AUTHOR=Amuasi Grebstad Rabbi , Dsani Esther , Owusu-Nyantakyi Christian , Owusu Felicia A. , Mohktar Quaneeta , Nilsson Pernille , Adu Bright , Hendriksen Rene S. , Egyir Beverly 

TITLE=Enterococcus species: insights into antimicrobial resistance and whole-genome features of isolates recovered from livestock and raw meat in Ghana

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1254896

DOI=10.3389/fmicb.2023.1254896

ISSN=1664-302X

ABSTRACT=<sec id="sec1"><title>Introduction</title><p><italic>Enterococcus</italic> spp. have gradually evolved from commensals to causing life-threatening hospital-acquired infections globally due to their inherent antimicrobial resistance ability and virulence potential. <italic>Enterococcus</italic> spp. recovered from livestock and raw meat samples were characterized using antimicrobial susceptibility testing and whole-genome sequencing.</p></sec><sec id="sec2"><title>Materials and methods</title><p>Isolates were confirmed using the MALDI-ToF mass spectrometer, and antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion method. Whole genome sequencing was performed on isolates resistant to two or more antibiotics. Bioinformatics analysis was performed to determine sequence types, resistance and virulence gene content and evolutionary relationships between isolates from meat and livestock samples, and other enterococci genomes curated by PATRIC. eBURST analysis was used to assign genomes to clonal complexes.</p></sec><sec id="sec3"><title>Results</title><p><italic>Enterococcus</italic> spp. were predominantly <italic>E. faecalis</italic> (96/236; 41%) and <italic>E. faecium</italic> (89/236; 38%). Overall, isolates showed resistance to erythromycin (78/236; 33%), tetracycline (71/236; 30%), ciprofloxacin (20/236; 8%), chloramphenicol (12/236; 5%), linezolid (7/236; 3%), ampicillin (4/236; 2%) and vancomycin (1/236, 0.4%). Resistance to two or more antimicrobial agents was detected among 17% (<italic>n</italic> = 40) <italic>Enterococcus</italic> spp. Resistance genes for streptogramins [<italic>lsa(A), lsa(E), msr(C)</italic>], aminoglycosides [<italic>aac(6′)-Ii, aph(3′)-III, ant(6)-Ia, aac(6′)-aph(2″), str],</italic> amphenicol [<italic>cat</italic>], macrolides [<italic>erm(B), erm(T), msr(C)</italic>], tetracyclines [<italic>tet(M), tet(L), tet(S)</italic>] and lincosamides [<italic>lsa(A), lsa(E), lnu(B)</italic>] were detected among the isolates. Genes for biofilm formation, adhesins, sex pheromones, cytolysins, hyaluronidase, oxidative stress resistance, quorum-sensing and anti-phagocytic activity were also identified. Potential plasmids with replicon sequences (<italic>rep1, rep2, repUS43, repUS47, rep9a, rep9b</italic>) and other mobile genetic elements (<italic>Tn917, cn_5536_ISEnfa1, Tn6009, ISEnfa1, ISEfa10</italic>) were detected. Clinically relevant <italic>E. faecium</italic> ST32 and ST416 clones were identified in meat samples.</p></sec><sec id="sec4"><title>Conclusion</title><p>The occurrence of antimicrobial-resistant <italic>Enterococcus</italic> spp. in livestock and raw meat samples, carrying multiple resistance and virulence genes, including known clones associated with hospital-acquired infections, underscores the critical need for employing robust tools like whole genome sequencing. Such tools provide detailed data essential for ongoing surveillance efforts aimed at addressing the challenge of antimicrobial resistance with a focus on one health.</p></sec>