Twenty years of Campylobacter research using sequencing data and PubMLST how far we have come!

Abstract T9

Presenter: Frances M Colles (University of Oxford)

Authors: Frances M. Colles, Kate E. Dingle and Martin C.J. Maiden.

In affectionate memory of Alison J. Cody.

Twenty years ago, the multilocus sequence typing (MLST) scheme for Campylobacter jejuni and Campylobacter coli was published (1). This scheme remains widely used, and curated sequencing typing data, and isolate provenance and phenotype information are available on the open-access PubMLST database (https://pubmlst.org/campylobacter) (2). Since its inception, the scope of the database has been greatly extended and as of June 2021, the database contained 100,822 isolate records, more than half of these (52,467) associated with whole genome sequence data, integrated with bioinformatics tools for downstream analyses. Before the introduction of sequence-based typing, first MLST, followed by flaA SVR and porA gene sequencing, the epidemiology and population structure of these principal causes of human gastroenteritis were poorly understood, obscured by bewildering and inconsistent phenotypic diversity. Sequence typing, now extended to whole genome sequence (WGS) approaches including core genome MLST (cgMLST) and ribosomal MLST (rMLST), has provided multiple and extensive insights into the host association, epidemiology, population biology, and pathogenesis of Campylobacter sp. In addition to high-resolution detection of disease clusters and outbreaks, which have been rarely described for Campylobacter, it is now possible to define capsule loci, antibiotic resistance loci, or indeed any biochemical pathway of interest. Very many primary research studies of C. jejuni and C. coli have been made possible by these resources, and the open access nature of these data enable extensive data reuse.

Of particular importance have been:

• (i) Campylobacter host-association studies and human campylobacteriosis infection source attribution;
• (ii) investigation of Campylobacter evolution and the relationships between isolates from wild and domesticated animals; and
• (iii) the long-term monitoring of human disease isolates with WGS, including trends in antimicrobial resistance. Recent events have confirmed the importance of long-term curated sequence-based resources for studying infectious diseases and implementing effective public health action heres to the next twenty years!
• 1 Dingle, K. E., Colles, F. M., Wareing, D. R. A., Ure, R., Fox, A. J., Bolton, F. J., Bootsma, H. J., Willems, R. J. L., Urwin, R. & Maiden, M. C. J. (2001). Multilocus sequence typing system for Campylobacter jejuni. J Clin Microbiol. 39, 14-23
• 2 Jolley, K. A., Bray, J. E. & Maiden, M. C. J. (2018). Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 3, 124

About the presenter

I am a professionally qualified microbiologist, having previously worked in NHS microbiology and veterinary diagnostic laboratories. My interest in zoonotic disease lead me pursue a career researching the epidemiology of Campylobacter on farms and in the human food chain. I helped set up the first Campylobacter MLST scheme which was published in 2001 and curate genomic data for the PubMLST Campylobacter database (https://pubmlst.org/) as a public resource for the community. I completed my DPhil at Oxford University and have continued to work there as part of a larger multidisciplinary team exploring the interaction between chicken health, welfare and behaviour, and the prevalence of Campylobacter.

Presenting in Speaking session 3 - Epidemiology and public health