Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)

Department / School

Biology and Microbiology

First Advisor

Radhey Shyam Kaushik

Second Advisor

Joy Scaria


cgMLST, Next generation sequencing, Pangenome, Salmonella Mbandaka, SNP analysis, Whole genome sequencing


Food borne salmonellosis is a global public health concern caused by Salmonella, that causes enteric disease both in humans and animals. Most of the pathogenic Salmonella serovars fall under Salmonella enterica subspecies enterica, a major subspecies group that includes more than 50% of total identified Salmonella serovars. New serovars are identified each year and overall incidence of salmonellosis may mask the outbreak incidences caused by individual serovars. Infrequently reported serovar outbreaks can be a significant threat to public health. Salmonella enterica serovar Mbandaka is one of the infrequently reported causative agents of non-typhoidal salmonellosis in USA. But it has been considered as one of the frequent human Salmonella serovar in other countries such as European countries, Israel, Africa as well as in New Zealand. Published researches about this serovar were very limited and no prior studies have been reported about S. Mbandaka isolates from USA especially at the genomic level. Knowledge about the population structure and intra serovar genetic diversity that exists within the S. Mbandaka isolates in a global context remains a mystery. This research was aimed to understand the population structure of globally distributed S. Mbandaka isolates with a hypothesis that isolates of this serovar from different geographical area may be genetically close and form specific clonal groups. Genome sequence data of 465 isolates from different parts of the world were collected from NCBI database and were used to analyze diversity at single nucleotide level. Phylogenetic tree, created based on SNP analysis, revealed partitioning of isolates into two major clusters and six sub clusters. Cluster formation was validated by further analysis with core genome MLST. This research was also aimed to understand the antimicrobial resistance gene pattern and distribution of virulence factors in S. Mbandaka isolates from different isolation sources. Analysis of ability to invade host cells and resistance to low pH environment in 76 USA isolates showed no major difference in these phenotypic properties irrespective of isolation source. Overall this research provides a solid platform for the epidemiological investigation of future Salmonella outbreaks caused by serovar S. Mbandaka.

Library of Congress Subject Headings

Salmonella infections.
Salmonella -- Epidemiology.
Virulence (Microbiology)


Includes bibliographical references (189-202)



Number of Pages



South Dakota State University

Included in

Microbiology Commons



Rights Statement

In Copyright