title: The structure and diversity of human, animal and environmental resistomes.
abstract: Antibiotic resistance genes (ARGs) are widespread but cause problems only when present in pathogens. Environments where selection and transmission of antibiotic resistance frequently take place are likely to be characterized by high abundance and diversity of horizontally transferable ARGs. Large-scale quantitative data on ARGs is, however, lacking for most types of environments, including humans and animals, as is data on resistance genes to potential co-selective agents, such as biocides and metals. This paucity prevents efficient identification of risk environments.
  
  
  
  We provide a comprehensive characterization of resistance genes, mobile genetic elements (MGEs) and bacterial taxonomic compositions for 864 metagenomes from humans (n = 350), animals (n = 145) and external environments (n = 369), all deeply sequenced using Illumina technology. Environment types showed clear differences in both resistance profiles and bacterial community compositions. Human and animal microbial communities were characterized by limited taxonomic diversity and low abundance and diversity of biocide/metal resistance genes and MGEs but a relatively high abundance of ARGs. In contrast, external environments showed consistently high taxonomic diversity which in turn was linked to high diversity of both biocide/metal resistance genes and MGEs. Water, sediment and soil generally carried low relative abundance and few varieties of known ARGs, whereas wastewater/sludge was on par with the human gut. The environments with the largest relative abundance and/or diversity of ARGs, including genes encoding resistance to last resort antibiotics, were those subjected to industrial antibiotic pollution and a limited set of deeply sequenced air samples from a Beijing smog event.
  
  
  
  Our study identifies air and antibiotic-polluted environments as under-investigated transmission routes and reservoirs for antibiotic resistance. The high taxonomic and genetic diversity of external environments supports the hypothesis that these also form vast sources of unknown resistance genes, with potential to be transferred to pathogens in the future.
authors.affiliation: Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden.|Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.
authors.forename: Chandan
authors.initials: C
authors.lastname: Pal
authors.affiliation: Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden.|Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Bengtsson-Palme
authors.affiliation: Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.|Department of Mathematical Sciences, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Kristiansson
authors.affiliation: Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden. joakim.larsson@fysiologi.gu.se.|Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden. joakim.larsson@fysiologi.gu.se.
authors.forename: D G Joakim
authors.initials: DG
authors.lastname: Larsson
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001419:Bacteria / Q000187:drug effects / Q000235:genetics*; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D000069196:Gastrointestinal Microbiome / Q000187:drug effects / Q000235:genetics*; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008670:Metals / Q000494:pharmacology; D012641:Selection, Genetic / Q000187:drug effects / Q000235:genetics*; D012722:Sewage / Q000382:microbiology; D012905:Smog; D012988:Soil Microbiology; D013753:Tetracycline Resistance / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents; D008670:Metals; D012722:Sewage; D012905:Smog
keywords: Antibiotic resistance; Biocide resistance; Environmental microbiome; Human microbiome; Metagenomics; Metal resistance; Resistome