Identification of Diverse Integron and Plasmid Structures Carrying a Novel Carbapenemase Among Pseudomonas Species.

Eleni Liapis,Katy Jeannot,Jean-Ralph Zahar,Maxime Bour,Benoît Valot,Thomas Jové,Patrick Plésiat,Pauline Triponney

doi:10.3389/fmicb.2019.00404

Abstract

A novel carbapenem-hydrolyzing beta-lactamase, called IMP-63, was identified in three clonally distinct strains of Pseudomonas aeruginosa and two strains of Pseudomonas putida isolated within a 4 year timeframe in three French hospitals. The blaIMP–63 gene that encodes this carbapenemase turned out to be located in the variable region of four integrons (In1297, In1574, In1573, and In1572) and to coexist with novel or rare gene cassettes (fosM, gcu170, gcuF1) and insertion elements (ISPsp7v, ISPa16v). All these integrons except one (In1574) were flanked by a copy of insertion sequence ISPa17 next to the orf6 putative gene, and were carried by non-conjugative plasmids (pNECK1, pROUSS1, pROUSS2, pROUE1). These plasmids exhibit unique modular structures and partial sequence homologies with plasmids previously identified in various non-fermenting environmental Gram-negative species. Lines of evidence suggest that ISPa17 promoted en bloc the transposition of IMP-63-encoding integrons on these different plasmids. As demonstrated by genotyping experiments, isolates of P. aeruginosa harboring the 28.9-kb plasmid pNECK1 and belonging to international “high-risk” clone ST308 were responsible for an outbreak in one hospital. Collectively, these data provide an insight into the complex and unpredictable routes of diffusion of some resistance determinants, here blaIMP–63, among Pseudomonas species.

Highlights

The Pseudomonas putida group is composed of several closely related species that live in the soil and surface waters as saprophytes within complex communities (Gomila et al, 2015)
We show that the diffusion of a rare variant of MBL IMP-12, named IMP-63, among clinical strains of P. aeruginosa and P. putida occurred through a complex scenario involving several genetic cargos
Seven multidrug resistant strains of P. aeruginosa isolated in hospital H1, Paris, between November 2011 and July 2012 were referred to the French National Reference Center for Antibiotic Resistance (NRC-AR, Besançon) for characterization of their resistance mechanisms to ß-lactams

Summary

Introduction

The Pseudomonas putida group is composed of several closely related species that live in the soil and surface waters as saprophytes within complex communities (Gomila et al, 2015). Though poorly pathogenic for humans these Gram-negative bacteria can occasionally generate acute or chronic infections in fragile patients. Species such as P. putida (sensu stricto), P. monteilii, and P. mosselii are regularly isolated from clinical samples (Yang et al, 1996). Metallo-ß-lactamases (MBLs) of VIMand IMP-types are the most prevalent carbapenemases in carbapenem-resistant P. aeruginosa and P. putida. Their genetic determinants can be borne by the bacterial chromosome or by plasmids (Lee et al, 2002; Docquier et al, 2003; Yomoda et al, 2003; Marchiaro et al, 2010). We show that the diffusion of a rare variant of MBL IMP-12, named IMP-63, among clinical strains of P. aeruginosa and P. putida occurred through a complex scenario involving several genetic cargos

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