Interconnected microbiomes and resistomes in low-income human habitats

Erica C. Pehrsson, Pablo Tsukayama, Sanket Patel, Melissa Mejía-Bautista, Giordano Sosa-Soto, Karla M. Navarrete, Maritza Calderon, Lilia Cabrera, William Hoyos-Arango, M. Teresita Bertoli, Douglas E. Berg, Robert H. Gilman and Gautam Dantas ()
Additional contact information
Erica C. Pehrsson: Center for Genome Sciences and Systems Biology, Washington University School of Medicine
Pablo Tsukayama: Center for Genome Sciences and Systems Biology, Washington University School of Medicine
Sanket Patel: Center for Genome Sciences and Systems Biology, Washington University School of Medicine
Melissa Mejía-Bautista: Center for Genome Sciences and Systems Biology, Washington University School of Medicine
Giordano Sosa-Soto: Center for Genome Sciences and Systems Biology, Washington University School of Medicine
Karla M. Navarrete: Facultad de Ciencias de la Salud “Dr. Luis Edmundo Vásquez”, Universidad Dr. José Matías Delgado
Maritza Calderon: Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres
Lilia Cabrera: Asociacion Benéfica PRISMA
William Hoyos-Arango: Facultad de Ciencias de la Salud “Dr. Luis Edmundo Vásquez”, Universidad Dr. José Matías Delgado
M. Teresita Bertoli: Facultad de Ciencias de la Salud “Dr. Luis Edmundo Vásquez”, Universidad Dr. José Matías Delgado
Douglas E. Berg: Washington University School of Medicine
Robert H. Gilman: Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres
Gautam Dantas: Center for Genome Sciences and Systems Biology, Washington University School of Medicine

Nature, 2016, vol. 533, issue 7602, 212-216

Abstract: 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.

Date: 2016
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DOI: 10.1038/nature17672

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