Emergence and evolution of antimicrobial resistance genes : insights from metagenomic approach

Abstract

Antimicrobial resistant (AMR) bacterial infections are associated with increased rates of mortality, morbidity, extended stays in hospitals, increased drug costs and limited choices of treatments, which became a critical issue in modern medicine. The increasing presence of pathogenic AMR bacteria in human and animal populations poses major threats to agriculture and global health. This thesis focuses on the dissemination of AMR bacteria through different sources, how they did this and how antibiotic resistance genes (ARGs) evolved by using metagenomic data as the primary tool. This allowed the factors involved in the spread and emergence of AMR to be determined, aiming to guide control, prevention and alternative treatment measures. Global animal metagenomic datasets available from online database were analyzed to measure the diversity and prevalence of ARGs in a range of animal hosts across domestic, peri-domestic and wild habitats. Domestic and peri-domestic animals carried similar ARG profiles, but those in wild animals were significantly different from the others, with a lower prevalence of ARGs related to antibiotics abundantly used in agriculture. Extended spectrum betalactamase (ESBL) genes were equally prevalent in all types of animals, with CfxA genes most prevalent in domestic and peri-domestic animals and TEM genes most prevalent in wild animals. Mobilized colistin resistance (mcr) genes were found, from earlier metagenomic data, in these animals prior to their initial recognition. Evolution of ARGs was examined for the mcr-1 to mcr-10 genes providing a novel insight into the origin of the mcr-3 and mcr-7 genes, which were from the product of homologous gene recombination events involving two different pairs of chromosomal Aeromonas spp. phosphoethanolamine transferase (PET) genes. How the PET genes evolved and recombined into mcr-3 and mcr-7 was examined by phylogenetic analysis of the genes. Longitudinal sampling of sewage from different outlets in a local major hospital complex and its downstream wastewater pretreatment works (PTW) was conducted for one year. Analyses on the sewage metagenomes showed that the discharge from the major clinical site had ARG and bacterial profiles different from the other sampling sites. Sewage from the downstream PTW gave a measure of the environmental persistence of ARGs. Metagenomes from the sewage collected from the PTW suggested the hospital might be the major source of the ARGs and related bacteria. These studies found mcr genes that were not previously identified by the hospital using standard culture-based screening for colistin-resistant bacteria. A metagenomic approach, studying sewage from a hospital and its PTW, allows comprehensive, and potentially more effective, surveillance without interfering in the operation of the hospital or affecting patients. An overview of AMR was obtained in a hospital that can discriminate by medical functions, give a comparison to the surrounding community, and with greater sensitivity than symptom-based surveillance.