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

• DOI: 10.1099/mgen.0.000237
• Publication Date: 2019-01-16T15:13:52Z
• Authors: Aleisha Reimer; Kelly Weedmark; Aaron Petkau; Christy-Lynn Pete...; Matthew Walker; Natalie Knox; Heather Kent; Philip Mabon; Chrystal Berry; Shaun Tyler; Lorelee Tschetter; Morganne Jerome; Vanessa Allen; Linda Hoang; Sadjia Bekal; Clifford Clark; Celine Nadon; Gary Van Domselaar; Franco Pagotto; Morag Graham; Jeff Farber; Matthew Gilmour
• Keywords: Subtyping; Prophage

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