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Use of whole-genome sequencing in the epidemiology of Campylobacter jejuni infections: state-of-knowledge

Ann-Katrin Llarena, View ORCID ProfileMirko Rossi
doi: https://doi.org/10.1101/078550
Ann-Katrin Llarena
Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjobergin katu 2, Helsinki, FI-00014, Finland.
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Mirko Rossi
Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjobergin katu 2, Helsinki, FI-00014, Finland.
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  • For correspondence: mirko.rossi@helsinki.fi
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ABSTRACT

High-throughput whole-genome sequencing (WGS) is a revolutionary tool in public health microbiology and is gradually substituting classical typing methods in surveillance of infectious diseases. In combination with epidemiological methods, WGS is able to identify both sources and transmission-pathways during disease outbreak investigations. This review provides the current state of knowledge on the application of WGS in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis in the European Union. We describe how WGS has improved surveillance and outbreak detection of C. jejuni infections and how WGS has increased our understanding of the evolutionary and epidemiological dynamics of this pathogen. However, the full implementation of this methodology in real-time is still hampered by a few hurdles. The limited insight into the genetic diversity of different lineages of C. jejuni impedes the validity of assumed genetic relationships. Furthermore, efforts are needed to reach a consensus on which analytic pipeline to use and how to define the strains cut-off value for epidemiological association while taking the needs and realities of public health microbiology in consideration. Even so, we claim that ample evidence is available to support the benefit of integrating WGS in the monitoring of C. jejuni infections and outbreak investigations.

Abbreviations
CC
clonal complex
cgMLST
core-genome MLST
DALY
Disability-adjusted life year
ECDC
European Centre for Disease Prevention and Control
EFSA
European Food Safety Authority
Epi-linked
epidemiologically linked
GWAS
genome-wide association study
MALDI-TOF
Matrix Associated Laser Desorption Ionization–Time of Flight
MLST
multilocus sequence typing
NGS
Next generation sequencing
SNPs
single nucleotide polymorphisms
SNV
single nucleotide variant
ST
Sequence type
PFGE
Pulsed-field gel electrophoresis
wgMLST
whole-genome MLST
WGS
Whole-genome sequencing
Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 01, 2016.
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Use of whole-genome sequencing in the epidemiology of Campylobacter jejuni infections: state-of-knowledge
Ann-Katrin Llarena, Mirko Rossi
bioRxiv 078550; doi: https://doi.org/10.1101/078550
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Use of whole-genome sequencing in the epidemiology of Campylobacter jejuni infections: state-of-knowledge
Ann-Katrin Llarena, Mirko Rossi
bioRxiv 078550; doi: https://doi.org/10.1101/078550

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