High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak

Matthew W Gilmour,Oscar Larios,Vanessa Allen,Gary Van Domselaar,Barbara Lee,Shaun Tyler,Heather Kent,Celine Nadon,Morag Graham,Keri M Trout-Yakel

doi:10.1186/1471-2164-11-120

Abstract

BackgroundA large, multi-province outbreak of listeriosis associated with ready-to-eat meat products contaminated with Listeria monocytogenes serotype 1/2a occurred in Canada in 2008. Subtyping of outbreak-associated isolates using pulsed-field gel electrophoresis (PFGE) revealed two similar but distinct AscI PFGE patterns. High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE.ResultsThe chromosomes were collinear, but differences included 28 single nucleotide polymorphisms (SNPs) and three indels, including a 33 kbp prophage that accounted for the observed difference in AscI PFGE patterns. The distribution of these traits was assessed within further clinical, environmental and food isolates associated with the outbreak, and this comparison indicated that three distinct, but highly related strains may have been involved in this nationwide outbreak. Notably, these two isolates were found to harbor a 50 kbp putative mobile genomic island encoding translocation and efflux functions that has not been observed in other Listeria genomes.ConclusionsHigh-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology.

Highlights

A large, multi-province outbreak of listeriosis associated with ready-to-eat meat products contaminated with Listeria monocytogenes serotype 1/2a occurred in Canada in 2008
Human listeriosis is relatively rare despite our likely frequent encounters with L. monocytogenes, which is ubiquitously present in the environment, farm and rural environments, and urban environments [2,3,4,5,6]
These data allowed for discovery of novel prophage and genomic islands, and the subsequent sequence closure and the confirmation of sequence variants allowed for annotation of polymorphisms and other traits associated with micro-diversity

Summary

Introduction

A large, multi-province outbreak of listeriosis associated with ready-to-eat meat products contaminated with Listeria monocytogenes serotype 1/2a occurred in Canada in 2008. The vast majority of human listeriosis is foodborne and the most commonly implicated vehicles are ready-to-eat food products such as meat, dairy, seafood, and fresh produce that are. There are 13 known serotypes of L. monocytogenes but the vast majority of human disease cases are caused by strains belonging to serotypes 4b, 1/2a, and 1/2b, severely limiting the utility of this subtyping method for differentiating L. monocytogenes [14]. Several molecular subtyping methods have been developed and applied to L. monocytogenes, including pulsed-field gel electrophoresis (PFGE), ribotyping, multilocus variable-number tandem repeat analysis (MLVA), and sequence-based subtyping [14,16,17]. PFGE has been adopted by PulseNet as the internationally standardized method for molecular subtyping of L.monocytogenes and has been essential in the detection and investigation of listeriosis outbreaks in Canada and worldwide [18,19,20]

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Results

Conclusion