Resistome in the indoor dust samples from workplaces and households: a pilot study

Abstract

The antibiotic resistance genes (ARGs) limit the susceptibility of bacteria to antimicrobials, representing a problem of high importance. Current research on the presence of ARGs in microorganisms focuses mainly on humans, livestock, hospitals, or wastewater. However, the spectrum of ARGs in the dust resistome in workplaces and households has gone relatively unexplored. This pilot study aimed to analyze resistome in indoor dust samples from participants' workplaces (a pediatric hospital, a maternity hospital, and a research center) and households and compare two different approaches to the ARGs analysis; high-throughput quantitative PCR (HT-qPCR) and whole metagenome shotgun sequencing (WMGS). In total, 143 ARGs were detected using HT-qPCR, with ARGs associated with the macrolides, lincosamides, and streptogramin B (MLSB) phenotype being the most abundant, followed by MDR (multi-drug resistance) genes, and genes conferring resistance to aminoglycosides. A higher overall relative quantity of ARGs was observed in indoor dust samples from workplaces than from households, with the pediatric hospital being associated with the highest relative quantity of ARGs. WMGS analysis revealed 36 ARGs, of which five were detected by both HT-qPCR and WMGS techniques. Accordingly, the efficacy of the WMGS approach to detect ARGs was lower than that of HT-qPCR. In summary, our pilot data revealed that indoor dust in buildings where people spend most of their time (workplaces, households) can be a significant source of antimicrobial-resistant microorganisms, which may potentially pose a health risk to both humans and animals.

Keywords: antibiotic resistance gene; antimicrobial resistance; hospital; indoor environment; microbiome.

Figure 1

Barplots of DNA taxonomical compositions of the pooled samples from the three workplaces (Work) and respective households (Home) at the domain level and genus level for Bacteria obtained by WMGS. Note the low levels of Archaea and Viruses DNA (< 1%). ENT, pediatric hospital; NEO, maternity hospital; and RCX, research center; WMGS, whole metagenome shotgun sequencing.

Figure 2

Radar chart containing 143 antibiotic resistance genes (ARGs) detected by HT-qPCR – Resistomap for the dust samples from three workplaces (Work) and households of workers from these workplaces (Home). ARGs were categorized based on the class of antibiotics they confer resistance to. ENT, pediatric hospital; NEO, maternity hospital; and RCX, research center; N, number of ARGs with relative quantity > 0 in any of the six pooled indoor dust samples; MDR, multidrug resistance; MLSB, genes associated with macrolides, lincosamides, and streptogramin B phenotype; HT-qPCR, high-throughput quantitative PCR.

Figure 3

Heatmap of antibiotic resistance genes (ARGs) with > 1% relative quantification in all pooled samples or found in both HT-qPCR and WMGS. Data scaled by the minimal non-zero value across all analyzed samples. The upper left part of each cell corresponds to the workplace (Work) samples, and the lower right part to the household (Home) samples, facilitating easy paired comparison. Circles inside cells indicate orders of magnitude for better readability. Cross marks (✘) denote ARGs that were found also by WMGS. ENT, pediatric hospital; NEO, maternity hospital; and RCX, research center; MDR, multidrug resistance; MLSB, genes associated with the phenotype resistant to macrolides, lincosamides, and streptogramin B; HT-qPCR, high-throughput quantitative PCR; WMGS, whole metagenome shotgun sequencing.