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Genomic Epidemiology and Detection of Antimicrobial Resistance Determinants in Salmonella Dublin Isolates Originating from Cattle

Byrne, Brianna
http://rave.ohiolink.edu/etdc/view?acc_num=osu1555410762319571

Abstract Details

2019, Master of Public Health, Ohio State University, Public Health.
Multidrug-resistant (MDR) Salmonella enterica is a threat to public health, in part due to a broad spectrum of resistance to antimicrobials critically important for treating infections. Salmonella Dublin is a bovine adapted S. enterica serotype. Human cases tend to manifest in a more invasive manner and the isolates have high prevalence of antimicrobial resistance (AMR). The aims of this study were to genetically characterize AMR features in MDR S. Dublin isolates from cattle in Ohio, assess the capacity of whole-genome sequencing (WGS) to predict AMR phenotypes, and characterize the genetic relatedness of the strains. Twenty-four S. Dublin isolates recovered from samples submitted to the Ohio Department of Agriculture by veterinarians from sick cattle were selected for WGS with Illumina MiSeq. Genotypic analysis of AMR determinants and plasmid replicons in each assembly was performed through Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/) and nucleotide BLAST analyses. Cohen’s kappa coefficient of agreement between phenotypic and genotypic AMR was calculated. The webtool CSIPhylogeny 1.4 was used for phylogenetic reconstruction to determine S. Dublin relatedness. Average genotype and phenotype agreement for characterization of AMR was 94.8%. Identification of a resistance gene had a mean 88.9% sensitivity and 84.2% specificity for the identification of the corresponding resistance phenotype. The majority of resistance genes were located on plasmid incompatibility group IncA/C2. IncFII(S) and IncX1 replicon groups were also present. WGS was able to identify chromosomal point mutations conferring resistance to quinolones and fluoroquinolones. All isolates were multilocus sequence type (MLST) ST-10 and showed close clustering in single nucleotide polymorphism (SNP) phylogenetic analyses. Results indicate that WGS is a robust method to accurately detect comprehensive AMR determinants in MDR S. Dublin isolates from bovine sources. WGS could also simultaneously generate additional molecular epidemiologic data from isolates, including identification of MLST type and plasmid replicons, making this method a fast and relatively inexpensive alternative to conventional phenotyping.
Gregory Habing, DVM, MS, PhD (Advisor)
Thomas Wittum, MS, PhD (Committee Member)
Jiyoung Lee, MS, PhD (Committee Member)
67 p.
Public Health
Salmonella, Whole Genome Sequencing, Antimicrobial Resistance, Plasmids

Recommended Citations

Citations

  • Byrne, B. (2019). Genomic Epidemiology and Detection of Antimicrobial Resistance Determinants in Salmonella Dublin Isolates Originating from Cattle [Master's thesis, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1555410762319571

    APA Style (7th edition)

  • Byrne, Brianna. Genomic Epidemiology and Detection of Antimicrobial Resistance Determinants in Salmonella Dublin Isolates Originating from Cattle. 2019. Ohio State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1555410762319571.

    MLA Style (8th edition)

  • Byrne, Brianna. "Genomic Epidemiology and Detection of Antimicrobial Resistance Determinants in Salmonella Dublin Isolates Originating from Cattle." Master's thesis, Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1555410762319571

    Chicago Manual of Style (17th edition)

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This open access ETD is published by The Ohio State University and OhioLINK.