Risk Assessment for Clinical Laboratories – Session Materials

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Date of session: 02/28/2023


Aufra C. Araujo, PhD

Centers for Disease Control and Prevention


Didactic Speaker

Crystal Fortune, MPH, MLS (ASCP)CM RBP (ABSA)

Montana Laboratory Services Bureau


Aufra Araujo: Good morning, good afternoon, and good evening, everyone. My name is Aufra Araujo, and I want to extend a warm welcome from the Centers for Disease Control and Prevention in Atlanta, Georgia to all of you.

I’m a Health Scientist in CDC’s Division of Laboratory Systems, and I am the facilitator for this Extension for Community Health Care Outcomes, or ECHO, Biosafety session. Thank you for joining our second session.

The topic for this interactive discussion today is Risk Assessment in Clinical Laboratories. Our subject matter expert today is Crystal Fortune. Crystal is the Newborn Screening Short-term Follow-up Coordinator and Biosafety Officer for the Montana Laboratory Services Bureau.

At this point, so we can get to know each other, I invite you to enter in chat how many years of experience you have working in biosafety. This way we get to know each other. So just next to your name, just enter the number of years.

All right. One year. Wow! 33 years! Laura Moody. One year, six years. 11 years. Six months! Wow! Four plus. Nine years. Another 11 years. Wow! We have some folks here with a lot of experience. Eight years. Excellent. Two months! Oh, I thought that nine months was the lowest. So we have a brand new, two months person.

All right. Thank you everybody for participating. I would welcome– I forget the name. I’m sorry, the person who entered 33 years, if you’d unmute yourself and turn on your camera if you can. Laura Moody, I’m going to put you on the spot. Just say hi to us and tell us where you work.

Laura Moody: Hi there. I work in New Hampshire and Vermont. I run two laboratories.

Aufra Araujo: Wow! Welcome we are glad you are here. Thank you so much for joining. 33 years. And Sonia Aleman. I’m sorry if I mispronounced your name. Two months. Would you unmute and turn on your camera if you can and say hi, and where you work?

Sonia Aleman: Good morning. My name is Sonia and I work in the Colorado Department of Public Health. And I just recently started there after working in a laboratory setting. So I’m very excited to join this meeting today.

Aufra Araujo: Yes. Welcome. All right. Thank you everyone. Unfortunately we don’t have time to have everybody introduce themselves, but little by little throughout the year I’m sure we are going to get to know each other.

I want to briefly mention some technical details related to our ECHO sessions. Please use the video capabilities of whatever device you are using for this session. All audience microphones are now muted. During the discussion, please unmute yourself to speak. If you are experiencing technical difficulties during the session, please send a private message to George Xiang, who is labeled as DLS ECHO Tech. He will do his best to respond to your issue. And he’s waving to you now.

If you are connecting to Zoom by phone only at the time of discussion, please announce yourself by name and institution when beginning to speak.

Briefly, how do these ECHO sessions differ from other sessions? These ECHO sessions are different from expert lecture teleconferences or webinars in that the discussion of cases or clinical laboratory challenges are the main feature. Our subject matter experts hope to share some solutions that will be translatable to all of you in your individual laboratories. We also hope you will participate in the discussion by sharing your knowledge and experience.

These ECHO sessions are focused exclusively on clinical and public health laboratories in the United States and the U.S. territories. Once again, we value the discussion amongst all of you and want to encourage you to share your own experience and challenges on this topic. We thank you for your interest and participation.

Now it looks like I am having some– all right. No. Okay. Here is a brief overview of today’s session. I will introduce our subject matter expert, Crystal Fortune, who will provide a didactic presentation followed by a case presentation. Then we will open the floor for discussion. And then CDR Sabrina DeBose from CDC will summarize the discussion. Closing comments and reminders we will follow these, and then we will adjourn this session.

Today’s session is being recorded. If you do not wish to be recorded, please disconnect now. Closed captioning will be provided for this session. Please find the link in the chat box. The transcript, audio recording, and slide deck will be posted on the DLS ECHO Biosafety web page. George will add that to the chat as well.

All right, so now it’s my pleasure to introduce Crystal Fortune, who will be our didactic speaker and case presenter for today’s session.

Crystal Fortune is the Newborn Screening Short-term Follow-up Coordinator and Biosafety Officer at the Montana Public Health Laboratory in Helena, Montana. Crystal worked in the clinical laboratory for 15 years prior to making the switch to public health. Crystal moved from North Carolina to Montana in 2009 and worked at the Montana Public Health Laboratory as a clinical laboratory scientist for six months before becoming the state training coordinator.

Crystal was part of the biosafety team that was formed in Montana after Ebola hit the United States and became the biosafety officer in 2016. During her time as the state training coordinator and now as the biosafety officer, Crystal has had the opportunity to collaborate and network with trainers and biosafety officers across the United States and has joined several of them in special projects, such as the conversion of the “Blue Book” to the Clinical Laboratory Preparedness Guide, and to the updates being done to the documents currently.

In her own words, she has a “sick passion” for packing and shipping of infectious substance and often offers her knowledge on the topic. Crystal received her bachelor’s degree in Clinical Laboratory Science from Winston-Salem State University and her Master’s in Public Health from the University of Montana.

She is married and has two adult children. One is a U.S. Marine, and one is a doctoral student at Montana State University. And two younger children, her dogs Thor and Ronan. Now we invite Crystal to describe her experience.

Please think about similar situations that you’ve encountered during Crystal’s presentation. We expect this to be a robust discussion. Please offer your questions in the discussion period. At this time CDC will not make any official comments around this discussion. Crystal, the floor is yours.

Crystal Fortune: Okay, good morning. Thank you for the introduction, and it is so nice to see a couple of names– Lisa Wallace and Michael Adjei are a couple of people that I’ve worked with throughout the APHL network of biosafety officers. So it’s awesome to see– Leila Filson, I see also. So just kind of going through some of the names I recognize.

Like Aufra said, this is kind of one of the passions that I have, even though now I’m working in newborn screening, which I kind of started on during my master’s in public health. But biosafety and packaging and shipping of infectious substances are always kind of the topics that are nearest and dearest to my heart, and so these kind of opportunities here allow me to stay connected to that network. And I appreciate this opportunity.

So today I’m going to talk to you a little bit about some of the concepts that we may be familiar with, but not always so familiar in the clinical lab. A lot of these were concepts that I was not necessarily familiar with when I worked in the clinical lab.

As she said, I have a son who’s a marine. If that tells you a little bit about my age, I actually started in this right about the time that they started the blood borne pathogens regulation, and well before the sharps injury laws came out. So I have some stories to tell you today that I hope that none of you will judge me by, but keep in mind that I was young and dumb.

Anyways, so it’s– again, safety– especially at that time– wasn’t necessarily– biosafety wasn’t a concept that was really reached out to clinical laboratories. And I’m thankful to see a lot of you guys are newer in this field, because a lot of the resources that I’m going to share with you are older resources that we were introduced to when we started the biosafety program through APHL. Some oldies but goodies for sure. So I’m going to share those with you.

First I’m going to try again to share my screen. And we practiced this before, so let me try this again. So hopefully everyone sees a slide that says Risk Assessment in Clinical Labs. Is that the case?

Aufra Araujo: Yes, Crystal, we can see.

Crystal Fortune: Okay, good. Thank you. So anyways, again, I’ll show you some screenshots of some of the resources that I’ve used here in my own biosafety outreach.

So first of all, just to kind of discuss the principles of biosafety we’re all aware of involves us being knowledgeable of the hazards that we encounter daily, as well as how to use the mitigations that are in place in order to protect ourselves and others, and to keep the pathogens contained within our laboratory environment.

In order to ensure successful containment all the staff need to be aware of what hazards are present and what we have in place to mitigate those hazards. So this includes understanding and respecting facility design and adhering to safety policies and procedures. Staff should also know how to properly use engineering controls, personal protective equipment, and they should adhere to good laboratory practices.

So just kind of an overview, those of us in biosafety have probably seen this chain of infection and how to break the chain. Also the pathogens entry points– the portals of entry. So we have skin. We know that intact skin is generally a barrier. But if you live in Montana and it’s cold outside, you may have some chapped skin. Any injuries– open injuries– are not considered a barrier. Also, if we’re looking at parenteral inoculation, there’s lots of opportunities for needle sticks, broken slides, sharps.

When we consider the mouth and GI system, we have to think about pathogens that are transmitted via the fecal, oral route. I saw recently an article about a man whose son passed away 33 years ago from an infection due to E. coli 0157. This was on CNN, and so people were very thankful to him– any time there’s a science article, I immediately jump to the comments.

People were very thankful to him because he suggested that E. coli 0157 could be spread person to person, because this other child in the daycare had eaten contaminated food, and his child didn’t, but his child actually– the baby who did eat the food had a leaky diaper. So his child came in contact, I’m sure, with the fecal matter either on toys or on the floor, and his child actually passed away of the hemolytic uremic syndrome because of that.

So it’s a good example of how science can be misconstrued. It’s not necessarily person to person contact. When we’re looking at mucous membranes, we want to consider splashes into the eyes or mouth. That will be considered in the risk assessment as far as what kind of protection we need to protect ourselves.

And then we think of Beth Griffin when we think of mucous membrane exposures. Of course, she was the young scientist who passed away from herpes virus after she got fecal matter in her eye from a macaque. And then inherent in the laboratory is the inhalational route, obviously through the lungs.

And we want to look at each of the work practices, facility design, engineering controls, PPE immunizations, and so on, to keep the pathogen from entering our body and then ultimately resulting in an infection and sickness. We also want to know more about that. We know that there’s kind of starting to become some mechanisms for reporting, but not a lot is necessarily known about all the routes of laboratorians becoming infected. So surveillance will help us to kind of protect ourselves and then protect others from becoming infected in the laboratory.

So here’s an example of how the agents differ. A lot of this is focused on micro because that’s what we deal with mostly in the public health lab. We’re looking at the different surveillance samples. Foodborne outbreaks, that kind of stuff.

So this slide then shows how E. coli only takes approximately 10 organisms to cause a person to be sick. So in that case, it kind of explains then how the baby would have become sick. Meningitis– we know infections can occur from Neisseria meningitidis type B. And also Shigella is a low infectious dose that– a lot of microbiologists are prone to Shigella infections if they’re not careful.

And this chart kind of demonstrates that risk for microbiologists. So when you consider the risk in the population, if someone needs to go to a salad bar or something, or eat contaminated meat to get sick, versus microbiologists who are actually dealing with a concentrated culture– that isolate from the culture, so direct exposure to that pathogen. And that’s a good reason why we want to do risk assessments in the lab.

So in order to protect ourselves, we have the practices that should be common in all laboratories, such as obviously not eating or drinking in the lab, no pipetting by mouth. We want to make sure that we wash our hands after we’ve dealt with infectious substances, after we’ve removed our gloves. Before we leave the laboratory we want to make sure that we leave all that stuff behind.

We also want to be careful with generation of aerosols. We want to decontaminate our work surfaces whenever they become contaminated or at the end of our shift. When you use, also, a disinfectant, you want to make sure that you have the correct contact time. Otherwise, you’re kind of negating the usefulness of that disinfectant.

We want to make sure that the infectious wastes are decontaminated before they’re taken out of the laboratory. The biohazard symbol that we have kind of warns other people that there’s stuff going on in this area that they may not want to come in contact with. So hopefully we’ll keep unauthorized people from entering.

With little pests, either bugs or small animals– we get squirrels that come into the building sometimes– we want to keep those guys from carrying pathogens out of the laboratory on their feet. And then also realizing that people are kind of the inherent risk after everything else is applied. So we want to make sure that they are trained and competent in the biosafety principles and practices.

So everything that we use during the day in the laboratory should be designated per risk, and then the biohazard symbols are used to indicate what’s contaminated. So like on your refrigerator, centrifuges, dirty sinks, computers, whatever might come in contact with pathogens during the day, need to be designated as something people want to be careful with, not to touch with bare hands, and so on.

The biological safety cabinets should be located away from doors and away from high traffic areas. Of course, we know that if someone walks behind a biosafety cabinet they can actually cause the error to walk through that curtain. So that could contaminate the environment. The biosafety cabinets need to be tested and certified at least annually in order to make sure that the air is safe to recirculate in the laboratory.

And then also our staff, if they get infected, then obviously they can take that infection and infect people outside of the laboratory. So we want to make sure that they’re protected with vaccination. We monitor conditions such as TB, and then if they have any incidents, we want to make sure that those get reported and that they are able to receive the prophylaxis, if needed, to avoid illness.

So facilities are all designed, of course, according to standards. And the design is intend to keep pathogens from escaping from higher containment to lower containment, or outside of the lab environment altogether.

So typically laboratories want to be separated from the public areas. They have directional airflow, self-closing lockable doors. That’s to keep people from coming into the laboratory. So it kind of defeats the purpose if we prop those open.

When I worked in the health department many years ago, I’d be drawing blood and people’s children would walk back into the lab because we would keep that door open so we could watch for people. So obviously not a good thing. So someone in the back would have to catch the baby or the toddler from running through the laboratory.

And we want the labs to be designed for easy cleaning and decontamination. We also want to make sure that whatever PPE we use in the laboratory doesn’t make it into office areas, so keep your PPE from coming out of the laboratory area. Or if the supervisor’s offices are within the lab, then you want to make sure you take your coat and gloves off before you enter the office.

So primary containment is kind of protection for personnel in the immediate laboratory environment from exposure to infectious agents. And I say immediate because, like I said before, if we have a higher containment lab– a BSL-3 lab and a BSL-2 lab, the same applies. We don’t want things to come from the higher to lower containment.

Two of the primary barriers we think of with protecting the worker in that media environment is the personal protective equipment and the biological safety cabinet, both of which can fail if they’re not used properly. We know about not having more than one person, for example, working in a biosafety cabinet. Not moving in and out of it. If you’re not trained in there, you don’t necessarily know that stuff. Even if you’re trained in the lab and someone is showing you they don’t necessarily show you, hey, don’t be moving around in here too much.

And I have a story. One of my coworkers could snap his gloves off and shoot them across to the garbage can. And I always thought that was the coolest thing that he could actually slingshot his gloves to the trash can. That’s also not a really good idea. If you’ve ever seen the “beaking” method you can’t snap your gloves actually if you take them off properly.

We also want to consider other engineering controls such as safety, centrifuge cups, to contain aerosols and exposure to broken tubes. When I was in the clinical lab– again, I started a long time ago– we used glass vacutainer tubes. And if you’ve ever heard the sound of a glass tube breaking inside of a centrifuge, that sound will actually make you move faster probably than anything in your life.

But then we didn’t have safety cups at that time. So we had an entire centrifuge with all the cracks and crevices filled with pulverized bloody glass that we then had to clean out of the centrifuge. So those are definitely useful.

Biosafety cabinets. The clinical labs typically have the class 2 biosafety cabinet, which is used to protect personnel, environment, and product. That has HEPA filtered air that circulates within the cabinet to protect you and your product, and also HEPA filtered exhaust air to protect the environment around you.

Secondary containment then is the protection of the environment external to the lab. Or like I said before, from higher to lower containment. So we want to make sure that everything generated inside the lab is disposed of properly and that it’s decontaminated before it leaves the laboratory, such as autoclaving, or if you’re going to package up your waste, you want to make sure that leaves the laboratory safely.

We also want to look at hand-washing sinks, clean sinks versus dirty sinks. We don’t want people to wash their hands at the same sink where someone maybe disposed of some hazardous waste. We also want the airflow to be directional so that it’s not going from one area– contaminated area– to an area that’s not supposed to be contaminated.

And also, as I mentioned before, we want to keep the doors closed and have badge access so that those people who have no business being in there don’t come in, because that actually then puts them at risk for an exposure.

So the information identified in the risk assessment provides a guide for a selection of the biosafety levels and microbiological practices. So I mentioned before that facility design is what factors into protection in the laboratory. So you kind of need to know– most of us come into a lab that’s already there– but that lab, you have to look at what you’re going to be dealing with to know how to design it to mitigate risk. So included also, we want to have the proper safety equipment, as I mentioned, and facility safeguards to prevent infections.

If you want to look at all of your operations to determine the risk, I’ll talk about that in a little more detail. So everything that you do from receiving the sample all the way up to disposal of the sample. And then you want to determine what risk is acceptable and which ones should be abated.

Everybody needs to be part of the process. It’s not just a couple of people that are going around doing everybody’s risk assessment. It needs to be involving leadership as well, because they’re the ones that are going to give you kind of their blessing in you doing what you need to do to mitigate these risks. And you want to make sure that you realize that risk can never be completely eliminated.

So the activities that are geared more towards microbiology then, is like sniffing plates, doing a catalase using biochemicals, and so on. Sniffing plates– I’ve always said that Pseudomonas smells to me more like corn chips than grapes, but we shouldn’t be sniffing those anyway.

Also, we may have seen the Harding and Byers study that showed that different– or how many people were infected with Neisseria meningitidis. 31 people, 11 of which passed away due to that infection. And the conclusion in that study was that tests were not being done inside of a biosafety cabinet.

And I actually did an experiment once in North Carolina where I set a bunch of sheep blood agar plates around behind the shield that I was using to do catalase testing, and there was actually growth on all of the plates. Some directly and some probably two feet away. Just kind of a small experiment. And I didn’t write it up or anything, but just to kind of show you that those little bubbles have some stuff in them that’s being imparted into the air.

So at this point I didn’t know if anybody would like to share any stories in their chat, or if they want to open their microphones to see if anyone has any silly stories that they’d like to talk about. I can’t actually– oh.

Somebody said they weren’t able to see, but I think Aufra said that you guys could see now. No one wants to divulge their secrets. All right, moving on.

So in 2016 APHL came out with a best practice regarding risk assessments, and they provided also examples from Alaska, Colorado, Florida, Iowa, and New York. We want to remember that the goal of risk assessment is to identify and mitigate risks, but because all the facilities are different, there’s not really a one size fits all.

So when we first started with the risk assessments, we were kind of trying to figure out ways that we could provide information to the clinical labs. So there was a bunch of, do we have examples of risk assessments? And again, because every facility is different, they always say it depends.

One thing, though, that risks assessment should all have in common is, you want to look at the common pathogens, the mode of transmission, likelihood of exposure, the activities that can result in exposure, staff training, their experience in that task. Also their health status. And remembering too that risk assessment is a continuous process. It’s not a one and done. So you do a risk assessment and then you need to go back and reevaluate it.

This is a snapshot from the APHL risk assessment over Ebola that was put out right after that. So I chose this because of the– it’s PPE, so that’s pretty common, of course, to all of the laboratories. So it was kind of relatable. The Ebola risk assessment was– obviously it’s public health labs that were doing the testing. But there was other stuff that clinical labs could glean.

This is a good resource when you’re working on your risk assessment. George is putting the links in the chat for you guys. Not only do these pathogen safety data sheets have information on the pathogen, they also list the host range, their route of infection. So like we were talking about, aerosol, or skin, or what have you.

The risk group. That kind of considers, like, what’s the consequences if you were to get exposed, if there’s treatment available, if there’s vaccines. Of course, the less chance for you to protect yourself against an organism, the higher the risk group.

The infectious dose. Again, like I showed you before, 10 organisms versus if something’s like 10,000, then obviously the one that has only 10 organisms to lead to illness is more dangerous.

There’s laboratory specific information in these pathogen safety data sheets. So including disinfectants and the contact time, you also have your survival time outside of the host and the level of containment and PPE that you want to consider. And, by the way, there’s an app for that with no ads and no in-app purchases. They have a link on their home page if you would like to download that. And I did, because I’m a nerd. And there’s no comments on it yet because we just use it, we don’t complain about it.

This is an example of the risk assessment like we do it in our laboratory. And we also provided this example to our clinical laboratories. So this is for our micro department.

And we have here two of the organisms that we consider hazardous in our laboratory. One is a microbial resistant organism. The other one is anything from a sterile source. And we have Neisseria meningitidis, so the breakdown– for example, the specimen processing, there’s a line there. So anything that can transmit the aerosols, then we would add then the N95, or working in a biosafety cabinet, or whatever.

So you see there then, we looked at the task itself, what was the route of exposure, and then based on that task, what was the likelihood for infection. So if they had a moderate risk, as you see with the sample processing of inhaling aerosols or getting something in their mouth, then we would add whatever mitigations to protect against that. And then all with the goal of bringing the risk down to low by the end.

So what challenges do you guys anticipate in your clinical labs? There’s one specific one that I’ve heard of many times in Montana. So I wondered if anybody has any ideas in their jurisdiction that they would like to share so that the rest of us can know what to cover.

I know everybody is being shy now, so they’re going to have a brain dump later. So we’ll return to this stuff.

So the major complaint that I’ve heard from my laboratories– somebody says difficult to get compliance where they process. And that’s true from leadership set in policies versus– I’ve had a lot of people– like, telephones cell phones in the lab is a huge issue. People want to have their cell phones.

I can’t remember who it was that told us once, you can have your cell phone in the lab, you just have to autoclave it at the end of the day. So it’s important then to have those policies so people will pay attention to them.

The other thing that I’ve heard then is people in the clinical labs– like, it’s fine and good in the public health lab because we generally know what’s coming in. We have our laboratories call us if they’re going to refer a rule out sample. And we kind of know the kind of stuff that’s being sent to us, whereas they don’t. They have no idea from one day to the next what they’re going to encounter.

So the sentinel lab definition after Ebola actually expanded to include any lab that can encounter an infectious disease irrespective of their facility. So any hospital, any laboratory could technically encounter any pathogen that can travel. I mean, people come to Montana all the time. And you think of us being a rural state, but someone could come here during the summertime with an exotic disease that they brought from overseas, or whatever. So any of our teeny tiny little labs can actually come in contact with something that they’re not prepared for.

These are some tips then that the clinical labs can use to prepare. In the same way that we ask people to call us if they have a pathogen that they suspect, an infectious disease in their patient. Clinical labs can request for their providers to give them a heads up.

Also laboratories can see the EMRs, the electronic medical records. Sometimes that may give them a little bit of background on what they’re looking for. We used to do– our health department had a deliverable where they had to do active surveillance, where they actually contacted the clinical labs on Fridays and said, hey, what’s circulating? I heard that this is circulating over in this area. Have you seen any of that? So kind of knowing what’s going on out there.

Also we want to consider trigger points. Anything that’s growing in a sterile source is bad. I mean, sterile should be sterile. So if something’s growing in the sterile source, if it’s not a contaminant, it’s probably pretty dangerous. So that in and of itself should be a trigger point for processing samples. And then of course, we know slow growers, small gram-negative rods, any of that stuff should then prompt someone to work with a culture inside of a biosafety cabinet.

You also want to know your staff. So how do they handle stress? What’s their comfort level? People with young children or elderly relatives at home, they may not want to deal with Ebola testing, for example. We had someone that wasn’t comfortable doing that. And if they’re not comfortable, you shouldn’t make them do that. There’s other people, maybe, that might be more willing.

We want to provide vaccine, of course, if they are interested in getting vaccinated. Obviously Hep-V vaccine. We also offer the meningitis and meningitis type B vaccine. And then if anything comes up that compromises their immune system, even if they’re pregnant– like, pregnant females are immunocompromised. So people need to be aware of that so that they can make sure that their immunocompromised workers have some additional protections, or that they do not work in that environment at all.

This is a great reference, obviously, that we have always looked at. But it may have been previously overlooked in the clinical labs. The sixth edition of the BMBL includes an appendix specific for the clinical labs. And I have a screenshot of that there.

It introduces bio-risk management, and kind of compares it to what clinical labs are already familiar with, which is the quality management and the individualized quality control plan. Both of those have elements of risk assessment and risk mitigation.

The BMBL emphasizes a multidisciplinary team to assess risk in all phases of testing for new instruments, new staff, and new processes. It addresses staff’s adherence to policies concerning PPE and engineering controls and to ensure that they properly use them to ensure effectiveness.

And then when one pillar of safety– a safety control– is lacking, that they can bulk up in others. For example, if someone doesn’t have a biosafety cabinet, can they use then, like a shield, or respiratory protection like a PAPR or an N95.

It also stresses the importance of non-punitive reporting, unanticipated, or unusual events, near-misses, injuries, and accidents. If your people are afraid of you, they’re probably not going to tell you that they had an accident that led to an exposure, especially if they weren’t adhering to policies. So we want to make sure that people feel safe to come and let us know if they were injured or exposed.

This one is also a really good resource. We use to refer clinical labs to this before. Then the BMBL came out with their index. The Blue Ribbon Panel, that was in 2012. The guidelines for safe work practices in human and animal medical diagnostic labs. This goes into great detail about risk assessments in the clinical labs, and it includes all the common areas that are in most laboratories, like micro, chemistry, hematology, blood banking.

It covers pre-analytical, analytical, and post analytical. So the risks inherent– like pre-analytical, you’re looking at sample collection, processing, transport to and within the laboratory. Analytical– so looking at testing platforms. If they’re open systems that might generate aerosols. If they have pipettes.

Some of the chemistry analyzers have the little pipette that goes down into the tubes. Hemo as well. So you want to be careful with that kind of stuff so you don’t scrape yourself. Then of course, obviously, glass slides. Sticks. Anything like that can cause a sharps injury or aerosol.

Post analytical, we want to look at sample and chemical disposal. And then waste handling. We talked about autoclaving.

We want to observe clean spaces such as offices, computers, sinks, versus dirty spaces. And it covers also, avoiding other hazards. So chemical, electrocution, explosion, slips, trips, and falls. Those are covered in pretty good detail in this document.

This one is a screenshot from the Blue Ribbon document, and it shows a breakdown of activities by portal of entry. So that’s kind of nice, giving you a clue like ingestion. These are the kind of things that can cause someone to accidentally get a pathogen in their mouth, and so on.

And then this screenshot then shows the kind of tasks that are associated with a hazard. And so here are some culturing– blood culture bottles. You have a likelihood of exposure– moderate likelihood of exposure– to percutaneous inoculation or inhalation. So this is kind of a nice break down. Kind of like the pathogen safety data sheets where it takes a lot of that guesswork out for the laboratorians who are doing the risk assessments.

I’m sorry, I have my chat window up here where probably everybody can see it. So other considerations are the biosafety lab competencies. So these kind of crossover a little bit to the public health professional competencies. The safety domain includes potential hazards, hazard controls, and administrative controls. And so this kind of crosswalks some of that then into the actual biosafety competencies.

It recognizes that people are the residual risk that’s in the laboratory after all the other controls are in place. And make sure that staff are appropriately trained in whatever capacity they serve. So whether they are beginners, and their job is just to recognize what’s dangerous, or if they need to adhere to the policies to protect themselves, if they need to actually affect some of the changes, write the policies, or if they’re in leadership where they need to ensure everyone is competent to work in the lab. This kind of breaks down each of the tasks and the responsibilities.

The checklists that are available also through APHL– you see this one on the left is published in April 2015. And then the one on the right actually didn’t have a date. And the links to both of these are in the chat as well. It goes through site checking, so kind of giving you different things to look at, such as the processes in your facility.

Are people using biosafety cabinets properly? Is there PPE available? Are they reporting incidents that might lead to exposures? How’s the infection control? Are they inventorying their stock cultures? Are people trained in what they’re supposed to be doing? And again, are they competent in what they’re supposed to be doing? Because they want to be comfortable in what they’re doing, right? So if they’re not comfortable, they’re not going to feel safe. They’re going to end up getting hurt or hurt someone else. Or they could even leave your institution if they have no confidence in their leadership to make sure that they’re trained and safe.

And this is the hierarchy of controls. I got this image off of the CDC website. It is showing then that the most effective thing we can do in the lab is eliminate any dangers. A lot of people think that PPE is the most important thing you can do to protect yourself, but you see here that’s actually the least effective.

Again, if people aren’t buttoning their coats, or they’re snapping their gloves, or they don’t know how to use a respirator, those things aren’t going to protect them. So the first thing we want to do is get rid of anything that can harm them. If we can’t get rid of it, then what can we use instead?

And of course, clinical labs don’t always have that luxury. So if you can’t protect yourself from a hazard by increasing the other controls, then you might need to just refer samples out if you don’t have the ability then, or the facilities, the mechanisms in place to protect you from testing.

I know a lot of stuff is point of care. But if all else fails and you don’t have the way to protect yourself, then you may need to refer those samples out.

And these were a couple of other documents that I found for you. So the one on the left, the Respiratory Protection Program Toolkit talks about the different respirators. What’s the conditions under which they should be worn, disposal, fit testing, all that kind of stuff. It’s a pretty comprehensive guide for health care workers.

And of course, the Clinical Lab Preparedness Guide is very comprehensive. It covers pathogen-specific information, safety, packaging, and shipping. It has some job aids and other references that laboratorians can use.

So I’m hoping then that someone can maybe say some resources that they’ve shared with their clinical labs. This is the end of my presentation. You also– hopefully you have something to add now.

Aufra Araujo: Thank you for your presentation, Crystal. Now we open for ideas and questions from the audience. As I mentioned before, we value the discussion amongst all of you and want to encourage you to share your own experience and challenges on this topic. We recommend turning on your camera and using your microphone to introduce yourself when you initially speak.

And if you are calling on the phone using the phone only, please, when you unmute yourself, say your name so we know who is speaking. Any thoughts? Any ideas you’d like to share? Either, like I said, unmute yourself, or write in the chat.

Crystal Fortune: Sonia shared earlier that she created a safety survey as a safe space for laboratorians to express concerns related to safety and security. She’s trying to understand dynamics on how people feel about safety. And I will say, in the clinical laboratory, you’re pretty darn busy. And people are calling, doctors are calling, everything is stat. And sometimes I think there’s not as much emphasis on safety as there should be in the clinical lab environment.

Like I said, even facility design. People don’t think about that stuff. So anyways, the kind of things that we need to stress the importance.

Lisa Wallace: This is Lisa Wallace. I had provided, of course, the Clinical Laboratory Preparedness and Response Guide. And some of the other biosafety guidance. The BMBL references.

One of the things that I found at the hospital was that very often I’d say, do you have a safety protocol where you’re coming and looking at the safety in the laboratory? And they say, oh, yeah. Infectious disease was just here. But infectious disease was looking at you not giving something to the people who were there at the hospital. Not keeping the people working in the laboratory safe.

So we need to kind of change the mindset of, it’s not just how do we not spread it to patients, but how do we keep the people who are doing the testing safe? When I was in the hospitals, what I found a lot was I’d ask, Okay, so do you use splash guards? Do you have splash guards? Well, we did. But they kind of got in the way. So they got shoved under cabinets, and we don’t even know where they are now.

So everything that was in place to try to protect them because they weren’t doing everything in a biosafety cabinet, they weren’t used to doing. And so they didn’t take the time to get used to it. They found it annoying and they just kind of pushed it to the side because it slowed them down.

Crystal Fortune: That’s a good point, Lisa. And thinking about, too– well, for one thing, working in a biosafety cabinet– as we know, it’s very hard on your body to not cover those grates and to keep your arms out straight and not move around too much.

But then when you talked about people negating stuff, if we make it too cumbersome for them as well, then they’re not going to use it either. They’re going to just say no. It’s too hard, or it’s too much stuff that they don’t know how to use. And that can actually end up getting them infected as well.

Marcia says, I’ve done a lot of one-on-one in the communication with labs struggling with exposure issues. Sponsored in person workshops that include lectures, biosafety drills, demos, and biosafety resources loading onto a flash drive, and that’s how I actually got a lot of my people some of the resources I shared with you today.

Carol says she gives the clinical labs the biosafety checklist and asks for someone to start– who are just starting their career, to go through it. It allows them to have hands-on and become familiar with the concepts.

And that’s a good point too. If you have someone who isn’t as familiar, they tend to look at things with a little bit more critical eye than the rest of us. The rest of us may say, oh, they’re not wearing their gloves right now, but that’s because, blah, blah, blah. They’re in between tasks, or you don’t actually have to wear gloves to look at a microplate. Which I personally disagree with. Or whatever. So people who have been in the lab for a long time like overlook stuff that newer people may look at more critically.

Oh, wow. And she purchased– oh, she bought the book. I thought you said you bought it for everybody. Marcia did. That’s a really good book too. The Biological Safety Principles and Practices. They just came out, I think, with the fourth edition of that within the last couple of years. Oh, she bought it for all of her staff. Very nice. Very nice. That’s a pretty expensive book, so that was very nice of you. With grant funding. Yeah. That would be necessary to purchase. I think it’s like $150, or something, new.

All right, well that’s all that I see right this second. So we can go into the case study now I think, if you guys are ready to do that.

So this is my introduction. We’ll have each of the questions, and then we’ll actually go into breakout rooms where we can discuss this a little bit further. I have on here DNA plugs. If you’ve done food testing before, I’m sorry, I explain this on a different slide. But basically they’re preparing the bacterial isolate to be able to type it out with DNA. So to do a fingerprint, a PFGE, where they actually can tell if the food bacteria is related to another to investigate an outbreak.

So a microbiologist is working a rotation in a lab that performs regulatory meat testing. Job duties in this section include making bacterial DNA plugs from enteric isolates received for DNA fingerprinting. What risks may be inherent in this type of work?

So with that, we’ll go into our breakout rooms. And that is George’s area of expertise.

Aufra Araujo: Crystal, thank you. I think this is very interesting case to discuss. How many minutes? And I just wanted to confirm with you for our operations purposes here. So how many minutes in the breakout room, and do you– so we go for this one question, and then come back in this room, right? Everybody?

Crystal Fortune: Yes.

Aufra Araujo: So how many minutes would you like the groups to stay in the breakout room for this question?

Crystal Fortune: I would say maybe four minutes.

Aufra Araujo: Four minutes. Okay. I also would like to suggest that when– shortly, we’ll be going in the breakout rooms, and I was going to suggest when I ask you, Crystal, what you think, in each room– each breakout room– one person is the designated speaker. So when we get back in this big room, we have one person from each group sharing their thoughts during the discussion. How does that sound?

Crystal Fortune: Right. So one person either on chat or open mic would probably be easier, I suppose, to give a summary of what their group talked about. And we’ll stress that again before we leave the breakout room.

Aufra Araujo: Yeah. And that’s nice as well, because this way people get to see each other and talk amongst themselves in the breakout room. Okay, so shortly we’ll be sent to these breakout rooms. You may see one of us in the room. We are there just listening. And if you need any technical assistance or anything– but the discussion is yours.

[No audio available for Breakout Room #1]

Crystal Fortune: Thank you. So in my room the sound quality wasn’t the best. I kind of asked Lisa, and if she’s not comfortable then I’ll present on our room. Lisa do you want to– how do you feel?

Lisa Wallace: I can tell you what I was saying. [Laughs]

Crystal Fortune: Okay.

Lisa Wallace: What I was talking about was whenever you’re working with any kind of food testing, you have to break that food down. So you’re doing some kind of emulsification. Of course, any time you’re adding energy into something, there’s the risk of creating aerosols. So that would be an inherent risk that you have within this testing that you’re going to have to take steps in order to contain the product that you’re trying to test so that you’re not creating aerosols outside of containment.

Crystal Fortune: Okay, thank you, Lisa. And I think Sonia had added to that– and Sonia, if I’m not representing properly, let me know– but she had added to that to say also because of the risk of splash, then we want to be careful with if we get stuff into our mouths or our eyes. So is there a– I don’t know how many groups there were. So I’ll let the next one present.

Michael Adjei: This is Michael here from DC public health labs. Our group, most of us within it have not done that DNA extraction routes before. But we all say that we look at the task, anything that is going to generate aerosols, and then potentially also present a puncturing of the skin, should be minimized to a minimum. So therefore those are the tasks that you want to contain. I hope I summarized it the way that we said it.

Crystal Fortune: Thank you, Michael. Does anyone else have anything to add? For any of the groups?

Marcia Pindling: Can everyone hear me?

Crystal Fortune: Marcia, are you trying to speak to the group?

Marcia Pindling: Yeah, can you hear me? I’m having audio issues. I apologize. Can you hear me?

Crystal Fortune: Barely. If you can project pretty loudly, I’ll translate for you.

Marcia Pindling: [Inaudible]

Crystal Fortune: Okay, I couldn’t hear everything that Marcia said. But she was talking about also the source. So basically when we have the meat testing– for regulatory meat testing for example, in Montana, we have beef. So people will send in– if they process, like, ground beef or beef sticks, anything like that, they have to have tested for USDA.

And then also, if we have a foodborne outbreak– like for example, we had the chicken at Costco. The chicken salad– I think that was caused by onions or celery or something– then we would want to test the different isolates that came in from different patients to see then– we would compare the electrophoresis to see if those isolates match up. So that’s how, then, foodborne illnesses are linked together.

So we’ll go ahead and move then to the next one. So a couple of days later, after this microbiologist was doing this work, he developed a fever and diarrhea, and he’s hospitalized overnight. So what information might the doctor need to know if he’s treating this microbiologist? So I would say maybe three minutes for the sake of time.

[No audio available for Breakout Room #2]

Aufra Araujo: So it looks like everyone is back. You want to take it over, Crystal? The room where I was very difficult to hear. I could not hear anybody. I’m not sure if they could hear me. I’m thinking, moving forward, it might be better to just continue the discussion in this big room, because at least in my room it was difficult to hear everybody. Sabrina has her hand raised.

Sabrina DeBose: Yes, I just wanted to share. The room that I was in, there was some comments placed in the chat, so I would like to read those for you. One, it says the doctor would need to know what was he working with? Meaning which pathogen. How long was the exposure in the lab? Does the person have any allergies to medication or antibiotics? Has he been in contact with others, and for how long? Over.

Michael Adjei: This is Michael here. We also had similar to what Sabrina said. Only that we did not discuss allergies. We had talked about occupation of the patient, what the patient does, and then the sample that the patient was working with. And then the potential route of infection. And if there are other past cases of exposure for the patient.

Crystal Fortune: Okay, my computer was doing something kind of funny during all of that discussion, so I have to find my slide back here again. And I agree, my group was also having a little bit of difficulty hearing. So thank you. And we’ll, probably for the sake of time, as well, it would be easier to just do it in a presentation. It’s not letting me advance my slide, so I’m not really sure what’s going on. But I’m just going to scootch this over here. Can you guys see that?

Oh, here we go.

Aufra Araujo: Not yet, Crystal.

Crystal Fortune: Can you see my case study investigation slide?

Aufra Araujo: No, we cannot. We’ll share on our end.

Crystal Fortune: Okay.

Aufra Araujo: It might be easier. Is this the slide? The one you want, Crystal.

Crystal Fortune: Yes, ma’am. Yes.

Aufra Araujo: Okay.

Crystal Fortune: So in the case of this microbiologist, when he had a stool culture done, it revealed that he had a co-infection with Salmonella and Campylobacter. Working in the food laboratory can result in exposure to either of these pathogens. When the microbiologist returns to work, the lab safety officer conducts an investigation to determine if this was a lab associated infection. And what– if you want to throw anything in the chat– what would you want to know if you were conducting this investigation? Or if you want to open your mic.

Michael Adjei: This is Michael here. First I would want to know whether the staff was wearing the right PPE and whether they were working under the hood.

Crystal Fortune: Okay. Anybody else?

Audience: Were they following all the procedure protocols, using the PPE properly? Did you have any close calls or exposures that they didn’t report?

Crystal Fortune: Okay. Oh, somebody says, what were the results of the extraction? Did either of these pathogens appear, or were they tested for? And that is key then to the next slide, George, if you want to take a look at that.

So he had been working with an isolate from a patient with Campylobacter jejuni, and we kind of already talked about the route of infection. So we won’t go into that too much. And to the next slide, George.

So the Salmonella, interestingly enough, was not a match to anything that the microbiologist had been recently working with. I think they said that there was a culture in a patient, but it was not accessed during this time. So it’s possible then that this person– and I told my group– this person was actually immunocompromised too. So just to kind of complicate things in this investigation. But the [C.] jejuni was actually something that they were working with.

And then the next slide. And these were kind of the exposures that happened when the person was doing their work. So it’s possible then he touched the gloves, touch something else in the garbage can, may not have washed his hands. So again, this is a hand-to-mouth infection. So there’s no telling then what could have led to this exposure.

And then you can go to the next slide. And any other discussion or comments either about that case or anything else? I think we timed this out nicely, and I believe Sonia was going to summarize. Any last minute comments? Okay, well that concludes my portion of today’s presentation. And thank you, guys.

Aufra Araujo: I’m sorry I was muted. Having trouble with the buttons here. Thank you so much for your presentation, Crystal. And discussion. It was productive, except for the difficulties in the room. But we are learning with this technology, and in the end, all worked out because we were able to come back in the room and discuss all together.

So that was good. Now my colleague, commander Sabrina DeBose, she’s the safety team lead in CDC’s Division of Laboratory Systems. She will summarize the discussion for us. Sabrina?

Sabrina DeBose: All right. Thank you, Aufra. Thank you, Crystal. And we want to thank you all for participating and giving us a robust discussion regarding risk assessment in clinical laboratories.

So I will provide a summary of today’s discussion. We did have one participant expressed concern for the difficulty of getting compliance where they’re processing the organisms in the laboratory. Someone also shared that they create a safety survey– that they’ve created a safety survey to create a safe space for laboratorians to express concerns related to any safety and security when working in the laboratory.

Someone also expressed that it’s important to change the mindset from spreading infection just to patients, but also keeping the workers safe as well. Someone expressed concern, or shared their experiences, of having a one-on-one conversation, conducting workshops, and trainings, to express and show how important safety and security in your laboratories are.

One of the other viewpoints that was shared with us is that when you have a new laboratory and it’s someone new in the field, you want to give them that opportunity of walking through the lab with fresh eyes so they can give you a different– so they can evaluate the situation from a different set of lenses. And it’s also important to provide resources and reference in the lab for everyone to have access to.

Once again, we want to thank you all for your discussion. And we are looking forward to continuing in these ECHO sessions with you all. Thank you very much. Back to you, Aufra.

Aufra Araujo: All right. Thank you all for taking part in our discussion today. We hope you find it valuable in the important work that you engage with, and in your individual laboratories. We look forward to your participation in future sessions as we dive into specific laboratory biosafety topics.

Soon you will receive an email message containing a post session survey link. It will take about two minutes to complete. If you have additional comments, please send an email to DLSbiosafety@cdc.gov. Please do complete the post session survey. Your response will help us understand your needs and improve these sessions. I now want to share the slides here. All right.

We are excited to have our next session in March. It will be on Wednesday, March 22nd at 12:00 p.m. Please note, our sessions are usually on Tuesdays. The last Tuesday of each month. But exceptionally next month, the session will be on Wednesday, March 22nd. Mark your calendars.

Also at this point, I want to remind you, you should have received the registration survey. If you complete the registration survey, you’ll receive calendar invites for all ECHO sessions throughout the year each month. If you have not received the registration survey, we will see your email address from today’s session, and we will send you an individual link so you can complete that registration survey and receive the calendar invites.

The topic for the March session will be safely implementing new diagnostic platforms commonly used in clinical laboratories, which will be presented by Dr. Christina Egan and Michael Perry from the New York [State] Department of Health.

Please visit the DLS ECHO Biosafety web page to view all upcoming sessions. George will put the link to the ECHO Biosafety web page in chat.

Again, if you have any questions, you can reach out to us at DLSbiosafety@cdc.gov.

Thank you so much, Crystal. It was a pleasure to meet you and work with you during the planning for this session. And thank you, everyone, for participating. Now we’ll adjourn. Thank you, and have a great day.

Additional Resources and Related Publications

  1. Association of Public Health Laboratories. Template for Public Health Laboratory Risk Assessment for Ebola Virus Disease (EVD) Testing.
  2. Public Health Agency of Canada. (2023, March 9). Pathogen Safety Data Sheets.
  3. Centers for Disease Control and Prevention. (2020, November 17). Biosafety in Microbiological and Biomedical Laboratories (BMBL) 6th Edition.
  4. Centers for Disease Control and Prevention. Guidelines for Safe Work Practices in Human and Animal Medical Diagnostic Laboratories. MMWR. 2012 Jan 6; 61(Suppl).
  5. Centers for Disease Control and Prevention. Guidelines for Biosafety Laboratory Competency. MMWR. 2011 Apr 15; 60(Suppl).
  6. Centers for Disease Control and Prevention. Competency Guidelines for Public Health Laboratory Professionals. MMWR. 2015 May 15; 64(Suppl).
  7. Association of Public Health Laboratories. (2015, April) A Biosafety Checklist: Developing A Culture of Biosafety.
  8. Association of Public Health Laboratories. Clinical Laboratory Biosafety Risk Management Program Assessment Checklist.
  9. Occupational Safety and Health Administration. (2022, April). Hospital Respiratory Protection Program Toolkit.
  10. Association of Public Health Laboratories. Clinical Laboratory Preparedness and Response Guide.