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 |

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


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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New Lab Matters: Time to welcome the next generation of public health laboratory scientists

New Lab Matters: Time to welcome the next generation of public health laboratory scientists |

The Bureau of Labor Statistics estimates that 12,000 new laboratory professionals are needed each year to meet consumer demand. At the same time, while automation has eliminated some less-skilled laboratory jobs, the growing sophistication of public health laboratory analyses has generated demand for scientists with highly specialized training. As our feature article shows, laboratories are recruiting new talent for the “hidden profession” by taking a hard look into what they really want, and how they want to work.

Here are just a few of this issue’s highlights:

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Stopping Listeria required an arsenal of tools and an army of experts

Stopping Listeria requires an arsenal of tools and an army of experts |

By several contributors from Maryland Department of Health and Mental Hygiene (DHMH), Division of Outbreak Investigation; State of Maryland Rapid Response Team (SMarRRT); Maryland Public Health Laboratory; Virginia Rapid Response Team; Virginia Department of Agriculture and Consumer Services (VDACS); and the Virginia Department of General Services Division of Consolidated Laboratory Services

While Listeria monocytogenes is not one of the most frequently occurring foodborne pathogens in the US, it is the third most deadly. Listeriosis, the infection caused by Listeria monocytogenes, primarily affects pregnant women and their newborns, adults over 65 and those with compromised immune systems – 90% of those who develop a severe Listeria infection fall into one of those groups. The severity of illnesses has focused US public health agency’s efforts to seek new and improved ways to identify outbreaks of Listeria and prevent additional illnesses.

In August 2014, the Maryland Department of Health and Mental Hygiene (DHMH) identified five cases of invasive listeriosis in Maryland residents from the same county. Of these five cases, four were related to a pregnancy (two mother-newborn pairs). The other illness was in a newborn. Data uploaded to the PulseNet database showed that the bacteria causing the illnesses were indistinguishable by pulsed-field gel electrophoresis (PFGE), indicating they could be caused by the same source. Because CDC implemented whole genome sequencing (WGS) for real-time Listeria surveillance in 2013, these isolates were also sequenced.
In keeping with the Listeria Initiative, a CDC program to aid in the investigation of listeriosis clusters and outbreaks by decreasing the time from outbreak detection to public health intervention, state epidemiologists promptly began conducting patient interviews. They used the standard case questionnaire, a valuable tool included as part of the Listeria Initiative, to gather detailed information about each case. Interviews showed some commonalities in the cases; notably, everyone was Hispanic. Hispanic women are 24 times more likely to get listeriosis than others. The questionnaire also included a checklist of foods that are frequent sources of Listeria, including a section on soft cheese, and more specifically, a section on Latin-style cheeses. Soft cheeses are a common source of Listeria, and pregnant women are advised not to consume them. This includes cheeses such as queso fresco, queso blanco and queso cotija, which are commonly used in Latin American cooking.

Stopping Listeria requires an arsenal of tools and an army of experts | www.APHLblog.orgOf the five initial cases, one patient reported consuming Latin-style soft cheese from an unlicensed vendor cart outside of a local Latin grocery store. However, cheese subsequently collected from the vendor was negative for Listeria.

Between October and December 2014, three additional cases were linked to the earlier cluster by PFGE in the PulseNet database. This prompted renewed concern that a product available by retail was contaminated and being broadly distributed. These patients were also all Hispanic. Two lived in the same Maryland county as the patients in the earlier cluster, one lived in California.

Intensive follow-up interviews in Spanish established that all five Maryland adults shopped at a common Latin grocery store chain in Maryland and Virginia, and consumed soft cheeses purchased there prior to illness. The patient from California died before an exposure history could be obtained.

The link between soft cheeses and a common grocery store chain prompted the Maryland Rapid Response Team to notify the Virginia Rapid Response Team of a potential food emergency. Established through a Food and Drug Administration (FDA) partnership, Rapid Response Teams (RRTs) are multi-agency, multi-disciplinary teams established to respond to food emergencies such as product tracebacks or recalls. Working together through the RRTs, the Virginia Department of Agriculture and Consumer Services and Maryland DHMH, in coordination with local health departments, collected retail samples of Latin-style soft cheeses from multiple retail chain locations.

Samples promptly tested by Virginia’s Division of Consolidated Laboratory Services (DCLS) were determined to be positive for Listeria. PFGE analysis confirmed the recovered isolates matched the outbreak strain, and WGS analysis further confirmed the relatedness of the pathogens recovered from both cheese and specimens from listeriosis cases. It was also revealed that the cheeses were from a single Delaware-based manufacturer, but had been repackaged by the retailer. This led to additional testing by Virginia DCLS and Maryland DHMH lab scientists who found the outbreak strain in cheese packaged by the original manufacturer. As a result of the identification of the outbreak strain in retail samples, the states of Maryland and Virginia issued consumer warnings for consumption of these products. FDA, in coordination with the Delaware Department of Public Health, investigated the manufacturer. Samples taken by FDA also found the outbreak strain (matched by PFGE and WGS at FDA) on multiple surfaces within the manufacturer’s facility which prompted a voluntary recall by the manufacturer.

While these findings supported previous PFGE results which linked this outbreak to the contaminated soft cheese, WGS was extremely valuable in confirming the inclusion of the California case.

Thanks to strong partnerships between state public health laboratory scientists, food safety officials and epidemiologists, this outbreak response effort was quick and successful. Each discipline contributed critical information during the investigation which allowed for timely resolution of the outbreak and the recall of contaminated products.

 This year we celebrate the 20th anniversary of PulseNet USA. Stories from highlighting PulseNet successes will be featured each month. Learn more about PulseNet from APHL and CDC.


Virginia: PFGE and whole genome sequencing show Salmonella outbreak who’s boss

Virginia: PFGE and whole genome sequencing show Salmonella outbreak who’s boss |
This year we celebrate the 20th anniversary of PulseNet USA. Stories from highlighting PulseNet successes will be featured each month. Learn more about PulseNet from APHL and CDC.

By Marshall P. Vogt, MPH, district epidemiologist, VDH; Krisandra J. Allen, MPH, foodborne and waterborne disease epidemiology specialist, VDH; Jessica Watson Rosner, MPH, foodborne disease epidemiologist, VDH; Angela Myrick-West, MPH, regional epidemiologist, VDH; Lauren Turner, PhD, foodborne and advanced pathogen characterization lead scientist, DCLS

In August 2015, public health laboratory scientists at the Virginia Division of Consolidated Laboratory Services (DCLS) notified foodborne disease epidemiologists at the Virginia Department of Health (VDH) that they were sending data on four Salmonella Enteritidis isolates from a single rural county in central Virginia. They all had matching PFGE patterns. During case review, the epidemiologists identified four additional cases of salmonellosis from the same central Virginia county, but without matching PFGE patterns. All of the isolates were Salmonella Enteritidis, and the timing of the cases was also significant with all eight patients becoming ill within a few weeks of each other. Despite these commonalities, the eight Salmonella Enteritidis isolates encompassed three different PFGE patterns, which generally wouldn’t link them as a cluster. Were these simply sporadic individual cases or was it an emerging outbreak? Given the similar (albeit slightly different) PFGE patterns, similar location of the patients and relatively short time period of illness onset, there was enough to prompt further investigation.

As a PulseNet participating laboratory, DCLS also submitted the PFGE patterns and corresponding data to the PulseNet national database. PulseNet data in conjunction with epidemiological data can be used to quickly connect similar cases of foodborne illness to link them back to a common source.

Epidemiologists followed up on their earlier initial case interviews by immediately performing more in-depth interviews with the eight patients to identify potential commonalities prior to the onset of illness. Of the first four individuals with whom they spoke, three reported eating at the same local restaurant. The epidemiologists then began asking the remaining patients if they too had eaten at this specific restaurant during the seven days prior to getting sick. Six of the eight said “yes.”

Virginia: PFGE and whole genome sequencing show Salmonella outbreak who’s boss | www.APHLblog.orgWithin Virginia’s public health system, there is constant two-way communication between the public health laboratory scientists and the foodborne disease epidemiologists. In any investigation, even after turning over cluster information, the public health lab wants to hear what the epis are finding in their investigation; and the epis might want to know if additional testing or analysis is available to support their investigation. In this case, the epis told the public health lab scientists about their findings: despite the Salmonella Enteritidis isolates from the patients having three different PFGE patterns, six out of eight patients reported visiting the same restaurant within the same time period before becoming ill. It was beginning to sound like this was an outbreak with a common source, but more testing was needed to confirm.

The public health lab staff and epidemiologists agreed this information supported further testing using whole genome sequencing (WGS) to better understand the relationship between isolates. WGS offers a fast, inexpensive way to improve PulseNet’s surveillance, and it allows participating laboratories like DCLS to use resources more efficiently. In Virginia, this was the first application of WGS to a local outbreak investigation. WGS analysis showed that seven of the eight Salmonella Enteritidis isolates were highly genetically related. The WGS data provided support for the epidemiologists’ hypothesis that there was a common-source outbreak, most likely associated with a single restaurant.

Upon inspection, it was revealed that the restaurant had two serious issues related to temperature monitoring and control that were later corrected. No specific food was implicated during this investigation, but temperature abuse could have been a factor in allowing the proliferation of Salmonella in the facility.

While PFGE data helped identify the cluster and prompted an investigation, WGS information strengthened the correlation between the isolates and supported the epidemiologists’ investigation results to complete the story. Frequent communication and collaboration between the epis and public health lab scientists proved critical to both the identification and resolution of the outbreak.

Due to the success with this outbreak, the use of WGS for other investigations is ongoing in Virginia. WGS has been successfully used for several other outbreaks and continues to deliver that knockout punch for outbreak detection.

Interested in learning more about food safety or reporting foodborne illness in Virginia? Check out the Virginia Department of Health’s My Meal Detective site for food safety videos, restaurant inspection information and more!

Do you have a PulseNet success story that could be featured? Please send your 500 word document and a photo that best represents the story to with subject line, “PulseNet Success Story- [Name of the State],” to be a part of the celebration!

Virginia: PFGE and whole genome sequencing show Salmonella outbreak who’s boss |

The Edgar Allen Poe Shrine in Richmond, Virginia,…

The Edgar Allen Poe Shrine in Richmond, Virginia, 1929.
Photograph by Charles Martin, National Geographic Creative

Neighbors Helping Neighbors

Busy Gym Testing for TB

When the Fairfax County Health Department (FCHD) in Virginia put out a call for volunteers to help conduct a tuberculosis (TB) contact investigation, Rosalia Parada, a long time Medical Reserve Corps (MRC) volunteer, jumped at the chance to serve her community.  The investigation was sparked when news of three students from Robert E. Lee High School acquired TB around the same time.

As a nurse and a resident of the Lee High School community, Parada saw firsthand the need for care and support throughout her neighborhood.  With a variety of ethnic groups and languages, the community is very diverse, lending itself to some challenges during a public health response of this scope.  For example, many families living in the community were from Spanish-speaking backgrounds.  In the same situation herself, , Parada felt that volunteering was an opportunity to provide interpretation, as well as nursing services for the contact investigation – when contacts like teachers, other students, and people who interacted with the students would be tested for TB.  “Many people don’t have access to health care,” Parada expressed, adding to the need for proper communication about the situation through interpretation. 

In the second phase of the contact investigation, screening and testing was provided at many sites around the community, one of which was located at Lee High School.  During the second phase, Parada volunteered as a screener.  She gathered information, distributed learning materials about what to do if someone has TB, and provided encouragement to those with concerns.  Her skills as a nurse permitted Parada to assist with TB testing, such as performing tuberculin skin testing (TST)

Although Parada is a practicing nurse, this was the first time she was involved in a response of this size.  During screening and testing, Parada saw the importance of providing comfort and reassurance for families, making them aware and helping build their knowledge about TB and the broad size and scope of signing upthe investigation.  Parada also stressed community awareness about TB vaccinations as a preventive measure for acquiring TB – and making the community aware of the consequences of not being tested, especially for those who were in close contact with the students who had acquired the active TB disease.

Among the many projects that Parada worked on as an MRC volunteer and as a practicing certified nurse, she says the Lee High School TB contact investigation is the largest and most unique. Parada explained that the gymnasium was very well organized for the screening and testing process, as volunteers kept the flow of students steady.   As a mother of three boys who graduated from Lee High School, she understood the worry, questions, and concerns from parents whose children may have been exposed to TB; but as a volunteer nurse, she knew the importance of making parents aware by gathering and providing accurate, helpful information while still being able to ease their worry.

Parada was extremely encouraged by the involvement of the community during the TB response.  She said the  investigation was a great learning experience for her community.  It combined the responsibility of the health department, along with the school and community, to help make people aware of good public health practice.

A sailor gets a tattoo on his arm in Virginia.Photograph by Paul…

A sailor gets a tattoo on his arm in Virginia.Photograph by Paul L. Pryor, National Geographic