Investigation using whole genome sequencing of a prolonged restaurant outbreak of Salmonella Typhimurium linked to the building drainage system, England, February 2015 to March 2016

Abstract

Following notification of a Salmonella enterica serovar Typhimurium gastroenteritis outbreak, we identified 82 cases linked to a restaurant with symptom onset from 12 February 2015 to 8 March 2016. Seventy-two cases had an isolate matching the nationally unique whole genome sequencing profile (single nucleotide polymorphism (SNP) address: 1.1.1.124.395.395). Interviews established exposure to the restaurant and subsequent case–control analysis identified an association with eating carvery buffet food (adjusted odds ratios (AOR): 20.9; 95% confidence interval (CI): 2.2 – ∞). Environmental inspections, food/water testing, and a food trace-back investigation were inconclusive. Repeated cycles of cleaning were undertaken, including hydrogen peroxide fogging, however, transmission continued. After 7 months of investigation, environmental swabbing identified 106 isolates from kitchen surfaces and restaurant drains matching the outbreak profile. We found structural faults with the drainage system and hypothesised that a reservoir of bacteria in drain biofilm and underfloor flooded areas may have sustained this outbreak. Ineffective drain water-traps (U-bends) may have also contributed by allowing transmission of contaminated aerosols into the kitchen environment. These findings suggest that routine swabbing of sink drain points and inspection of drainage systems should be considered in future outbreak scenarios.

Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges

“…However, as demonstrated here and elsewhere, variant calling pipelines and the various mapping/alignment, SNP calling, and SNP filtering practices that they employ (e.g., removal of recombination and clustered SNPs) can influence the identification of SNPs in WGS data and, thus, the topology of a resulting phylogeny (Pightling et al, 2014, 2015; Croucher et al, 2015; Hwang et al, 2015; Katz et al, 2017; Sandmann et al, 2017). This can be particularly problematic for outbreak and cluster detection in bacterial pathogen surveillance: pairwise SNP thresholds are currently widely used to make initial decisions regarding the inclusion or exclusion of isolates in a given outbreak (Taylor et al, 2015; Gymoese et al, 2017; Mair-Jenkins et al, 2017; McCloskey and Poon, 2017; Walker et al, 2018). In such scenarios, just a few SNPs can be the deciding factor in whether a bacterial pathogen is included or excluded as part of an outbreak or cluster (Katz et al, 2017), rendering the choice of variant calling method as non-trivial.…”

Perceived utility and feasibility of pathogen genomics for public health practice: a survey among public health professionals working in the field of infectious diseases, Belgium, 2019

“…Current and future NGS activities represented in this national survey were mainly in the context of food-and waterborne outbreak detections and investigations, reflecting the priority for these diseases across Europe and beyond [63,64]. Several criteria should be considered in the process of integrating WGS in a routine laboratory setting [11] in order to know in which situations and for which pathogens it is worthwhile to use NGS. Identifying a set of key drivers that cover all aspects related to the implementation of NGS (utility and feasibility) can help to guide prioritization of pathogens and to efficiently allocate resources.…”

“…The main added value of implementing WGS during surveillance activities or outbreak investigations is inherent in the higher resolution of the WGS output itself, leading to an increased sensitivity and specificity to identify transmission clusters compared to conventional subtyping methods [6]. As such, there are numerous success stories of outbreak investigations applying WGS that were able to identify to the source of infection and implement targeted control measures to stop further spread, saving resources at the health protection and local authority level [10][11][12][13][14][15][16][17]. Other concrete examples of the utility of WGS for national surveillance and local infection control include the guidance of vaccination strategies [18][19][20][21] and antibiotic stewardship [22,23].…”

An outbreak of norovirus infection caused by ice cubes and a leaking air ventilation valve

“…Norovirus infection can be a huge burden in a community and a major reduction in the illness may be able to be obtained if even a modest proportion of cases can be prevented. A recently published paper suggests that a salmonella outbreak spread from contaminated drains and leaking U-traps [40]. However, as the authors of that paper did not mention why cases only occurred in carvery meat eaters and did not mention the sampling of the carvery (only significant exposure in the case-control study), the source's validity remained somewhat uncertain.…”