Microbiome Dispersal and Resistome Transmission Risk in Built Environments

建築環境內微生物的傳播途徑及其耐藥基因的傳播風險研究

Student thesis: Doctoral Thesis

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Award date6 Aug 2019

Abstract

The global trend towards urbanization and industrialization has prompted modern people to spend most of their times indoors. Built environments encompass all different types of manufactured structures, such as residential buildings and public transit systems constructed by humans. Built environments are not only the habitats for human individuals, but also the hosts for a myriad of microorganisms. Bacteria, fungi, archaea, and viruses collectively constitute the built environment microbiome. Although predominantly consisting of commensal microbes, built environment microbiome also contains microbial pathogens, allergens and endotoxins that may be transmitted to and between human occupants. In addition, the emergence and spread of abundant and diverse antibiotic resistant bacteria and antibiotic resistance genes (ARGs) in built environments may pose a threat to human health. Thus, high-throughput sequencing approaches were applied to understand the dispersal pattern and transmission risk of indoor microbiome and resistome (the collection of ARGs present in a microbial community), and their relationships with the physical environments and human individuals.

In the first section of this thesis, the dispersal routes and distribution pattern of fungal communities (mycobiomes) in residential buildings were studied. Biological samples were collected from indoor air, residential surfaces and occupant skin of 19 Hong Kong households, and the first internal transcribed spacer (ITS1) region was sequenced. In this study, SourceTracker algorithm was applied to predict the transmission potentials of microbial communities between different sample types, and the microbial biogeography of indoor air was investigated on a city-wide scale. The results indicate that occupants exert a weaker influence on surface fungal communities compared to bacterial communities, and air currents are stronger determinants of indoor airborne mycobiome than ventilation strategy, human occupancy, and room type.

To further understand the ecology of the skin mycobiomes, skin swabs were collected from five body sites (forehead, left/right forearm and left/right palm) of 24 healthy Chinese individuals across four seasons (from winter to autumn) and amplicon sequencing of the ITS1 region was applied. In this study, the temporal stability of the skin mycobiomes was investigated on an individual basis, and both the abundant and rare species were considered. In addition, a neutral model was applied to predict the assembly pattern of the skin mycobiomes over seasons, and identify the ecological processes underlying skin fungal community dynamics. The results suggest that the skin mycobiome assembly is predominantly a neutral process, and rare taxa, which could be under the influence of selective forces, are potentially key to the structure of a community network.

Given the health threat of antimicrobial resistance, the air microbiomes and resistomes in urban transit environments were investigated. Bioaerosol samples were collected from the public transits of six cities (Denver, Hong Kong, London, New York, Oslo and Stockholm), and processed using shotgun metagenomic sequencing. The results highlighted the importance of geography in governing the air microbial composition of public transits on a global scale. In contrast, air resistome of public transits was influenced less by geography, and subway surface, soil and human skin were predicted to be the major sources of ARGs detected in the subway air. In addition, the transmission risk of ARGs between bacteria varied across cities but remained at a low level, and the abundance of ARGs in chromosome and plasmid was found to be positively correlated with human antibiotic use. The results suggest that urban transit air seems to be a reservoir of ARGs, and their abundances may be used as indicators of local antimicrobial usage patterns for public health surveillance.

Overall, the work conducted in this thesis provided insights into the dispersal and transmission of indoor microbiomes and resistomes in residential and public transit environments at both local and global scales. The results of this research provided an important framework to understand the microbial interactions between human occupants and the indoor environment, the complex relationships between indoor microbiome and resistome, and the exposure and transmission risk of ARGs and their influences on human health.

    Research areas

  • Microbiome, microbial dispersal, Resistome, Antibiotic resistance, Built environment