DIVERSITY AND EVOLUTION OF MULTIDRUG RESISTANCE PLASMIDS IN PANDEMIC ESCHERICHIA COLI ST131

Kira Kondratyeva Shiri Navon-Venezia
Molecular Biology Department, Ariel University, Ariel, Israel

Background: Escherichia coli sequence type ST131 is a pandemic clone colonizing and infecting humans. In order to understand the local and international spread of this important pathogen, we aimed to study the diversity and evolution of ST131 MDR plasmids circulating in Israel, and compare them with global E.coli ST131 plasmids, focusing on plasmids encoding blaCTX-M genes, the most widespread extended-spectrum-β-lactamases (ESBL).

Methods: The study was based on a local collection of 20 sequenced MDR E.coli ST131 plasmids isolated in Israel from clinical and animal origins (2003-2016), and on global E.coli ST131 whole genome sequences (WGS) retrieved from NCBI Sequence Read Archive (n=657). WGS (local and global) were sequenced by Illumina and assembled using SPAdes-v3.10.1. In silico analysis included: (i) ST131 subclone classification based on fimH-typing; (ii) plasmid replicon typing; (iii) blaCTX-M-genes identification. Plasmid phylogeny was studied using reference-free SNP-analysis (kSNP3.1), followed by maximum-likelihood bootstrap methods (PhyML-20131022, IQ-TREE-v1.6.2).

Results: Israeli sequenced plasmids were large (100-150Kb) and carried one to 10 ARGs. Eighteen plasmids belonged to IncF group with the following combinations of IncF replicon types and blaCTX-M-genes: IncF[F2:A1:B-] and CTX-M-15 (n=6); IncF[F1:A2:B20] and CTX-M-27 (n=7), and additional unique combinations (n=5). Two remaining identical plasmids (recovered from a human bloodstream infection and from a horse gut) showed 100% identity with a phage-like blaCTX-M-15-encoding plasmid from Germany. Focusing only on E.coli ST131 IncF plasmids and the encoded blaCTX-M genes (n=328), we found interesting correlations between the ST131 subclones (fimH30, fimH41, fimH22 and others) and the distribution of different IncF replicon types and blaCTX-M. Phylogenetic trees of local and global blaCTX-M-encoding plasmids were constructed with the designated country of origin and year of isolation if available.

Conclusions: Highly diverse ESBL-encoding plasmids circulate in E.coli ST131 in Israel and worldwide. This study demonstrates the complex evolution and spread of E.coli ST131 subclones and MDR plasmids.









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