Abstract
The emergence of antimicrobial-resistant, livestock-associated Enterococcus faecalis represents a public health concern. Here, we report the isolation, molecular detection of virulence and antimicrobial resistance determinants, in addition to the phylogenetic analyses of 20 Enterococcus species using whole genome sequencing analysis of 15 Enterococcus faecalis strains including six strains of three novel sequence types, three Enterococcus faecium and two Enterococcus durans. All strains were isolated from food chain animals in South Africa. Enterococcus strains were isolated on bile aesculin azide agar, followed by identification using MALDI-TOF MS analysis. Antibiotic susceptibility testing was performed using the Kirby–Bauer disk diffusion method. The genomic DNA of the isolates was extracted and sequencing was performed using the Illumina MiSeq platform. Sequence reads were trimmed and de novo assembled. The assembled contigs were analyzed for antimicrobial resistance genes and chromosomal mutations, extra-chromosomal plasmids, and multi-locus sequence type (MLST). Multidrug antimicrobial resistance genes conferring resistance to aminoglycosides (ant(6)-Ia, aph(3′)-IIIa, sat4, and spw), lincosamides (lnu(B), lsa(A), and lsa(E)), macrolides (erm(B)), trimethoprim (dfrG) and tetracyclines (tet(L) and tet(M)) were identified. Plasmid replicons were detected in seven E. faecalis and three E. faecium isolates. The sequence type (ST) of each isolate was determined using the Enterococcus PubMLST database. Ten STs were identified in the collection, three of which (ST1240, ST1241, and ST1242) have not been previously reported and are described in the present study for the first time. To compare the sequenced strains to other previously sequenced E. faecalis strains, assembled sequences of E. faecalis from livestock were downloaded from the PubMLST database. Core genome-based phylogenetic analysis was performed using ParSNP. The detection of multiple drug-resistance in Enterococcus including E. faecalis and E. faecium highlights the significance of genomic surveillance to monitor the spread of antimicrobial resistance in food chain animals. In addition, the genome sequences of Enterococcus strains reported in the present study will serve as a reference point for future molecular epidemiological studies of livestock-associated and antibiotic-resistant E. faecalis in Africa. In addition, this study enables the in-depth analysis of E. faecalis genomic structure, as well as provides valuable information on the phenotypic and genotypic antimicrobial resistance, and the pathogenesis of livestock-associated E. faecalis and E. faecium.
| Original language | English |
|---|---|
| Article number | 18609 |
| Journal | Scientific Reports |
| Volume | 13 |
| Issue number | 1 |
| DOIs | |
| State | Published - Dec 2023 |
Bibliographical note
Publisher Copyright:© 2023, The Author(s).
Funding
The authors thank the South African livestock farm owners for their cooperation in the study. Authors thank Keith D. Perret, DVM from the Epidemiology Section, KwaZulu-Natal Veterinary Services and the Department of Agriculture and Rural Development, KwaZulu-Natal, South African Department of Agriculture, Forestry and Fisheries (DAFF) for their support and help. Authors would like to thanks the two anonymous reviewers for their insightful comments which significantly improved the manuscript. We thank staff members from the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, and the Genomics Center at the University of Minnesota (St. Paul, MN, USA) for their cooperation and help throughout the project. We thank staff members from the Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University (Raleigh, NC, USA), the GenomeTrakr Network, and the WGS Program for Foodborne Pathogen Traceback and the Center for Food Safety and Applied Nutrition (CFSAN), U.S. FDA, for their cooperation and support. We thank the NCBI GenBank submission staff for their help with the genome submission, decontamination, and deposition process. Prof. Mohamed E. El Zowalaty and co-authors thank Sean G Young, Ph.D., from Peter O’Donnell Jr. School of Public Health, the University of Texas Southwestern Medical Center, Dallas, TX, USA for his help and collaboration. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the organizations or agencies that provided support for the project. No other person had any role in the study concept, study design, data collection, experimental work, data analysis, data interpretation or the decision to publish. Any use of commercial names, commercial diagnostic products, or firm names is for descriptive purposes only and does not imply endorsement by the funding agencies, the National Institutes of Health, Food and Drug Administration, or the United States Government. Any opinions, findings and conclusions, or recommendations expressed in this material are those of the authors and do not necessarily reflect the view of the funding agencies, the National Institutes of Health, or the United States Government. The funders of the study had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The corresponding author had full access to all the data in the study project and had the final responsibility for the decision to submit for publication. The project was supported in part by funding from the United States National Institutes of Health/Food and Drug Administration (USA/NIH/FDA) under award 1U18FD006780-01, the Hessian Ministry of Higher Education, Research and Arts within the project HuKKH (Hessisches Universitaeres Kompetenzzentrum Krankenhaus Hygiene), and the South African National Research Foundation for supporting this research through the Thuthuka Funding Instrument (grant number TTK170411226583). The project was also supported by discretionary funds from Prof. Dr Mohamed Ezzat El Zowalaty and from Dr Yosra A. Helmy through start-up fund from the Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, USA. The Open access publication charges of this article were made possible by support from the University of KwaZulu-Natal, South Africa.
| Funders | Funder number |
|---|---|
| Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky | |
| GenomeTrakr Network | |
| Hessian Ministry of Higher Education, Research and Arts | |
| Hessisches Universitaeres Kompetenzzentrum Krankenhaus Hygiene | |
| KwaZulu-Natal Sharks Board | |
| KwaZulu-Natal Veterinary Services | |
| NCBI | |
| National Institutes of Health and Food and Drug Administration | |
| South African Department of Agriculture, Forestry and Fisheries | |
| U.S. FDA | |
| USA/NIH/FDA | 1U18FD006780-01 |
| Veterinary Diagnostic Laboratory | |
| National Institutes of Health (NIH) | |
| U.S. Food and Drug Administration | |
| College of Veterinary Medicine, Cornell University | |
| University of North Carolina and North Carolina State University | |
| University of Texas Southwestern Medical Center | |
| Department of Agriculture and Rural Development Northern Ireland | |
| Genomics Center, University of Minnesota | |
| Center for Food Safety and Applied Nutrition | |
| National Research Foundation South African Research Chair | TTK170411226583 |
| National Research Foundation South African Research Chair | |
| Inyuvesi Yakwazulu-Natali | |
| Department of Agriculture, Forestry and Fisheries |
ASJC Scopus subject areas
- General
