The bacterial microbiome and resistome of house dust mites in Irish homes

Abstract

Dust samples were collected from Irish homes. House Dust Mite and storage mites were separated from the dust. The microbiome and resistome of mites and originating dust were assessed using a culture-independent approach. The bacterial microbiome of mites and dust were predominantly populated by Staphylococci. There was a highly significant (P = 0.005; Spearman's rank test) correlation between the bacterial microbiome of mites and the dust. One-hundred and eighteen antimicrobial resistance genes (ARGs) were associated with mites and 176 with dust. Both contained ARGs encoding resistance for multi drug resistances, macrolide-lincosamide-streptogramin B, mobile genetic elements, Beta-lactam, Tetracycline and Aminoglycosides. By contrast, 15 ARGs were found for a laboratory-grown strain of Dermatophagoides pteronyssinus. A significant difference (P = 0.03; t test) was found in means between the resistome of mites and the household dust from which they emanated. No significant correlations (P = 0.23 and P = 0.22; Mantel test) were observed between the microbiome and resistome of mite and dust samples. There was not a significant difference (P = 0.54; t-test) between the means of ARGs for homes with and without a history of antibiotic use.

Keywords: 16 S rRNA microbiome; Antibiotic resistant genes; Dust mites; Dust samples; Resistome; qPCR SmartChip.

Fig. 1

The ten most abundant bacterial species found for dust mite and household dust samples (n = 12). Samples 4 and 4D represented the laboratory strain (control).

Fig. 2

Number of detected genes in environmental HDM, dust samples (n = 12) according to different antibiotic classes: 1–6 represented mite samples and 1D-6D represented dust samples, 4&4D showed the laboratory strain (control).

Fig. 3

Relative abundances of the genes detected in the HDM in proportion to the 16S rRNA gene (as log values) in mite and dust samples (n = 12). 1–6 represented mite samples and 1D–6D represented dust samples, 4&4D showed the laboratory strain (control).

Fig. 4

Resistome composition of HDM and dust in Galway homes (n = 12), Ireland. The colours in the heatmap show gene abundances relative to 16S rRNA gene. The X axis represents the sample ID and the Y axis represents the antibiotic group. 1–6 represented mite samples and 1D–6D represented dust samples, 4 and 4D showed the laboratory strain (control).

Fig. 5

NMDS ordination of microbiome and resistome of mite and dust samples. Circles show 95% confidence area for standard error of the centroids of the microbiome and resistome in different sample types. 1-6D_m and 1-6_m = microbiome for dust and dust mite for samples (n = 12), respectively. 1-6D_r and 1-6_r = resistome for dust and dust mite for samples (n = 12), respectively.