Surveillance of Pathogenic Bacteria and Antimicrobial Resistance Determinants in Surface Water and Human Plasma Using Metagenomic Sequencing in the Ngamiland and Okavango Delta Regions

(1) Background: Antimicrobial resistance poses a critical global public health threat, with surface water acting as a potential reservoir for pathogenic, zoonotic, and AMR determinants and transmission pathways between humans and animals. We aimed to detect bacterial DNA of clinically relevant taxa and putative AMR determinants in surface water and human beings to support the expansion of One Health environmental surveillance in the Ngamiland and Okavango Delta regions. (2) Methods: We performed a cross-sectional environmental surveillance study using metagenomic sequencing. We collected 28 surface-water samples from Thamalakane River and Moremi Game Reserve sampling sites: 12 samples from Mall of Maun, Island Safari Lodge, and Police Bridge sites along the Thamalakane River, and 16 samples from Xakanaxa, Maxwexwana, Paradise, and Jessie’s Pools sites in Moremi Game Reserve. Additionally, 72 human plasma samples from Letsholathebe II Memorial District Hospital in Maun were also sequenced. Taxonomic classification was performed using Kraken2, and predictive AMR gene identification was performed using the CZ ID AMR module. Beta-diversity was assessed using Principal Coordinates Analysis and PERMANOVA for significant differences in bacterial and AMR gene composition. A p-value of less than 0.05 was considered to be statistically significant. (3) Results: Thamalakane River was dominated by Acinetobacter schindleri (~27%), Acinetobacter lwoffii (~67%), and the toxic cyanobacterium Microcystis aeruginosa (~99%). Moremi Game Reserve had greater bacterial diversity, including Stenotrophomonas maltophilia at two sites (~26% and ~29%), Microcystis aeruginosa (~60%), P. aeruginosa (~20%), P. putida (~13%), and A. baumannii (~10%). Beta diversity analysis demonstrated distinct bacterial communities between locations (PERMANOVA: R2 = 0.261, p = 0.001). Only 5 out of 28 bacterial species identified were shared between surface water and human plasma samples. No putative AMR genes were detected in human samples. However, only intrinsic efflux pump genes (mex-, sme-, ade-families, etc.) dominated surface water. AMR beta diversity was significantly associated with location (PERMANOVA: R2 = 0.101, p = 0.007), but explained only a small proportion of the observed variation. (4) Conclusions: Detection of bacterial DNA of clinically relevant bacterial taxa in both surface water and human samples and putative AMR determinants in surface water samples only highlights the need for expanded One Health environmental surveillance. Even though no putative AMR genes were detected in human plasma, monitoring the emergence and transmission of pathogens and resistance-associated genes between One Health interfaces remains a significant research area that requires further investigation.