Abstract
The decreased costs of genome sequencing have increased the capability to apply whole-genome sequencing to epidemiological surveillance of zoonotic Campylobacter jejuni. However, knowledge of the genetic diversity of this bacteria is vital for inferring relatedness between epidemiologically linked isolates and a necessary prerequisite for correct application of this methodology. To address this issue in C. jejuni we investigated the spatial and temporal signals in the genomes of a major clonal complex and generalist lineage, ST-45 CC, by analysing the population structure and genealogy as well as applying genome-wide association analysis of 340 isolates from across Europe collected over a wide time range. The occurrence and strength of the geographical signal varied between sublineages and followed the clonal frame when present, while no evidence of a temporal signal was found. Certain sublineages of ST-45 formed discrete and genetically isolated clades containing isolates with extremely similar genomes regardless of time and location of sampling. Based on a separate data set, these monomorphic genotypes represent successful C. jejuni clones, possibly spread around the globe by rapid animal (migrating birds), food or human movement. In addition, we observed an incongruence between the genealogy of the strains and multilocus sequence typing (MLST), challenging the existing clonal complex definition and the use of whole-genome gene-by-gene hierarchical nomenclature schemes for C. jejuni.
Highlights
The use of whole-genome sequencing (WGS) in genomic epidemiology is revolutionizing surveillance and outbreak investigations of bacterial threats to public health
In Dataset one, all publicly accessible genomes of sequence type (ST)-45 clonal complex (CC) with available metadata and Finnish and Baltic genomes of the ST-45 CC were included, resulting in a collection of 340 genomes of 22 STs of ST-45 CC, of which 13 were considered singleton STs as they accounted for two or fewer isolates, and one genome of the outgroup ST-21. This database consisted of 199 C. jejuni genomes acquired from the PubMLST database [http:// www.pubmlst.org/; accessed May 2015 (Jolley & Maiden, 2010)] obtained between 2000 and 2012 in the United Kingdom (UK), of which some strains were collected from human campylobacteriosis cases between June 2011 and June 2014 in Oxford, UK, as part of the Oxfordshire sentinel surveillance study
We have identified problems with the use of a Multilocus sequence typing (MLST)-based hierarchical nomenclature system for C. jejuni within ST-45 CC, since the WGS genealogy harbored both polyphyletic http://mgen.microbiologyresearch.org and paraphyletic STs, complicating the use of such systems in genomic epidemiology
Summary
The use of whole-genome sequencing (WGS) in genomic epidemiology is revolutionizing surveillance and outbreak investigations of bacterial threats to public health. WGS is currently used in real-time surveillance of Listeria monocytogenes and Salmonella enteritidis by the American Centers for Disease Control and Prevention and the US Food and Drug Administration (http://www.fda.gov/ Food) and similar approaches for E. coli, Campylobacter, Vibrio and Cronobacter, etc., are expected to come into use in the near future. Our findings highlight the difficulty of establishing a common framework for WGS-based epidemiological surveillance of zoonotic C. jejuni This arises from the limited genetic variability of monomorphic genotypes and differences in the strength of phylogeographic signals, which complicate the development of a joint cut-off value for determining epidemiological linkage between C. jejuni isolates
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