Undetectable Production of the VIM-1 Carbapenemase in an Atlantibacter hermannii Clinical Isolate.

Delphine Girlich,Thierry Naas,Alexis Proust,Laurent Dortet,Rémy A Bonnin

doi:10.3389/fmicb.2021.741972

Abstract

The differential expression of VIM-1 in Atlantibacter hermannii WEB-2 and Enterobacter hormaechei ssp. hoffmannii WEB-1 clinical isolates from a rectal swab of a hospitalized patient in France was investigated. A. hermannii WEB-2 was resistant to all β-lactams except carbapenems. It produced ESBL SHV-12, but the Carba NP test failed to detect any carbapenemase activity despite the production of VIM-1. Conversely, E. hormaechei WEB-1, previously recovered from the same patient, was positive for the detection of carbapenemase activity. The blaVIM–1 gene was located on a plasmid and embedded within class 1 integron. Both plasmids were of the same IncA incompatibility group and conferred the same resistance pattern when electroporated in Escherichia coli TOP10 or Enterobacter cloacae CIP7933. Quantitative RT-PCR experiments indicated a weaker replication of pWEB-2 in A. hermannii as compared to E. hormaechei. An isogenic mutant of A. hermannii WEB-2 selected after sequential passages with increased concentrations of imipenem possessed higher MICs for carbapenems and cephalosporins including cefiderocol, higher levels of the blaVIM–1 gene transcripts, and detectable carbapenemase activity using the Carba NP test. Assessment of read coverage demonstrated that a duplication of the region surrounding blaVIM–1 gene occurred in the A. hermannii mutant with detectable carbapenemase activity. The lack of detection of the VIM-1 carbapenemase activity in A. hermannii WEB-2 isolate was likely due to a weak replication of the IncA plasmid harboring the blaVIM–1 gene. Imipenem as selective pressure led to a duplication of this gene on the plasmid and to the restoration of a significant carbapenem-hydrolyzing phenotype.

Highlights

Atlantibacter hermannii belongs to the distinct genus Atlantibacter in Enterobacterales (Brenner et al, 1982; Hata et al, 2016)
Phylogenetic analysis revealed that E. cloacae complex WEB-1 corresponds to E. hormaechei ssp. hoffmannii WEB1 (Supplementary Figure 1)
A. hermannii WEB-2 showed resistance to amoxicillin, ticarcillin, ceftazidime, and aztreonam, which was only slightly reversed by clavulanate; a moderate susceptibility to piperacillin and other cephalosporins; and susceptibility to carbapenems and cefiderocol (MICs at 0.12 mg/L)

Summary

Introduction

Atlantibacter (formerly Escherichia) hermannii belongs to the distinct genus Atlantibacter in Enterobacterales (Brenner et al, 1982; Hata et al, 2016). A. hermannii harbors a chromosome-encoded class A β-lactamase (HER-1-like), VIM-1 Expression conferring resistance to amoxicillin and ticarcillin, which is reversed by clavulanate, and a moderate susceptibility to piperacillin. The VIM-1 enzyme is a metallo-β-lactamase (MBL) identified for the first time in 1997, in a carbapenem-resistant Pseudomonas aeruginosa isolate at the Verona University Hospital (Lauretti et al, 1999). This enzyme exhibits a very broad substrate specificity, including carbapenems, and was found to be encoded by a determinant carried on a mobile gene cassette inserted into an integron located on the chromosome or on plasmids (Di Pilato et al, 2014, 2015). Infection with VIM-1-producing Klebsiella pneumoniae has become endemic in some European countries, especially in intensive care units of tertiary care hospitals in Greece (Souli et al, 2008), and sporadic cases of infection due to multidrug-resistant Enterobacterales carrying blaVIM−1 have been reported (Perilli et al, 2002; Souli et al, 2008)

Objectives

Results

Conclusion