Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria.

Aleisha Reimer,Heather Kent,Matthew Walker,Morag Graham,Christy-Lynn Peterson,Linda Hoang,Kelly Weedmark,Lorelee Tschetter,Franco Pagotto,Gary Van Domselaar,Chrystal Berry,Vanessa Allen,Morganne Jerome,Natalie Knox,Jeff Farber,Shaun Tyler,Philip Mabon,Clifford G Clark ,Sadjia Békal ,Céline Nadon ,A Petkau ,Matthew W Gilmour

doi:10.1099/mgen.0.000237

Abstract

The persuasiveness of genomic evidence has pressured scientific agencies to supplement or replace well-established methodologies to inform public health and food safety decision-making. This study of 52 epidemiologically defined Listeria monocytogenes isolates, collected between 1981 and 2011, including nine outbreaks, was undertaken (1) to characterize their phylogenetic relationship at finished genome-level resolution, (2) to elucidate the underlying genetic diversity within an endemic subtype, CC8, and (3) to re-evaluate the genetic relationship and epidemiology of a CC8-delimited outbreak in Canada in 2008. Genomes representing Canadian Listeria outbreaks between 1981 and 2010 were closed and manually annotated. Single nucleotide variants (SNVs) and horizontally acquired traits were used to generate phylogenomic models. Phylogenomic relationships were congruent with classical subtyping and epidemiology, except for CC8 outbreaks, wherein the distribution of SNV and prophages revealed multiple co-evolving lineages. Chronophyletic reconstruction of CC8 evolution indicates that prophage-related genetic changes among CC8 strains manifest as PFGE subtype reversions, obscuring the relationship between CC8 isolates, and complicating the public health interpretation of subtyping data, even at maximum genome resolution. The size of the shared genome interrogated did not change the genetic relationship measured between highly related isolates near the tips of the phylogenetic tree, illustrating the robustness of these approaches for routine public health applications where the focus is recent ancestry. The possibility exists for temporally and epidemiologically distinct events to appear related even at maximum genome resolution, highlighting the continued importance of epidemiological evidence.

Highlights

Innovations in, and the cost-effectiveness of, DNA sequencing technologies have quickly tipped the scales to favour bacterial genome sequencing as the inevitable replacement of conventional subtyping for infectious disease surveillance and outbreak response
Our finding supports smaller previous studies concluding that sequencing technologies and read quality are of little consequence in the application of whole-genome sequence (WGS) for distinguishing disease outbreaks with moderate genetic similarity [42], such technical robustness has not been previously validated for highly clonal groups as is reported in this study
The comparative analyses presented in this study demonstrate that listeriosis outbreaks are typically monophyletically distinct events with very few Single nucleotide variants (SNVs) present between isolates from the same event, an unusually high level of SNV diversity within an event might be due to the microbial diversity inherent to the source of contamination and/or the investigative environment sampled

Summary

Introduction

Innovations in, and the cost-effectiveness of, DNA sequencing technologies have quickly tipped the scales to favour bacterial genome sequencing as the inevitable replacement of conventional subtyping for infectious disease surveillance and outbreak response. Listeria species are opportunistic pathogens ubiquitous in the natural environment, present in up to 5 % of healthy human carriers, and of particular concern to public health authorities and the food production industry as they are difficult to control using traditional food preservation means (salt and low temperatures). Listeriacontaminated food can result in large food product recalls, severe illness and high-profile fatal outbreak events [5,6,7]

Methods

Results

Conclusion