Comparative bacterial community profiling of hospital, community, and abattoir wastewater in Mbarara, Uganda, using 16S rRNA amplicon sequencing
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Wastewater-based surveillance is increasingly being explored as a complementary approach for monitoring microbial communities and strengthening antimicrobial resistance (AMR) surveillance. However, wastewater bacterial community data from Uganda remain limited. This study characterized and compared bacterial communities in hospital, community, and abattoir wastewater in Mbarara, Uganda. Forty-five wastewater samples were collected over five consecutive weeks from TASO hospital, Kizuungu community, and Ruti abattoir wastewater lagoons. Bacterial communities were characterized using 16S rRNA gene amplicon sequencing. Taxonomic composition and microbial diversity were analysed using nf-core/ampliseq and QIIME2, while functional potential was inferred using PICRUSt2. A total of 9,870 amplicon sequence variants were identified. Bacterial community composition differed significantly among TASO, Kizuungu, and Ruti across Bray–Curtis, Jaccard, weighted UniFrac, and unweighted UniFrac metrics, whereas alpha-diversity measures did not differ significantly among the three wastewater sources. Among 13 genera targeted for their relevance to wastewater-based AMR surveillance, Acinetobacter and Enterobacter showed significant source-associated differences after false-discovery-rate correction. Acinetobacter was relatively abundant in both TASO and Ruti lagoons wastewater but low in Kizuungu, while Enterobacter had the highest mean relative abundance in TASO lagoon. PICRUSt2 predicted broadly overlapping metabolic potential across the three wastewater systems. Hospital, community, and abattoir wastewater in Mbarara harbour compositionally distinct bacterial communities and provide complementary microbial signals for environmental surveillance. These findings establish baseline wastewater microbiome data and support further genomic surveillance integrating direct characterization of antimicrobial resistance determinants.
