A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales

Abstract

In Enterobacterales, the most common carbapenemases are Ambler's class A (KPC-like), class B (NDM-, VIM- or IMP-like) or class D (OXA-48-like) enzymes. This study describes the characterization of twenty-four OXA-23 or OXA-58 producing-Proteus mirabilis isolates recovered from human and veterinary samples from France and Belgium. Twenty-two P. mirabilis isolates producing either OXA-23 (n = 21) or OXA-58 (n = 1), collected between 2013 and 2018, as well as 2 reference strains isolated in 1996 and 2015 were fully sequenced. Phylogenetic analysis revealed that 22 of the 24 isolates, including the isolate from 1996, belonged to a single lineage that has disseminated in humans and animals over a long period of time. The bla_OXA-23 gene was located on the chromosome and was part of a composite transposon, Tn6703, bracketed by two copies of IS15∆II. Sequencing using Pacbio long read technology of OXA-23-producing P. mirabilis VAC allowed the assembly of a 55.5-kb structure encompassing the bla_OXA-23 gene in that isolate. By contrast to the bla_OXA-23 genes, the bla_OXA-58 gene of P. mirabilis CNR20130297 was identified on a 6-kb plasmid. The acquisition of the bla_OXA-58 gene on this plasmid involved XerC-XerD recombinases. Our results suggest that a major clone of OXA-23-producing P. mirabilis is circulating in France and Belgium since 1996.

Figure 1

Geographic distribution of the 24 OXA-23- or OXA-58-producing P. mirabilis isolates. Bolded isolates correspond to animal isolates, while OXA-58-producing isolates were boxed.

Figure 2

(A) Comparative genomic of P. mirabilis VAC. Genome analysis of P. mirabilis VAC and its comparison with P. mirabilis S4 (1996), P. mirabilis BCT17 (2017) and P. mirabilis BB2000 reference genome (CP004022). Circular representation was obtained using CGViewer. Inner circles represent CG content (black circle) and CG Skew (green & purple circle). GI = Genomic Island (B) Schematic representation of IS15∆II-based composite transposon (Tn6703) and its insertion site. Red boxes represent resistance genes and orange boxes represent mobile elements. (C) Schematic representation of Tn7. Genes are indicated by arrows. Red arrows represent resistance genes and orange arrows represented mobile elements. (D) Analysis of the genetic context of bla_OXA-58 in P. mirabilis 1091 and 20130297 isolates. XerC-XerD binding sites are indicated by triangles. Dashed lines represent DNA insertions.

Figure 3

Phylogenetic relationship of the 24 OXA-23 and OXA-58-producing P. mirabilis isolates with 121 reference genomes of P. mirabilis from GenBank. The phylogenetic tree was obtained using CSI phylogeny v1.4. Carbapenemase producing isolates are labelled with their respective coloured symbols.