National surveillance of clinical isolates of Enterococcus faecalis resistant to linezolid carrying the optrA gene in Colombia, 2014-2019

Abstract

Objective. To describe the epidemiological, phenotypical and genetic characteristics of clinical isolates carrying the optrA gene identified in antimicrobial resistance surveillance by the laboratory of the National Institute of Health of Colombia. Methods. Between October 2014 and February 2019, 25 isolates of Enterococcus spp. resistant to linezolid were received. Antimicrobial identification and sensitivity were determined using Vitek 2 and the minimum inhibitory concentration (MIC) to linezolid was established with E-test. The optrA gene was detected by PCR, and the genetic diversity of optrA-positive isolates was tested with Diversilab®. Six isolates were selected to perform whole genome sequencing. Results. The optrA gene was confirmed in 23/25 isolates of E. faecalis from seven departments in Colombia. The isolates presented a MIC to linezolid between 8 and >256μg/mL. Typing by Diversilab® showed a wide genetic variability. All the isolates analyzed by whole genome sequencing showed the resistance genes fexA, ermB, lsaA, tet(M), tet(L) and dfrG in addition to optrA and were negative for other mechanisms of resistance to linezolid. Three type sequences and three optrA variants were identified: ST16 (optrA-2), ST476 (optrA-5) and ST618 (optrA-6). The genetic environment of the optrA-2 (ST16) isolates presented the impB, fex, optrA segment, associated with plasmid, while in two isolates (optrA-6 and optrA-5) the transferable chromosomal element Tn6674-like was found. Conclusion. OptrA-positive clinical isolates present a high genetic diversity, with different optrA clones and variants related to two types of structures and different mobile genetic elements.