Thomas Inns

A multi-country Salmonella Enteritidis phage type 14b outbreak associated with eggs from a German producer: 'near real-time' application of whole genome sequencing and food chain investigations, United Kingdom, May to September 2014.

We report an outbreak of Salmonella Enteritidis phage type 14b (PT14b) in the United Kingdom (UK) between May and September 2014 where Public Health England launched an investigation to identify the source of infection and implement control measures. During the same period, outbreaks caused by a Salmonella Enteritidis strain with a specific multilocus variable-number tandem repeat analysis (MLVA) profile occurred in other European Union Member States. Isolates from a number of persons affected by the UK outbreak, who had initially been tested by MLVA also shared this particular profile. Cases were defined as any person infected with S. Enteritidis PT14b, resident in England or Wales and without history of travel outside of this geographical area during the incubation period, reported from 1 June 2014 onwards, with a MLVA profile of 2–11–9-7–4-3–2-8–9 or a single locus variant thereof. In total, 287 cases met the definition. Food traceback investigations in the UK and other affected European countries linked the outbreaks to chicken eggs from a German company. We undertook whole genome sequencing of isolates from UK and European cases, implicated UK premises, and German eggs: isolates were highly similar. Combined with food traceback information, this confirmed that the UK outbreak was also linked to a German producer.

Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis.

Since April 2015, whole genome sequencing (WGS) has been the routine test for Salmonella identification, surveillance and outbreak investigation at the national reference laboratory in England and Wales. In May 2015, an outbreak of Salmonella Enteritidis cases was detected using WGS data and investigated. UK cases were interviewed to obtain a food history and links between suppliers were mapped to produce a food chain network for chicken eggs. The association between the food chain network and the phylogeny was explored using a network comparison approach. Food and environmental samples were taken from premises linked to cases and tested for Salmonella. Within the outbreak single nucleotide polymorphism defined cluster, 136 cases were identified in the UK and 18 in Spain. One isolate from a food containing chicken eggs was within the outbreak cluster. There was a significant association between the chicken egg food chain of UK cases and phylogeny of outbreak isolates. This is the first published Salmonella outbreak to be prospectively detected using WGS. This outbreak in the UK was linked with contemporaneous cases in Spain by WGS. We conclude that UK and Spanish cases were exposed to a common source of Salmonella-contaminated chicken eggs.

Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network

Outbreaks of Salmonella Enteritidis have long been associated with contaminated poultry and eggs. In the summer of 2014 a large multi-national outbreak of Salmonella Enteritidis phage type 14b occurred with over 350 cases reported in the United Kingdom, Germany, Austria, France and Luxembourg. Egg supply network investigation and microbiological sampling identified the source to be a Bavarian egg producer. As part of the international investigation into the outbreak, over 400 isolates were sequenced including isolates from cases, implicated UK premises and eggs from the suspected source producer. We were able to show a clear statistical correlation between the topology of the UK egg distribution network and the phylogenetic network of outbreak isolates. This correlation can most plausibly be explained by different parts of the egg distribution network being supplied by eggs solely from independent premises of the Bavarian egg producer (Company X). Microbiological sampling from the source premises, traceback information and information on the interventions carried out at the egg production premises all supported this conclusion. The level of insight into the outbreak epidemiology provided by whole-genome sequencing (WGS) would not have been possible using traditional microbial typing methods.

Outbreak of mumps in a school setting, United Kingdom, 2013

Effective protection against mumps can be achieved through 2 doses of the measles-mumps-rubella (MMR) vaccine. However, outbreaks of mumps have recently been described among populations with high vaccination coverage, including 2 doses of MMR. Here we describe an outbreak at a school in the East of England, UK. The school was attended by 540 pupils aged 10–19 years and had 170 staff. In total, 28 cases of mumps (24 pupils and 4 staff) were identified during 10 January to 16 March 2013. Vaccination status was known in 25 of the cases, and among these 21 (84.0%) had a documented history of 2 doses of MMR while the remaining had a history of one dose (2/25 cases, 8.0%) or no doses (2/25, 8.0%) of MMR. An outbreak control team recommended that MMR vaccine should be offered to all pupils whose parents consented to it, regardless of previous vaccination status. Additional MMR vaccines were administered to 103 pupils, including 76 (73.8%) third doses of MMR. Offering an additional dose of MMR appeared to be acceptable to parents, and we found it feasible to administer the intervention in a timely manner with resources from the local Public Health Centre (Primary Care Trust). An additional dose of MMR to all individuals at risk can be considered as an acceptable control measure for mumps outbreaks in schools even if the vaccination coverage is high. However, further evidence on the effectiveness, acceptability, and safety of this intervention is needed.

Outbreak of Salmonella enterica Goldcoast infection associated with whelk consumption, England, June to October 2013.

An increase in the number of cases of Salmonella enterica serotype Goldcoast infection was observed in England during September 2013. A total of 38 cases were reported, with symptom onset dates between 21 June and 6 October 2013. Epidemiological, environmental, microbiological and food chain evidence all support the conclusion that this outbreak was associated with eating whelks processed by the same factory. Whelks are a novel vehicle of Salmonella infection and should be considered when investigating future outbreaks.

The potential impact of media reporting in syndromic surveillance: an example using a possible Cryptosporidium exposure in North West England, August to September 2015

During August 2015, a boil water notice (BWN) was issued across parts of North West England following the detection of Cryptosporidium oocysts in the public water supply. Using prospective syndromic surveillance, we detected statistically significant increases in the presentation of cases of gastroenteritis and diarrhoea to general practitioner services and related calls to the national health telephone advice service in those areas affected by the BWN. In the affected areas, average in-hours general practitioner consultations for gastroenteritis increased by 24.8% (from 13.49 to 16.84) during the BWN period; average diarrhoea consultations increased by 28.5% (from 8.33 to 10.71). Local public health investigations revealed no laboratory reported cases confirmed as being associated with the water supply. These findings suggest that the increases reported by syndromic surveillance of cases of gastroenteritis and diarrhoea likely resulted from changes in healthcare seeking behaviour driven by the intense local and national media coverage of the potential health risks during the event. This study has further highlighted the potential for media-driven bias in syndromic surveillance, and the challenges in disentangling true increases in community infection from those driven by media reporting.

Introduction of a new Rotavirus vaccine: Initial results of uptake and impact on laboratory confirmed cases in Anglia and Essex, United Kingdom, July 2015.

abstract Rotavirus gastroenteritis accounts for an estimated 130,000 GP consultations and 13,000 hospitalisations for children under 5 y old each year in England and Wales. In July 2013, an oral live attenuated rotavirus vaccine (Rotarix®) was introduced into the UK infant immunisation program as a 2 dose schedule at 2 and 3 months of age. We collected vaccination uptake from October 2013 to March 2015 and laboratory confirmed cases data on children under the age of 5 y from 1 January 2004 to 31 May 2015. The vaccine uptake rates and laboratory confirmed cases were compared to provide evidence of the impact of this vaccination program. Vaccine uptake rates were available from sentinel data with between 91–98% of GP practices in Anglia and Essex providing data every month. These data showed from February 2014 to March 2015 between 90–92% of infants received the recommended 2 doses of Rotarix® each month. The numbers of rotavirus cases reported by laboratories decreased on average by 82% in the post vaccination seasons. The mean number of cases reported in weeks 1–22 for 2004–2013 in Anglia and Essex was 1,318. For the same period in 2014, 256 cases were reported and initial data for 2015 report 226 cases. In the first 5 months 2014 the greatest reduction in cases (89%) was seen in those under 1 yr (who would have been directly affected by vaccination) with case numbers falling to 59 from a mean 537 cases in the equivalent period for 2004–2013. Initially data suggests a 92% reduction in 2015 compared to the same pre-vaccination periods. For those aged 1 to <5 y who would not have been vaccinated, a reduction of 75% was also evident in 2014 and 77% in 2015, suggesting indirect protection in this group. In conclusion, initial results following the introduction of the Rotavirus vaccine clearly indicates a very good uptake of the vaccine and a significant reduction in the numbers of laboratory confirmed cases.

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.

Novel application of the matched case–control design to compare food supply chains during an Escherichia coli O157 outbreak, United Kingdom, 2016

There is a need for innovative methods to investigate outbreaks of food-borne infection linked to produce with a complex distribution network. The investigation of a large outbreak of Escherichia coli O157 PT34 infection in the United Kingdom in 2016 indicated that catering venues associated with multiple cases had used salad leaves sourced from one supplier. Our aim was to investigate whether catering venues linked to cases were more likely to have used salad leaves from this supplier. We conducted a matched case–control study, with catering venues as the units of analysis. We compared venues linked to cases to those without known linked cases. We included 43 study pairs and obtained information on salad leaf products received by each venue. The odds of a case venue being supplied with salad leaves by Supplier A were 7.67 times (95% confidence interval: 2.30–25.53) those of control venues. This association provided statistical evidence to support the findings of the other epidemiological investigations undertaken for this outbreak. This is a novel approach which is labour-intensive but which addresses the challenge of investigating exposures to food across a complex distribution network.

First use of whole-genome sequencing to investigate a cluster of Yersinia enterocolitica, Liverpool, United Kingdom, 2017

Purpose. In May 2017 we were notified of a cluster of Yersinia enterocolitica‐positive isolates from Liverpool. The purpose of this work was to investigate this cluster of cases and find a possible common source. We combined epidemiological information with whole‐genome sequencing (WGS) results, which indicated that these cases were unlikely to be from the same source. This investigation provides evidence that WGS could be used to investigate future clusters of Y. enterocolitica cases. Methods. A case was defined as a person with a laboratory‐confirmed isolate of Y. enterocolitica, sampled in 2017, who is a resident in Liverpool local authority at the time of sampling. Faecal samples were cultured at the local laboratory and presumptive isolates of Yersinia sp. were identified using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). Positive isolates were whole‐genome sequenced by the reference laboratory. Results. Nine cases were identified, which was significantly greater (P<0.0001) than the average number of cases in this area from the last 10 years. Six cases were female (66.67 %) and the ages of the patients ranged from 20 to 81 (median 54). The sample dates ranged from 29 April to 1 August 2017. The WGS results showed that Y. enterocolitica isolates belonged to different sequence types. Conclusion. This was the first time that WGS was used to investigate a cluster of Y. enterocolitica cases; the cases were clustered in time, person and place, but the WGS results indicate that these cases were not from the same source. This result informed the Outbreak Control Teams decision‐making and resulted in the investigation being closed.