Assessment of feedlots cattle in the development and spread of Vancomycin resistant Enterococci

Abstract

Enterococci are commensals of the gastrointestinal tract of warm-blooded animals. They have been incriminated in a wide range of community-aquired infections and nosocomial diseases, especially in immunocompromised individuals and stressed animals. If enterococci have been able to survive and thrive in different ecological niches to date, it is due mainly to their outstanding capability to adapt to these various environmental settings by incorporating into their genetic constitution, resistance genes to many currently used antimicrobials. The widespread use of antibiotics in industrial animal husbandry has contributed significantly to the emergence of resistant isolates, such as vancomycin-resistant enterococci (VREs) worldwide and in South Africa, specifically. Despite the fact that Avoparcin, which is a glycopeptide and analogue of vancomycin, was identified as the source of the emergence of VREs and was forbidden worldwide in industrial animal farming decades ago, VREs are regularly screened in environmental samples in the North West Province, South Africa. This study, therefore, sheds some light on the various reasons why VREs are continuously detected n environmental samples in the North West Province of South Africa. Very few studies in South Africa have focused on the involvement of cattle feedlots in the spread and dissemination of such strains in the environment. In this regard, we aseptically collected 384 faecal samples, 24 drinking troughs water and 24 soil/liter samples from six registered feedlots of the North West Province, South Africa. Thereafter, we used biochemical and molecular methods to identify and categorise the isolated enterococci. Furthermore, we determined their antibiotic resistance and their virulence profiles with phenotypic and genotypic methods as well as Next Generation Sequencing platforms. Five humdred and twenty-seven (527) presumptive isolates were recovered, while two hundred and eighty-nine (289) isolates were confirmed as members of the genus Enterococcus. Species specific PCR protocols were used to identify them as E. faecalis (9%), E. faecium (10%), E. durans (69%), E. gallinarum (6%), E. casseliflavus (2%), E. mundtii (2%) and E. avium (2%). Vancomycin resistance genes were detected through PCR assays in 176 isolates, precisely vanA (62%), vanB (17%) and vanC (21%). Moreover, four Tetracycline efflux pump genetic determinants were also detected through PCR methods in 138 of the screened VREs and these included tetK (26), tetL (57), msrA/B (111) and mefA (9). All the VREs of this study were multidrug resistant and four antibiotic resistance profiles were identified. Furthermore, cylA, hyl, esp, gelE and asa1 virulence genes were detected in 86 VREs, with some harbouring more than one virulence gene. The cluster analysis of the VREs of this study was based on the diameters of the antibiotic inhibition zones and revealed a similar exposure history to the antibiotics tested. Data on antimicrobials currently used in the feedlots under investigation, either for prophylactic purposes or for therapeutic purposes as well as for growth promoting purposes, was collected. Data was assessed along with the bioinformatical analysis of the whole genome sequences of VR E. durans strain NWUTAL1 and VR E. gallinarum strain S52016, isolated from feedlot cattle faeces and feedlot soil/liter samples respectively. The data derived from these analyses revealed that some of the antibiotics used in the feedlots, were responsible for the resurgence of VREs. Specifically, plasmids with resistance genes to Tetracycline, Tylosin and Erythromycin were detected in these VREs. These antibiotics wield a sort of selective pressure on their specific antibiotic resistance genetic determinants that are co-selected with Vancomycin resistance genes. The fact that potentially pathogenic multidrug resistant VREs were detected in this study, demonstrates that practices such as the extensive usage of antibiotics in industrial animal husbandry, have a significant impact on the environment and its ecological niches. This may, consequently, affect humans and other living organisms since it enhances the availability of antimicrobial resistance genes in the environment, which is taken up and exchanged among commensals that were not initially harmful. Since such commensals find their way through direct and indirect contacts into the food chain, issues of this nature cannot be undermined, especially in the context of South Africa, where the occurrence of AIDS/HIV and diabetes is high.