Molecular Characterization of Enterococcus Isolates From Different Sources in Estonia Reveals Potential Transmission of Resistance Genes Among Different Reservoirs

Erki Aun; Veljo Kisand; Mailis Laht; Kaidi Telling; Piret Kalmus; Ülo Väli; Age Brauer; Maido Remm; Tanel Tenson

doi:10.3389/fmicb.2021.601490

Molecular Characterization of Enterococcus Isolates From Different Sources in Estonia Reveals Potential Transmission of Resistance Genes Among Different Reservoirs

Front Microbiol. 2021 Mar 26:12:601490. doi: 10.3389/fmicb.2021.601490. eCollection 2021.

Authors

Erki Aun¹, Veljo Kisand², Mailis Laht², Kaidi Telling³, Piret Kalmus⁴, Ülo Väli⁵, Age Brauer¹, Maido Remm¹, Tanel Tenson²

Affiliations

¹ Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
² Institute of Technology, University of Tartu, Tartu, Estonia.
³ Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.
⁴ Department of Clinical Veterinary Medicine, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia.
⁵ Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia.

Abstract

In this study, we aimed to characterize the population structure, drug resistance mechanisms, and virulence genes of Enterococcus isolates in Estonia. Sixty-one Enterococcus faecalis and 34 Enterococcus faecium isolates were collected between 2012 and 2014 across the country from various sites and sources, including farm animals and poultry (n = 53), humans (n = 12), environment (n = 24), and wild birds (n = 44). Clonal relationships of the strains were determined by whole-genome sequencing and analyzed by multi-locus sequence typing. We determined the presence of acquired antimicrobial resistance genes and 23S rRNA mutations, virulence genes, and also the plasmid or chromosomal origin of the genes using dedicated DNA sequence analysis tools available and/or homology search against an ad hoc compiled database of relevant sequences. Two E. faecalis isolates from human with vanB genes were highly resistant to vancomycin. Closely related E. faecalis strains were isolated from different host species. This indicates interspecies spread of strains and potential transfer of antibiotic resistance. Genomic context analysis of the resistance genes indicated frequent association with plasmids and mobile genetic elements. Resistance genes are often present in the identical genetic context in strains with diverse origins, suggesting the occurrence of transfer events.

Keywords: E. faecalis; E. faecium; antibiotic resistance; multi-locus sequence typing; phylogenetic analysis; van genes; virulence factors; whole-genome sequencing.