zzl2516/dust-2015

Analysis of dust samples collected from a mixed-use athletic facility at the University of Oregon

Antimicrobial chemicals and the dust microbiome

This repository contains processed data and code to reproduce figures and analyses in the following paper: "Antimicrobial chemicals are associated with elevated resistance in the indoor dust microbiome" (in revision as of April 2016)

Authors: Erica M. Hartmann,^1,2 Roxana Hickey,^1,2 Tiffany Hsu,^3,4 Clarisse M. Betancourt Román,^1,2 Jing Chen,⁵ Randall Schwager,³ Jeff Kline,^1,6 G. Z. Brown,^1,6 Rolf U. Halden,⁵ Curtis Huttenhower,^3,4 Jessica L. Green,^1,2

¹ Biology and the Built Environment Center, University of Oregon, Eugene, OR 97403, USA; ² Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA; ³ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; ⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; ⁵ Center for Environmental Security and Global Security Initiative, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; ⁶ Energy Studies in Buildings Laboratory, University of Oregon, Eugene, Oregon 97403, USA

Abstract

Antibiotic resistance is increasingly widespread, largely due to human influence. Here, we explore the relationship between antibiotic resistance and the antimicrobial chemicals triclosan, triclocarban, and methyl-, ethyl-, propyl-, and butylparaben in the dust microbiome. Dust samples from a mixed-use athletic and educational facility were subjected to microbial and chemical analyses using a combination of 16S rRNA amplicon sequencing, shotgun metagenome sequencing, and liquid chromatography tandem mass spectrometry. The dust resistome was characterized by identifying antibiotic resistance genes from the metagenomes of each sample using ShortBRED and the Comprehensive Antibiotic Resistance Database (CARD). The three most highly abundant antibiotic resistance genes were tetW, SRT-1, and ermB. The complete dust resistome was then compared against the measured concentrations of antimicrobial chemicals. We uncovered several positive associations between the occurrence of antimicrobial chemicals and antibiotic resistance genes, including one between the ubiquitous antimicrobial triclosan and 23S ribosomal RNA methyltransferases implicated in resistance to several antibiotics. Results indicate that increased antibiotic resistance correlates with increased antimicrobial chemicals in the built environment. This study is the first to look for an association between antibiotic resistance genes and antimicrobial chemicals in dust.