Lab Culture Ep. 17: Exploring bioinformatics: From fellow to full time in Virginia

Lab Culture Ep. 17: Exploring bioinformatics: From fellow to full time in Virginia | www.APHLblog.org

Kevin Libuit went from the APHL-CDC Bioinformatics Fellowship to a contractor to working full-time as a bioinformatician at the Virginia state lab (VA Division of Consolidated Laboratory Services (DCLS)). First he talks about when he discovered bioinformatics as a field and how the fellowship propelled his career. Then Kevin takes the mic and interviews Dr. Denise Toney, director of Virginia DCLS, about the value and growing need for bioinformaticians in public health labs.

 

 

Kevin G. Libuit, M.S.
Bioinformatics Lead Scientist, Division of Consolidated Laboratory Services (DCLS), Virginia Department of General Services

Denise Toney, PhD
Director, Division of Consolidated Laboratory Services (DCLS), Virginia Department of General Services

Links:

APHL-CDC Fellowships

APHL-CDC Bioinformatics Fellowships

Virginia Division of Consolidated Laboratory Services (DCLS)

APHL Off the Bench (new Facebook group!)

 

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Lab Culture Ep. 12: Bitten by the public health bug — How I found my lab niche

Lab Culture Ep. 12: Bitten by the public health bug -- How I found my lab niche | www.APHLblog.org

The people who work in public health laboratories make a difference in your community daily. In this third episode, members of the Emerging Leader Program cohort 10 sit down with their peers to hear how their public health laboratory careers have made an impact.

You can listen to our show via the player embedded below or on iTunes, Stitcher or wherever you get your podcasts. Please be sure to subscribe to Lab Culture so you never miss an episode.

ELP cohort 10 members featured in this episode:

Interviewees:

  • Degina Booker has been working in the public health lab for 40 years and is now the administrative services director for the Mississippi Public Health Lab.
  • Dr. Burton Wilcke, Jr., now retired, has worked in public health laboratories for over 35 years in Vermont, Michigan and California. Dr. Wilcke remains active in the public health laboratory community as a member of both the APHL Workforce Development Committee  and the Global Health Committee.
  • Dr. Musau WaKabongo, now retired, was the Public Health Laboratory Director at the Placer County Public Health Laboratory  and has worked in several public health laboratories in California for 13 years.
  • Dr. Maria Ishida has been working in public health for 11 years and is now the director of the New York State Food Laboratory.

Are you thinking about a career in a public health laboratory?

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Lab Culture Ep. 11: What if there were no public health labs?

Lab Culture Ep. 11: What if there were no public health labs? | www.APHLblog.org

Maybe the saying is true: you don’t know what you had until it is gone. For the families in this episode, the absence of public health laboratories turned their worlds upside down and negatively impacted both the present and future. These families represent us all and highlight the vulnerabilities that would exist if there were no public health laboratories working continuously to keep our communities and populations safe.

This is the second episode in the series produced by members of the Emerging Leader Program cohort 10.

You can listen to our show via the player embedded below or on iTunes, Stitcher or wherever you get your podcasts. Please be sure to subscribe to Lab Culture so you never miss an episode.

Lab Culture Ep. 11: What if there were no public health labs? | www.APHLblog.orgEmerging Infectious Disease Response:

APHL’s Infectious Disease Program

Laboratory Response Network (LRN)

Interviewer: Kate Wainwright, PhD, D(ABMM), HCLD (ABB), MPH, MSN, RN, deputy director, Public Health Protection and Laboratory Services, Indiana State Department of Health

Expert: Peter Shult, PhD, director, Communicable Disease Division; associate director, Wisconsin State Laboratory of Hygiene, School of Medicine and Public Health, University of Wisconsin-Madison

 

Lab Culture Ep. 11: What if there were no public health labs? | www.APHLblog.orgNewborn Screening:

APHL’s Newborn Screening Program

NewSTEPs

Baby’s First Test

Interviewer: Josh Rowland, MBA, MT(ASCP), manager, Training and Workforce Development, Association of Public Health Laboratories

Expert: Miriam Schachter, PhD, research scientist 3, New Jersey Department of Health, Newborn Screening Laboratory

 

Lab Culture Ep. 11: What if there were no public health labs? | www.APHLblog.orgFoodborne Illness:

APHL’s Food Safety Program

5 Things You Didn’t Know (but Need to Know) About Listeria

Interviewer: Samir Patel, PhD, FCCM, (D)ABMM, clinical microbiologist, Public Health Ontario; Toronto, Canada

Expert: Vanessa Allen, MD, MPH, medical microbiologist, chief of microbiology, Public Health Ontario; Toronto, Canada

 

Narrator:  Erin Bowles, B.S., MT(ASCP), Wisconsin Clinical Laboratory Network coordinator and co-biosafety officer, Communicable Disease Division, Wisconsin State Laboratory of Hygiene, School of Medicine and Public Health, University of Wisconsin-Madison

Contributor: Emily Travanty, PhD, scientific director, Laboratory Services Division, Colorado Department of Public Health and Environment

Special thanks to Jim Hermanson at the Wisconsin State Laboratory of Hygiene for his help in recording this episode.

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How my fellowship and an interest in oysters took me to France

How my fellowship and an interest in oysters took me to France | www.APHLblog.org

By Chelsea Carman

When I applied to APHL’s Infectious Diseases Laboratory Fellowship in 2017, I had no idea I’d find myself spending three weeks in Nantes, France, with a leading expert in norovirus detection in oysters. While I love to travel, and France had been on my list of places to explore, I never anticipated that I would have this opportunity during my fellowship or that the opportunity would be made possible through the network of researchers connected through it.

I began my year-long fellowship at the Massachusetts Department of Public Health State Laboratory last summer. Less than a year before, the state faced a norovirus outbreak linked to consumption of raw oysters from Wellfleet, MA. Oysters are filter feeders, so whatever is in their surrounding environment will filter through their body and possibly bioaccumulate, (i.e., accumulate in the oyster rather than being excreted). When people eat the oysters raw, they can be exposed to a potentially infectious dose of the virus.

The state public health lab did not have a protocol to test oysters for norovirus, so I was tasked with this project. I was invited to visit the Shellfish Purification Plant in Newburyport, MA, which is the oldest depuration facility in the world and the largest in the US. I thought this hour and a half trip to the tip of Plum Island on the north shore of Massachusetts would be the furthest I would travel during this fellowship, and was happy to enjoy this fascinating field trip.

As part of my research, I began contacting experts in similar fields. Upon connecting with an international expert in norovirus detection in oysters, I was invited to visit and train at IFREMER, a French research and national reference lab. I was thrilled to accept!

A few months later I was in Nantes, France, a beautiful and green city on the Loire River, approximately 30 miles inland from the western Atlantic coast. There I spent three weeks learning the ISO method for detection of norovirus in oysters along with another visiting researcher from Morocco. I also learned about other research projects at the lab, and its responsibilities as a national reference lab.

On my second day there, the public transportation workers went on strike, so I joined some of the lab scientists and walked to work through the morning mist on a forest trail. I happened to mention that it was my birthday that day, and soon one of the students had organized a group dinner to celebrate. I gained a strong sense of inclusiveness from the group and had a truly memorable experience. It was wonderful to be able to ask as many questions as I wanted about their work (sometimes with the aid of Google translate because my French was quite limited), which was enormously helpful for my own project.

From my time training in the IFREMER lab, I learned the nuances of dissecting out the digestive tissue of an oyster, as well as two different homogenization and ribonucleic acid (RNA) extraction techniques. It was an opportunity to work with people that routinely work with both oysters and norovirus. While I could have read and interpreted the protocols from Massachusetts, it was extremely helpful to observe the intricate steps and ask the experts questions to fully understand the protocol. I’m now back in Massachusetts and have implemented much of what I learned into my project.

Once I returned and shared my experience with friends and family, they had one question for me: Do I still eat oysters? I did eat oysters but then I started finding live pea crabs inside them. Pea crabs are a parasite in the oyster and I felt they represented a large physical manifestation of all the other potential parasites, bacteria or viruses that can reside in oysters. That was enough to make me avoid them, at least for a while. I might begin eating them again after I complete this project; I’m still young and have a relatively good immune system to protect me from whatever might be lurking in an oyster!

 

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Lab Culture Ep. 10: Public health labs do that?!

Lab Culture Ep. 10: Public health labs do that?! | www.APHLblog.org

Public health laboratories do a great deal of work that impacts the daily lives of everyone in America. Do you know exactly how much they’re doing? The first episode produced by members of the Emerging Leader Program cohort 10 looks at some of the work performed by public health lab scientists.

You can listen to our show via the player embedded below or on iTunes, Stitcher or wherever you get your podcasts. Please be sure to subscribe to Lab Culture so you never miss an episode.

Links

(*indicates ELP cohort 10 member)

Water Quality Testing

Interviewer: *Amanda Hughes, program manager of ambient air quality monitoring, State Hygienic Lab at the University of Iowa

Experts:
Michael Schueller, assistant director of operations, State Hygienic Lab at the University of Iowa
Nancy Hall, program manager, Environmental Microbiology, State Hygienic Lab at the University of Iowa

Water quality testing at the State Hygienic Lab at the University of Iowa

Alcohol Testing

Interviewer: *Gitika Panicker, microbiologist, Centers for Disease Control and Prevention

Expert: Laura Bailey, director, Office of Alcohol Testing, Arkansas State Public Health Laboratory

Alcohol testing at the Arkansas State Public Health Laboratory

 

Influenza Testing

Interviewer: *Shondra Johnson, laboratory information management system administrator, Missouri State Public Health Laboratory

Expert: Jessica Bauer, molecular unit manager, Missouri State Public Health Laboratory

Seasonal influenza testing at the Missouri State Public Health Laboratory

 

Bioterrorism

Interviewer: Avi Singh, food lab lead microbiologist, Washington State Public Health Laboratory

Expert: *Denny Russell, bioterrorism coordinator, Washington State Public Health Laboratory

 

Foodborne Outbreak Linked to Flour

Interviewer: *Rebecca Lindsey, Whole Genome Sequence Project lead, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC)

Experts:

Heather A. Carleton, bioinformatics team lead, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC)
Samuel J. Crowe, National Outbreak Reporting System team lead, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC)

E. coli outbreak linked to flour (CDC)

Shiga Toxin–Producing E. coli Infections Associated with Flour

 

 

 

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Lab Culture Ep. 9: What is the APHL Emerging Leader Program?

Lab Culture Ep. 9: What is the APHL Emerging Leader Program? | www.APHLblog.org

What is the Emerging Leader Program (ELP)? APHL staff, Pandora Ray and Kajari Shah, share how the ELP got its start and how it has progressed. This year’s ELP cohort is producing three episodes for Lab Culture that will be released over the coming weeks. Stay tuned!

APHL Emerging Leader Program

(Cohort 9 is pictured above. Pan and Kajari are kneeling in the center.)

You can listen to our show via the player embedded below or on iTunes, Stitcher or wherever you get your podcasts. Please be sure to subscribe to Lab Culture so you never miss an episode.

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Do you have questions about packaging and shipping regulations that are not easily answered?  

Do you have questions about packaging and shipping regulations that are not easily answered? | www.APHLblog.org

By Patricia Payne, president, JBM Associates, Inc.; consultant, APHL

In some circumstances, when a question arises about classification, hazardous material (hazmat) compliance or how to package a specimen, time is of the essence. You need answers quickly to facilitate getting a response on a test result for patient diagnosis or treatment. Fortunately, there are several options for receiving help fast.

It is often possible to get answers to specific questions on-demand by contacting the regulatory agency involved in hazmat transportation compliance. Questions regarding transport of infectious substances by motor vehicle and air transport can be directed to one of the agencies below:

  • Department of Transportation (DOT) issues federal regulations for motor vehicle, air and water transport of any hazardous material in the Hazardous Materials Regulations (HMR, 49 CFR Parts 100-185). Those regulations are freely accessible at the US Government Publishing Office website. For immediate answers to questions regarding hazmat packaging instructions, rulemakings or how to use the HMR, contact the Hazardous Materials Information Center Monday through Friday from 9:00 AM to 5:00 PM (EST) at 1-800-HMR-4922 (1-800-467-4922) or 202-366-4488 for Washington, DC residents.
  • International Air Transport Association (IATA) issues airline carrier regulations in the Dangerous Goods Regulations (DGR), which is required to be followed by all IATA member airlines. The DGR is available in print and electronically. Both are copyright materials that can be purchased online from the IATA website. Questions regarding the IATA regulations can be asked by calling +1 (514) 390-6770 or email at dangood@iata.org.

In my experience, the DOT information center is very responsive to questions. It is rare to wait to speak with a DOT employee or receive an answer. The IATA phone number is answered by IATA staff in Montreal, Canada who most often take your question and pass it on to the appropriate staff in a different location. I have found that IATA responds faster to questions sent by email than by phone. I usually receive a response within 1-2 days, sometimes within a few hours, after sending an email to IATA. The silver lining of the longer wait for an IATA vs DOT response is that the question and answer are in writing, which can be filed for future reference and to share with others.

The cargo agencies used to transport our samples, including FedEx and UPS, also have hazmat hotlines.  Their hotlines are staffed seven days a week and nearly 24 hours a day. Hotline employees provide answers to questions related to packaging, documentation and transport. Contact the FedEx Dangerous Goods/Hazardous Materials Hotline at 1-800-463-3339 and then press 81. The UPS Hazardous Materials Support Center can be reached at 1-800-554-9964.

None of the agencies mentioned above will provide advice on questions concerning classification. For assistance with classification, it is best to contact the reference laboratory that will be testing your specimen or identifying microorganisms. All state public health departments have staff who are trained to help you classify. For many pathogens, including new and emerging pathogens, check the CDC website. By placing the microorganism name in the upper right search box, you will be directed to a page with links to information related to laboratory and medical personnel. Those links often, but not always, provide the classification of a specific microorganism.

In addition, APHL accepts questions regarding classification, packaging, documentation and transport of infectious substances at seminar@aphl.org. Last but not least, this blog has a comment section that can be used to post questions. The advantage of posting a comment to the blog is that multiple people who may have the same comment can view the answer, make additional comments and share their experiences. This not only provides a forum for sharing packaging questions but also helps to facilitate uniform regulatory compliance.

 

The post Do you have questions about packaging and shipping regulations that are not easily answered?   appeared first on APHL Lab Blog.

When and why is it legal to not follow the DOT packaging instructions? 

When and why is it legal to not follow the DOT packaging instructions? | www.APHLblog.org

By Patricia Payne, president, JBM Associates, Inc.; consultant, APHL

If you have completed any packaging and shipping training, you are undoubtedly aware that you must always follow the packaging instructions as written in the hazardous materials transportation regulations. However, sometimes it may be as safe, less costly or more efficient to do it another way. In some instances, it may be impossible to follow the current regulations.

If you have ever encountered any of those situations, a legal alternative is available in the form of a special permit. A special permit is a document that permits a person to perform a function that is not otherwise allowed under the Hazardous Materials Regulations (HMR). A special permit sets forth alternative requirements, or variances, to the requirements of the HMR. The Pipeline and Hazardous Materials Safety Administration (PHMSA) is authorized to issue such variances if the proposed method achieves a safety level that is at least equal to that required under federal hazmat law or is in the public interest if a required safety level does not exist.

In the past, special permits have been issued to clinical and research laboratories and medical facilities for a variety of reasons. Two of the reasons were:

  1. To allow transport of a Category A infectious substance in non-Class 6.2 packaging, and
  2. To conduct exercises with mock specimens to test preparedness for chemical exposure due to a terrorist event.

Clinical and research labs maintain stocks of infectious substances for a variety of reasons, including quality control, method validation and training purposes. Permits have been requested and issued for the motor vehicle transport of stocks of Biological Substances Category B from one location to another in the freezers in which they were stored instead of packaging separately, according to the HMR. This saved both time and money in transporting those cultures to a new facility.

When the first patients with Ebola were being treated in the US, it became apparent that packaging did not exist to hold the quantities of Category A infectious substances being generated from the biological waste produced by patient treatment. The biological waste generated from treatment of patients with most infectious agents is classified as Regulated Medical Waste. However, the waste generated from an Ebola patient is classified as an Infectious Substance Affecting Humans and must be packed in Class 6.2 UN specification packaging. Because packaging did not exist to hold the quantities being generated, a special permit was issued to package that waste in a manner not otherwise allowed by the HMR.

For preparedness purposes, public health agencies often develop exercises or drills to prepare for shipping infectious agents in the event of a public health threat or outbreak. Because the drills evaluate the participants’ ability to correctly package an infectious agent being sent to a reference lab without delay but are not evaluating the actual testing of those agents, infectious agents are not required to be placed in the package during these exercises. However, the HMR prohibits offering a package marked as containing hazardous materials if it does not contain a known or suspected hazardous material. In the past, special permits have been issued to allow chemical terrorism exercises to test preparedness for shipping samples for Rapid Toxic Screens using mock Category B infectious substances. Currently, a special permit request is in preparation for drills testing preparedness for correctly packaging a Category A infectious substance, such as Ebola. For obvious reasons, the permit will request that mock non-infectious agents be substituted for the purposes of the drill.

It is important to note that special permits must be requested in writing at least 120 days in advance and that you must wait for approval before packaging in a non-compliant manner. Permits are generally issued for the use of one agency. However, other agencies can request to use the same permit and be granted party status to use it.

The PHMSA website provides information on the process for requesting a special permit, a searchable database of previously issued permits and contact information for support.

Learn more about APHL trainings.

 

This post wasn’t written by an APHL staff member and the views expressed in the post are those of the guest author and do not necessarily reflect the views or opinions of APHL. If the post contains an evaluation or opinion about a product or service, this represents the guest blogger’s personal belief and does not represent APHL’s endorsement or critique.

 

Lab sciences grad program brought me from the yogurt factory to public health

by Joe Shea, MS, research assistant, Wadsworth Center, New York State Department of Health

My career as a laboratory scientist started in a yogurt factory. Yes, you read that correctly. And no, it was definitely not your typical lab experience. Instead of putting on a lab coat each day, I would change from my street clothes into freshly cleaned white pants, a button-down shirt, steel-toe boots and a hairnet. I’d begin my day walking through large rooms crowded with industrial steel pipes carrying yogurt in every direction, a site I initially found intimidating. I spent my time measuring the pH, fat content, protein content and bacterial contamination of milk, heavy cream and yogurt. The skills I gained as an undergraduate biology student at Siena College were being applied to quality assurance and ensuring that our products were safe for human consumption.

It was a great job, but I had the urge to move into something I would find more meaningful.

Lab sciences grad program brought me from the yogurt factory to public health | www.APHLblog.orgDuring a visit to my alma mater, I heard about a seminar for students who were interested in public health graduate programs. On a whim I decided to go. At the seminar I learned about the Wadsworth Center’s (New York’s state public health laboratory) Master of Science in Laboratory Sciences (MLS) program, which at the time was only in its first year of existence. The MLS program combines coursework and laboratory rotations in fields ranging from biomonitoring, clinical chemistry and genetics to infectious disease and immunology, while also providing courses in laboratory management. Shortly after, I completed my application and was accepted into the MLS class of 2015 – the second class in the history of the program.

The highlight of the program was my capstone project, an eight-month project in the lab of my choosing. I chose to rotate through the Mycobacteriology Laboratory, and became fascinated with the amount of testing it takes to diagnose and confirm cases of tuberculosis (TB), and to perform drug susceptibility testing on each of those confirmed samples. I decided to focus on utilizing whole genome sequencing (WGS) to identify Mycobacterium tuberculosis, the causative agent of TB, and detect mutations associated with drug resistance in clinical isolates.

Drug resistant strains of TB represent a global health concern, as there are fewer treatment options and a higher likelihood of poor outcomes. Conventional drug susceptibility testing can take eight weeks or longer in some cases, which means that patients may receive ineffective treatment until these results are available. Currently, several different tests are needed to assess drug resistance; WGS, however, could be used to detect these potential mutations while also identifying the M. tuberculosis species and strain type. WGS would take far less time and provide more useful and detailed information than current methods and could decrease the time it takes for tuberculosis patients to receive appropriate treatments.

Having the opportunity to work alongside public health laboratory scientists at the New York State Department of Health’s Wadsworth Center was an invaluable experience. I believe in the importance of this work, and I loved having the chance to contribute to the groundbreaking work being done at the Wadsworth Center.

Lab sciences grad program brought me from the yogurt factory to public health | www.APHLblog.org

I recently graduated from the MLS program and am continuing to work in the Mycobacteriology Laboratory. I’ll be focusing on using WGS to identify and detect TB in clinical specimens (rather than pure isolates) which is challenging due to the presence of other sources of DNA in the sample. This position will also enable me to contribute to other ongoing projects in the lab using WGS, including the study of other pathogenic bacteria such as Legionella pneumophila.

Sometimes I think about that last-minute decision to attend the seminar at Siena College where I learned about this great program; it changed the course of my career by exposing me to a whole world of laboratory science that I had never considered.

Moving from academia to public health: Did I make the right choice?

By Lixia Liu, PhD, MP (ASCP), D(ABMM), deputy director, Indiana Department of Health Laboratories

Lixia Liu is a member of APHL’s Emerging Leaders Program (Cohort 6). The group developed an educational website called That’s Sick! to introduce students and young scientists to the exciting world of public health laboratory careers.
________

In 1996 I completed my PhD in molecular biology and bacterial genetics, and later received postdoctoral training on bacterial pathogenesis. Among my peers, becoming a professor in an academic institution was the ultimate career goal; non-academic professions were considered to be less competitive. While I knew that this was the perception, I never gave it much thought as I later transitioned from academia to public health… That is, until I ran into an old acquaintance at the American Society of Microbiology (ASM) annual meeting.

She was a fellow student who worked at the same lab where I did my postdoctoral training. By that time, I had been away from academia and working in a public health laboratory for three years. We met up later that day to update each other on our recent endeavors. During our conversation, she paused for a moment and then asked with a sympathetic look on her face, “You are now working in a public health laboratory, not staying in academia?”

In the following days, I couldn’t erase that look from my mind. I began to question my decision and wondered if I made the wrong move in choosing public health laboratory science as my career. I began to think back about how I first stepped onto this career path.

After my postdoctoral training, I continued basic research in a new academic lab conducting a study on virulence-related genetic markers. I was also involved in method development for molecular diagnosis and a molecular epidemiological study of infections of cystic fibrosis (CF) patients. During this study, we found bacterial strains from two CF patients – one from the East coast and another from the West coast – with the same genetic fingerprints, which linked these two CF centers together. The transmission from one patient to the other occurred when one patient visited a camp attended by the other. Seeing how this bacterial strain moved and infected these patients caught my attention. This discovery was my first true exposure to the field of public health. I was intrigued.

Three years later, my husband was relocated for work so we moved from Michigan to Indiana. With my newfound interest in mind, I extended my job search to include public health. I came across a listing for a job that included molecular method development and molecular finger printing; it was a contractor position at the Indiana State Department of Health Laboratories. I pursued the opportunity and started my trial-run at the public health laboratory.

Although the method development and molecular epidemiological study of CF patients in the previous lab bridged the gap between academia and public health for me, the culture shock was still intense.

While academic research dives down deep to understand the fundamentals of a basic scientific mechanism (a vertical look at science), public health spans across disciplines to look for wide-reaching answers to real-life questions (a horizontal look at science).

In the public health lab, we seek answers to questions like: How severe is the flu season? Is a particular food product the cause of an outbreak or is it still safe for consumers? Is the drinking water safe to drink? To me, the most striking aspect of a public health laboratory is the impact generated by the test results. In clinical care, an individual patient’s sample may reveal the cause of their illness, their infection status or the reason that treatment has failed. In public health, aggregated results from multiple patients can reveal a trend, the health status of an entire community, a common link among infections or even the cause of an outbreak.

This trial-run introduced me to the field of public health laboratory science where I have stayed for 11 years because it is so fulfilling. I am now the deputy director of the Indiana State Department of Health Laboratories. One of my proudest moments was being a part of the team that detected MERS-CoV in Indiana, the first case in the US. While every situation isn’t as newsworthy, everything we do promotes public health and that is why I am glad to be here.

So while that question, “You are now working in a public health laboratory, not staying in academia?,” has come up again with friends, particularly among my former PhD classmates and postdocs, it doesn’t bother me anymore. If asked to choose again, I would still pursue this career path. I am proud of my choice and would encourage other scientists to consider this rewarding field.