Dissemination of OXA-23 carbapenemase-producing Proteus mirabilis and Escherichia coli is driven by transposon-carrying lineages in the UK

Abstract

Carbapenem-resistant Enterobacterales are a significant threat to global public health. Here, we characterize bla _OXA-23-positive Proteus mirabilis (n=8) and Escherichia coli (n=3) isolates from human clinical samples collected between 2021 and 2024 in the UK. Whole-genome sequencing (WGS) was used to generate data, and a phylogenetic tree inferred from SNPs filtered for recombination was constructed to assess the genomic relatedness among the isolates. To provide an international context, we included publicly available genomes. Short-read mapping to a reference genome enabled reconstruction of the genomic neighbourhood around bla _OXA-23. Minimum inhibitory concentration (MIC) determination was performed using broth microdilution and results interpreted using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. UK P. mirabilis isolates belonged to ST142 and formed a sub-clade descending from an ancestral cluster of French isolates with relatively few SNPs between them (9-39). E. coli ST38 isolates harboured bla _OXA-23 and showed close genetic relatedness (12-15 SNPs) among themselves. In P. mirabilis, bla _OXA-23 was associated with transposon Tn6703, while E. coli harboured a novel composite transposon, designated Tn7816, bordered by two copies of IS26 and with three copies of bla _OXA-23. bla _OXA-23 was integrated into the chromosome in all isolates. All isolates were resistant to amoxicillin/clavulanic acid (>32 mg l^-1) and with meropenem MICs above the EUCAST screening cut-off (0.5-1 mg l^-1). In conclusion, UK bla _OXA-23-positive P. mirabilis isolates belong to the same clonal lineage (ST142) previously reported in Belgium, Germany, Switzerland and France, suggesting introduction of this lineage into the UK. This is the first report of an E. coli ST38 lineage with chromosomally encoded bla _OXA-23 located within a novel transposon Tn7816. WGS plays an important role in identifying the mechanism(s) of transmission of emerging carbapenemase genes.

Keywords: Escherichia coli; OXA-23; Proteus mirabilis; carbapenemase; transposon.

Fig. 1.. Recombination-filtered SNP-based rooted phylogeny of 62 bla_OXA-23-positive P. mirabilis isolates. The phylogenetic relationship analysis included bla_OXA-23-positive ST142 isolates from the UK (n=8) and isolates obtained from prior studies (n=54) conducted in various European countries. Next to the tree are represented the metadata such as country, source, year, ST and AMR determinants. ‘NA’ label within the year field indicated that year-related information was not available, while ‘NA’ in ST indicates that it was not feasible to establish the ST due to missing or incomplete MLST loci. This includes the absence or partial coverage (44 –86 %) of recA in 11 genomes, the absence of pyrC in one genome or partial coverage (75 –58 %) of dnaJ in two genomes, possibly attributable to fragmented contigs. Bootstrap support ≥95 % (blue dots) indicates well-supported clades, with the clade of interest highlighted in pale blue. Scale bars represent a phylogenetic distance of 10 SNPs.

Fig. 2.. Genomic context associated with bla_OXA-23 in the UK isolates. (a) Composite transposon Tn6703 is present in P. mirabilis ST142 isolates from the UK (n=8) and France (with the VAC isolate as a reference), carrying AMR genes, and specifically Tn6704, which harbours bla_OXA-23. Boundaries of Tn6704 are indicated by the 9-bp TSD GATGAAGCG and for Tn6703 by the 8-bp TSD TAATTTCC. (b) A novel composite transposon Tn7816 associated with bla_OXA-23 in bla_OXA-23-positive E. coli ST38 in UK isolates (n=3). The two bla_OXA-23-negative isolates yielded contig-level sequence assemblies, where the operon yjiGHJKLMN and genetic configuration yjiGHJKLM–IS15DIV–yjiN were in a single contig, respectively. Genes are represented by arrows indicating the direction of transcription. bla_OXA-23 is indicated by the orange arrow, ATPase by the light green arrow, ISAba1 by the dark green arrow, IS15DII and IS26 by the light blue arrows, other insertion sequences and additional AMR genes are indicated by the dark blue arrows, other genes within the transposon by the grey arrows and other genes outside the transposon by the white arrows. Grey areas between the linear plots represent nucleotide sequence identity (mostly >90 %).