Assessment of Bacterial Diversity and Antibiotic Resistance Genes in Water Used by Eateries and Open Markets in Juja

Abstract

Water is an important bacterial habitat and a major avenue of dissemination of antibiotic resistant bacteria between and among different environments. Contamination of drinking water used in open market eateries with antibiotic resistant bacteria pose a direct threat to human health. This is because antimicrobial resistome monitoring in drinking water is not currently a routine standard inspection protocol of drinking water. This study aimed to investigate the occurrence of antibiotic resistance genes (ARGs) and variation in the composition of bacterial communities in drinking water collected from eighty-two sampling points in Juja. Water samples were collected using purposive sampling. Special media of MacConkey, Thioglycollate and Lauryl Tryptose Broth media were used for isolation of bacteria from the collected water samples. Culture and molecular techniques were used to profile the bacteria and detect antibiotic resistant bacteria (ARBs) and antibiotic resistant genes (ARGs) present in samples. Metagenomics sequencing and analysis was applied to investigate the ARB genetic profiles. Morphological, biochemical characterization, antimicrobial susceptibility and molecular detection of ARGs data (qualitative & quantitative) were analyzed using R software to generate heat maps (Manhattan metric) showing characteristic relationships and antibiotic susceptibility or resistance among bacterial isolates. QIIME (version 2021.4) software and DADA2 were used to analyze microbial profiles in collected water samples. Detection of antibiotic resistance genes data were analyzed using R software to generate heat maps highlighting their presence in water samples. Results showed abundance of bacterial phylum Proteobacteria (above 86%) across all the collected water samples from the open markets and eateries. The dominant phylum documented by this study belonged to Proteobacteria and comprised of; Wakulima Eateries (WE) (Acinetobacter 44.180%), Wakulima Open Markets (WOM) (Duganella 28.201%), Gachororo Eateries (GE) (Acinetobacter 15.189%), Gachororo Open Markets (GOM) (Acinetobacter 30.675%) Mwerevu Eateries (ME) (Acinetobacter 40.823%) and Mwerevu Open Markets (MOM) (Curvibacter 48.785%). This study reported the presence of antibiotic resistant priority pathogens from the WHO list; Priority 1 (Critical) where Pseudomonas spp detected in samples ME (12.163%) and WOM (0.323%), Acinetobacter baumannii detected in samples GE (2.975%) and WE (5.495%), Enterobacteriaceae detected in samples WE (0.125%), MOM (0.326%), WOM (0.875%), GE (0.452%) and ME (0.206%). The genus of Escherichia, Klebsiella, Raoultella and Enterobacter dominated in Enterobacteriaceae. Priority 2 (High) pathogen detected was the genus Staphylococcus in samples MOM (1.826%) and GE (0.962%). The ARGs of qnrD and sul2 were detected in all six samples (WOM, WE, GOM, GE, MOM and ME), int1 and FloR genes were present in five samples except in MOM and GOM samples respectively while those of strB (MOM), catA (MOM) and blaTEM (GOM) were found in one sample each using qualitative PCR assays. Findings of this study form a critical reference point for policy development and rapid mitigation strategies to prevent a possible outbreak of water-borne diseases in the area.