Abstract
ABSTRACTHuman campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterization methods. Whole-genome sequencing (WGS) data enable the improvement of sequence-based typing approaches, such as multilocus sequence typing (MLST), by substantially increasing the number of loci examined. A core genome MLST (cgMLST) scheme defines a comprehensive set of those loci present in most members of a bacterial group, balancing very high resolution with comparability across the diversity of the group. Here we propose a set of 1,343 loci as a human campylobacteriosis cgMLST scheme (v1.0), the allelic profiles of which can be assigned to core genome sequence types. The 1,343 loci chosen were a subset of the 1,643 loci identified in the reannotation of the genome sequence of C. jejuni isolate NCTC 11168, chosen as being present in >95% of draft genomes of 2,472 representative United Kingdom campylobacteriosis isolates, comprising 2,207 (89.3%) C. jejuni isolates and 265 (10.7%) C. coli isolates. Validation of the cgMLST scheme was undertaken with 1,478 further high-quality draft genomes, containing 150 or fewer contiguous sequences, from disease isolate collections: 99.5% of these isolates contained ≥95% of the 1,343 cgMLST loci. In addition to the rapid and effective high-resolution analysis of large numbers of diverse isolates, the cgMLST scheme enabled the efficient identification of very closely related isolates from a well-defined single-source campylobacteriosis outbreak.
Highlights
Human campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterization methods
A secondary minor peak, indicating that an additional 72 loci were identified in only 89% of the isolates, was observed, and reanalysis to establish the presence of these loci in isolates belonging to C. jejuni or C. coli determined that these loci were predominantly present only in C. jejuni isolates (Fig. 1B)
Of the 19 pseudogenes identified in the reannotation of the reference strain NCTC 11168 [28], only one (Cj0072c) of the candidate loci for inclusion in the core genome MLST (cgMLST) scheme was identified as a paralogue and excluded
Summary
Human campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterization methods. In high-income countries such as the United Kingdom (UK) and the United States, the majority (90%) of human disease is caused by Campylobacter jejuni, with Campylobacter coli responsible for most of the remaining cases [2] Both of these organisms are ubiquitously present in the intestines of wild and domesticated animals, where they are thought to be harmless commensal members of the microbiota. The advent of whole-genome sequencing (WGS) technologies for clinical microbiology application [21] has greatly increased the volume of genetic information available for the characterization of bacterial isolates, with simultaneous reductions in cost [22] This has the potential to improve surveillance by the introduction of cost-effective, high-resolution typing systems. For Campylobacter, universal single- and multiple-locus typing schemes, including antigen gene typing [24], conventional seven-locus MLST [5], and ribosomal sequence typing (rMLST) [25, 26], have been designed and implemented with internationally accepted Web-based nomenclature servers available [27], but none of these has the resolution to identify diffuse outbreaks or diversity within outbreaks
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