Genomic investigations of the role of disinfectant-induced antibiotic resistance for public health

Abstract

Microorganisms occupy almost every habitat on earth such as soils, ocean, freshwater, and engineered systems (e.g., wastewater treatment systems), and are often associated with other multicellular organisms. Their communities play various important roles in controlling the biogeochemical cycles, and human and animal wellbeing (e.g., food fermentation, preventing infectious disease agents). Even though the great majority of microorganisms are beneficial to human and animal life and health, there have been rising public health concerns such as the recent emergence and spreading of antimicrobial resistant pathogens. The advent of high-throughput sequencing technology and the accompanying development of bioinformatics tools for the analysis of the resulting sequence data in the past decade have enabled the high throughput characterization of the complex microbiota in various environments. Rapid analysis of microbial isolate genomes from various environments through whole-genome sequencing (WGS) has provided new insights into their ecological roles, identified novel species, and tracked the source of disease outbreak. For example, the identification of genomic islands (GIs) and single nucleotide polymorphisms (SNPs) among genomes of the same species can be used to identify the genomic determinants of antimicrobial resistance and to distinguish highly virulent from commensal strains of the species. Moreover, the rise of metagenomics (sequencing of the total microbial community DNA extracted from a target sample) has transformed our understanding of the microbial ecology and physiology of diverse ecosystems, by bypassing the need to isolate the organisms in the lab, a major limitation of traditional lab-based approaches. Although a substantial amount of work has been done in public and environmental health microbiology with omics techniques, there are still unresolved or debatable issues remaining. In this thesis, we combined traditional, culture-based laboratory techniques with cutting-edge, culture-independent omics tools to provide insight into several important research questions. Specifically, in chapter 2, we did metagenomic analysis of bioreactors, MinION-based long-read sequencing of microbial isolates, and molecular cloning to provide molecular evidence that exposure to the widely used disinfectant benzalkonium chlorides (BAC), a member of QAC family, can co-select for antibiotic resistant bacteria. These results contribute toward solving a high debatable issue in the literature for the past two decades, i.e., whether or not exposure to disinfectants promotes antibiotic resistance. In chapter 3, we assessed the effects of BAC-exposure of two different Pseudomonas aeruginosa strains, i.e., one pre-exposed to sub-inhibitory concentrations of BAC for three years vs. its non-exposed counterpart, to increasing concentrations of BAC for about two hundred generations (1-2 months) and applied transcriptomic analysis to reveal molecular mechanisms for the microbial BAC resistance at the whole cell level, including BAC-degradation by microbial enzymes. This work also identified microbial taxa and genes to BACs in non-target environments such as natural sediments and freshwater ecosystems. Finally, in chapter 4, we applied whole community DNA (metagenome) sequencing to 122 stool samples from young children in a low-income, urban neighborhood setting in Maputo, Mozambique, to assess the effect of shared, on-site sanitation intervention on bacterial gut infections. Our findings suggested that the intervention induce small but significant differences in abundance of at least several microbial species, including Veillonella parvula, an opportunistic pathogen. However, pathogen load remain high in children with intervention compared to their matched controls, indicating alternative routes of infection that remain uncontrollable.