title: Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture.
abstract: Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundance of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk.
  
  
  OBJECTIVE
  Agricultural antibiotic use results in clusters of cooccurring resistance genes that together confer resistance to multiple antibiotics. The use of a single antibiotic could select for an entire suite of resistance genes if they are genetically linked. No links to bacterial membership were observed for these clusters of resistance genes. These findings urge deeper understanding of colocalization of resistance genes and mobile genetic elements in resistance islands and their distribution throughout antibiotic-exposed microbiomes. As governments seek to combat the rise in antibiotic resistance, a balance is sought between ensuring proper animal health and welfare and preserving medically important antibiotics for therapeutic use. Metagenomic and genomic monitoring will be critical to determine if resistance genes can be reduced in animal microbiomes, or if these gene clusters will continue to be coselected by antibiotics not deemed medically important for human health but used for growth promotion or by medically important antibiotics used therapeutically.
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, Iowa, USA.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Johnson
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, USA.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Stedtfeld
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Cole
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, USA.
authors.forename: Syed A
authors.initials: SA
authors.lastname: Hashsham
authors.affiliation: Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, Iowa, USA.
authors.forename: Torey
authors.initials: T
authors.lastname: Looft
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yong-Guan
authors.initials: YG
authors.lastname: Zhu
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA tiedjej@msu.edu.
authors.forename: James M
authors.initials: JM
authors.lastname: Tiedje
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001419:Bacteria / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D001426:Bacterial Proteins / Q000235:genetics*; D002681:China; D024881:Drug Resistance, Bacterial; D020071:Interspersed Repetitive Sequences; D010802:Phylogeny; D013552:Swine / Q000254:growth & development / Q000382:microbiology*
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins