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

Abstract

IntroductionEnterococcus spp. have gradually evolved from commensals to causing life-threatening hospital-acquired infections globally due to their inherent antimicrobial resistance ability and virulence potential. Enterococcus spp. recovered from livestock and raw meat samples were characterized using antimicrobial susceptibility testing and whole-genome sequencing.Materials and methodsIsolates 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.ResultsEnterococcus spp. were predominantly E. faecalis (96/236; 41%) and E. faecium (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% (n = 40) Enterococcus spp. Resistance genes for streptogramins [lsa(A), lsa(E), msr(C)], aminoglycosides [aac(6′)-Ii, aph(3′)-III, ant(6)-Ia, aac(6′)-aph(2″), str], amphenicol [cat], macrolides [erm(B), erm(T), msr(C)], tetracyclines [tet(M), tet(L), tet(S)] and lincosamides [lsa(A), lsa(E), lnu(B)] 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 (rep1, rep2, repUS43, repUS47, rep9a, rep9b) and other mobile genetic elements (Tn917, cn_5536_ISEnfa1, Tn6009, ISEnfa1, ISEfa10) were detected. Clinically relevant E. faecium ST32 and ST416 clones were identified in meat samples.ConclusionThe occurrence of antimicrobial-resistant Enterococcus 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.

Antimicrobial susceptibility and resistome of Actinobacillus pleuropneumoniae in Taiwan: a next-generation sequencing analysis

“…Previous studies also reported similar findings, in which several ARGs tended to occur more often on the same contig with MGEs, such as ISs (Amuasi et al. 2023 ). Nevertheless, few studies have revealed the co-occurrence of plasmid replicons and/or MGEs associated with ARGs encoding resistance to antimicrobials in A. pleuropneumoniae .…”

“…However, a similar association between macrolide resistance gene [ erm(B) ] and repUS43 and rep9b plasmid replicons was proposed (Amuasi et al. 2023 ). Furthermore, we found that co-occurrence between one MGE (ISVsa5) and ARGs on the same contig was observed in 94.4% (17/18) of the isolates ( Table S3 ).…”

Antibacterial Activity and Action Mechanism of Bacteriocin Paracin wx7 as a Selective Biopreservative against Vancomycin-Resistant Enterococcus faecalis in Fresh-Cut Lettuce

“…It can cause life-threatening infections, such as bacteremia, endocarditis, sepsis, meningitis, surgical wound infections, and intra-abdominal infections [4,5]. Up to now, a large number of genes resistant to ampicillin, gentamicin, cephalothin, ofloxacin, teicoplanin, tetracycline, vancomycin, linezolid, daptomycin, etc., have been found among the E. faecalis strains [6][7][8][9]. Antibiotic resistance has made E. faecalis more dangerous.…”