Project_2021_8_9_13_46_24
Identification of a subset of Escherichia coli sequence type 131 harbouring genomic island GI-pheU with higher antimicrobial resistance and virulence genes contents
Escherichia coli sequence type 131 (ST131) is a pandemic clone which has been known for its contribution to the worldwide dissemination of multidrug resistance. Understanding trends among ST131 clades will help to design strategies to prevent its rapid dissemination. In this study, comparative genomic analysis was performed for 72 ST131. We also systematically compared 64 clade C with those clade C strains reported from other regions using publicly available whole genome sequencing data for ST131 strains. C1 (n=31, %48.4) and C2 (n=33, %51.5) strains had equal prevalence in our collection and C1-M27 (n=22) strains were closely related, carried a unique plasmid type (F1: A2: B20) and displayed virotype C. By removing 11 C2 strains with varied virotype patterns and heterogeneous IncF type, 22 closely related virotype E/F strains with replicon type F31/F36: A4: B1 were identified, forming what we denote the C2-subset. This subpopulation accounted for excess resistance/virulence of subclade C2 relative to C1 strains. In the global context, C2-subset, constituted distinct cluster with international virotype E strains and harboured a genomic island, GI-pheU. Association of cnf1/hlyCABD genes with 1 to 7 mobile genetic elements within GI-pheU was identified. Furthermore, a conserved chromosomal IS26-mediated composite transposon (IS15DIV- intact ISEcp1-blaCTX-M-15-WbuC cupin fold metalloprotein-Tn2-IS15DIV) was observed. The C2-subset locally circulating in the studied hospital with carriage of higher virulence/resistance markers and a peculiar F-type plasmid, highlighting the potential for diversification of ST131 lineage and appearance of subpopulations with higher survival potential to cause outbreaks associated with healthcare environments.
Escherichia coli sequence type 131 (ST131) is a pandemic clone which has been known for its contribution to the worldwide dissemination of multidrug resistance. Understanding trends among ST131 clades will help to design strategies to prevent its rapid dissemination. In this study, comparative genomic analysis was performed for 72 ST131. We also systematically compared 64 clade C with those clade C strains reported from other regions using publicly available whole genome sequencing data for ST131 strains. C1 (n=31, %48.4) and C2 (n=33, %51.5) strains had equal prevalence in our collection and C1-M27 (n=22) strains were closely related, carried a unique plasmid type (F1: A2: B20) and displayed virotype C. By removing 11 C2 strains with varied virotype patterns and heterogeneous IncF type, 22 closely related virotype E/F strains with replicon type F31/F36: A4: B1 were identified, forming what we denote the C2-subset. This subpopulation accounted for excess resistance/virulence of subclade C2 relative to C1 strains. In the global context, C2-subset, constituted distinct cluster with international virotype E strains and harboured a genomic island, GI-pheU. Association of cnf1/hlyCABD genes with 1 to 7 mobile genetic elements within GI-pheU was identified. Furthermore, a conserved chromosomal IS26-mediated composite transposon (IS15DIV- intact ISEcp1-blaCTX-M-15-WbuC cupin fold metalloprotein-Tn2-IS15DIV) was observed. The C2-subset locally circulating in the studied hospital with carriage of higher virulence/resistance markers and a peculiar F-type plasmid, highlighting the potential for diversification of ST131 lineage and appearance of subpopulations with higher survival potential to cause outbreaks associated with healthcare environments.