Serotyping and genotyping of salmonellae of poultry and poultry product origin


Thesis Type: Doctorate

Institution Of The Thesis: Uludağ Üniversitesi, Turkey

Approval Date: 2016

Thesis Language: Turkish

Student: ZAFER ATA

Supervisor: AYŞE GÜL EYİGÖR

Abstract:

The first aim of this study was to identify the serogroup/serotype of the Salmonella spp. isolates of animal and animal-derived food origin in our laboratory by conventional serotyping, as well as to perform a S. Enteritidis-specific realtime PCR (SE-rPCR), then to determine their performance and evaluate their relevance. The second aim of this study was to genotype the same Salmonella isolates by a multilocus sequence typing (MLST), and to compare these results with high resolution melting (HRM) analysis performed after MLST, and to finally determine the usefulness of HRM analysis in MLST. For this, a total of 58 isolates of chicken meat, turkey meat, egg, and poultry origin was used. SE-rPCR, which was performed for the first time by using SefB-gene specific primers, was almost in perfect agreement with conventional serotyping (Cohen's kappa index = 0,86). Only 3 of the 50 isolates (isolate number 6, 122 ve 151) showed 100% similarity to sequence type (ST)11 in the STs in MLST database. All of the isolates used in this study showed 43 different genotypes, where MLST had high resolution in Salmonella enterica typing. As a part of the MLST, DNA sequences were classified under 40 different sequences after HRM analysis. Since HRM analysis resulted the same as the DNA sequence analysis, by only sequencing the DNA with different HRM analysis results, the analysis cost would be reduced by 83%. Results of this study indicate that SE-rPCR is a rapid alternative diagnostic tool to be used in surveillance and research purposes, which would reduce the requirement for agglutination tests performed by specific antisera, thus the time and the cost. Additionally, this study reports the use of HRM analysis in combination with MLST for the first time in literature as an advantageous approach in reducing the overall cost of the test.