Genomic characterisation of lytic bacteriophages isolated from wastewater in Kilifi, Kenya

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Background Multidrug-resistant (MDR) pathogens such as Escherichia coli , Pseudomonas aeruginosa , and Klebsiella pneumoniae pose significant challenges to infection control and environmental sanitation, particularly in regions with high antimicrobial resistance (AMR) burdens. In 2021, Kenya reported approximately 28,500 deaths attributed to AMR, with K. pneumoniae accounting for the highest toll at 5220 deaths, followed by P. aeruginosa with 2,690, according to the Institute of Health Metrics. These pathogens are frequently detected in wastewater and hospital effluents, contributing to environmental persistence and transmission. Objective To isolate and descriptively characterise lytic bacteriophages (phages) targeting high-priority MDR bacteria from wastewater sources in Kilifi County, Kenya, with emphasis on genomic features that inform their safety, taxonomy, and potential relevance for future evaluation in applied contexts. Methods Four lytic phages were isolated using enrichment techniques against environmental MDR strains and purified by plaque assays. Whole-genome sequencing was performed using Oxford Nanopore technology, followed by annotation and comparative genomic analysis to determine taxonomic placement, conserved domains, and safety profiles. Results All four phages belong to the class Caudoviricetes and have genomic features consistent with obligately lytic replication, including the absence of lysogeny-associated genes and conserved structural modules. Comparative genomic analysis revealed global relatedness to previously described lytic phages. Preliminary spot-test observations demonstrated lytic activity against a limited set of local MDR isolates, providing initial descriptive evidence of their biological activity. Conclusion This study provides a genomics-based, preliminary characterisation of four wastewater-derived lytic phages. While their genomic profiles and observed activity suggest potential relevance for future evaluation in environmentally associated systems, further functional validation and application-orientated studies are required.

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