title: Comparative genomics of Enterococcus spp. isolated from bovine feces.
abstract: 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.
  
  
  
  We 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.
  
  
  
  This 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.
authors.affiliation: Faculty of Veterinary Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.|Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
authors.forename: Alicia G
authors.initials: AG
authors.lastname: Beukers
authors.affiliation: Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
authors.forename: Rahat
authors.initials: R
authors.lastname: Zaheer
authors.affiliation: Canadian Food Inspection Agency, National Center for Animal Disease, Lethbridge Laboratory, Lethbridge, AB, Canada.
authors.forename: Noriko
authors.initials: N
authors.lastname: Goji
authors.affiliation: Canadian Food Inspection Agency, National Center for Animal Disease, Lethbridge Laboratory, Lethbridge, AB, Canada.
authors.forename: Kingsley K
authors.initials: KK
authors.lastname: Amoako
authors.affiliation: Faculty of Veterinary Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
authors.forename: Alexandre V
authors.initials: AV
authors.lastname: Chaves
authors.affiliation: Faculty of Veterinary Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Ward
authors.affiliation: Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada. tim.mcallister@agr.gc.ca.
authors.forename: Tim A
authors.initials: TA
authors.lastname: McAllister
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001435:Bacteriophages; D064113:CRISPR-Cas Systems; D002417:Cattle / Q000382:microbiology*; D002418:Cattle Diseases / Q000382:microbiology; D016000:Cluster Analysis; D004251:DNA Transposable Elements / Q000235:genetics; D004269:DNA, Bacterial / Q000302:isolation & purification; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics; D016983:Enterococcus / Q000145:classification* / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification*; D013293:Enterococcus faecalis / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity; D016984:Enterococcus faecium / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity; D000070076:Enterococcus hirae / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity; D005243:Feces / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D055231:Lincosamides / Q000494:pharmacology; D018942:Macrolides / Q000494:pharmacology; D008826:Microbial Sensitivity Tests; D058885:Multilocus Sequence Typing / Q000379:methods; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D025381:Streptogramin B / Q000494:pharmacology; D013753:Tetracycline Resistance / Q000235:genetics; D037521:Virulence Factors / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D055231:Lincosamides; D018942:Macrolides; D037521:Virulence Factors; D025381:Streptogramin B
keywords: Bovine feces; Comparative genomics; Enterococcus