Metagenomic Assessment of Antibiotics Resistance Genes from Four Ecosystems in the Niger Delta Area of Nigeria

Abstract

Antibiotics resistance genes (ARGs) in environmental samples have been implicated in the clinical spread of resistance to antibiotics. This study was therefore aimed at the metagenomic assessment of ARGs from various environmental samples. Benthic, epipellic, estuary and soil samples were collected and analyzed for physicochemical parameters using standard techniques and ARGs via metagenomics. Metagenomic DNA was extracted from the various samples and sequenced on Miseq Illumina platform. Following next generation sequencing, gene calling was performed on the assembled sequence reads using FragGeneScan to predict open reading frames (ORFs), which were functionally annotated to various taxonomic groups using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Ghost KOALA databases. Results of physicochemical analysis showed anthropogenic influence in the various environments. Furthermore, a total of 12 types of ARGs were identified, that belongs to the RND and ABC superfamilies of ARGs. These were dominated by five classes of bacteria which were Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and the Firmicutes (Clostridia). Our findings suggest that ARGs diversity differs with samples; with soil being the most abundant and only sample with the multidrug resistant efflux pumps. Further studies aimed at building a repository of ARGs genes in various environments should be carried out.