Evaluation of Genomic Typing Methods in the Salmonella Reference Laboratory in Public Health, England, 2012–2020

Abstract

We aim to provide an evidence-based evaluation of whole genome sequence (WGS) methods, employed at the Salmonella reference laboratory in England, in terms of its impact on public health and whether these methods remain a fit for purpose test under UKAS ISO 15189. The evaluation of the genomic methods were mapped against the value of detecting microbiological clusters to support the investigation of food-borne outbreaks of Salmonella in England between 2012–2020. The analysis of WGS with both SNP- and allelic-based methods provided an unprecedented level of strain discrimination and detection of additional clusters when comparing to all of the previous typing methods. The robustness of the routine genomic sequencing at the reference laboratory ensured confidence in the microbiological identifications, even in large outbreaks with complex international food distribution networks. There was evidence that the phylogeny derived from the WGS data can be used to inform the provenance of strains and support discrimination between domestic and non-domestic transmission events. Further insight on the evolutionary context of the emerging pathogenic strains was enabled with a deep dive of the phylogenetic data, including the detection of nested clusters. The public availability of the WGS data linked to the clinical, epidemiological and environmental context of the sequenced strains has improved the trace-back investigations during outbreaks. The global expansion in the use of WGS-based typing in reference laboratories has shown that the WGS methods are a fit for purpose test in public health as it has ensured the rapid implementation of interventions to protect public health, informed risk assessment and has facilitated the management of national and international food-borne outbreaks of Salmonella.

Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi

“…The level of SNP variation within clusters showed concordance/congruence to the level of allele variation determined using cgMLST. These concordance of results have previously been reported when investigating clusters and outbreaks of enteric bacterial pathogens [18, 40–45].…”

Genomic perspectives on foodborne illness

“…Choosing a SNP threshold that implies that two isolates share a similar source of contamination in this analysis has been discussed in the context of outbreak detection and source tracking (Pightling et al 2018; Chattaway et al 2023) In this analysis, we are using the SNP threshold to generate clusters from very large sets of clinical isolates and then examining statistical trends in the metadata associated with these clusters. To understand the robustness of the results, we compared thresholds set at 2, 4, and 8 SNPs for most analyses.…”

Occurrence of a New Variant of Salmonella Infantis Lacking Somatic Antigen

“…WGS has enhanced studies about genomic diversity among Salmonella , allowing us to identify and subtype strains and to assess their relatedness. In addition, WGS can be useful to streamline the laboratory process and reduce processing and turnaround times [ 5 ].…”

“…S. Infantis (6,7:r:1,5) is a Salmonella enterica serovar and, with S. Enteritidis (1,9,12:g,m:-), S. Typhimurium (1,4, [5],12:i:1,2), monophasic S. Typhimurium (1,4,[5],12:i:-) and S. Derby (1,4,[5],12:f,g: [1,2]), belongs to the five most frequently reported Salmonella serovars in human salmonellosis cases acquired in the EU in 2020 [3]. It accounted for 31.5% of the human infections from food-animal sources that occurred in the EU in 2020.…”