title: Interconnected microbiomes and resistomes in low-income human habitats.
abstract: Antibiotic-resistant infections annually claim hundreds of thousands of lives worldwide. This problem is exacerbated by exchange of resistance genes between pathogens and benign microbes from diverse habitats. Mapping resistance gene dissemination between humans and their environment is a public health priority. Here we characterized the bacterial community structure and resistance exchange networks of hundreds of interconnected human faecal and environmental samples from two low-income Latin American communities. We found that resistomes across habitats are generally structured by bacterial phylogeny along ecological gradients, but identified key resistance genes that cross habitat boundaries and determined their association with mobile genetic elements. We also assessed the effectiveness of widely used excreta management strategies in reducing faecal bacteria and resistance genes in these settings representative of low- and middle-income countries. Our results lay the foundation for quantitative risk assessment and surveillance of resistance gene dissemination across interconnected habitats in settings representing over two-thirds of the world's population.
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63110, USA.
authors.forename: Erica C
authors.initials: EC
authors.lastname: Pehrsson
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63110, USA.
authors.forename: Pablo
authors.initials: P
authors.lastname: Tsukayama
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63110, USA.|Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA.
authors.forename: Sanket
authors.initials: S
authors.lastname: Patel
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63110, USA.|Facultad de Ciencias de la Salud "Dr. Luis Edmundo Vásquez", Universidad Dr. José Matías Delgado, El Salvador.
authors.forename: Melissa
authors.initials: M
authors.lastname: Mejía-Bautista
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63110, USA.|Facultad de Ciencias de la Salud "Dr. Luis Edmundo Vásquez", Universidad Dr. José Matías Delgado, El Salvador.
authors.forename: Giordano
authors.initials: G
authors.lastname: Sosa-Soto
authors.affiliation: Facultad de Ciencias de la Salud "Dr. Luis Edmundo Vásquez", Universidad Dr. José Matías Delgado, El Salvador.
authors.forename: Karla M
authors.initials: KM
authors.lastname: Navarrete
authors.affiliation: Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima 31, Peru.
authors.forename: Maritza
authors.initials: M
authors.lastname: Calderon
authors.affiliation: Asociacion Benéfica PRISMA, San Miguel, Lima 32, Peru.
authors.forename: Lilia
authors.initials: L
authors.lastname: Cabrera
authors.affiliation: Facultad de Ciencias de la Salud "Dr. Luis Edmundo Vásquez", Universidad Dr. José Matías Delgado, El Salvador.
authors.forename: William
authors.initials: W
authors.lastname: Hoyos-Arango
authors.affiliation: Facultad de Ciencias de la Salud "Dr. Luis Edmundo Vásquez", Universidad Dr. José Matías Delgado, El Salvador.
authors.forename: M Teresita
authors.initials: MT
authors.lastname: Bertoli
authors.affiliation: Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri 63110, USA.|Department of Medicine, University of California San Diego, La Jolla, California 92093, USA.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Berg
authors.affiliation: Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima 31, Peru.|Asociacion Benéfica PRISMA, San Miguel, Lima 32, Peru.|Department of International Health, Johns Hopkins School of Public Health, Baltimore, Maryland 21205, USA.
authors.forename: Robert H
authors.initials: RH
authors.lastname: Gilman
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63110, USA.|Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA.|Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri 63110, USA.|Department of Biomedical Engineering, Washington University, St Louis, Missouri 63105, USA.
authors.forename: Gautam
authors.initials: G
authors.lastname: Dantas
mesh_terms: D000383:Agriculture; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D003906:Developing Countries / Q000191:economics*; D004352:Drug Resistance, Microbial / Q000235:genetics*; D017753:Ecosystem; D004544:El Salvador; D004784:Environmental Monitoring; D005243:Feces / Q000382:microbiology; D022761:Gene Transfer, Horizontal; D006801:Humans; D056186:Metagenomics; D064307:Microbiota / Q000235:genetics*; D017720:Molecular Epidemiology; D010568:Peru; D010802:Phylogeny; D012111:Residence Characteristics; D018570:Risk Assessment; D012722:Sewage / Q000382:microbiology; D012959:Socioeconomic Factors
chemical_list: D012722:Sewage