Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome

Abstract

Antibiotic resistance is increasingly widespread, largely due to human influence. Here, we explore the relationship between antibiotic resistance genes 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 annotated in the Comprehensive Antibiotic Resistance Database (CARD) from the metagenomes of each sample using the Short, Better Representative Extract Data set (ShortBRED). The three most highly abundant antibiotic resistance genes were tet(W), blaSRT-1, and erm(B). The complete dust resistome was then compared against the measured concentrations of antimicrobial chemicals, which for triclosan ranged from 0.5 to 1970 ng/g dust. We observed six significant positive associations between the concentration of an antimicrobial chemical and the relative abundance of an antibiotic resistance gene, including one between the ubiquitous antimicrobial triclosan and erm(X), a 23S rRNA methyltransferase implicated in resistance to several antibiotics. This study is the first to look for an association between antibiotic resistance genes and antimicrobial chemicals in dust.

Figure 1

Influx of outdoor air, and thus outdoor microbes, likely had a large influence on the microbiome of the building in this study. a) The proportion of bacteria attributed to a human source using SourceTracker by sample. b) Violin plot, showing the median (white dot) and interquartile ranges (box and whiskers) as well as the density distribution (shaded area) of the proportion of bacteria of putative human origin in the present study (purple, n = 42), other athletic facilities (red, n = 308), and private homes (yellow, n = 1366).

Figure 2

Antibiotic resistance gene families (identified in ARDB) were identified throughout the building but at lower relative abundances than observed elsewhere. a) Dot plot of the relative abundance (in RPKM) of each antibiotic gene class by sample. b) Violin plot, showing the median (white dot) and quartile ranges (box and whiskers) as well as the density distribution (shaded area) of the relative abundance of all antibiotic resistance gene families (in RPKM) from the present study (purple, n = 36), other built environment microbiomes (blue, n = 40), and the human microbiome (teal, n = 552).

Figure 3

A 23S ribosomal RNA methyltransferase (erm(33)) was significantly associated with triclosan.