Outbreak of Shiga toxin-producing E. coli O157 associated with consumption of watercress, United Kingdom, August to September 2013

Quantitative risk assessment of haemolytic uremic syndrome associated with beef consumption in Argentina

We developed a quantitative microbiological risk assessment (QMRA) of haemolytic uremic syndrome (HUS) associated with Shiga toxin-producing Escherichia coli (STEC)-contaminated beef (intact beef cuts, ground beef and commercial hamburgers) in children under 15 years of age from Argentina. The QMRA was used to characterize STEC prevalence and concentration levels in each product through the Argentinean beef supply chain, including cattle primary production, cattle transport, processing and storage in the abattoir, retail and home preparation, and consumption. Median HUS probability from beef cut, ground beef and commercial hamburger consumption was <10-15, 5.4x10-8 and 3.5x10-8, respectively. The expected average annual number of HUS cases was 0, 28 and 4, respectively. Risk of infection and HUS probability were sensitive to the type of abattoir, the application or not of Hazard Analysis and Critical Control Points (HACCP) for STEC (HACCP-STEC), stx prevalence in carcasses and trimmings, storage conditions from the abattoir to retailers and home, the joint consumption of salads and beef products, and cooking preference. The QMRA results showed that the probability of HUS was higher if beef cuts (1.7x) and ground beef (1.2x) were from carcasses provided by abattoirs not applying HACCP-STEC. Thus, the use of a single sanitary standard that included the application of HACCP-STEC in all Argentinean abattoirs would greatly reduce HUS incidence. The average number of annual HUS cases estimated by the QMRA (n = 32) would explain about 10.0% of cases in children under 15 years per year in Argentina. Since other routes of contamination can be involved, including those not related to food, further research on the beef production chain, other food chains, person-to-person transmission and outbreak studies should be conducted to reduce the impact of HUS on the child population of Argentina.

Investigation into a national outbreak of STEC O157:H7 associated with frozen beef burgers, UK, 2017

In November 2017, Public Health England identified an outbreak of Shiga toxin-producing Escherichia coli O157:H7 in England where whole genome sequencing results indicated cases were likely to be linked to a common source, and began investigations. Hypothesis generation included a review of enhanced surveillance data, a case-case study and trawling interviews. The hypothesis of interest was tested through the administration of focussed questionnaires and review of shopping history using loyalty card data. Twelve outbreak cases were detected, eight were hospitalised and four developed haemolytic uraemic syndrome. Frozen beef burgers supplied by a national retailer were identified as the vehicle of the outbreak. Testing of two left-over burger samples obtained from the freezers of two separate (unlinked) cases and a retained sample from the production premises were tested and found to be positive for the outbreak strain. A voluntary recall of the burgers was implemented by the retailer. Investigations at the production premises identified no contraventions of food safety legislation. Cooking guidance on the product packaging was deemed to be adequate and interviews with the cases/carers who prepared the burgers revealed no deficiencies in cooking practices at home. Given the long-shelf life of frozen burgers, the product recall likely prevented more cases.

Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: Neisseria meningitidis as a Proof of Concept

Whole genome sequencing is increasingly recognized as the most informative approach for characterization of bacterial isolates. Success of the routine use of this technology in public health laboratories depends on the availability of well-characterized and verified data analysis methods. However, multiple subtyping workflows are now often being used for a single organism, and differences between them are not always well described. Moreover, methodologies for comparison of subtyping workflows, and assessment of their performance are only beginning to emerge. Current work focuses on the detailed comparison of WGS-based subtyping workflows and evaluation of their suitability for the organism and the research context in question. We evaluated the performance of pipelines used for subtyping of Neisseria meningitidis, including the currently widely applied cgMLST approach and different SNP-based methods. In addition, the impact of the use of different tools for detection and filtering of recombinant regions and of different reference genomes were tested. Our benchmarking analysis included both assessment of technical performance of the pipelines and functional comparison of the generated genetic distance matrices and phylogenetic trees. It was carried out using replicate sequencing datasets of high- and low-coverage, consisting mainly of isolates belonging to the clonal complex 269. We demonstrated that cgMLST and some of the SNP-based subtyping workflows showed very good performance characteristics and highly similar genetic distance matrices and phylogenetic trees with isolates belonging to the same clonal complex. However, only two of the tested workflows demonstrated reproducible results for a group of more closely related isolates. Additionally, results of the SNP-based subtyping workflows were to some level dependent on the reference genome used. Interestingly, the use of recombination-filtering software generally reduced the similarity between the gene-by-gene and SNP-based methodologies for subtyping of N. meningitidis. Our study, where N. meningitidis was taken as an example, clearly highlights the need for more benchmarking comparative studies to eventually contribute to a justified use of a specific WGS data analysis workflow within an international public health laboratory context.

Escherichia coli strains producing a novel Shiga toxin 2 subtype circulate in China

Shiga toxin (Stx) is the key virulence factor in Shiga toxin producing Escherichia coli (STEC), which can cause diarrhea and hemorrhagic colitis with life-threatening complications. Stx comprises two toxin types, Stx1 and Stx2. Several Stx1/Stx2 subtypes have been identified in E. coli, which are variable in sequences, toxicity and host specificity. Here, we report the identification of a novel Stx2 subtype, designated Stx2k, in E. coli strains widely detected from diarrheal patients, animals, and raw meats in China over time. Stx2k exhibits varied cytotoxicity in vitro among individual strains. The Stx2k converting prophages displayed considerable heterogeneity in terms of insertion site, genetic content and structure. Whole genome analysis revealed that the stx_2k-containing strains were genetically heterogeneous with diverse serotypes, sequence types, and virulence gene profiles. The nine stx_2k-containing strains formed two major phylogenetic clusters closely with strains belonging to STEC, enterotoxigenic E. coli (ETEC), and STEC/ETEC hybrid. One stx_2k-containing strain harbored one plasmid-encoded heat-stable enterotoxin sta gene and two identical copies of chromosome-encoded stb gene, exhibiting STEC/ETEC hybrid pathotype. Our finding enlarges the pool of Stx2 subtypes and highlights the extraordinary genomic plasticity of STEC strains. Given the wide distribution of the Stx2k-producing strains in diverse sources and their pathogenic potential, Stx2k should be taken into account in epidemiological surveillance of STEC infections and clinical diagnosis.

Outbreaks of Shiga Toxin-Producing Escherichia coli Linked to Sprouted Seeds, Salad, and Leafy Greens: A Systematic Review

Shiga toxin-producing Escherichia coli (STEC) outbreaks involving ready-to-eat salad products have been described in the scientific literature since 1995. These products typically do not undergo a definitive control step such as cooking to eliminate pathogens. To reduce the number of STEC infections from salad products, efforts will need to focus on preventing and reducing contamination throughout the food chain. We performed a systematic review of STEC outbreaks involving sprouted seeds, salad, or leafy green products to determine whether there were recurrent features, such as availability of microbiological evidence or identification of the contamination event, which may inform future investigations and prevention and control strategies. Thirty-five STEC outbreaks linked to contaminated leafy greens were identified for inclusion. The outbreaks occurred from 1995 to 2018 and ranged from 8 to more than 8,500 cases. Detection of STEC in the food product was rare (4 of 35 outbreaks). For the remaining outbreaks, the determination of leafy greens as the source of the outbreak mainly relied on analytical epidemiology (20 of 35) or descriptive evidence (11 of 35). The traceback investigation in 21 of 32 outbreaks was not able to identify possible routes leading to where the STEC bacteria came from or how the leaves were contaminated. Investigations in eight outbreaks found poor practice during processing that may have contributed to the outbreak, such as insufficient postharvest disinfection of the product. Six outbreak investigations were able to identify the outbreak strain in animal feces near the growing fields; two of these were also able to find it in irrigation water on the farms, providing a likely route of contamination. These results highlight the limitations of relying on microbiological confirmation as a basis to initiate investigations of upstream production to understand the source of contamination. This review also demonstrates the importance of, and difficulties associated with, food-chain traceback studies to inform control measures and future prevention.

National outbreak of Shiga toxin-producing Escherichia coli O157:H7 linked to mixed salad leaves, United Kingdom, 2016

We investigated a large outbreak of Escherichia coli O157 in the United Kingdom (UK) with 165 cases between 31 May and 29 July 2016. No linked cases were reported in other countries. Cases were predominately female (n = 128) and adult (n = 150), 66 attended hospital and nine had features of haemorrhagic uraemic syndrome. A series of epidemiological studies (case-control, case-case, ingredients-based and venue-based studies) and supply chain investigations implicated mixed salad leaves from Supplier A as the likely outbreak vehicle. Whole genome sequencing (WGS) indicated a link with strains from the Mediterranean and informed the outbreak control team to request that Supplier A cease distributing salad leaves imported from Italy. Microbiological tests of samples of salad leaves from Supplier A were negative. We were unable to confirm the source of contamination or the contaminated constituent leaf although our evidence pointed to red batavia received from Italy as the most likely vehicle. Variations in Shiga toxin-producing E.coli surveillance and diagnosis may have prevented detection of cases outside the UK and highlights a need for greater standardisation. WGS was useful in targeting investigations, but greater coverage across Europe is needed to maximise its potential.

Online market research panel members as controls in case-control studies to investigate gastrointestinal disease outbreaks: early experiences and lessons learnt from the UK

Established methods of recruiting population controls for case–control studies to investigate gastrointestinal disease outbreaks can be time consuming, resulting in delays in identifying the source or vehicle of infection. After an initial evaluation of using online market research panel members as controls in a case–control study to investigate a Salmonella outbreak in 2013, this method was applied in four further studies in the UK between 2014 and 2016. We used data from all five studies and interviews with members of each outbreak control team and market research panel provider to review operational issues, evaluate risk of bias in this approach and consider methods to reduce confounding and bias. The investigators of each outbreak reported likely time and cost savings from using market research controls. There were systematic differences between case and control groups in some studies but no evidence that conclusions on the likely source or vehicle of infection were incorrect. Potential selection biases introduced by using this sampling frame and the low response rate are unclear. Methods that might reduce confounding and some bias should be balanced with concerns for overmatching. Further evaluation of this approach using comparisons with traditional methods and population-based exposure survey data is recommended.

Epidemiological and Microbiological Investigation of an Outbreak of Severe Disease from Shiga Toxin-Producing Escherichia coli O157 Infection Associated with Consumption of a Slaw Garnish

Investigating outbreaks of Shiga toxin-producing Escherichia coli (STEC) in England is a priority due to the potential severity of disease. However, there are often challenges in investigating outbreaks due to the small numbers of cases, poor patient recall, and low levels of bacteria that are challenging to detect in food samples using traditional laboratory culture techniques, and frequently a source is not identified. In September 2014, we investigated an STEC O157 outbreak associated with consuming a slaw garnish, and we report our findings here. Twenty confirmed cases were identified. Outbreak cases were interviewed, and menus reviewed to identify dishes consumed outside the home. Cases shared a history of eating meals at different chain restaurants. Analysis of menu items indicated shared consumption of slaw garnishes by 85.6% cases, although just 35.7% reported consuming them during interviews. Whole-genome sequencing linked cases where interpretation of the multilocus variable number tandem repeat analysis profile was obscured and indicated that the strain originated from a domestic (i.e., United Kingdom) source. Traceback identified that carrots and cabbages grown in the United Kingdom were the likely source of infection. Samples of products were examined, but STEC was not recovered. Epidemiological investigations linked the outbreak to consumption of a slaw garnish, which was poorly recalled by cases, and likely comprised of domestically produced raw vegetables. The causative organism was not isolated from food samples, and we conclude that future investigations should include sampling of animals and wildlife in the vicinity of farms where implicated produce is grown.

Are ready-to-eat salads ready to eat? An outbreak of Salmonella Coeln linked to imported, mixed, pre-washed and bagged salad, Norway, November 2013

We investigated a nationwide outbreak of Salmonella Coeln in Norway, including 26 cases identified between 20 October 2013 and 4 January 2014. We performed a matched case-control study, environmental investigation and detailed traceback of food purchases to identify the source of the outbreak. In the case-control study, cases were found to be more likely than controls to have consumed a ready-to-eat salad mix (matched odds ratio 20, 95% confidence interval 2·7-∞). By traceback of purchases one brand of ready-to-eat salad was indicated, but all environmental samples were negative for Salmonella. This outbreak underlines that pre-washed and bagged salads carry a risk of infection despite thorough cleaning procedures by the importer. To further reduce the risk of infection by consumption of ready-to-eat salads product quality should be ensured by importers. Outbreaks linked to salads reinforce the importance of implementation of appropriate food safety management systems, including good practices in lettuce production.

A large Great Britain-wide outbreak of STEC O157 phage type 8 linked to handling of raw leeks and potatoes

Between December 2010 and July 2011, 252 cases of STEC O157 PT8 stx1 + 2 infection were reported in England, Scotland and Wales. This was the largest outbreak of STEC reported in England and the second largest in the UK to date. Eighty cases were hospitalized, with two cases of haemolytic uraemic syndrome and one death reported. Routine investigative data were used to generate a hypothesis but the subsequent case-control study was inconclusive. A second, more detailed, hypothesis generation exercise identified consumption or handling of vegetables as a potential mode of transmission. A second case-control study demonstrated that cases were more likely than controls to live in households whose members handled or prepared leeks bought unwrapped [odds ratio (OR) 40, 95% confidence interval (CI) 2·08-769·4], and potatoes bought in sacks (OR 13·13, 95% CI 1·19-145·3). This appears to be the first outbreak of STEC O157 infection linked to the handling of leeks.

Public Health Investigation of Two Outbreaks of Shiga Toxin-Producing Escherichia coli O157 Associated with Consumption of Watercress

An increase in the number of cases of Shiga toxin-producing Escherichia coli (STEC) O157 phage type 2 (PT2) in England in September 2013 was epidemiologically linked to watercress consumption. Whole-genome sequencing (WGS) identified a phylogenetically related cluster of 22 cases (outbreak 1). The isolates comprising this cluster were not closely related to any other United Kingdom strain in the Public Health England WGS database, suggesting a possible imported source. A second outbreak of STEC O157 PT2 (outbreak 2) was identified epidemiologically following the detection of outbreak 1. Isolates associated with outbreak 2 were phylogenetically distinct from those in outbreak 1. Epidemiologically unrelated isolates on the same branch as the outbreak 2 cluster included those from human cases in England with domestically acquired infection and United Kingdom domestic cattle. Environmental sampling using PCR resulted in the isolation of STEC O157 PT2 from irrigation water at one implicated watercress farm, and WGS showed this isolate belonged to the same phylogenetic cluster as outbreak 2 isolates. Cattle were in close proximity to the watercress bed and were potentially the source of the second outbreak. Transfer of STEC from the field to the watercress bed may have occurred through wildlife entering the watercress farm or via runoff water. During this complex outbreak investigation, epidemiological studies, comprehensive testing of environmental samples, and the use of novel molecular methods proved invaluable in demonstrating that two simultaneous outbreaks of STEC O157 PT2 were both linked to the consumption of watercress but were associated with different sources of contamination.

Control selection methods in recent case-control studies conducted as part of infectious disease outbreaks

Successful investigation of national outbreaks of communicable disease relies on rapid identification of the source. Case-control methodologies are commonly used to achieve this. We assessed control selection methods used in recently published case-control studies for methodological and resource issues to determine if a standard approach could be identified. Neighbourhood controls were the most frequently used method in 53 studies of a range of different sizes, infections and settings. The most commonly used method of data collection was face to face interview. Control selection issues were identified in four areas: method of identification of controls, appropriateness of controls, ease of recruitment of controls, and resource requirements. Potential biases arising from the method of control selection were identified in half of the studies assessed. There is a need to develop new ways of selecting controls in a rapid, random and representative manner to improve the accuracy and timeliness of epidemiological investigations and maximise the effectiveness of public health interventions. Innovative methods such as prior recruitment of controls could improve timeliness and representativeness of control selection.

Veterinary Public Health Approach to Managing Pathogenic Verocytotoxigenic Escherichia coli in the Agri-Food Chain

Verocytoxigenic Escherichia coli (VTEC) comprises many diverse serogroups, but seven serogroups, O157, O26, O103, O145, O111, O21, and O45, have been most commonly linked to severe human infections, though illness has also been reported from a range of other VTEC serogroups. This poses challenges in assessing the risk to humans from the diverse range of VTEC strains that may be recovered from animals, the environment, or food. For routine assessment of risk posed by VTEC recovered from the agri-food chain, the concept of seropathotype can be used to rank the human risk potential from a particular VTEC serogroup on the basis of both serotype (top seven serogroups) and the presence of particular virulence genes (vt in combination with eae, or aaiC plus aggR). But for other VTEC serogroups or virulence gene combinations, it is not currently possible to fully assess the risk posed. VTEC is shed in animal feces and can persist in the farm environment for extended periods ranging from several weeks to many months, posing an ongoing reservoir of contamination for grazing animals, water courses, and fresh produce and for people using farmland for recreational purposes. Appropriate handling and treatment of stored animal waste (slurries and manures) will reduce risk from VTEC in the farm environment. Foods of animal origin such as milk and dairy products and meat may be contaminated with VTEC during production and processing, and the pathogen may survive or grow during processing operations, highlighting the need for well-designed and validated Hazard Analysis Critical Control Point management systems. This article focuses on a veterinary public health approach to managing VTEC, highlighting the various routes in the agri-food chain for transmission of human pathogenic VTEC and general approaches to managing the risk.

E. coli O157 outbreaks in the United Kingdom: past, present, and future

This review describes Escherichia coli O157 outbreaks in the United Kingdom, beginning from the first, in the 1980s, to those recorded in 2013. We point out that the United Kingdom differs from other countries, particularly the United States, in that it has had a considerable number of outbreaks associated with butchers, but very few caused by contaminated burgers. Two of the butcher-associated outbreaks (in central Scotland in 1996 and South Wales in 2005) were very large and are considered here in detail; the reviewer conducted detailed investigations into both outbreaks. Also considered is the very large outbreak that occurred in visitors to an open farm in Surrey in 2009. Detailed descriptions of some milk-borne outbreaks and incidents connected with camping and childrens' nurseries have been published, and these are also considered in this review. Large outbreaks in the United Kingdom have sometimes led to policy developments regarding food safety, and these are considered, together with public reactions to them, their health effect, and their value, as examples to follow or eschew in terms of the procedures to be adopted in response to incidents of this kind. Regulatory and legal consequences are also considered. As a wise man said, making predictions is difficult, particularly about the future. This review follows this position but points out that although human infections caused by E. coli O157 are rare in the United Kingdom, their incidence has not changed significantly in the last 17 years. This review points out that although a response to an outbreak is to say "lessons must be learned", this response has been tempered by forgetfulness. Accordingly, this review restricts its recommendations regarding outbreaks to two: the crucial importance of a rapid response and the importance of experience, and even "gut feeling", when an inspector is evaluating the safety of a food business.

Reducing the barriers against analytical epidemiological studies in investigations of local foodborne disease outbreaks in Germany – a starter kit for local health authorities

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