Environmental occurrence of optrA-mediated linezolid resistance in Enterococcus isolates and genomic insights into Enterococcus faecium ST54 co-harboring optrA, poxtA, and cfr(D) genes

TL;DR

This study finds linezolid-resistant Enterococcus bacteria in Brazilian aquatic environments, highlighting the spread of antibiotic resistance genes in nature.

Contribution

The study reports the first environmental occurrence of Enterococcus faecium ST54 co-harboring optrA, poxtA, and cfr(D) genes in South America.

Findings

181 Enterococcus isolates were obtained, with 37% carrying the optrA gene.

One E. faecium isolate (EW1587) co-harbored optrA, poxtA, and cfr(D) genes and belonged to ST54.

The resistance genes were plasmid-borne and remained stable in vitro for 30 days.

Abstract

Linezolid-resistant Enterococcus species have emerged worldwide, with resistance mainly driven by plasmid-borne optrA, poxtA, and cfr genes. While the optrA gene has been increasingly identified in humans and animals, its presence in the environmental sector remains poorly studied, especially in South America. This study aimed to investigate and characterize linezolid resistance genes in isolates of Enterococcus faecium and Enterococcus faecalis obtained from aquatic ecosystems in 51 cities in the state of São Paulo, Brazil. Phenotypic, molecular, and genomic analyses were used for this proposal. Accordingly, 181 Enterococcus isolates were obtained, with 67 (37%) harboring the optrA gene. Most isolates exhibited multidrug resistance, and the minimum inhibitory concentration to linezolid ranged from 0.5 to > 64 mg/L. Several virulence genes and plasmid replicons were observed, with gelE and rep9 being most prevalent, respectively. Ten isolates co-harbored the optrA and poxtA genes and belonged to the known sequence type (ST) 1221 (E. faecium) and ST283, ST253, ST234, and ST1230 (E. faecalis), as well as to the new ST3018, ST3022, ST3026, and ST3027 (E. faecium), and ST2126 (E. faecalis). Moreover, one E. faecium isolate (EW1587) carried optrA, poxtA, and cfr(D) genes and, therefore, was submitted to genomic characterization. Isolate EW1587 belonged to ST54 and was closely related to an animal-derived Brazilian strain. In silico analysis predicted that optrA, poxtA, and cfr(D) genes were plasmid-borne, whereas in vitro stability tests demonstrated that these genes remained stable for 30 days. These results highlight the environmental spread of transferable oxazolidinone resistance genes, with E. faecium ST54 co-carrying optrA, poxtA, and cfr(D) genes. Therefore, continuous monitoring is essential to fully elucidate the mechanisms driving the spread and evolution of linezolid resistance across environmental reservoirs.

The online version contains supplementary material available at 10.1007/s11274-026-04786-4.

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