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Nature. 2016 May 12;533(7602):212-6. doi: 10.1038/nature17672.

Interconnected microbiomes and resistomes in low-income human habitats.

Author information

1
Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63110, USA.
2
Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA.
3
Facultad de Ciencias de la Salud "Dr. Luis Edmundo Vásquez", Universidad Dr. José Matías Delgado, El Salvador.
4
Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima 31, Peru.
5
Asociacion Benéfica PRISMA, San Miguel, Lima 32, Peru.
6
Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri 63110, USA.
7
Department of Medicine, University of California San Diego, La Jolla, California 92093, USA.
8
Department of International Health, Johns Hopkins School of Public Health, Baltimore, Maryland 21205, USA.
9
Department of Biomedical Engineering, Washington University, St Louis, Missouri 63105, USA.

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.

PMID:
27172044
PMCID:
PMC4869995
DOI:
10.1038/nature17672
[Indexed for MEDLINE]
Free PMC Article

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