Enterococcus faecalis ST21 harbouring Tn6009 isolated from a carriage sample in South Africa.

Abstract

98 February 2021, Vol. 111, No. 2 Enterococcus faecalis ST21 harbouring Tn6009 isolated from a carriage sample in South Africa To the Editor: Enterococcus faecalis is an opportunistic pathogen included in the ESKAPE (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) group that is commonly observed as a commensal in the gastrointestinal tract, but can also opportunistically cause serious infections.[1,2] E. faecalis has been implicated globally in difficult-to-treat infections through acquired multidrug resistance (MDR) as well as the numerous virulence factors it expresses.[3] Several reports have shown that the high virulence and resistance in E. faecalis were associated with pathogenicity islands and mobile genetic elements (MGEs).[2] We report on a virulent, vancomycinresistant E. faecalis (VRE) ST21 (A113R1B0) isolate, carrying several resistance determinants and integrative conjugative elements Tn6009, colonising a patient admitted to a medical ward at a district hospital in uMgungundlovu district, South Africa (SA). The isolate was one of 38 non-duplicate VREs isolated in a larger study on colonisation with ESKAPE pathogens in hospitalised patients in medical and surgical wards.[4] Enterococci from rectal swabs were phenotypically screened for resistance to a panel of antibiotics as previously described. [4] A selected sample of isolates underwent whole-genome sequencing (WGS) and bio informatics analysis, with Comprehensive Antibiotic Resistance Database (CARD), ResFinder, VirulenceFinder, PlasmidFinder and MGEFinder being used to detect resistance genes, virulence factors, plasmids and MGE. The isolate carried several resistance genes encoding for resistance to tetracycline (tetM) and macrolides (ermB), as well as the insertion sequence (IS) IsaA encoding efflux systems such as MATE, MFS and pmrA that conferred resistance to lincosamides and streptogramins. A total of 14 putative virulence genes including ace and efaA genes that are involved in facilitating cell wall adhesion and thereby human pathogenicity were detected. The bacterial sex pheromone genes cCF10, CamE, cad and cOB1 that drive the transfer of resistance and virulence genes through horizontal transfer of the plasmid pCF10 among enterococci and other bacteria were additionally detected. The ebpA, ebpB and ebpC genes associated with sortase (srtC) assist in adherence and biofilm formation and contribute significantly to the pathogenicity of E. faecalis in nosocomial infection. In addition, the thiol peroxidase (tpx), antiphagocytosis (cpsA/uppS, cpsB/cdsA) were also detected involved in the regulation of oxidant-inducible expression of genes (Table 1). Furthermore, in silico genomic analysis revealed that the isolate harboured a plasmid repUS43 that encodes for the tetracycline resistance gene tet(M) and harbours a highly transmissible non-composite conjugative transposon Tn6009 linked to an S. aureus mer and previously identified in in Gram-negative bacteria from Nigeria and Gram-negative and positive bacteria from Portugal.[6] The isolate further harboured an array of MGEs such as CRISPR, phages and insertion sequences, as set out in Table 1. VRE is a serious public health threat worldwide, although there is a dearth of information regarding the clonal structure of Enterococcus spp. in Africa. To the best of our knowledge, this is the first report of a VRE ST21 harbouring repUS43 together with Tn6009, cCF10 and tet(M) in SA. A study from Norway revealed that E. faecalis ST21 involved in peripheral periodontitis in hospitalised patients harboured rep9 plasmids and carried Tn916 coupled with tet(M), erm(B) and integrase genes intTn.[5] Another report showed that Tn6009 was associated to Tn916like elements in S. aureus contributing to the dissemination of MDR determinants that could be transferred from numerous bacteria, including K. pneumoniae, Serratia liquefaciens, Pseudomonas spp. and Streptococcus spp.,[6] with the maximum transmissibility rate occurring in Enterococcus spp. Our findings suggest that the presence of Tn6009 in the microbiome coupled with immunocompromised host status may facilitate transfer of resistance and virulence factors and consequently contribute to the fitness and pathogenicity of commensal bacteria that could subsequently lead to outbreaks not only due to E. faecalis but also other bacteria present in the microbiome. Further molecular studies are warranted to monitor the genomic and pathogenicity trends of both clinical and carriage isolates across geographical locations, in order to prevent outbreak situations. Rational use of antibiotics in community and clinical settings is also essential to curtail antimicrobial resistance emergence and spread.