Analysis of antibiotic resistance from a rural community and wastewater contaminated environment linked to human and animal activities

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Antimicrobial resistance poses serious socioeconomic and ecological threat globally, warranting innovative approaches for surveillance and monitoring. One Health concept was considered in the analysis of soil, animal feces, pond water, wastewater and vegetable samples from a rural community and the environment in Palapye, Botswana. Culture-dependent and next-generation sequencing approaches were used for characterization of bacteria and antibiotic resistance genes. Viable potentially pathogenic bacteria exhibiting multi-drug resistance profiles corresponding to various clinically relevant antibiotics were observed. Next-generation sequence analysis also reveals occurrence and diversity of bacterial communities and acquired antibiotic resistance genes corresponding to clinically important classes of antibiotics (beta-lactam, aminoglycoside, tetracycline, fosfomycin, trimethoprim, sulfonamide, quinolone, macrolide, and phenicol). High diversity was observed for beta-lactamase encoding (bla) genes from pond water in a rural community. Phylum gammaproteobacteria was revealed as the most abundant from metagenomics sequences of both community and environment samples. Multi-drug and heavy metal resistance encoding Serratia mercensens DM6 was identified from whole genome sequence data. This study serves as proof-of-concept for the application of next-generation sequencing in low- and middle-income countries and supports the One Health surveillance of antimicrobial resistance. The data generated can contribute towards antimicrobial stewardship programs and implementation of National Action Plan on antimicrobial resistance.