title: The genomic epidemiology of nontyphoidal Salmonella serovars and their association with invasive disease
Creators: name: Pulford, Caisey
Publisher: name: University of Liverpool Repository
Year: 2020

description: Nontyphoidal Salmonella (NTS) is a globally important bacterial pathogen, typically associated with foodborne gastroenteritis. However, NTS can also invade normally sterile sites in humans, resulting in an extraintestinal infection known as invasive nontyphoidal Salmonella (iNTS) disease. The majority of cases of iNTS disease in humans are caused by a small minority of Salmonella pathovariants, which exhibit genomic signatures of adaptation to a systemic lifestyle within a restricted host-range. With the increasing availability of whole genome sequencing (WGS)-based pathogen surveillance, it has become possible to use genomic approaches to investigate the adaptive process that occurred when NTS serovars evolved to exploit a new niche. I aimed to determine the temporal, geographical and evolutionary trends in nontyphoidal Salmonella serovars, in order to understand the genomic signatures acquired on the trajectory towards extraintestinal adaptation. My genome-based analysis began with a phylogenetic approach to differentiate a broad range of NTS serovars. Specifically, I assembled a unique dataset of 133 reptilian isolates to study S. enterica species-level evolution and ecology, with a focus on Salmonella that colonised the guts of venomous snakes. The serovars belonged to four of the six S. enterica subspecies and included a small number of multidrug resistant isolates of clinical relevance. The subspecies enterica isolates were distributed between two distinct phylogenetic clusters, clade A and clade B, and exhibited different levels of metabolic flexibility reflecting distinctive host-ranges. My species-level analysis provided a context for a more detailed study of two epidemiologically important serovars responsible for iNTS disease in humans; S. Typhimurium and S. Panama. By studying the stepwise evolution of 680 S. Typhimurium isolates that caused bloodstream infection in sub-Saharan Africa, I uncovered the timeline of crucial loss-of-function genetic events that facilitated the emergence of the invasive ST313 S. Typhimurium pathovariant in the immunocompromised human niche. The findings link the acquisition of particular nucleotide changes with gene function during the evolution of ST313 lineage 2 (ST313 L2). A recently emerged pan-susceptible ST313 lineage (ST313 L3) was discovered in Malawi, with evidence of genome degradation in important virulence genes which had not occurred in other ST313 lineages. My work describes the evolutionary dynamics of S. Typhimurium ST313 and highlights epidemiological shifts in the circulation of ST313 lineages in Malawi. To compare and contrast with my work in S. Typhimurium, I explored an understudied serovar responsible for extraintestinal infection globally. Specifically, I described the population structure, phylodynamics and invasiveness potential of 489 S. Panama isolates from 27 countries. The findings revealed 6 geographically associated clades, and regional trends in AMR. Finally, I determined the genetic markers of invasiveness that varied between S. Panama clades, highlighting the importance of prophage presence and genome degradation, as was the case in S. Typhimurium. Taken together, my study provides new insights into the evolution of niche-adaptation in a globally important pathogenic genus. My findings highlight the need for an integrated approach for pathogen surveillance and scientific research that combines the power of genome-level discrimination, with epidemiological rigour, clinical observation and functional analysis.