Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak

Madison E Pearce,Nabil-Fareed Alikhan,Timothy J Dallman,Zhemin Zhou,Kathie Grant,Martin C.J Maiden

doi:10.1016/j.ijfoodmicro.2018.02.023

Abstract

Multi-country outbreaks of foodborne bacterial disease present challenges in their detection, tracking, and notification. As food is increasingly distributed across borders, such outbreaks are becoming more common. This increases the need for high-resolution, accessible, and replicable isolate typing schemes. Here we evaluate a core genome multilocus typing (cgMLST) scheme for the high-resolution reproducible typing of Salmonella enterica (S. enterica) isolates, by its application to a large European outbreak of S. enterica serovar Enteritidis. This outbreak had been extensively characterised using single nucleotide polymorphism (SNP)-based approaches. The cgMLST analysis was congruent with the original SNP-based analysis, the epidemiological data, and whole genome MLST (wgMLST) analysis. Combination of the cgMLST and epidemiological data confirmed that the genetic diversity among the isolates predated the outbreak, and was likely present at the infection source. There was consequently no link between country of isolation and genetic diversity, but the cgMLST clusters were congruent with date of isolation. Furthermore, comparison with publicly available Enteritidis isolate data demonstrated that the cgMLST scheme presented is highly scalable, enabling outbreaks to be contextualised within the Salmonella genus. The cgMLST scheme is therefore shown to be a standardised and scalable typing method, which allows Salmonella outbreaks to be analysed and compared across laboratories and jurisdictions.

Highlights

Members of the bacterial genus Salmonella are a major threat to human health, causing an estimated 80.3 million cases of foodborne gastroenteritis annually (Majowicz et al, 2010)
The single nucleotide polymorphism (SNP) addresses provided a greater resolution than core genome multilocus typing (cgMLST) single linkage clusters
Short insertions or deletions in the core genes are ignored by many SNP analyses but captured by a cgMLST scheme, because they change the sequences of the genes

Summary

Introduction

Members of the bacterial genus Salmonella are a major threat to human health, causing an estimated 80.3 million cases of foodborne gastroenteritis annually (Majowicz et al, 2010). Salmonella enterica (S. enterica) serovar Enteritidis is the largest single cause of Salmonella infection globally, accounting for between 40% and 60% of human cases (Galanis et al, 2006; Hendriksen et al, 2011) and many foodborne disease outbreaks. The first broadly accepted Salmonella typing scheme, the Kauffmann-White scheme, was based on the serological detection of somatic and flagella antigens (Grimont and Weill, 2007) This scheme facilitated international communication and comparison due to annual updates and maintenance by the World Health Organization (WHO) coordinated reference laboratory, located at the Insitut Pasteur (Paris, France); serotyping does not always reflect the genetic relatedness of S. enterica lineages (Harbottle et al, 2006; Sangal et al, 2010). Pulse-field gel electrophoresis (PFGE) fingerprinting provided increased resolution and achieved success with the PulseNet initiative (Gerner-Smidt et al, 2006), but these data were difficult to compare among laboratories (Harbottle et al, 2006) as they required highly standardised approaches (Swaminathan et al, 2001) and a global PFGE database proved too complex and costly to implement (Nadon et al, 2017)

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Discussion

Conclusion