Systematic review in South Africa reveals antibiotic resistance genes shared between clinical and environmental settings

A systematic review was conducted to determine the distribution and prevalence of antibiotic-resistant bacteria (ARB), antimicrobial-resistant genes (ARGs), and antimicrobial-resistant gene determinants (ARGDs) in clinical, environmental, and farm settings and to identify key knowledge gaps in a bid to contain their spread. Fifty-three articles were included. The prevalence of a wide range of antimicrobial-resistant bacteria and their genes was reviewed. Based on the studies reviewed in this systematic review, mutation was found to be the main genetic element investigated. All settings shared 39 ARGs and ARGDs. Despite the fact that ARGs found in clinical settings are present in the environment, in reviewed articles only 12 were found to be shared between environmental and clinical settings; the inclusion of farm settings with these two settings increased this figure to 32. Data extracted from this review revealed farm settings to be one of the main contributors of antibiotic resistance in healthcare settings. ARB, ARGs, and ARGDs were found to be ubiquitous in all settings examined.

Although data could not be found for the Northern Cape and Mpumalanga Provinces, genes conferring AR were found to be ubiquitous across SA. The available data present a broader scope on isolation and prevalence information on ARGs in ARB and emphasize the dire need for surveillance and documentation of ARGs, ARB, and ARGDs in all provinces. Owing to the lack of sequence analysis in the current review, future reviews will investigate shared ARB, ARGs, and ARGDs based on related sequence data. One of the main findings in this review was the discrepancy between phenotypic and genotypic patterns. This calls for a move toward complementing the gold standard PCR with the use of WGS in examining ARB as well as shotgun metagenomics technologies  then dealing with a consortium of bacteria. In extending this tracking and genetic characterization of ARB, ARGs, and ARGDs, this study suggests the adoption of an AR genomic epidemiology  application

Source: Dovepress