‘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.

 

Expediting detection of pathogens in food supply

Angelo Gaitas, a research assistant professor at Florida International University’s Electrical and Computer Engineering Department, along with Gwangseong Kim, a research scientist, are commercializing a device that reduces the screening process of foods to just a few hours at the same cost as current devices.

FIU says that if you have ever suffered from food poisoning, you will appreciate why it is so important to inspect food before it reaches the consumer. Food producers have to check for bacteria and signs of contamination before they are able to ship out any perishable food. Some common bacteria that can lead to foodborne illnesses include E.coli, salmonella and listeria. In fact, according to the Centers for Disease Control, each year, one in six Americans gets sick by consuming contaminated foods or beverages, that is forty-eight million people, out of whom 128,000 are hospitalized.

Typically, the inspection process, which involves putting samples in a solution and placing it in an incubator to see if bacteria grows, takes anywhere from 18 hours to several days. The reason is that it takes time for bacteria to grow at detectable levels. Current detection techniques are limited – you may need about 1,000 to a million bacteria present, depending on the technique, in a small volume before bacteria can be successfully detected. To reach that level, it takes time.

With this new device, food producers are able to run the whole solution through a smaller container inside the incubator oven. Antibodies in the device capture the target bacteria. This procedure allows bacteria to be concentrated in a smaller volume enabling same day detection.

“We are focused on helping food producers reduce storage cost and get fresher food to consumers,” Gaitas says. “We are addressing a major and well documented need in a very large market. There are about 1.2 billion food tests conducted worldwide and about 220 million tests in the United States.”

By shortening the detection time by one day, the team believes that the device can save the food industry billions. For example, meat producers, as a collective industry, could save up to $3 billion in storage costs by shortening the detection to one day. This device can also be used to expedite the detection of bloodborne illnesses such as sepsis and viral infections; however, currently the commercial focus is on food due to the lower barriers to entry.

Gaitas formed a company, Kytaro Inc – an FIU startup – which spent the last few years creating and testing the device and publishing the results in scientific journals. Besides Gaitas and Kim, the company has been employing FIU undergraduates.

FIU notes that this April, with the support of Henry Artigues of the Office of Research and Economic Development and Shekhar Bhansali, chair of the Electrical and Computer Engineering Department, Kytaro was recognized as one of “40 Best University Startups 2017” at the University Startups Conference and Demo Day in Washington, D.C. About 200 startups applied to the national competition.

Surf cops: Investigating microbes of surfers and the sea to understand resistance

Peter Andrey Smith of the New York Times writes that on a recent trip, Cliff Kapono hit some of the more popular surf breaks in Ireland, England and Morocco. He’s proudly Native Hawaiian and no stranger to the hunt for the perfect wave. But this time he was chasing something even more unusual: microbial swabs from fellow surfers.

Mr. Kapono, a 29-year-old biochemist earning his doctorate at the University of California, San Diego, heads up the Surfer Biome Project, a unique effort to determine whether routine exposure to the ocean alters the microbial communities of the body, and whether those alterations might have consequences for surfers — and for the rest of us.

Mr. Kapono has collected more than 500 samples by rubbing cotton-tipped swabs over the heads, mouths, navels and other parts of surfers’ bodies, as well as their boards. Volunteers also donate a fecal sample.

He uses mass spectrometry to create high-resolution maps of the chemical metabolites found in each sample. “We have the ability to see the molecular world, whether it’s bacteria or a fungus or the chemical molecules,” he said.

Then, working in collaboration with U.C.S.D.’s Center for Microbiome Innovation — a quick jaunt across the quad from his lab — Mr. Kapono and his colleagues sequence and map the microbes found on this unusually amphibious demographic.

He and his colleagues are looking for signs of antibiotic-resistant organisms. Part of their aim is to determine whether, and to what extent, the ocean spreads the genes for resistance.

Many antibiotics used today derive from chemicals produced by microbes to defend themselves or to attack other microorganisms. No surprise, then, that strains of competing bacteria have also evolved the genetic means to shrug off these chemicals.

While drug resistance comes about because of antibiotic overuse, the genes responsible for creating resistance are widely disseminated in nature and have been evolving in microbes for eons. Startlingly, that means genes giving rise to drug resistance can be found in places untouched by modern antibiotics.

Several years ago, researchers identified antibiotic-resistant genes in a sample of ancient permafrost from Nunavut, in the Canadian Arctic. William Hanage, an epidemiologist at the Harvard School of Public Health, was among those showing that these genes conferred a resistance to amikacin, a semi-synthetic drug that did not exist before the 1970s.

“There was a gene that encoded resistance to it in something that was alive 6,000 years ago,” he said in an interview.

Another group led by Hazel Barton, a microbiologist at the University of Akron, discovered microorganisms harboring antibiotic-resistance genes in the Lechuguilla Cave in New Mexico. These bacteria, called Paenibacillus sp. LC231, have been isolated from Earth’s surface for four million years, yet testing showed they were capable of fending off 26 of 40 modern antibiotics.

It’s all cool research, but all I could think of was Celebrity, a skit by The Kids in the Hall.

Hang 10, you’re booked.

Kids, kids: Foodnet report is out

It’s my favorite day of the year: The annual U.S. Foodnet report, where data is presented, mulled over, and then crammed into politically suitable food safety fairytales.

When a scientific report leads with, “The incidence of infections transmitted commonly through food has remained largely unchanged for many years,” isn’t it time to try something different?

The U.S. Centers for Disease Control reports reducing foodborne illness depends in part on identifying which illnesses are decreasing and which are increasing. Yet recent changes in the use of tests that diagnose foodborne illness pose challenges to monitoring illnesses and progress toward preventing foodborne disease, according to a report published today in CDC’s Morbidity and Mortality Weekly Report.

Rapid diagnostic tests help doctors diagnose infections quicker than traditional culture methods, which require growing bacteria to determine what is causing illness. But without a bacterial culture, public health officials cannot get the detailed information needed to detect and prevent outbreaks, monitor disease trends, and identify antibiotic resistance.

The MMWR article includes the most recent data from CDC’s Foodborne Diseases Active Surveillance Network, or FoodNet, which collects data on 15% of the U.S. population. It summarizes preliminary 2016 data on nine germs spread commonly through food. In 2016, FoodNet reported 24,029 infections, 5,512 hospitalizations, and 98 deaths. This is the first time the numbers used for calculations of trends include bacterial infections diagnosed only by rapid diagnostic tests as well as those confirmed by traditional culture-based methods. Previously, these calculations used only those bacterial infections confirmed by culture-based methods. The most frequent causes of infection in 2016 were Salmonella and Campylobacter, which is consistent with previous years.

 Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food and the Effect of Increasing Use of Culture-Independent Diagnostic Tests on Surveillance — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2013–2016

Marder EP, Cieslak PR, Cronquist AB, et al.

MMWR Morb Mortal Wkly Rep 2017;66:397–403. DOI: http://dx.doi.org/10.15585/mmwr.mm6615a1

https://www.cdc.gov/mmwr/volumes/66/wr/mm6615a1.htm?s_cid=mm6615a1_e#suggestedcitation

The incidence of infections transmitted commonly through food has remained largely unchanged for many years. Culture-independent diagnostic tests (CIDTs) are increasingly used by clinical laboratories to detect enteric infections.

What is added by this report?

Compared with the 2013–2015 average annual incidence, the 2016 incidence of confirmed Campylobacter infections was lower, incidences of confirmed Shiga toxin-producing Escherichia coli (STEC), Yersinia, and Cryptosporidium infections were higher, and incidences of confirmed or CIDT positive–only STEC and Yersinia infections were higher. However, CIDTs complicate the interpretation of surveillance data; testing for pathogens might occur more frequently because of changes in either health care provider behaviors or laboratory testing practices. A large proportion of CIDT positive specimens were not reflex cultured, which is necessary to obtain isolates for distinguishing pathogen subtypes, determining antimicrobial resistance, monitoring trends, and detecting outbreaks.

What are the implications for public health practice?

Some information about the bacteria causing infections, such as subtype and antimicrobial susceptibility, can only be obtained for CIDT positive specimens if reflex culture is performed. Increasing use of CIDTs affects the interpretation of public health surveillance data and ability to monitor progress toward prevention measures.

Foodborne diseases represent a substantial public health concern in the United States. CDC’s Foodborne Diseases Active Surveillance Network (FoodNet) monitors cases reported from 10 U.S. sites* of laboratory-diagnosed infections caused by nine enteric pathogens commonly transmitted through food. This report describes preliminary surveillance data for 2016 on the nine pathogens and changes in incidences compared with 2013–2015. In 2016, FoodNet identified 24,029 infections, 5,512 hospitalizations, and 98 deaths caused by these pathogens. The use of culture-independent diagnostic tests (CIDTs) by clinical laboratories to detect enteric pathogens has been steadily increasing since FoodNet began surveying clinical laboratories in 2010 (1). CIDTs complicate the interpretation of FoodNet surveillance data because pathogen detection could be affected by changes in health care provider behaviors or laboratory testing practices (2). Health care providers might be more likely to order CIDTs because these tests are quicker and easier to use than traditional culture methods, a circumstance that could increase pathogen detection (3). Similarly, pathogen detection could also be increasing as clinical laboratories adopt DNA-based syndromic panels, which include pathogens not often included in routine stool culture (4,5). In addition, CIDTs do not yield isolates, which public health officials rely on to distinguish pathogen subtypes, determine antimicrobial resistance, monitor trends, and detect outbreaks. To obtain isolates for infections identified by CIDTs, laboratories must perform reflex culture; if clinical laboratories do not, the burden of culturing falls to state public health laboratories, which might not be able to absorb that burden as the adoption of these tests increases (2). Strategies are needed to preserve access to bacterial isolates for further characterization and to determine the effect of changing trends in testing practices on surveillance.

FoodNet is a collaboration among CDC, 10 state health departments, the U.S. Department of Agriculture’s Food Safety and Inspection Service, and the Food and Drug Administration. FoodNet personnel conduct active, population-based surveillance for laboratory-diagnosed infections caused by Campylobacter, Cryptosporidium, Cyclospora, Listeria, Salmonella, Shiga toxin-producing Escherichia coli (STEC), Shigella, Vibrio, and Yersinia for 10 sites covering approximately 15% of the U.S. population (an estimated 49 million persons in 2015). Confirmed bacterial infections are defined as isolation of the bacterium from a clinical specimen by culture. Confirmed parasitic infections are defined as detection of the parasite from a clinical specimen by direct fluorescent antibody test, polymerase chain reaction, enzyme immunoassay, or light microscopy. CIDTs detect bacterial pathogen antigen, nucleic acid sequences, or for STEC, Shiga toxin or Shiga toxin genes, in a stool specimen or enrichment broth.§ A CIDT positive–only bacterial infection is a positive CIDT result that was not confirmed by culture. Hospitalizations occurring within 7 days of specimen collection are recorded. The patient’s vital status at hospital discharge (or 7 days after specimen collection if not hospitalized) is also recorded. Hospitalizations and deaths occurring within 7 days of specimen collection are attributed to the infection. FoodNet also conducts surveillance for physician-diagnosed postdiarrheal hemolytic uremic syndrome (HUS), a potential complication of STEC infection, by review of hospital discharge data through a network of nephrologists and infection preventionists. This report includes HUS cases among persons aged <18 years for 2015, the most recent year with available data.

Incidence of infection for each pathogen is calculated by dividing the number of infections in 2016 by the U.S. Census estimates of the surveillance area population for 2015. Incidence is calculated for confirmed infections alone and for confirmed or CIDT positive–only infections combined. A negative binomial model with 95% confidence intervals (CIs) was used to estimate changes in incidence of confirmed bacterial and parasitic infections and confirmed or CIDT positive–only bacterial infections in 2016 compared with 2013–2015, adjusting for changes in the surveillance population over time. For STEC, incidence is reported for all STEC serogroups combined because it is not possible to distinguish between serogroups using CIDTs. Insufficient data were available to assess change for Cyclospora. For HUS, the 2015 incidence was compared with incidence during 2012–2014.

Cases of Infection, Incidence, and Trends

During 2016, FoodNet identified 24,029 cases, 5,512 hospitalizations, and 98 deaths caused by confirmed or CIDT positive–only infections. The largest number of confirmed or CIDT positive–only infections in 2016 was reported for Campylobacter (8,547), followed by Salmonella (8,172), Shigella (2,913), STEC (1,845), Cryptosporidium (1,816), Yersinia (302), Vibrio (252), Listeria (127), and Cyclospora (55). The proportion of infections that were CIDT positive without culture confirmation in 2016 was largest for Campylobacter (32%) and Yersinia (32%), followed by STEC (24%), Shigella (23%), Vibrio (13%), and Salmonella (8%). The overall increase in CIDT positive–only infections for these six pathogens in 2016 was 114% (range = 85%–1,432%) compared with 2013–2015. Among infections with a positive CIDT result in 2016, a reflex culture was attempted on approximately 60% at either a clinical or state public health laboratory. The proportion of attempted reflex cultures differed by pathogen, ranging from 45% for Campylobacter to 86% for STEC and 88% for Vibrio. Among infections for which reflex culture was performed, the proportion of infections that were positive was highest for Salmonella (88%) and STEC (87%), followed by Shigella (64%), Yersinia (59%), Campylobacter (52%), and Vibrio (46%).

The incidence of confirmed infections and of confirmed or CIDT positive–only infections per 100,000 persons was highest for Campylobacter (confirmed = 11.79; confirmed or CIDT positive–only = 17.43) and Salmonella (15.40; 16.66), followed by Shigella (4.60; 5.94), Cryptosporidium (3.64; N/A**), STEC (2.85; 3.76), Yersinia (0.42; 0.62), and lowest for Vibrio (0.45; 0.51), Listeria (0.26; N/A), and Cyclospora (0.11; N/A). Compared with 2013–2015, the 2016 incidence of Campylobacter infection was significantly lower (11% decrease) when including only confirmed infections, yet was not significantly different when including confirmed or CIDT positive–only infections. Incidence of STEC infection was significantly higher for confirmed infections (21% increase) and confirmed or CIDT positive–only infections (43% increase). Similarly, the incidence of Yersinia infection was significantly higher for both confirmed (29% increase) and confirmed or CIDT positive–only infections (91% increase). Incidence of confirmed Cryptosporidium infection was also significantly higher in 2016 compared with 2013–2015 (45% increase).

Among 7,554 confirmed Salmonella cases in 2016, serotype information was available for 6,583 (87%). The most common serotypes were Enteritidis (1,320; 17%), Newport (797; 11%), and Typhimurium (704; 9%). The incidence in 2016 compared with 2013–2015 was significantly lower for Typhimurium (18% decrease; CI = 7%–21%) and unchanged for Enteritidis and Newport. Among 208 (95%) speciated Vibrio isolates, 103 (50%) were V. parahaemolyticus, 35 (17%) were V. alginolyticus, and 26 (13%) were V. vulnificus. Among 1,394 confirmed and serogrouped STEC cases, 503 (36%) were STEC O157 and 891 (64%) were STEC non-O157. Among 586 (70%) STEC non-O157 isolates, the most common serogroups were O26 (190; 21%), O103 (178; 20%), and O111 (106; 12%). Compared with 2013–2015, the incidence of STEC non-O157 infections in 2016 was significantly higher (26% increase; CI = 9%–46%) and the incidence of STEC O157 was unchanged.

FoodNet identified 62 cases of postdiarrheal HUS in children aged <18 years (0.56 cases per 100,000) in 2015; 33 (56%) occurred in children aged <5 years (1.18 cases per 100,000). Compared with 2012–2014, in 2015, no significant differences in incidence among all children or children aged <5 years were observed.

Discussion

The number of CIDT positive–only infections reported to FoodNet has been increasing markedly since 2013, as more clinical laboratories adopt CIDTs. Initially, increases were primarily limited to Campylobacter and STEC; followed by substantial increases in Salmonella and Shigella beginning in 2015 (6). The pattern continued in 2016, with large increases in the number of CIDT positive–only Vibrio and Yersinia infections. When including both confirmed and CIDT positive–only infections, incidence rates in 2016 were higher for each of these six pathogens. The increasing use of CIDTs presents challenges when interpreting the corresponding increases in incidence. For example, the incidence of confirmed Campylobacter infections in 2016 was significantly lower than the 2013–2015 average. However, when including CIDT positive–only infections, a slight but not significant increase occurred. For STEC and Yersinia, the incidence of confirmed infections alone and confirmed or CIDT positive–only infections in 2016 were both significantly higher than the 2013–2015 average; the magnitude of change approximately doubled when analyzing CIDT positive–only infections.

Because of the ease and increasing availability of CIDTs, testing for some pathogens might be increasing as health care provider behaviors and laboratory practices evolve (2). Among clinical laboratories in the FoodNet catchment, the use of CIDTs to detect Salmonella, for which the only CIDTs available are DNA-based gastrointestinal syndrome panels, increased from 2 per 460 laboratories (<1%) in 2013 to 59 per 421 laboratories (14%) in 2016 (FoodNet, unpublished data). This increased use paralleled significant increases in incidence of Cryptosporidium, STEC, and Yersinia, and slight but not significant increases in incidence of Campylobacter, Salmonella, Shigella, and Vibrio, all of which are also included in these panel tests. The increase in STEC incidence is driven by the increase in STEC non-O157, which is not typically included in routine stool culture testing because it requires specialized methods. Routine stool cultures performed in clinical laboratories typically include methods that identify only Salmonella, Campylobacter, Shigella, and for some laboratories, STEC O157 (4,5). The increased use of the syndrome panel tests might increase identification, and thus, improve incidence estimates of pathogens for which testing was previously limited.

Results are more quickly obtained using CIDTs than traditional culture methods (3). Because of this, health care providers might be more likely to order a CIDT than traditional culture (2). Increased testing might identify infections that previously would have remained undiagnosed. However, sensitivity and specificity vary by test type. Evaluations of DNA-based syndrome panel tests have indicated high sensitivity and specificity for most targets (3). However, among pathogens for which antigen-based CIDTs are often used, such as Campylobacter and Cryptosporidium, sensitivity and specificity have varied more widely, with a large number of false positive results (7,8). Including CIDT positive infections to calculate incidence, some of which could be false positives, might provide an inaccurate estimate. When interpreting incidence and trends in light of changing diagnostic testing, considering frequency of testing, sensitivity, and specificity of these tests is important. The observed increases in incidence of confirmed or CIDT positive–only infections in 2016 compared with 2013–2015 could be caused by increased testing, varying test sensitivity, an actual increase in infections, or a combination of these reasons.

These changes in testing are also important to consider when monitoring progress toward Healthy People 2020 objectives.†† The current objectives were created before the use of CIDTs and were based on confirmed infections. In the future, just as incidence measures should adjust for these changes, objectives should also be evaluated in light of changing diagnostics.

CIDTs pose additional challenges because they do not yield the bacterial isolates necessary for essential public health surveillance activities, such as monitoring trends in pathogen subtypes, conducting molecular testing, detecting outbreaks and implicating vehicles, and determining antimicrobial susceptibility. Reflex culture performed to yield an isolate places an additional burden on laboratories’ budgets, personnel, and time. Specimen submission requirements differ by state and pathogen, and this responsibility often falls to state public health laboratories (9). As CIDT use increases and more pathogens are affected, state public health laboratories will be challenged to sufficiently increase their testing capacity and will likely have to prioritize specimens on which to perform reflex culture (10). Clinical laboratories should review state specimen submission requirements and the Association of Public Health Laboratories guidelines§§ for reflex culture and submission of CIDT positive specimens.

The findings in this report are subject to at least two limitations. First, the changing diagnostic landscape with unknown changes in frequency of testing, varying test performance, and decreasing availability of isolates for subtyping make interpreting incidence and trends more difficult. Second, changes in health care–seeking behavior, access to health services, or other population characteristics might have changed since the comparison period, which could affect incidence.

Foodborne illness remains a substantial public health concern in the United States. Previous analyses have indicated that the number of infections far exceeds those diagnosed; CIDTs might be making those infections more visible (11). Most foodborne infections can be prevented, and substantial progress has been made in the past in decreasing contamination of some foods and reducing illness caused by some pathogens. More prevention measures are needed. Surveillance data can provide information on where to target these measures. However, to accurately interpret FoodNet surveillance data in light of changes in diagnostic testing, more data and analytic tools are needed to adjust for changes in testing practices and differences in test characteristics. FoodNet is collecting more data and developing those tools. With these, FoodNet will continue to track the needed progress toward reducing foodborne illness.

Acknowledgments

Foodborne Diseases Active Surveillance Network staff members, Emerging Infections Program; Brittany Behm, Staci Dixon, Elizabeth Greene, Jennifer Huang, Clare Wise, and FoodNet Fast Development Team, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC.

Veal products recalled due to possible E. coli O26 and O45 contamination

Gold Medal Packing Inc., a Rome, N.Y. establishment, is recalling approximately 4,607 pounds of boneless veal products that may be contaminated with E. coli O26 and O45, the U.S. Department of Agriculture’s Food Safety and Inspection Service (FSIS) announced today.

veal-cutsThe veal trim and top bottom sirloin (TBS) products were produced and packaged on August 16, 2016, and October 25, 2016. The following products are subject to recall: [View Label (PDF only)]

60-lb. boxes containing “BONELESS VEAL”.

2,387-lb. bin containing “TBS”.

The products subject to recall bear establishment number “EST. 17965” inside the USDA mark of inspection. The “BONELESS VEAL” items were shipped to a warehouse in California and the “TBS” items were shipped to distributor locations in Pennsylvania.

The problem was discovered during routine sample testing. There have been no confirmed reports of illness or adverse reactions due to consumption of these products.

Many clinical laboratories do not test for non-O157 Shiga toxin-producing E. coli (STEC), such as STEC O26 or O45, because they are harder to identify than STEC O157. People can become ill from STECs 2–8 days (average of 3–4 days) after consuming the organism. Most people infected with STEC O26 or O45 develop diarrhea (often bloody), and vomiting. Some illnesses last longer and can be more severe. Infection is usually diagnosed by testing of a stool sample. Vigorous rehydration and other supportive care is the usual treatment; antibiotic treatment is generally not recommended.

Cook it: Toxo in pork

Toxoplasma gondii is one of the leading foodborne pathogens in the United States.

The Centers for Disease Control and Prevention (CDC) reported that T. gondii accounts for 24% of deaths due to foodborne illness in the United States.

raw-meat-120607Consumption of undercooked pork products in which T. gondii has encysted has been identified as an important route of human exposure. However, little quantitative evaluation of risk due to different pork products as a function of microbial quality at the abattoir, during the production process, and due to consumer handling practices is available to inform risk management actions.

The goal of this study was to develop a farm-to-table quantitative microbial risk assessment (QMRA) model to predict the public health risk associated with consumption of fresh pork in the United States.

T. gondii prevalence in pigs was derived through a meta-analysis of existing data, and the concentration of the infectious life stage (bradyzoites) was calculated for each pork cut from an infected pig. Logistic regression and log-linear regression models were developed to predict the reduction of T. gondii during further processing and consumer preparation, respectively. A mouse-derived exponential dose-response model was used to predict infection risk in humans. The estimated mean probability of infection per serving of fresh pork products ranges from 3.2 × 10−7 to 9.5 × 10−6, corresponding to a predicted approximately 94,600 new infections annually in the U.S. population due to fresh pork ingestion. Approximately 957 new infections per year were estimated to occur in pregnant women, corresponding to 277 cases of congenital toxoplasmosis per year due to fresh pork ingestion.

In the context of available data, sensitivity analysis suggested that cooking is the most important parameter impacting human health risk. This study provides a scientific basis for risk management and also could serve as a baseline model to quantify infection risk from T. gondii and other parasites associated with meat products.

Quantifying the risk of human Toxoplasma gondii infection due to consumption of fresh pork in the United States

Food Control, Volume 73, Part B, March 2017, Pages 1210–1222

Miao Guo, Elisabetta Lambertini, Robert L. Buchanan, Jitender P. Dubey, Dolores E. Hill, H. Ray Gamble, Jeffrey L. Jones, Abani K. Pradhan

http://www.sciencedirect.com/science/article/pii/S0956713516305825

Campy increasing in Sweden

An unusually high number of people have been struck by Campylobacter in Sweden this winter, resulting in a less than festive combination of vomiting, diarrhea and stomach pains.

vomit-birdThe number of infections usually peaks during the late summer months then drops off, but this year has yet to see a notable downward curve, Sweden’s Public Health Agency (Folkhälsomyndigheten) warns.

The growth coincides with an increase in campylobacter among flocks of chicken in Sweden, and fresh chicken is therefore thought to be a culprit.

 “The explanation we have right now is that we eat a lot of chicken. We eat a lot of fresh chicken, and campylobacter can be found in the fresh chicken to a certain extent,” Folkhälsomyndigheten spokesperson Britta Björkholm noted.

“If you’re not careful with your hygiene you risk coming down with it,” she added.

Between August and November 2016 twice as many cases were reported as normal, and that pattern has continued into the last month of the year.

About 100 cases are usually reported in December, but in December 2016 the number was almost 300 by the middle of the month.

“People are not being sufficiently careful about separating raw chicken from utensils and work surfaces,” Björkholm insisted.

Resistant Salmonella causes 6,200 illnesses a year in US

Chris Dall of the Center for Infectious Disease Research Policy reports the U.S. Centers for Disease Control and Prevention (CDC) has published new estimates of the incidence of antibiotic-resistant Salmonella infections in the United States, putting the burden at about 6,200 cases annually.

ab-res-salmIn a report in Emerging Infectious Diseases, CDC researchers estimate the overall incidence of resistant salmonella infections as roughly 2 for 100,000 persons per year from 2004 to 2012They also determined that clinically important resistance was linked to four specific Salmonella serotyopes: Enteritidis, Newport, Typhimurium, and Heidelberg.

Nontyphoidal Salmonella causes an estimated 1.2 million foodborne illnesses and about 450 deaths each year, according to the CDC. While most people who get Salmonella infections recover within a week and do not require antibiotics, more severe infections are generally treated with either ampicillin, ceftriaxone, or ciprofloxacin. Resistance to these drugs can result in increased hospitalization, invasive illnesses, and death.

The new estimates are based on data from the US Census Bureau and from two surveillance systems the CDC uses to track Salmonella and drug-resistant Salmonella: The National Antimicrobial Resistance Monitoring System (NARMS) and the Laboratory-based Enteric Disease Surveillance (LEDS) system. NARMS monitors resistance in Salmonella by testing isolates from infected individuals and determining the percentage of isolates that show resistance. LEDS collects Salmonella surveillance data, including serotypes, from state and territorial public health labs.

The researchers defined three mutually exclusive categories of resistance for the study: ampicillin-only resistance, ceftriaxone/ampicillin resistance, and ciprofloxacin nonsusceptibility.

According to the LEDS data, there were 369,254 culture-confirmed Salmonella infections from 2004 through 2012. Four primary serotypes—Enteritidis, Typhimurium, Newport, and Heidelberg—accounted for 52% of all fully serotyped isolates. NARMS tested 19,410 isolates from 2004 through 2012, and overall resistance was detected in 2,320 isolates. Ampicillin-only resistance was the most common resistance pattern detected, followed by ceftriaxone/ampicillin resistance and ciprofloxacin nonsusceptibility.

Using these data, the researchers determined that from 2004 to 20012 there were approximately 6,200 resistant culture-confirmed infections annually. Overall incidence was 1.93/100,000 person-years for any clinically important resistance, 1.07 for ampicillin-only resistance, .51 for ceftriaxone/ampicillin resistance, and .35 for ciprofloxacin nonsusceptibility.

The authors note that while Enteritidis, Typhimurium, Newport, and Heidelberg account for only half of all culture-confirmed Salmonella infections, the four serotypes accounted for 73% of the Salmonella infections that involved clinically important resistance.

The predominance of these four serotypes, they write, reflects their ability to persist in food animals, be transmitted through the food system, and cause illness. It also suggests that strategies to reduce Salmonella infections caused by these four serotypes could have an impact on the incidence of resistant infections overall.

“The 4 major serotypes that have been driving the incidence of resistant infections should continue to be high priorities in combating resistance,” the authors write.

The report also notes that two of these serotypes—Typhimurium and Newport—have been associated with outbreaks of drug-resistant Salmonella infections linked to contaminated meat, which highlights the need for NARMS to continue monitoring emerging resistance patterns by serotype.

The authors caution, however, that while this estimate of resistant Salmonella infection incidence will help define the magnitude of the problem and guide prevention efforts, it might be telling only part of the story. That’s because it relies on culture-confirmed infections only.

The CDC has estimated that for every culture-confirmed case of Salmonella, there may as many as 29 undetected cases. That could put the annual US incidence as high as 180,000 cases.

E. coli O26, HUS and dairy

In their recent article in Eurosurveillance, Germinario et al. describe a community-wide outbreak of Shiga toxin 2-producing Escherichia coli (STEC) O26:H11 infections associated with haemolytic uraemic syndrome (HUS) and involving 20 children between 11 and 78 months of age in southern Italy during the summer 2013 [1]. The investigation identified an association between STEC infection and consumption of dairy products from two local milk-processing establishments. We underline striking similarities to a recent multi-country STEC O26 outbreak in Romania and Italy and discuss the challenges that STEC infections and their surveillance pose at the European level.

e-coli-colbertIn March 2016, Peron et al. published, also in Eurosurveillance, early findings of the investigation of a community-wide STEC infection outbreak in southern Romania [2]. As at 29 February 2016, 15 HUS cases with onset of symptoms after 24 January 2016, all but one in children less than two years of age, had been identified, three of whom had died. Aetiological confirmation was retrospectively performed through serological diagnosis and six cases were confirmed with STEC O26 infection. Shortly after this publication, and following the identification of the first epidemiologically-linked case in central Italy, the European Centre for Disease Prevention and Control (ECDC) and the European Food Safety Authority (EFSA) published a joint Rapid Outbreak Assessment [3]. The Italian and Romanian epidemiological, microbiological and environmental investigations implicated products from a milk-processing establishment in southern Romania as a possible source of infection. The dairy plant exported milk products to at least four European Union (EU) countries. The plant was closed in March 2016 and the implicated food products recalled or withdrawn from the retail market.

Pulsed Field Gel Electrophoresis (PFGE) and whole genome sequencing (WGS) analyses did not establish a microbiological link between the Italian (2013) and the Romanian/Italian (2016) outbreaks (personal communication, Stefano Morabito, October 2016). However, the epidemiological similarities between the two community-wide outbreaks associated with HUS and STEC O26 infections, mostly affecting young children and implicating dairy products, are notable. While raw milk and unpasteurised dairy products are well known potential sources of STEC infection, milk products, as highlighted by Germinaro et al. [1], have been rarely implicated in community-wide STEC outbreaks in the past, emphasising an emerging risk of STEC O26 infection associated with milk products.

Reporting of STEC O26 infections has been steadily increasing in the EU since 2007, partly due to improved diagnostics of non-O157 sero-pathotypes [4]. The attention to non-O157 STEC sero-pathotypes rose considerably after the severe STEC O104 outbreak that took place in Germany and France in 2011 during which almost 4,000 cases and more than 50 deaths were reported [5]. In light of the recently published outbreaks related to dairy products and the simultaneous increased reporting of isolations of STEC O26 from milk and milk products in the EU/European Economic Area (EEA) [6], strengthening STEC surveillance in humans and food and enhancing HUS surveillance in children less than five years of age is warranted. Paediatric nephrologists should be sensitised to this effect

Community-wide outbreaks of haemolytic uraemic syndrome associated with Shiga-toxin producing Escherichia coli O26 in Italy and Romania: A new challenge for the European Union

Eurosurveillance, Volume 21, Issue 49, 08 December 2016, DOI: http://dx.doi.org/10.2807/1560-7917.ES.2016.21.49.30420

E Severi, F Vial, E Peron, O Mardh, T Niskanen, J Takkinen

http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22664

Data says so: Australia does have a raw egg problem

Statistics show that the consumption of foods containing raw or minimally cooked eggs is currently the single largest source of foodborne Salmonella outbreaks in Australia.

garlic_aioliI based a large part of my research career on verifying the soundbite, ‘we have released guidelines’ or, ‘we follow all recommendations’ by arranging to have students see what actually goes on.

In October 2014, the New South Wales Food Authority released Food Safety Guidelines for the Preparation of Raw Egg Products (the Guidelines). Despite this, outbreaks continued to take place, particularly where business hygiene and temperature control issues were apparent. In addition, businesses and councils approached the Food Authority for advice on desserts containing raw eggs and other unusual raw egg dishes. As a result, the Guidelines were recently updated and give specific reference to Standard 3.2.2, Division 3, clause 7 of the Australia New Zealand Food Standards Code to ensure that only safe and suitable food is processed.

To reduce the risk of foodborne illness outbreaks caused by Salmonella, retail businesses are advised to avoid selling food containing raw or minimally cooked eggs. The Guidelines give food businesses that do sell food containing raw egg specific safety steps for its preparation and clear guidance and advice on what they must do to meet food safety regulations. The revised Food Safety Guidelines for the Preparation of Raw Egg Products is available at www. foodauthority.nsw.gov.au/_Documents/ retail/raw_egg_guidelines.pdf.

raw-eggsOr as the Australian Food Safety Information Council now says, buy, don’t make aioli or mayonnaise.

This is nice but of no use to consumers at a restaurant who order fish and chips  with a side of mayo or aioli. I’ve already begun an ad hoc investigation – because I don’t want my family to get sick – and can say that out of the 15 times I’ve asked over the past few years – is the aioli or mayo made at the restaurant or bought commercially – the server invariably returns and proclaims, We only use raw eggs in our aioli or mayo.

Wrong answer.

Only once, so far, has an owner or chef said, we know of the risk, we only use the bought stuff. And they’re ex-pat Canadians.

Giv’r, eh.

A table of Australian egg outbreaks is available at http://barfblog.com/wp-content/uploads/2015/10/raw-egg-related-outbreaks-australia-10-9-15.xlsx