Genomic Analysis of Carbapenem-Resistant Environmental Gram-Negative Bacteria

Hem, Sopheak

Genomic Analysis of Carbapenem-Resistant Environmental Gram-Negative Bacteria

Hem, Sopheak

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Publication Type:: Thesis
Issue Date:: 2023

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Field	Value	Language
dc.contributor.author	Hem, Sopheak
dc.date.accessioned	2024-06-18T02:19:47Z
dc.date.available	2024-06-18T02:19:47Z
dc.date.issued	2023
dc.identifier.uri	http://hdl.handle.net/10453/179542
dc.description	University of Technology Sydney. Faculty of Science.	en_US.UTF-8
dc.description.abstract	The contamination of water bodies with antibiotics, biocides/pesticides, metals, pharmaceuticals, as well as antibiotic-resistant bacteria creates constant selection pressures that promote horizontal gene transfer, a major driver of microbial evolution. Consequently, contaminated water may introduce multiple drug resistant pathogens into healthcare facilities, food production environments, wildlife and agriculture. There is also a growing concern that healthy human and food animal microbial flora harbour considerable antibiotic resistance and virulence gene loads. These developments enhance reliance on carbapenem and other last line antibiotics, which play a crucial role in treating severe Gram-negative bacterial infections This study aimed to investigate the issue using whole genome sequencing (WGS) on carbapenem-resistant Gram-negative bacterial isolates from environmental water sources. The investigation focused on three genera: Elizabethkingia (n=94), Comamonas (n=39), and Citrobacter (n=77). Comprehensive genomic analyses were performed to explore phylogenetics, species typing, SNP distances, and to characterise mobile genetic elements (MGEs), virulence-associated genes, and antibiotic resistance genes (ARGs). The study revealed intriguing findings concerning carbapenem-resistant bacteria. In Elizabethkingia, environmental isolates closely related to clinical strains causing sepsis were identified, indicating the significance of natural water bodies as potential sources for pathogenic Elizabethkingia. Furthermore, a novel species, E. umeracha, was identified, carrying novel metallo β-lactamase and extended-spectrum cephalosporin gene alleles. The investigations into Comamonas revealed blaGES-5 and blaOXA present on unique putative genomic islands. Additionally, one C. denitrificans isolate carried an IncP-1 plasmid with metal resistant genes involved in xenobiotic degradation. Regarding Citrobacter, it was observed that isolates from wastewater exhibited a substantial burden of ARGs, and several novel multidrug-resistant lineages were identified. Notably, C. freundii isolates carried two carbapenemase genes, blaIMP-4 located within a class 1 integron on IncM plasmids, and blaKPC-2 on IncP plasmids. Additionally, our study identified a C. portucalensis isolate carrying blaNDM-1, blaSHV-12, and mcr-9 genes. Our study provided valuable insights into the presence of carbapenem-resistant species in environmental waters. The identification of new species and novel ARG alleles enriched our understanding of the genetic diversity within these bacterial genera. Moreover, the investigation shed light on the MGEs that harbour and presumably transmit these genes. We also identified phylogenetic and genotypic connections between environmental isolates and other sources, unveiling potential origins and transfer mechanisms of MGEs. These findings contribute to our knowledge of the spread of antibiotic resistance in water environments which is crucial for implementing effective measures to mitigate the impact of this growing public health concern.	en_US.UTF-8
dc.format	Thesis (PhD)
dc.language.iso	en_US	en_US.UTF-8
dc.relation	https://opus.lib.uts.edu.au/bitstream/10453/179542/1/thesis.pdf
dc.rights	info:eu-repo/semantics/openAccess
dc.rights	The author owns the copyright in this thesis including all reproduction and reuse rights for the work. The work may not be altered without the permission of the copyright owner. Attribution is essential when quoting or paraphrasing from this thesis.
dc.rights	© 2023 Sopheak Hem
dc.rights	au.edu.uts.lib/cph
dc.title	Genomic Analysis of Carbapenem-Resistant Environmental Gram-Negative Bacteria	en_US.UTF-8
dc.type	Thesis
utslib.copyright.status	open_access	*

Abstract:

The contamination of water bodies with antibiotics, biocides/pesticides, metals, pharmaceuticals, as well as antibiotic-resistant bacteria creates constant selection pressures that promote horizontal gene transfer, a major driver of microbial evolution. Consequently, contaminated water may introduce multiple drug resistant pathogens into healthcare facilities, food production environments, wildlife and agriculture. There is also a growing concern that healthy human and food animal microbial flora harbour considerable antibiotic resistance and virulence gene loads. These developments enhance reliance on carbapenem and other last line antibiotics, which play a crucial role in treating severe Gram-negative bacterial infections This study aimed to investigate the issue using whole genome sequencing (WGS) on carbapenem-resistant Gram-negative bacterial isolates from environmental water sources. The investigation focused on three genera: Elizabethkingia (n=94), Comamonas (n=39), and Citrobacter (n=77). Comprehensive genomic analyses were performed to explore phylogenetics, species typing, SNP distances, and to characterise mobile genetic elements (MGEs), virulence-associated genes, and antibiotic resistance genes (ARGs). The study revealed intriguing findings concerning carbapenem-resistant bacteria. In Elizabethkingia, environmental isolates closely related to clinical strains causing sepsis were identified, indicating the significance of natural water bodies as potential sources for pathogenic Elizabethkingia. Furthermore, a novel species, E. umeracha, was identified, carrying novel metallo β-lactamase and extended-spectrum cephalosporin gene alleles. The investigations into Comamonas revealed blaGES-5 and blaOXA present on unique putative genomic islands. Additionally, one C. denitrificans isolate carried an IncP-1 plasmid with metal resistant genes involved in xenobiotic degradation. Regarding Citrobacter, it was observed that isolates from wastewater exhibited a substantial burden of ARGs, and several novel multidrug-resistant lineages were identified. Notably, C. freundii isolates carried two carbapenemase genes, blaIMP-4 located within a class 1 integron on IncM plasmids, and blaKPC-2 on IncP plasmids. Additionally, our study identified a C. portucalensis isolate carrying blaNDM-1, blaSHV-12, and mcr-9 genes. Our study provided valuable insights into the presence of carbapenem-resistant species in environmental waters. The identification of new species and novel ARG alleles enriched our understanding of the genetic diversity within these bacterial genera. Moreover, the investigation shed light on the MGEs that harbour and presumably transmit these genes. We also identified phylogenetic and genotypic connections between environmental isolates and other sources, unveiling potential origins and transfer mechanisms of MGEs. These findings contribute to our knowledge of the spread of antibiotic resistance in water environments which is crucial for implementing effective measures to mitigate the impact of this growing public health concern.

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