Browsing by Subject "Antimicrobial resistance"

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    Development And Application Of Targeted Dna Sequencing Tools To Profile Microbiome-Wide Antimicrobial Resistance And Pathogens Of Public Health Importance
    (2024-02) Slizovskiy, Ilya
    Antimicrobial resistance (AMR) poses critical health challenges as drivers of frequent and severe global outbreaks. In the U.S. alone, AMR accounts for one infection every eleven seconds, and one death every fifteen minutes. Bacterial antimicrobial resistance genes (ARGs) are the underpinning determinants of AMR, and traditionally prevention and surveillance efforts have focused on cultivating and studying resistant pathogens harboring DNA-encoded ARGs, isolated from human, animal, food, and environmental sources. However, across most compartments of the biosphere, bacteria reside as community members of complex microbial ecosystems with diverse ecological interactions and defined niche profiles. The perspective of the community-level composition and processes that lead to AMR rise and dissemination is rarely accounted for. Though culture-independent methods like PCR have been used for decades, recent advances in the field of metagenomics offers the possibility of directly sequencing the entire genetic milieu across the total microbiota within a sample (i.e. the ‘metagenome’). This technique offers an ecosystem-wide glimpse into bacterial community members, their genes, and their functional potential. However, metagenomic sequencing is rarely adopted in public health surveillance and tracking of pathogens, as well as risk assessment of AMR. The resulting sequencing data offers a low resolution and fragmented view of AMR hazard potential within microbial communities which is not conducive to motivating quality evidence-based decision-making for clinicians, public health practitioners, food producers, and policy makers. This dissertation consists of four integrated studies that attempt to: (1) Formalize the major impediments precluding informative metagenomic sequencing and data analysis in the study of AMR and its hazard potential; (2) Demonstrate an improved metagenomic approach to elucidate epidemiological trends in a major public health context of AMR; (3) Innovate and implement a novel metagenomic sequencing platform and associated bioinformatic tools to address impediments to metagenomic sequencing and enhance risk characterization of AMR; and (4) Extend technical metagenomic innovations for deployment in public health surveillance and monitoring activities. All metagenomic methods involved the use of unique human, animal, environmental, and food safety-related samples, and all studies were conducted using systems in vivo, in vitro, and / or in silico.
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    Monitoring of phenotypic and genotypic changes in antimicrobial resistance in clinical swine bacterial isolates circulating in the U.S.
    (2019-08) Hayer, Shivdeep Singh
    Starting 2017, a Veterinary Feed Directive was implemented in food animal production in the U.S. This directive prohibits the extra-label use and use of medically important antimicrobials for growth promotion. Analysis of long-term trends of antimicrobial resistance (AMR) can help in evaluating the success of such policies. The objectives of this dissertation were to monitor phenotypic and genotypic changes in antimicrobial resistance in clinical swine bacterial isolates (Escherichia coli, Streptococcus suis, Actinobacillus suis, Pasteurella multocida and Haemophilus parasuis) circulating in the U.S. between 2006 to 2016. For E. coli, the prevalence of resistance to most of the antimicrobials remained constant or changed only modestly, with the exception of enrofloxacin resistance which increased from nearly 0% in 2006 to 21% in 2016. For S. suis and P. multocida, prevalence of resistance did not change drastically except for a few antimicrobials. For A. suis and H. parasuis, statistically significant changes were estimated for several antimicrobials. However, a lack of clinical breakpoints or epidemiological cut-offs hindered in the making any clinical or epidemiological inferences. E. coli isolates resistant to ceftiofur and enrofloxacin were selected and whole genome sequencing was conducted on these isolates. Nearly 25% of the ceftiofur resistant E. coli isolates carried ESBL genes and 24% of enrofloxacin resistant isolates carried qnr genes. These genes have been reported only rarely in food animals in USA. Select plasmids carrying ESBL genes were assembled and these were similar to ESBL plasmids present globally. Additionally, these isolates were also found to be carrying mcr-9 and fosA7 genes, which have not been reported in food animals in USA previously. In addition to these studies, a systematic review on global prevalence of AMR in E. coli of swine origin is also presented. This review highlights the disparity between AMR prevalence in high income versus lower-middle income countries and a clear lack of harmonization in studies conducted worldwide.