39 sick: You’re a cute puppy, yes you are, but you have Campylobacter

The Ohio Department of Health, several other states, the U.S. Centers for Disease Control, and USDA-APHIS are investigating a multistate outbreak of human Campylobacter infections linked to puppies sold through Petland stores.

Investigators are looking for the source of infections in people and puppies so they can recommend how to stop the outbreak and prevent more illnesses in order to protect human and animal health.

As of September 11, 2017, the outbreak includes 39 cases in 7 states (Florida, Kansas, Missouri, Ohio, Pennsylvania, Tennessee, and Wisconsin).

Illnesses began on dates ranging from September 15, 2016 through August 12, 2017. The most recent illness was reported on September 1, 2017.

Ill people range in age from <1 year to 64 years, with a median age of 22 years; 28 (72%) are female; and 9 (23%) report being hospitalized. No deaths have been reported.

Epidemiologic and laboratory findings have linked the outbreak to contact with puppies sold through Petland stores. Among the 39 ill people, 12 are Petland employees from 4 states and 27 either recently purchased a puppy at Petland, visited a Petland, or visited or live in a home with a puppy sold through Petland before illness began.

Whole genome sequencing showed samples of Campylobacter isolated from the stool of puppies sold through Petland in Florida were closely related to Campylobacter isolated from the stool of an ill person in Ohio. Additional laboratory results from people and dogs are pending.

Regardless of where they are from, any puppies and dogs may carry Campylobacter germs.

 

‘Are you sure Hank done it this way’ Whole genome sequencing and better global foodborne disease surveillance

In 1993, I thought the consummation of Hollywood and Nashville was complete when starlet Julia Roberts wed country music’s ugly duckling, Lyle Lovett.

They divorced less than two years later.

As the NHL Stanley Cup playoffs progressed, the last-seeded Nashville Predators demolished foe-after-foe, with star couple captain Mike Fischer and partner Carrie Underwood paving the way for another coupling of the weirdness and greatness that is America: Nashville and Smashville.

But I don’t think that Hank do it like that.

It didn’t happen, as Nashville finally lost to Pittsburgh in 6-games to close out a grueling National Hockey League season.

I write this while watching Sorenne and Amy on the ice, taking extra skating lessons, in the sub-tropics of Brisbane, as likely a hockey hotspot as Nashville.

Amy is happy Pittsburgh won because, she hates country music.

But baby … Lyle isn’t country, he’s something different.

I’ve been to Nashville several times, hung out on Music Row, hung out a Titans tailgate, and saw Lyle Lovett one night and John Prine the next at the Ryman Auditorium, The Mother Church of Country Music.

Now that my Nashville Predators have lost the Stanley Cup in a valiant, country-heartbreak ballad to Pittsburgh, I return to the more mundane mattes of foodborne illness.

PulseNet International advocates for public health institutes and laboratories around the world to move together towards the use of whole genome sequencing (WGS) to improve detection of and response to foodborne illnesses and outbreaks in the latest edition of Eurosurveillance.

This will save lives and money due to the superior ability of WGS to link human cases with contaminated food sources.

PulseNet International is a global network of public health laboratory networks, dedicated to bacterial foodborne disease surveillance. The network is comprised of the national and regional laboratory networks of USA, Canada, Latin America and the Caribbean, Europe, Africa, the Middle-East and Asia Pacific.

The European Centre for Disease Prevention and Control (ECDC) manages the EU/EEA food- and waterborne diseases and zoonoses network of public health institutes and laboratories, which work to ensure comparability of data and further ties to the global health community.

Mike Catchpole, Chief Scientist at ECDC says, “it is important for all partners worldwide to continue to work together towards the implementation and standardised analysis of whole genome sequencing.”

The article also states that a global standard method for primary sequence data analysis based on whole genome Multiple Locus Sequence Typing (wgMLST) and derived public nomenclature will be adopted.

This will facilitate the sharing of information within regional and global public health laboratory networks, increasing efficiency and enabling data to be compared across countries in real-time which is currently not the case. This is especially important due to international travel and trade.

Common steps for validation studies, development of standardised protocols, quality assurance programmes and nomenclature have been agreed.

Pulsenet international: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

Eurosurveillance, vol. 22, issue, 23, 08 June 2017, C Nadon , I Van Walle, P Gerner-Smidt, J Campos, Chinen, J Concepcion-Acevedo, B Gilpin, AM Smith, KM Kam, E Perez, E Trees, K Kubota, J Takkinen, EM Nielsen, H Carleton, FWD-NEXT Expert Panel, DOI: http://dx.doi.org/10.2807/1560-7917.ES.2017.22.23.30544

http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22807

PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies. WGS data are suitable for surveillance and outbreak purposes and for answering scientific questions pertaining to source attribution, antimicrobial resistance, transmission patterns, and virulence, which will further enable the protection and improvement of public health with respect to food-borne disease.

 

Whole genome sequencing (WGS) for food-borne pathogen surveillance and control- Taking the pulse

Eurosurveillance, vol 22, issue 23, 08 June 2017, J Moran-Gilad, DOI: http://dx.doi.org/10.2807/1560-7917.ES.2017.22.23.30547

http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22811

Next-generation sequencing (NGS) is transforming microbiology [1]. With the increased accessibility and decrease in the costs of sequencing and the optimisation of the ‘wet laboratory’ components of NGS i.e. the quality and throughput of DNA extraction, library preparation and sequencing reactions, whole genome sequencing (WGS) of bacterial isolates is rapidly revolutionising clinical and public health microbiology. WGS is a ‘disruptive technology’ that has the potential to become a one-stop-shop for routine bacterial analysis. By replacing multiple parallel steps in the microbiology diagnostic cycle, which currently involves traditional and molecular methods, it achieves accurate and speedy species identification, inference of antimicrobial susceptibility and virulence and high-resolution subtyping [2].

Typing of food-borne pathogens was one of the earliest applications of WGS [3] and proof-of-concept has been demonstrated for the superiority of WGS over traditional typing methods such as pulsed-field gel electrophoresis (PFGE), multilocus variable-number tandem repeat analysis (MLVA) and multilocus sequence typing (MLST), for a range of high priority food-borne pathogens, including Salmonella enterica, Listeria monocytogenes, Campylobacter species and Shiga-toxin producing Escherichia coli [4]. Applications of WGS include the investigation of food-related outbreaks and surveillance to delineate the local, regional and global genomic epidemiology of pathogens and to attribute the infection source. WGS thus supports risk assessment and guides interventions for prevention and control of infections.

A growing number of (public health microbiology) laboratories and governmental agencies employ WGS in their routine practice and food-borne pathogen surveillance and even more are expected to enter this field in the near future. Thus the maturation of food-borne pathogen surveillance into the WGS era is very timely.

In order for WGS to be adopted as the new gold standard for tracking of food-borne pathogens, a key element of food-borne disease control, there is a need for robust, standardised, portable and scalable methods for analysing WGS data. However, the notable diversity of bioinformatics tools and approaches used for bacterial WGS to date, as evident from a recent survey by the Global Microbial Identifier project [5], creates a tremendous challenge for harmonising surveillance and investigation of food-borne illness, especially across geographical borders and different sectors. Calling variants based on analysis of single nt polymorphisms (SNPs) as it is being done in many food-borne outbreak investigations, offers maximal resolution and discriminatory power but is very difficult to standardise. Therefore, approaches based on gene-by-gene analyses, collectively referred to as ‘extended MLST’, such as core genome (cg) or whole genome (wg)MLST may be advantageous [6], and have been advocated in other public health settings, such as Legionnaires’ disease control [7].

PulseNet was established in the United States (US) more than 20 years ago as a laboratory network for molecular epidemiology based on standardised PFGE analysis and later expanded globally. PulseNet has been successful in engaging many players in the field of food safety on a global scale and in creating a platform for data sharing and comparison of clinical, veterinary and food isolates in over 80 countries and it has a proven track-record in supporting molecular surveillance [8]. Nevertheless, some issues remained unresolved such as creation and implementation of a global nomenclature, which is important for communicating molecular epidemiology results, both scientifically as well as operationally.

In this issue of Eurosurveillance, an article by Nadon et al. [9] describes the next generation of PulseNet International, which is evolving into harnessing WGS. This initiative represents a wide collaboration between many leading agencies and stakeholders in this area, including the US Centers for Disease Control and Prevention (CDC), the European Centre for Disease Prevention and Control (ECDC) and the Public Health Agency Canada (PHAC), just to name a few. The authors illustrate the technical and practical aspects of adapting the network. Notably, PulseNet International has chosen an extended MLST approach, specifically, wgMLST, as its default phylogenetic analysis tool, which should underpin a standardised and efficient nomenclature-based system. Different technical and practical aspects are reviewed and discussed, mainly focusing on information technology (IT) and bioinformatics aspects (data storage, computing power, nomenclature, data sharing), methods for validation and quality control/quality assurance. Nadon et al. highlight complexities surrounding the implementation of WGS for food-borne disease surveillance, with respect to readiness at individual country and regional levels and delineate how PulseNet plans to address these.

The evolution of PulseNet International is very encouraging and will reinforce the use of NGS in the area of food safety. That said, challenges remain that need to be addressed by the public health community. There is a need for user-friendly bioinformatics solutions that will enable automated analysis of bacterial genomes by non-experts in bioinformatics to extract valuable information in a time-efficient manner. Such solutions should offer as much backwards compatibility as possible with current typing methods since the global transition to WGS is expected to be gradual. It should also offer an efficient strain/allele nomenclature that facilitates inter-laboratory work. Moreover, bioinformatics solutions should also factor in the developments in the field of DNA sequencing, particularly long-read single molecule sequencing platforms and portable sequencing devices which are increasingly being used. While WGS of food-borne pathogens has now become the new gold standard for food-borne pathogen typing, other techniques such as strain typing and characterisation using proteomics (particularly matrix-assisted laser desorption/ionisation (MALDI) time-of-flight (TOF) mass spectroscopy) or DNA arrays are rapidly evolving and should be carefully evaluated [10]. The field of metagenomics is also rapidly advancing and culture-independent microbiology, enabling genomic analysis of pathogens directly from sequenced clinical or environmental samples (as opposed to cultured isolates), is just around the corner [11]. When laying the foundations for global food pathogen surveillance networks for the coming years, we need to be mindful of such future developments.

Different from current protocols in which only typing results are shared, the transition to genome-based surveillance inevitably involves the sharing of complete sequence data. This has many implications, not only with respect to data storage, analysis and sharing infrastructures, but also aspects such as data ownership, privacy and transparency, pertaining to both genomic sequences and the related metadata. These issues should be proactively addressed in order to provide reassurance concerning data protection and create flexible solutions that will facilitate the timely sharing of public health data by as many partners as possible.

Finally, the transition to WGS-based surveillance needs to ensure sufficient quality is maintained in order to meet national and international regulatory requirements. Nadon et al. rightfully emphasise in their paper, the importance of validation, quality control and standardisation. One major aspect in making this transition and that needs to be considered is the human factor. The successful implementation of WGS-based surveillance on a global scale requires careful planning, building of capacity and training of public health and microbiology personnel to develop local readiness, especially in limited resource settings. Care should be taken to address the ‘softer’ issues, including possible cultural, political and cross-sector barriers, which together with economical, management and operational aspects could greatly influence the successful implementation of WGS.

This is a fascinating time for public health microbiology, and initiatives such as the integration of WGS as proposed by PulseNet International, are central for leveraging recent technological advancements for the benefit of public health surveillance.

 

Seek and ye shall find: STEC in Ireland

The recent paradigm shift in infectious disease diagnosis from culture-based to molecular-based approaches is exemplified in the findings of a national study assessing the detection of verotoxigenic Escherichia coli infections in Ireland. The methodologic changes have been accompanied by a dramatic increase in detections of non-O157 verotoxigenic E. coli serotypes.

wgsChanging diagnostic methods and increased detection of verotoxigenic Escherichia coli, Ireland

Emerg Infect Dis., Volume 22, Number 9, September 2016, DOI: 10.3201/eid2209.160477

T Rice, N Quinn, RD Sleator, B Lucey

http://wwwnc.cdc.gov/eid/article/22/9/16-0477_article

Whole genome sequencing to determine food sources of Salmonella

Salmonella Typhimurium (STM) is an important cause of foodborne outbreaks worldwide. Subtyping of STM remains critical to outbreak investigation, yet current techniques (e.g. multilocus variable number tandem repeat analysis, MLVA) may provide insufficient discrimination. Whole genome sequencing (WGS) offers potentially greater discriminatory power to support infectious disease surveillance.

wgsMethods

We performed WGS on 62 STM isolates of a single, endemic MLVA type associated with two epidemiologically independent, foodborne outbreaks along with sporadic cases in New South Wales, Australia, during 2014. Genomes of case and environmental isolates were sequenced using HiSeq (Illumina) and the genetic distance between them was assessed by single nucleotide polymorphism (SNP) analysis. SNP analysis was compared to the epidemiological context.

Results

The WGS analysis supported epidemiological evidence and genomes of within-outbreak isolates were nearly identical. Sporadic cases differed from outbreak cases by a small number of SNPs, although their close relationship to outbreak cases may represent an unidentified common food source that may warrant further public health follow up. Previously unrecognised mini-clusters were detected.

Conclusions

WGS of STM can discriminate foodborne community outbreaks within a single endemic MLVA clone. Our findings support the translation of WGS into public health laboratory surveillance of salmonellosis.

Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014

BMC Microbiology, Published 15 September 2016, DOI: 10.1186/s12866-016-0831-3

http://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-016-0831-3

Cause unknown: 72 sickened by Salmonella in Australian state

Matt Johnston of the Herald Sun reports that Victoria is battling a major outbreak of salmonella and bacteria-related illnesses which has experts desperately searching for a cause.

mayonnaise.raw.eggIn the past two months 72 cases of foodborne infections have been reported to the Department of Health — including 46 identified in one June week alone.

The average number of ­salmonella reports each month is about six.

Despite the outbreak, a clear pattern has not been identified and experts have been unable to pin down a suspect food source.

Health Minister Jill Hennessy has issued a blanket food-safety warning. “All Victorians should remember to take care when preparing food at home, especially during the winter months, to prevent food turning nasty,” she said.

In the first six months of this year there were 67 per cent more cases compared to the last six months of 2015.

Also, Melbourne’s opulent Langham Hotel has been charged over a salmonella outbreak that left 90 diners ­violently ill.

The high tea crisis, which was triggered by raw egg mayonnaise, put 16 people in hospital last year.

The Sunday Herald Sun can reveal Melbourne City Council has charged the hotel over its handling and service of unsafe food and noncompliance with the Food Standards Code.

The case will be heard in the Melbourne Magistrates’ Court in October.

Whole genome sequencing key to delineating E. coli O26 in cattle

Escherichia coli O26 is the second most important enterohemorrhagic E. coli (EHEC) serogroup worldwide.

cow.say.whatSerogroup O26 strains are categorized mainly into two groups: enteropathogenic (EPEC) O26, carrying a locus of enterocyte effacement (LEE) and mostly causing mild diarrhea, and Shiga-toxigenic (STEC) O26, which carries the Shiga toxin (STX) gene (stx), responsible for more severe outcomes. stx-negative O26 strains can be further split into two groups. One O26 group differs significantly from O26 EHEC, while the other O26 EHEC-like group shows all the characteristics of EHEC O26 except production of STX.

In order to determine the different populations of O26 E. coli present in U.S. cattle, we sequenced 42 O26:H11 strains isolated from feedlot cattle and compared them to 37 O26:H11 genomes available in GenBank. Phylogenetic analysis by whole-genome multilocus sequence typing (wgMLST) showed that O26:H11/H− strains in U.S. cattle were highly diverse. Most strains were sequence type 29 (ST29). By wgMLST, two clear lineages could be distinguished among cattle strains. Lineage 1 consisted of O26:H11 EHEC-like strains (ST29) (4 strains) and O26:H11 EHEC strains (ST21) (2 strains), and lineage 2 (36 strains) consisted of O26:H11 EPEC strains (ST29).

Overall, our analysis showed U.S. cattle carried pathogenic (ST21; stx1+ ehxA+ toxB+) and also potentially pathogenic (ST29; ehxA+ toxB+) O26:H11 E. coli strains. Furthermore, in silico analysis showed that 70% of the cattle strains carried at least one antimicrobial resistance gene.

Our results showed that whole-genome sequence analysis is a robust and valid approach to identify and genetically characterize E. coli O26:H11, which is of importance for food safety and public health.

Virulence gene profiles and clonal relationships of Escherichia coli O26:H11 isolates from feedlot cattle as determined by whole-genome sequencing

Appl. Environ. Microbiol. July 2016 vol. 82 no. 13 3900-3912, DOI: 10.1128/AEM.00498-16

Narjol Gonzalez-Escalona, Magaly Toro, Lydia V. Rump, Giojie Cao, T.G. Nagaraja, Jianghong Meng

http://aem.asm.org/content/82/13/3900.abstract?etoc

Lots of recalls but ‘100 times more likely to detect an outbreak than 20 years ago’

Martin Wiedmann, a professor of food safety at Cornell University’s food science department, told CBC News we really are seeing far more food recalls and outbreaks these days, “But that doesn’t mean our food is less safe. It’s the opposite. What happened over the last 20 years and really accelerated over the last two years is the use of completely new DNA fingerprinting tools to detect disease outbreaks. Today, we are 100 times more likely to detect an outbreak than we were 20 years ago.”

riskHealth officials have developed a system to track the genetic makeup of salmonella, Listeria and E. coli. Once a food-related illness outbreak is identified, scientists can match the DNA from contaminated food with the bacteria making people sick, and potentially trace it to the originating food processing plant.

In light of that long list of recalls, and the fact that we’re detecting more outbreaks, shouldn’t they also be steering us away from salad and cantaloupes? After all, based on the recalls, they might sound like risky foods.

Wiedmann says that’s not really so. He points to the reason we see few cases of issues arising from raw milk consumption as an example of why.

“Much, much fewer people consume raw milk,” he said.

“So we don’t hear much about raw milk outbreaks. But we hear about outbreaks with lettuce, so [people think] lettuce must be less safe. Quite the opposite, because you need to consider the total amount of the food produced — what is your chance of getting sick from eating one of these servings.”

Wiedmann also points out that a recall isn’t the same as an outbreak. In most cases, food recalls are precautionary, and the products haven’t actually made anyone sick.

We call them outbreaks now because we can easily link a specific product in California, for example, with a handful of sick people in separate provinces or states, thanks to the DNA fingerprinting Wiedmann mentioned.

The bottom line, he says, is that those high-risk products health officials advise against, like unpasteurized cheese, are actually riskier than the products making news headlines.

A cheese that’s acceptable in the French countryside isn’t in urban Canada, largely because of our cultural biases.

“The challenge is that risk isn’t binary,” Wiedmann said.

“It’s just not like ‘risk’ or ‘no-risk.’ There’s a gradation… And then somewhere in the middle, someone puts a line. And that line is arbitrary, because no food is risk free.”

I don’t eat raw oysters: Gross and may have Vibrio

Following up a scientific report, Timothy B. Wheeler of the Bay Journal reports a 6-year-old outbreak of food poisoning linked to eating raw Chesapeake Bay oysters has left behind a lingering mystery. Scientists seeking to identify the water-borne pathogen that sickened a pair of Baltimore restaurant patrons have tracked the culprit to Asia.

Raw oystersHow a potent strain of Vibrio bacteria seemingly from so far away wound up in the Bay continues to puzzle Maryland health officials, who worked with researchers at the U.S. Food and Drug Administration to investigate the 2010 cases.

The microorganism could have gotten here in the ballast water of the many oceangoing ships that ply the Chesapeake every year, state and federal scientists suggested in a recently published journal article. Or, they added, perhaps it came via the introduction of non-native oysters or some exotic fish.

“It really is speculation,” acknowledged Dr. Clifford Mitchell, environmental health bureau director for the Maryland Department of Health and Mental Hygiene. “We didn’t sample ballast water. We didn’t take specimens that would lead us to know that we had fish coming over, or migration.”

But the case, published in the June issue of Applied and Environmental Microbiology, illustrates how disease-carrying organisms may travel around the world, researchers said. And while steps have been taken since 2010 to prevent the unintentional transport of pathogens, parasites and other potentially harmful organisms via ships’ ballast water, those safeguards still have significant gaps in them.

The bacterium involved in the 2010 food poisoning outbreak was Vibrio parahaemolyticus, strains of which are commonly found in coastal waters worldwide — including the Bay — though only some have been found to cause illness. When those are ingested, they can cause acute gastrointestinal distress, including diarrhea, stomach pain, nausea, fever and chills. It usually passes within a few days, but in rare cases can be more severe, especially in people with weakened immune systems.

There were 45 cases of Vibrio infections reported in Maryland in 2010, but it’s not that often, state health officials said, that they’re able to pinpoint the source of the bacteria that may have sickened a particular person. By the time laboratory tests identify Vibrio as the cause of someone’s GI distress and the information gets reported to the state, days or even weeks may have passed, and the food that person had eaten is long gone.

In this case, though, state health investigators got a lucky break. Two individuals who got sick said that shortly before they became ill that summer, they had eaten raw oysters at different Baltimore restaurants. They hadn’t traveled out of state or done anything else that likely could have exposed them.

When investigators visited the restaurants, they found the half-shells eaten by the two victims were from the Bay. And when they visited the Maryland aquaculture operation that supplied both eateries, investigators pulled some oysters from the water and discovered that they had Vibrio in them as well — 11 different potentially disease-causing strains, in fact. One of those appeared to match the Asian strain found in the two food poisoning victims.

Coos Bay Oyster Co.The investigation ended there, for the time being. Even though the Vibrio involved were similar, researchers couldn’t positively identify them as the same, using the analytic techniques they had at the time. “The chromosome patterns matched, but we weren’t sure how common that pattern was in the environment,” explained Robert Myers, director of the state health department’s laboratory administration. “We hadn’t seen it before.”

A few years later, though, “whole genome sequencing” technology became available, Myers said, giving researchers the ability to draw a more detailed map of an organism’s genetic makeup.

With that new, more powerful analytical tool, FDA researchers re-examined the Vibrio strains involved in the 2010 outbreak and those from the oysters that state health investigators had sampled. They identified them as belonging to a family of strains known as “sequence type 8.” 

When researchers consulted a worldwide Vibrio database, they found that the Maryland strains were unlike any seen to date in the United States. Instead, they were closely related to strains reported only in Asia, most recently in Hong Kong about four years before the outbreak.

Changes were made to shellfish safety protocols after a larger outbreak in 2013of Vibrio parahaemolyticus illnesses associated with eating raw oysters harvested along the Atlantic Coast. More than 100 people in 13 states, including Maryland and Virginia, became ill.  According to a spokesman for the Maryland Department of the Environment, which regulates shellfish harvest waters in the state, the Interstate Shellfish Sanitation Conference, a joint state-federal body, tightened its requirements for investigating such cases, closing implicated harvest areas and ordering a product recall when more than 10 cases are traced to a given area. 

But officials caution that the protocols are not foolproof, and cases like this are a reminder of the risk people run in consuming raw seafood, Mitchell said, especially if they have underlying health conditions.

The number of reported Vibrio infections in the state varies from year to year, but has been trending upward since 2005, according to state health data. Concentrations of the bacteria increase in warmer weather, and climate change could be a factor as Bay water temperatures tick upward. But Mitchell cautioned that the bacteria are present year-round.

“Given the number of people who eat oysters, certainly it’s a relatively small number of infections, but it can be a very significant one,” Mitchell said.

WGS, Vibrio and traceback in oysters

In the summer of 2010, Vibrio parahaemolyticus caused an outbreak in Maryland linked to the consumption of oysters. Strains isolated from both stool and oyster samples were indistinguishable by pulsed-field gel electrophoresis (PFGE). However, the oysters contained other potentially pathogenic V. parahaemolyticusstrains exhibiting different PFGE patterns.

Oyster-Vancouver, B.C.- 07/05/07- Joe Fortes Oyster Specialist Oyster Bob Skinner samples a Fanny Bay oyster at the restuarant. Vancouver Coastal Health now requires restaurants to inform their patrons of the dangers of eating raw shellfish.  (Richard Lam/Vancouver Sun)   [PNG Merlin Archive]

In order to assess the identity, genetic makeup, relatedness, and potential pathogenicity of the V. parahaemolyticusstrains, we sequenced 11 such strains (2 clinical strains and 9 oyster strains). We analyzed these genomes by in silico multilocus sequence typing (MLST) and determined their phylogeny using a whole-genome MLST (wgMLST) analysis. Ourin silico MLST analysis identified six different sequence types (STs) (ST8, ST676, ST810, ST811, ST34, and ST768), with both of the clinical and four of the oyster strains being identified as belonging to ST8.

Using wgMLST, we showed that the ST8 strains from clinical and oyster samples were nearly indistinguishable and belonged to the same outbreak, confirming that local oysters were the source of the infections. The remaining oyster strains were genetically diverse, differing in >3,000 loci from the Maryland ST8 strains. eBURST analysis comparing these strains with strains of other STs available at the V. parahaemolyticus MLST website showed that the Maryland ST8 strains belonged to a clonal complex endemic to Asia. This indicates that the ST8 isolates from clinical and oyster sources were likely not endemic to Maryland. Finally, this study demonstrates the utility of whole-genome sequencing (WGS) and associated analyses for source-tracking investigations.

A nonautochthonous U.S. strain of Vibrio parahaemolyticus isolated from Chesapeake Bay oysters caused the outbreak in Maryland in 2010

Appl. Environ. Microbiol. June 2016 vol. 82 no. 11 3208-3216

Julie Haendiges, Jessica Jones, Robert A. Myers, Clifford S. Mitchell, Erin Butler, Magaly Toro and Narjol Gonzalez-Escalona

http://aem.asm.org/content/82/11/3208.abstract?etoc

The power of whole genome sequencing: 1 dead 1 sick from Listeria-in-raw milk, 2014

The U.S. Centers for disease Control reports that raw milk produced by Miller’s Organic Farm in Bird-In-Hand, Pennsylvania, is the likely source of this outbreak.

colbert.raw.milkTwo people infected with the outbreak strain of Listeria were reported from California (1) and Florida (1). Both illnesses occurred in 2014.

Both people were hospitalized, and the ill person in Florida died as a result of listeriosis.

Although the two illnesses occurred in 2014, the source of these illnesses wasn’t known until January 29, 2016, when the U.S. Food and Drug Administration informed CDC that whole genome sequencing of Listeria bacteria from raw chocolate milk produced by Miller’s Organic Farm showed that it was closely related genetically to Listeria bacteria from the two ill people described above.

Because Listeria was recently found in raw milk produced by Miller’s Organic Farm, CDC is concerned that conditions may exist at the farm that may cause further contamination of raw milk and raw dairy products distributed by this company and make people sick.

In November 2015, samples of raw chocolate milk were collected from a raw milk conference held in Anaheim, California. The raw chocolate milk was produced by Miller’s Organic Farm. The U.S. Food and Drug Administration (FDA) isolated Listeria from the raw chocolate milk and conducted WGS testing on the isolate to get more genetic information about the bacteria. On January 29, 2016, FDA informed CDC that WGS determined that the Listeria bacteria from the raw chocolate milk was closely related genetically to Listeria bacteria from two people in two states who got sick in 2014, one from California and one from Florida.