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

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

Erki Aun  1 , Veljo Kisand  2 , Mailis Laht  2 , Kaidi Telling  3 , Piret Kalmus  4 , Ülo Väli  5 , Age Brauer  1 , Maido Remm  1 , Tanel Tenson  2
Affiliations

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

Erki Aun et al. Front Microbiol. .

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.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Isolation sources and hosts of the collected Enterococcus strains.
FIGURE 2
FIGURE 2
Core-genome phylogenetic tree of our collected 61 Enterococcus faecium isolates and 16 reference genomes with the distribution matrix of the antimicrobial resistance and virulence genes detected in their whole-genome sequences.
FIGURE 3
FIGURE 3
Core-genome phylogenetic tree of our collected 34 Enterococcus faecium isolates and 16 reference genomes with the distribution matrix of the antimicrobial resistance and virulence genes detected in their whole-genome sequences.
FIGURE 4
FIGURE 4
The genomic context of the resistance genes in the antibiotic resistance islands. Most of the clustered resistance genes were found in the same genetic context in strains of different origins and were flanked by mobile genetic elements and plasmid-related genes. The figure illustrates only the context and is not scaled to the actual length of the genes and intergenic sequences. (A–D) a lsa(E), lnu(B) and aminoglycoside resistance genes harboring genomic islands found in husbandry and human related strains, (E,F,L) a tetracycline resistance gene cluster variants found in human and husbandry related strains, (G) a erm(B) and aminoglycoside resistance genes harboring genomic in human related strains, (H) a cat_5 and str_1 genes harboring genomic island in human and husbandry related strains, (I) a tetracycline resistance cluster and cat_5 gene harboring genomic island found in husbandry related strains, (J) a erm(B) and dfr(G) genes harboring genomic island found in poultry related strains, (K) an aminoglycoside resistance genes harboring genomic island found in human related strains, (M) cat(pc221)_1 and erm(B) genes harbouring genomic island found in human related strains.
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