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

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

doi:10.3389/fmicb.2023.1254896

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

Front Microbiol. 2023 Dec 5:14:1254896. doi: 10.3389/fmicb.2023.1254896. eCollection 2023.

Authors

Grebstad Rabbi Amuasi¹, Esther Dsani², Christian Owusu-Nyantakyi¹, Felicia A Owusu¹, Quaneeta Mohktar³, Pernille Nilsson⁴, Bright Adu³, Rene S Hendriksen⁴, Beverly Egyir¹

Affiliations

¹ Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.
² Veterinary Services Department, Ministry of Food and Agriculture, Accra, Ghana.
³ Department of Immunology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.
⁴ National Food Institute, Research Group for Global Capacity Building, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kongens Lyngby, Denmark.

Abstract

Introduction: Enterococcus 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 methods: 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.

Results: Enterococcus 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.

Conclusion: The 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.

Keywords: Africa; Enterococcus spp.; antimicrobial resistance; livestock; raw meat; whole-genome sequencing.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by the University of Ghana Research Fund [URF/9/ ILG-067/2015–2016] and a grant from the International Society for Infectious Disease Research. Whole-genome sequencing of the Enterococcus spp. was funded by SeqAfrica. The SeqAfrica project is funded by the Department of Health and Social Care’s Fleming Fund using UK aid. The views expressed in this publication are those of the authors and not necessarily those of the UK Department of Health and Social Care or its Management Agent, Mott MacDonald.