Genomic Surveillance of Antimicrobial Resistance at the Human–Animal–Environmental Interface in Low- and Middle-income Countries: A One Health Review of Intensive Livestock Systems

Abstract

Antimicrobial resistance is increasingly shaped by connected microbial ecosystems rather than by isolated clinical, veterinary or environmental compartments. Intensive livestock systems in low- and middle-income countries occupy a particularly important position in this ecology because they combine rising demand for animal-source foods, dense animal populations, variable veterinary oversight, uneven antimicrobial stewardship, concentrated manure production, informal slaughter and retail pathways, and close contact between animals, workers and households. Genomic surveillance can sharpen understanding of these interfaces by resolving bacterial lineages, resistance determinants, plasmids, integrons and metagenomic resistomes at a level that phenotypic surveillance alone cannot provide. Yet its usefulness depends on sampling design, metadata quality, laboratory standards, bioinformatics capacity, data governance and careful interpretation of transmission directionality. This narrative review critically examines how whole-genome sequencing, long-read sequencing, shotgun metagenomics and wastewater-based approaches can be used to characterise antimicrobial resistance across human, animal and environmental sectors in intensive livestock systems in low- and middle-income countries. It synthesises evidence on antimicrobial use, selection pressure, co-selection, environmental dissemination, mobile genetic elements, occupational exposure, food-chain contamination and the practical constraints of implementing genomic surveillance in resource-limited settings. The review argues that genomics should not be treated as a stand-alone technological solution. Its greatest public-health value lies in integrated sentinel systems that connect microbiological, epidemiological, ecological, production and policy data, and that are designed to inform feasible interventions such as antimicrobial-use reduction, improved biosecurity, safer manure handling, slaughter-hygiene reform and targeted environmental monitoring. A One Health genomic surveillance agenda for low- and middle-income countries must therefore be scientifically rigorous, locally useful and attentive to inequities in resources, data ownership and policy influence.