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

• Published in: Scientific reports Vol. 10; no. 1; pp. 9160 - 9
• Main Authors: Bonnin, Rémy A., Girlich, Delphine, Jousset, Agnès B., Gauthier, Lauraine, Cuzon, Gaëlle, Bogaerts, Pierre, Haenni, Marisa, Madec, Jean-Yves, Couvé-Deacon, Elodie, Barraud, Olivier, Fortineau, Nicolas, Glaser, Philippe, Glupczynski, Youri, Dortet, Laurent, Naas, Thierry
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 08.06.2020; Nature Publishing Group; Nature Portfolio
• Subjects: 45; 45/23; 45/77; 631/326/107; 631/326/22/1434; Animals; Antibiotics; Bacterial Proteins - biosynthesis; Bacterial Proteins - classification; Bacterial Proteins - genetics; Bacteriology; Belgium; beta-Lactamases - biosynthesis; beta-Lactamases - classification; beta-Lactamases - genetics; Carbapenemase; Chromosomes, Bacterial - genetics; DNA Transposable Elements - genetics; DNA, Bacterial - genetics; Enterobacterales; Enzymes; France; Genes; Genes, Bacterial - genetics; Genomes; Human health and pathology; Humanities and Social Sciences; Humans; Hépatology and Gastroenterology; Life Sciences; Microbiology and Parasitology; multidisciplinary; Phylogenetics; Phylogeny; Plasmids - genetics; Proteus mirabilis; Proteus mirabilis - enzymology; Proteus mirabilis - genetics; Proteus mirabilis - isolation & purification; Science; Science (multidisciplinary); Urine; Belgium; France; Clinical microbiology; Antimicrobial resistance
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-66161-z

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, Tn 6703 , bracketed by two copies of IS 15∆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.