Genome analysis of multidrug resistant Enterococcus faecium and Enterococcus faecalis circulating among hospitalized patients in uMgungundlovu District, KwaZulu-Natal, South Africa

• Published in: BMC infectious diseases 2024-07, Vol.24 (1), p.671-13, Article 671
• Main Authors: Founou, Raspail Carrel, Founou, Luria Leslie, Allam, Mushal, Ismail, Arshad, Essack, Sabiha Yusuf
• Format: Article
• Language: English
• Subjects: Adolescent; Adult; Aged; Analysis; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antibiotics; Bacteria; Carriage; Circulation; CRISPR; Cross-Sectional Studies; DNA sequencing; Drug resistance; Drug resistance in microorganisms; Drug Resistance, Multiple, Bacterial - genetics; Efflux; Enterococcus; Enterococcus faecalis; Enterococcus faecalis - drug effects; Enterococcus faecalis - genetics; Enterococcus faecalis - isolation & purification; Enterococcus faecium; Enterococcus faecium - drug effects; Enterococcus faecium - genetics; Enterococcus faecium - isolation & purification; Esculin; Ethylenediaminetetraacetic acid; Female; Gene sequencing; Genes; Genetic aspects; Genetic diversity; Genetic testing; Genome, Bacterial; Genomes; Genomic analysis; Genomics; Glycopeptides; Gram-Positive Bacterial Infections - epidemiology; Gram-Positive Bacterial Infections - microbiology; Health aspects; Hospital patients; Hospitalization; Hospitals; Humans; Laboratories; Lincosamides; Male; Medical research; Medicine, Experimental; Microbial Sensitivity Tests; Middle Aged; Mobilome; Multidrug resistance; Nosocomial infections; Nucleotide sequencing; Pathogenicity; Pathogens; Patients; Phylogenetics; Plasmids; Polymerase chain reaction; Questionnaires; Real time; Resistance factors; Risk factors; Sample preparation; Software; South Africa - epidemiology; Surgical equipment; Testing; Tetracyclines; Transposons; Vancomycin; Vancomycin-Resistant Enterococci - drug effects; Vancomycin-Resistant Enterococci - genetics; Vancomycin-Resistant Enterococci - isolation & purification; Varieties; Virulence; Virulence (Microbiology); Virulence - genetics; Virulence factors; Virulence Factors - genetics; WGS; Whole Genome Sequencing; Young Adult
• ISSN: 1471-2334; 1471-2334
• DOI: 10.1186/s12879-024-09380-3

Vancomycin-resistant enterococci (VRE) are important pathogens categorized as high-priority bacteria in the Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics published by the World Health Organization. The aim of this study was to determine the risk factors, resistance, virulence, mobilomes associated with multidrug-resistant and clonal lineages of Enterococcus faecium and faecalis circulating among hospitalized patients following the health system in South Africa, using whole genome sequencing (WGS). A cross-sectional study was conducted during a two-month periods among hospitalized patients in 2017. Rectal swabs were collected from patients admitted to medical and surgical wards in an urban tertiary hospital, and a rural district hospital in uMgungundlovu district, South Africa. Enterococci were screened for vancomycin resistance on bile esculin azide agar supplemented with 6 mg/L of vancomycin and confirmation of VRE was done using ROSCO kits. Conventional and real-time PCR methods were used to ascertain the presence of VanA, VanB, VanC-2/3 and VanC-1 genes. All six multidrug-resistant Enterococcus faecalis and faecium selected were identified using multiplexed paired-end libraries (2 × 300 bp) with the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA, USA) and genome sequencing was done using Illumina MiSeq instrument with 100× coverage at the National Institute of Communicable Diseases Sequencing Core Facility, South Africa. Antibiotic resistance genes, virulence factors, plasmids, integrons and CRISPR were characterized using RAST, ResFinder, VirulenceFinder, PlasmidFinder, PHAST and ISFinder respectively. Sequencing analysis revealed that these strains harbouring numerous resistance genes to glycopeptides (vanC[100%], vex3[100%], vex2[83,33%] and vanG[16,66%]), macrolides, lincosamides, sterptogramine B (ermB[33,32%], Isa[16,66%], emeA[16,66%]) and tetracyclines (tetM[33,32%]) in both district and tertiary hospitals. Multidrug efflux pumps including MATE, MFS and pmrA conferring resistance to several classes of antibiotics were also identified. The main transposable elements observed were in the Tn3 family, specifically Tn1546. Four single sequence types (STs) were identified among E. faecium in the district hospital, namely ST822, ST636, ST97 along with a novel ST assigned ST1386, while one lineage, ST29 was detected in the tertiary hospital. The study reveals the ge