Genetic features of the poxtA linezolid resistance gene in human enterococci from France

Abstract

Objectives To describe the prevalence of poxtA among clinical linezolid-resistant enterococci (LRE) collected in France from 2016 to 2020 and to extensively characterize its genetic supports and environments. Methods All LRE clinical isolates received at the National Reference Centre for Enterococci from French hospitals between 2016 and 2020 were included. LRE isolates were screened for linezolid resistance genes (cfr-like, optrA and poxtA) by real-time PCR and phenotypically characterized. A collection of 11 representative poxtA-positive isolates (10 Enterococcus faecium and 1 Enterococcus faecalis) underwent WGS by hybrid assembly combining short-read (Illumina MiSeq) and long-read (MinION) approaches. Transferability of poxtA was attempted by filter-mating experiments. Results Out of 466 LRE received at the National Reference Centre for Enterococci over the period, 47 (10.1%) were poxtA-positive, including 42 E. faecium. The 11 isolates characterized by WGS were confirmed to be epidemiologically unrelated by core genome analysis and eight different STs were assigned to E. faecium isolates. The poxtA gene was found to be plasmid carried and flanked by IS1216E transposase genes in all isolates and frequently linked with fexB, tet(M) and tet(L). A total of seven distinct poxtA-harbouring plasmids were obtained after hybrid assembly and plasmid transfer of poxtA was successful in three cases. For the two poxtA/optrA-positive isolates, those genes were carried by different plasmids. Conclusions The poxtA gene has been circulating among clinical enterococci in France since at least 2016, mostly in E. faecium and independently from optrA. The poxtA-carrying plasmids often co-carried resistance genes to phenicols and tetracyclines, and could have been co-selected through their veterinary use.

Plasmid Fusion and Recombination Events That Occurred during Conjugation of poxtA -Carrying Plasmids in Enterococci

“…The prevalence of the poxtA gene has been investigated in enterococci from food-producing animal farms in China, Italy, and Korea, as well as in linezolid-resistant Enterococcus spp. (LRE) from patients in Ireland, Spain, and France ( 13 , 16 – 22 ). In China, Lei et al reported that the poxtA gene was present in 5.5% (19/345) of enterococci isolated from 36 food-producing animal farms across 12 provinces in 2017 ( 16 ).…”

“…In Spain, clinical LRE isolates from different hospitals were submitted to the Spanish Reference Laboratory from 2015 to 2018, and 6.2% of them (6/97) were poxtA -positive ( 21 ). In France, out of 466 LRE received by the National Reference Centre for Enterococci from French hospitals between 2016 and 2020, 47 (10.1%) were poxtA -positive ( 22 ).…”

“…Previously, all of the poxtA genes described in enterococci have been plasmid-borne, suggesting that plasmids play an important role in the dissemination of the poxtA gene among enterococci ( 22 , 23 ). In this study, two mobilizable poxtA -carrying plasmids were identified in E. faecalis and E. lactis , respectively.…”

Emergence of optrA-Mediated Linezolid Resistance in Enterococcus faecium: A Molecular Investigation in a Tertiary Hospital of Southwest China from 2014–2018

“…The IS1216E-PoxtA-IS1216E segment in our study is similar to S. aureus AOUC-0915, and clinical E. faecium from Italy, Spain, indicating that the genetic background of poxtA is relatively single. 8,16,41 In addition to the conjugative plasmid pE035 detected in China, Enterococcus harboring both the optrA and poxtA genes were also found in the environment and human samples from Pakistan, Ireland, Spain, France 17,[42][43][44][45] Unexpectedly, there does not seem to be any obvious synergistic effect when optrA and poxtA coexist. Because the MIC of EFM_7150 is not only similar to optrA or poxtA alone isolates in our study but also to E. faecium C10004 isolated from Spain (8mg/L).…”

Comparison of the Intestinal Pharmacokinetics of Two Different Florfenicol Dosing Regimens and Its Impact on the Prevalence and Phenotypic Resistance of E. coli and Enterococcus over Time

“…For example, linezolid resistant human strains of Enterococcus spp. may carry plasmids with co-resistance genes to florfenicol [5]. The cfr gene (named for chloramphenicol and florfenicol resistance) also mediates resistance to both linezolid and florfenicol in methicillin-resistant staphylococci [6].…”