Genetic analyses of antimicrobial resistance and virulence genes in Enterococcus species isolated from livestock production systems in South Africa.

Abstract

Enterococcus species are widely dispersed in the environment this includes soil, water, plants, food and animals. Although Enterococcus constitute mostly as a commensal bacterium; over the past years the bacterium has evolved to cause nosocomial infections. The proliferation of this pathogen is attributed to its ability in successfully transferring antimicrobial and virulence genes using several channels such as mobile genetic elements. This study investigated the prevalence of Enterococcus spp. in small-scale commercial farms in rural South Africa. The dissemination of virulent E. faecium and E. faecalis isolates allied with livestock production in the Eastern Cape and KwaZulu-Natal provinces was investigated. A total of 276 samples randomly sampled from livestock and their associated environments (feed, soil and water) were screened for Enterococcus spp. using selective media and using DNA molecular methods. E. faecalis and E. faecium prevalence was confirmed by the amplification of the tuf and sodA genes. Sixty-one percent of total presumptive isolates were E. faecalis (n=61) and only 8% (n=8) were identified as E. faecium. The presence of virulence determining factors such as asa1, ccf, cylA, esp, gelE and hyl was screened in all samples that tested positive for Enterococcus species. Presumptive E.faecalis and E. faecium isolates were mostly recovered from Amandawe (KZN). E. faecalis isolates harboured the most virulence genes asa1 (25%; n=), ccf (84%; n=), esp(4%;n= ), gelE (69%; n=) and hyl (12%; n= ). Whilst E. faecium isolates only harboured of asa1(12.5%; n=1), ccf (100%; n=8), gelE (75%;n=6 ) and hyl (25%;n=2). The current study also evaluated the antibiotic resistance profiles and their associated genes in these two species. Antibiotic susceptibility profiles of E. faecium and E. faecalis were assessed using Kirby-Bauer disk-diffusion assay as per the CSLI guidelines. Erythromycin had the highest occurrence of resistant isolates in both species with 75% (n=6) and 54.1% (n=33) respectively. Isolates were least resistant to ampicillin, with 0.03% resistance in E. faecalis and 0% in E. faecium. E. faecalis had the highest prevalence of Multi Drug Resistance (MDR), exhibiting phenotypic resistance to macrolides, aminoglycoside, tetracyclines and fluoroquinolones. TET-CIP-ERY was the most observed antibiotic resistance pattern. Furthermore, the isolates were screened for vanA, vanB, vanC1, vanC2/3, aac(6”)-aph(2”) ,ermA and ermB. The resistance genes that amplified in E. faecalis included vanB (8%;n=5), vanC1 (37%;n=23), vanC2/3 (37%; n=23), ermB (96%;n=58), ermA (8%;n=5) and aac(6”)-aph(2”) (1.6%;n=1). The immense dissemination of E. faecalis that has potentially pathogenic virulent determinants is a cause for concern in livestock production systems. In addition, faecal contamination from livestock poses a threat to the dissemination of virulent strains. The study demonstrated that E. faecium and E. Faecalis isolated from livestock and their associated environment were predominantly resistant to macrolides, glycopeptides, tetracyclines and fluroquinolones. In addition to be the first study in South Africa to document the emergence of inducible vanC determinants in Vancomycin Resistant Enterococci isolates.