Profiles of antibiotic resistome and microbial community in groundwater of CKDu prevalence zones in Sri Lanka

Highlights: • CKDu prevalence significantly affected antibiotic resistome and microbial community. • The cphA acted as the biomarker of the antibiotic resistome in the high CKDu zones. • The mexF dominated and acted as the intrinsic ARG in the groundwater. • Specific enrichment of cphA in CKDu prevalence zones was associated with Aeromonas. • Microbial community and MGEs contributed most to the antibiotic resistome. The chronic kidney disease of unknown etiology (CKDu) prevalent in certain regions of Sri Lanka poses a serious threat to human health. Previous epidemiological studies focused on the search of causative agents for CKDu etiology from the viewpoint of groundwater composition, but how CKDu prevalence affected the groundwater microbial composition, especially the antibiotic resistome, has never been illuminated. This study investigated the response of microbial community and antibiotic resistome to CKDu prevalence in the groundwater through the high throughput sequencing and qPCR (HT-qPCR), respectively. Results showed that CKDu prevalence significantly influenced the distribution of antibiotic resistome and microbial community composition. The mexF dominated in all the groundwater samples and could be considered as an intrinsic ARG, and the β-lactamase cphA was specially enriched and closely associated with the antibiotics used for CKDu patients. The Acinetobacter was a potential human pathogen common in the groundwater of CKDu affected regions, while CKDu prevalence specially enriched the Aeromonas. Statistical analysis indicated that CKDu prevalence impacted antibiotic resistome through the microbial community as a whole, and MGEs contributed to the occurrence of mexF, while the enrichment of cphA could be attributed to the increase of Aeromonas.