How will–
INTERVIEWER: Yeah, sure. So, “how will supply chains improve for small clinical laboratories or even tribal laboratories?”
JOE SAAD: Well, I would say that we have seen improvements. And it’s a matter of, obviously, the manufacturing. We need to have the manufacturing capacity, and then the ability to get those to the appropriate laboratories. And I think the whole supply chain is a mess everywhere.
Some supplies may be stuck on boats waiting outside of the LA harbor. And once they get to the harbor, you may need the trucks and the truck drivers to transport them to the appropriate things. So I think that the manufacturing has certainly improved. Perhaps the distribution is still a problem. But in general I sense that there’s been pretty substantial easing in supply chain issues.
MATTHEW PETTENGILL: Yeah, it fortunately has improved. Part of the question being the small labs. I think small labs are at a disadvantage, because they have less ability to have the flexibility of having multiple platforms. In some cases, they just don’t have the budget for that.
And also to be honest, big vendors, when they’re allocating reagents, are going to favor the larger accounts. And so I do think there’s pressure on smaller labs. And maybe that’s something that the government or other organizations like CAP can try to help advocate for those small labs, where they may be disadvantaged, and be kind of at the end of the line when are shortages.
INTERVIEWER: Great, thank you both. And I guess the follow-up question to that is, “when do you know if it’s time to execute a backup plan for supplies?”
MATTHEW PETTENGILL: Almost the entire pandemic we’ve been on our backup plan for supplies, for various things. So it’s– I mean, I guess just emphasizing the need to have a backup plan. You know reagents, that we never thought we would run out of, we have. And so that’s kind of forced us to make a list of, what’s the alternate for a variety of things. So it’s hard to come up with some kind of numeric or something, to say when you would switch, but you do need to have one.
JOE SAAD: Yeah. And I would add, please don’t accuse me of hoarding, but we typically like to keep four to six weeks of supplies on hand. When we start to drop below about four weeks, we start to look at a backup plan, and look at outsourcing some of our testing. That’s kind of our threshold, is about four weeks.
INTERVIEWER: OK, great. Thank you both. “Can I use expired COVID-19 tests, and if so, how do I monitor this?”
JOE SAAD: I’ll go ahead and start out, because this did come up in our practice over summer. During the September surge, we were desperate. One of the manufacturers was switching from outsourcing the reagent production to doing it in-house. And there was an acute shortage all of a sudden. So there was a lab in town that offered us expired reagents.
And actually, CLIA has come out with some guidance during the public health emergency. Otherwise it’s a very, very narrow circumstance in which you can use it. But CLIA did come out with some guidance during this public health emergency, to allow under certain conditions, the use of expired reagents. Number one, on condition you don’t deviate from the manufacturer’s instructions, otherwise it’s not covered by the EUA. And then number two, very importantly, that it’s only temporary until unexpired reagents become available.
So the laboratory must have a written policy in place to ensure that the reagents are performing as expected. And the kits and reagents must pass all the quality controls for each run. So for a short period of time, until they become available, you can use expired reagents if you have the appropriate policies in place in your laboratory.
MATTHEW PETTENGILL: Yeah, I would say we had to do that for some non-COVID reagents, just because we couldn’t perform susceptibility testing for a brief period of time without it. But we added extra quality control material runs every day. And those had to be checked before any patient results could be released. And it was only for a few days.
So we did have to do that. But COVID reagents, we used them all up far in advance of their expiration date. I don’t think we ever got near an expiry on a COVID test. [INAUDIBLE] OK.
INTERVIEWER: Great. And then I think our last question is, “how do we prioritize between stocking COVID-19 testing supplies and influenza testing supplies?”
MATTHEW PETTENGILL: That’s difficult to predict. We don’t really know what this flu season is going to be like. You know, we had almost no flu from February of 2020 on last year, maybe a little in early March. And there started to be some cases of influenza in the Midwest.
Unclear what this season is going to be like. Probably depends a lot on how people are utilizing masks and things like that, which will probably diminish over time. And what this season will be like, we don’t know, because the southern hemisphere flu season was not normal as well. So it’s hard to predict.
You kind of have to have the flexibility to have [INAUDIBLE] available. So you may try to stock up on some influenza testing supplies that have long out dates. Or keep, as Dr. Saad said, four to six weeks– have some kind of buffer. But it’s really unclear at this time, how much influenza activity there’s going to be.
JOE SAAD: I would add, Matthew is absolutely right. It is hard to predict. But right now, what we’re seeing is COVID. We don’t have much circulating flu. I can tell you in Dallas County, I’m not aware of– at least in our hospitals– I’m not aware of a single positive flu test that we’ve had recently.
So we are stocking up on COVID as our highest priority. We’re also stocking up on the COVID and flu combo tests. So we have some of those in stock as well. And at one of our hospitals, we’re kind of running the combo test, just reporting the COVID if that’s what’s requested.
So far, we haven’t had any positive. I think once we start to get positive tests from those combos, then we’ll probably roll out the combo test more widely. So we’re looking at the County Health Department, we’re looking at CDC statistics numbers, other regions of the country. And we’re doing our own kind of mini surveillance in one of our hospitals, to try to predict when we need to switch to the combo testing.
MATTHEW PETTENGILL: Some labs actually may not have a choice. Because some of the vendors, depending on what platforms you have in your lab– if you’ve only got one or two or three. Many of the vendors are switching to only manufacturing combined flu and COVID testing, so you may not have a choice.
INTERVIEWER: Thank you both. In the interest of time, I’m going to pass this back to Triona. And thanks, you both, again for presenting. Back to you, Triona.
TRIONA HENDERSON-SAMUEL: Thank you, [? Jay Z. ?] And thank you, Dr. Saad and Dr. Pettengill. For our members, please look out for more information regarding our next OneLab event, a collaborative educational event about point-of-care testing.
As a reminder, all of these slides with links will be posted to www.cdc.gov/onelab within the next two weeks. If we weren’t able to get to your questions today– and there were a lot of questions, so thank you so much for the robust discussion. Please send your questions to firstname.lastname@example.org.
We will also be using the information gathered from the Mentimeter to develop a supply chain Q&A job aid, which we will send out to the network once complete. We’re looking forward to our continued collaboration, being able to assist you in all of your training needs. Thank you and have a great day.
JOE SAAD: Thank you.
MATTHEW PETTENGILL: Thank you.