Date of Award




Document Type

Master's Thesis

Degree Name

Master of Science (MS)


Department of Biological Sciences

Content Description

1 online resource (v, 26 pages) : color illustrations.

Dissertation/Thesis Chair

Cheryl Andam

Committee Members

Alex Valm, Pascal Lapierre


Salmonella, Salmonella infections, Salmonella enteritidis, Microbial genomics, Genomics

Subject Categories

Biology | Epidemiology | Microbiology


Antimicrobial resistance in Salmonella enterica remains a challenging public health threat. We aim to characterize the population structure and evolutionary history of 394 genomes of S. enterica isolates recovered from human clinical cases in New Hampshire, USA from 2017 to 2020. The population is phylogenetically diverse, consisting of 78 STs and 67 serotypes. We detected 61 genes associated with resistance to14 different antimicrobial classes. Rather than a single multidrug resistant clone expanding in the state, we found multiple lineages carrying different combinations of independently acquired resistance determinants. New or emerging lineages can therefore rapidly spread over relatively short timeframes. In the case of the predominant lineage serotype Enteritidis ST 11 (n = 126 genomes), its effective population size has been increasing in the last five decades. Integrating whole genome sequencing in state-level public health efforts is critical to elucidating the origins and spread of high-risk clones.