Comparative genomics of Enterococcus spp. isolated from bovine feces

Abstract

Background Enterococcus is ubiquitous in nature and is a commensal of both the bovine and human gastrointestinal (GI) tract. It is also associated with clinical infections in humans. Subtherapeutic administration of antibiotics to cattle selects for antibiotic resistant enterococci in the bovine GI tract. Antibiotic resistance genes (ARGs) may be present in enterococci following antibiotic use in cattle. If located on mobile genetic elements (MGEs) their dissemination between Enterococcus species and to pathogenic bacteria may be promoted, reducing the efficacy of antibiotics.ResultsWe present a comparative genomic analysis of twenty-one Enterococcus spp. isolated from bovine feces including Enterococcus hirae (n = 10), Enterococcus faecium (n = 3), Enterococcus villorum (n = 2), Enterococcus casseliflavus (n = 2), Enterococcus faecalis (n = 1), Enterococcus durans (n = 1), Enterococcus gallinarum (n = 1) and Enterococcus thailandicus (n = 1). The analysis revealed E. faecium and E. faecalis from bovine feces share features with human clinical isolates, including virulence factors. The Tn917 transposon conferring macrolide-lincosamide-streptogramin B resistance was identified in both E. faecium and E. hirae, suggesting dissemination of ARGs on MGEs may occur in the bovine GI tract. An E. faecium isolate was also identified with two integrative conjugative elements (ICEs) belonging to the Tn916 family of ICE, Tn916 and Tn5801, both conferring tetracycline resistance.ConclusionsThis study confirms the presence of enterococci in the bovine GI tract possessing ARGs on MGEs, but the predominant species in cattle, E. hirae is not commonly associated with infections in humans. Analysis using additional complete genomes of E. faecium from the NCBI database demonstrated differential clustering of commensal and clinical isolates, suggesting that these strains may be specifically adapted to their respective environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-017-0962-1) contains supplementary material, which is available to authorized users.

Comparative Genome Analysis Reveals Important Genetic Factors Associated with Probiotic Property inEnterococcus faeciumstrains

“…growth, DNA replication, transcription, translation, carbohydrate and amino acid metabolism, stress response and transporters. In contrast to earlier reports, core genes were also found in the functional categories of secondary metabolism and motility (Palmer et al 2012; Beukers et al 2017). Categories representing transport and metabolism of coenzyme, lipid, amino acid, nucleotide comprised of 16.24% of the core genes, while 11.30% of core genes were ascribed to carbohydrate metabolism which is in agreement with an earlier report (Beukers et al 2017).…”

“…Mobile genetic elements (MGEs) play an important role in HGT of genes within and between bacteria (Beukers et al 2017; Jiang et al 2017; Kaplan 2014; Von Wintersdorff et al 2016). A number of MGEs have been described in E. faecium including transposons, plasmids, and bacteriophage (Hegstad et al 2010b; Beukers et al 2017).…”

Metagenomic analysis of enteric bacterial pathogens affecting the performance of dairy cows in smallholder productions systems

“…faecium were detected both in the rumen fluid and feces. Similar findings were also reported by Goskel et al (2016) and Beukers et al (2017). They were also reported infecal and cecal samples of chickens by Diarra et al (2010).…”

Short communication: Antimicrobial resistance and virulence genes of Enterococcus faecalis isolated from subclinical bovine mastitis cases in China

“…Although Enterococcus spp. have low-level intrinsic resistance to aminoglycosides, lincosamides, and trimethoprim, emergence and prevalence of antimicrobial resistance is closely related to the use of antimicrobial agents (Klibi et al, 2015;Beukers et al, 2017). A variety of antimicrobials is available for therapeutic use in veterinary medicine in China (MOA, 2013).…”