Mitigation of Antimicrobial Resistance in Dorper Sheep Manure Using Black Soldier Fly Larvae: Insights from Shotgun Metagenomic Profiling

Abstract

Antimicrobial resistance (AMR) is a critical global health challenge, with livestock manure acting as a significant reservoir for antimicrobial-resistant bacteria (ARBs) and resistance genes (ARGs). In Kenya and other low- and middle-income countries, untreated manure is widely applied in agriculture, accelerating the spread of resistance across soil, water, and food systems. This study evaluated the efficacy of Black Soldier Fly Larvae (BSFL; Hermetia illucens) in mitigating AMR in Dorper sheep manure using shotgun metagenomic profiling. A controlled experimental design was employed involving three treatments: untreated manure, manure treated with BSFL for 10 days, and post-treatment incubated manure. High-throughput Illumina MiSeq sequencing and bioinformatics analyses were used to assess microbial diversity, community structure, and resistome dynamics. Findings revealed that BSFL treatment significantly restructured microbial communities, reducing Proteobacteria while increasing Firmicutes and Bacteroidetes, indicating enhanced stabilization. Microbial diversity increased following treatment and incubation. Resistome analysis showed a mixed response: reductions in aminoglycoside, fluoroquinolone, and sulfonamide resistance genes, but persistence or enrichment of tetracycline and β-lactam resistance genes. Notably, zoonotic pathogens such as Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, and Pseudomonas aeruginosa declined in relative abundance after treatment. The study concludes that BSFL bioconversion partially mitigates AMR by altering microbial ecology and reducing key resistance determinants, though it does not achieve complete elimination. Integrating BSFL treatment with post-processing strategies is recommended to enhance biosafety. These findings contribute to sustainable manure management practices within a One Health framework.