Surveillance and monitoring of antimicrobial-resistant human pathogenic and zoonotic bacteria in the Ngamiland and Okavango Delta

Antimicrobial resistance is a critical global health threat. Surface water from eight Okavango/Ngamiland sites was sequenced (Illumina NextSeq2000); taxonomy used Kraken2 and ARGs AMRFinder. Seasonal variation influenced salinity and conductivity. Abundant pathogens included Acinetobacter lwoffii and A. johnsonii; clinically significant zoonotic taxa were detected at low abundance. The resistome was dominated by efflux genes MexF and MexB alongside β-lactamase TEM-116. Co-detection of TEM-116 and transposase TniB raises HGT concerns. Freshwater metagenomic surveillance is a valuable early-warning system for AMR in Botswana and comparable LMICs.