Whole genome analysis of ExPEC ST73 from a single hospital over a 2-year period identified different circulating clonal groups

Bogema, D.; McKinnon, J.; Liu, M. Y.; Hitchick, N.; Miller, N.; Venturini, C.; Iredell, J.; Darling, A. E.; Roy Chowdury, P.; Djordjevic, S.

doi:10.1101/428599

bioRxiv · 10.1101/428599

Whole genome analysis of ExPEC ST73 from a single hospital over a 2-year period identified different circulating clonal groups

Bogema, D.·McKinnon, J.·Liu, M. Y.·Hitchick, N.·Miller, N.·Venturini, C.·Iredell, J.·Darling, A. E.·Roy Chowdury, P.·Djordjevic, S.

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Abstract

ST73 has emerged as one of the most frequently isolated extraintestinal pathogenic E. coli (ExPEC). To examine the localised diversity of ST73 clonal groups including their mobile genetic elements profile, we sequenced the genomes of 16 multiple drug-resistant ST73 isolates from patients with urinary tract infection from a single hospital in Sydney, Australia between 2009 and 2011. Genome sequences were used to generate a SNP-based phylogenetic tree to determine the relationship of these isolates in a global context with ST73 sequences (n=210) from public databases. There was no evidence of a dominant outbreak strain of ST73 in patients from this hospital, rather we identified at least eight separate groups, several of which reoccur, over a two-year period. The inferred phylogeny of all ST73 strains (n=226) including the ST73 Clone D i2 reference genome shows high bootstrap support and clusters into four major groups which correlate with serotype. The Sydney ST73 strains carry a wide variety of virulence-associated genes but the presence of iss, pic and several iron acquisition operons was notable.\n\nImpactST73 is a major clonal lineage of ExPEC that causes urinary tract infections often with uroseptic sequelae but has not garnered substantial scientific interest as the globally disseminated ST131. Isolation of multiple antimicrobial resistant variants of ExPEC ST73 have increased in frequency, but little is known about the carriage of class 1 integrons in this sequence type and the plasmids that are likely to mobilise them. This pilot study examines the ST73 isolates within a single hospital in Sydney Australia and provides the first large-scale core-genome phylogenetic analysis of ST73 utilizing public sequence read datasets. We used this analysis to identify at least 8 sub-groups of ST73 within this single hospital. Mobile genetic elements associated with antibiotic resistance were less diverse and only three class 1 integron structures were identified, all sharing the same basic structure suggesting that the acquisition of drug resistance is a recent event. Genomic epidemiological studies are needed to further characterise established and emerging clonal populations of multiple drug resistant ExPEC to identify sources and aid outbreak investigations.

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Bogema, D., McKinnon, J., Liu, M. Y., Hitchick, N., Miller, N., Venturini, C., Iredell, J., Darling, A. E., Roy Chowdury, P., Djordjevic, S.. 2018-09-27. Whole genome analysis of ExPEC ST73 from a single hospital over a 2-year period identified different circulating clonal groups. https://doi.org/10.1101/428599

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