Abstract
Whole-genome sequencing (WGS) via next-generation sequencing (NGS) technologies is a powerful tool for determining the relatedness of bacterial isolates in foodborne illness detection and outbreak investigations. WGS has been applied to national outbreaks (for example, Listeria monocytogenes); however, WGS has rarely been used in smaller local outbreaks. The current study demonstrates the superior resolution of genetic and evolutionary relatedness generated by WGS data analysis, compared to pulsed-field gel electrophoresis (PFGE). The current study retrospectively applies WGS and a reference-free bioinformatic analysis to a Utah-specific outbreak of Campylobacter jejuni associated with raw milk and to a national multistate outbreak of Salmonella enterica subsp. enterica serovar Typhimurium associated with rotisserie chicken, both of which were characterized previously by PFGE. Together, these analyses demonstrate how a reference-free WGS workflow is not reliant on determination of a reference sequence, like WGS workflows that are based on single-nucleotide polymorphisms, or the need for curated allele databases, like multilocus sequence typing workflows.
Highlights
Whole-genome sequencing (WGS) via next-generation sequencing (NGS) technologies is a powerful tool for determining the relatedness of bacterial isolates in foodborne illness detection and outbreak investigations
pulsed-field gel electrophoresis (PFGE) analysis of 79 isolates associated with the 99 identified Campylobacter jejuni cases (61 clinical isolates and 18 environmental isolates) related to a raw milk outbreak revealed that 75 isolates, including 16 environmental isolates, shared identical PFGE profiles for both SmaI and KpnI enzyme digestions, designated UTDBDS16.944 and UTDBDK02.053, respectively (Fig. 1)
PFGE has been used since the inception of the Centers for Disease Control and Prevention (CDC) PulseNet program as the method of choice for bacterial “fingerprinting”; PFGE has limitations, compared to WGS
Summary
Whole-genome sequencing (WGS) via next-generation sequencing (NGS) technologies is a powerful tool for determining the relatedness of bacterial isolates in foodborne illness detection and outbreak investigations. Timely analysis of WGS data at the local level is crucial to identify linked cases of illness, which can be an early indication of an outbreak, and to provide phylogenetic and evolutionary relationship information, which can give epidemiological context to an ongoing investigation. This analysis becomes critical as PulseNet moves closer to ending the use of PFGE. Between 9 May and 6 November 2014, 99 cases of C. jejuni infections were identified [11]
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