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.
Highlights
Enterococcus is a genus of Gram-positive bacteria, with 67 species, belonging to the lactic acid bacteria from the phylum Firmicutes (Arias and Murray, 2012; Parte, 2014)
For E. faecium, in total, 34 isolates were recovered from the collected samples, and these included four isolates from environmental sources, three isolates from farm animals (B. taurus = 1, S. scrofa = 2), 23 isolates from poultry, one isolate from free living pigeon Columba livia, and three isolates from human samples
This is in accordance with previous findings that E. faecalis strains of the same sequence type can be found in humans as well as in other animal species, while E. faecium strains tend to be more host specific (Hammerum, 2012)
Summary
Enterococcus is a genus of Gram-positive bacteria, with 67 species, belonging to the lactic acid bacteria from the phylum Firmicutes (Arias and Murray, 2012; Parte, 2014). Enterococcus faecium and Enterococcus faecalis are the two most abundant Enterococcus commensals of the gastrointestinal and genitourinary tracts, the oral cavity, the vagina, and the skin In addition to their commensal role, these two Enterococcus species have recently emerged as important human pathogens causing infectious diseases, including endocarditis and bacteremia. Their ability to withstand harsh environmental conditions and their high intrinsic resistance or tolerance to many antimicrobials accompanied by their ability to acquire high-level resistance to new antimicrobial agents via horizontal gene transfer have enabled them to survive and spread within hospital settings and become one of the leading causes of nosocomial infections (Kayser, 2003; Ørstavik, 2004; Heikens et al, 2007). The last-resort antibiotics against enterococcal infections that cannot be treated with β-lactams or glycopeptides include, for example, oxazolidinones like tedizolid and linezolid, daptomycin, tigecycline, and a synergistic combination of streptogramin A and streptogramin B (Cetinkaya et al, 2000; Arias et al, 2010; Rybak and Roberts, 2015; Ahmed and Baptiste, 2018; Bender et al, 2018; Abbo et al, 2019)
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