Genomic epidemiology of clinical Campylobacter spp. at a single health trust site.

Steven J Dunn,Georgina Manning,Vicki Fleming,Alan Mcnally,James Turton,Ben Pascoe,Mathew Diggle,Samuel K Sheppard

doi:10.1099/mgen.0.000227

Abstract

Campylobacter is the leading cause of bacterial enteritis in the developed world, and infections with the organism are largely sporadic in nature. Links between sporadic cases have not been established, with the majority of infections thought to be caused by genetically distinct isolates. Using a read-mapping approach, 158 clinical isolates collected during 2014 from the greater Nottinghamshire area were analysed to assess the local population structure and investigate potential case linkages between sporadic cases of campylobacteriosis. Four instances (2.5 %) of case linkage were observed across the dataset. This study demonstrates that case linkage does occur between sporadic Campylobacter infections, and provides evidence that a dual multi-locus sequence typing/within-lineage single nucleotide polymorphism typing approach to Campylobacter genomic epidemiology provides a benefit to public-health investigations.

Highlights

Campylobacter is the leading cause of bacterial enteritis in the developed world
This study demonstrates that case linkage does occur between sporadic Campylobacter infections, and provides evidence that a dual multi-locus sequence typing/within-lineage single nucleotide polymorphism typing approach to Campylobacter genomic epidemiology provides a benefit to public-health investigations
The complex epidemiology of Campylobacter can be resolved using multi-locus sequence typing (MLST), which assigns house-keeping loci with an arbitrary allele number based on iterative differences in their constituent nucleotide sequences [5, 6]

Summary

Introduction

Campylobacter is the leading cause of bacterial enteritis in the developed world. In the UK, it is responsible for approximately 65 000 illnesses, 22 000 hospitalizations and more than 100 deaths each year – it is a significant burden to the UK economy, costing tax payers an estimated £900 milllion per annum [1, 2]. Query sequences are compared against a central repository [7] containing previously identified alleles, providing an allelic profile of identified loci, and allowing pairwise comparison of other isolates processed in the same manner This methodology has been expanded to include additional loci in both core-genome MLST (cgMLST), which assesses a curated set of alleles that are present in >95 % of the species, and whole-genome MLST (wgMLST), which utilises all identified Campylobacter jejuni and Campylobacter coli loci irrespective of absolute presence [8, 9]. This type of analysis is useful in a clinical environment, as the computational resources required are significantly lower than alternative approaches (e.g. read mapping), and the results are comparable and reproducible across laboratories [8,9,10]

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