title: Application of genomic technologies to measure and monitor antibiotic resistance in animals.
abstract: One of the richest reservoirs of antibiotic-resistant bacteria and genes, animal intestinal microbiota contributes to the spread of antibiotic resistance in the environment and, potentially, to human pathogens. Both culture-based genomic technology and culture-independent metagenomics have been developed to investigate the abundance and diversity of antibiotic resistance genes. The characteristics, strengths, limitations, and challenges of these genomic approaches are discussed in this review in the context of antibiotic resistance in animals. We also discuss the advances in single-cell genomics and its potential for surveillance of antibiotic resistance in animals.
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
authors.forename: Jian-Qiang
authors.initials: JQ
authors.lastname: Su
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
authors.forename: Li
authors.initials: L
authors.lastname: Cui
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
authors.forename: Qing-Lin
authors.initials: QL
authors.lastname: Chen
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
authors.forename: Xin-Li
authors.initials: XL
authors.lastname: An
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.|State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yong-Guan
authors.initials: YG
authors.lastname: Zhu
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents; D001419:Bacteria / Q000235:genetics*; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans
chemical_list: D000900:Anti-Bacterial Agents
keywords: animals; antibiotic resistance; metagenomics, single-cell genomics