Meta-analysis of Multidrug Resistant Plasmids Circulating in Pandemic Escherichia coli Sequence Type 131

Background: WGS databases allow to investigate plasmid dynamics in bacterial populations. We aimed to study the plasmidome of a worldwide pandemic pathogen Escherichia coli sequence type (ST) 131 focusing on its multidrug resistance plasmids.

Methods: Our meta-analysis included raw E.coli ST131 WGS data (NCBI Sequence Read Archive, SRA, n=880) using two approaches: (i) assembly (SPAdes-v3.10.1); (ii) read-mapping to reference plasmids/genes (bwa 0.7.17-r1188). We identified ST131 clonal features, plasmid replicon types, and CTX-M extended-spectrum-β-lactamase genes. The concordance rate of the two approaches was evaluated and SNPs-based phylogenetic analyses of differently processed data were compared. In addition, to add local plasmidome data, we sequenced and analyzed 20 Israeli ST131 plasmids (2003-2016) using Illumina-HiSeq and Nanopore technologies.

Results: We characterized SRA ST131 plasmidome and showed associations between bacterial clades, plasmid replicon types and CTX-M genes. Two major ST131 IncF plasmid groups were further investigated: Group1- CTX-M-27-encoding IncF[F1:A2:B20] plasmids; and Group2- CTX-M-15-encoding IncF[F2:A1:B-]. SRA analysis revealed strong plasmid-clade associations where Group1 features were found only in clade C1, and Group2- in clade C2, suggesting adaptations to be identified. NCBI Nucleotide database and Israeli collection analyses supported Group1 and Group2 associations with the expected clades. We found a new CTX-M-15-encoding phage-like plasmid group (Group3) among Israeli isolates and followed its spread in global SRA data.

Conclusions: This study offers a comprehensive approach to decipher plasmid-bacterium associations and can be applied to diverse bacterial populations. We demonstrate that ST131 CTX-M-encoding Group1 and Group2 plasmids are clade-restricted and potentially contributing to the worldwide success of this clone.