Genomics and host response of S. Typhi infections

Abstract: Genomics and host response to S. Typhi infections Mailis Maes, Department of Medicine, St. Edmunds College, University of Cambridge Around 20 million people are diagnosed annually with typhoid fever, caused by the Gram-negative bacterial pathogen Salmonella enterica serovar Typhi (S. Typhi). Typhoid is endemic in regions of the world with poor infrastructure and the disease sporadically occurs in travellers to these regions. Latin America is known to have endemic typhoid, although information about circulating S. Typhi genotypes and the actual incidence of typhoid in the region is limited by poor surveillance infrastructure. To begin to narrow this data gap, I investigated the genetics of S. Typhi in two Latin American countries, Chile and Colombia, placing this analysis into a global context. I report an analysis of the molecular epidemiology of Colombian S. Typhi, based on pulse field gel electrophoresis (PFGE) patterns of S. Typhi DNA using isolates collected throughout the country between 2012 and 2015. This is followed by further analysis of a second data set using isolates collected between 1997 and 2018. Here, PFGE results were compared to whole genome sequences (WGS) derived from ~70 Colombian S. Typhi isolates placed into a global phylogenetic context. This analysis forms parts of efforts to implement WGS for routine S. Typhi surveillance in this country. In addition, I used genomic analysis to define S. Typhi populations collected in Chile. Chile almost succeeded in eliminating S. Typhi infections in the 1990’s by implementing an ambitious control program. The distribution of S. Typhi genotypes using isolates collected before the implementation of broad typhoid control measures (1980’s isolates) was compared with recent sporadically identified isolates. In addition to identifying three independent haplotype H58 introductions into the country, which are the first reported H58 isolates from Latin America, I show that the current sporadic isolates are likely the result of lingering endemic S. Typhi. This new data has important implications for future typhoid control strategies in the region. This analysis also identified a novel plasmid pHCM2 variant and a potential virulence related single nucleotide polymorphism (SNP) was detected in ancient clades 1.2.1 and 1.1.0. All in all, this part of the thesis highlights the importance of better genetic surveillance in Latin America. In Chapter 5, I investigated the cell-specific responses of human induced pluripotent stem cell (hIPSC)-derived intestinal organoids and human gallbladder organoids to distinct typhoidal Salmonella isolates. By using single cell RNAseq I found that Salmonella down regulates the expression of the Macrophage migration inhibiting factor (MIF), an important regulator of innate immunity, in both models. MIF has previously been shown to contribute to the control of Salmonella infections. Furthermore, indications of infection-associated enhanced lymphotoxin B (LTB) expression by goblet cells were observed. LTB has previously been shown enhance the clearance of Salmonella from the gut. Finally, these results indicate a possible role for the poorly characterised gene Lipocalin 15 (LCN15) in Salmonella control. The last results chapter focusses on the establishment of a high throughput imaging method to evaluate the use of therapeutic monoclonal antibodies against Gram negative bacteria. Functional antibody binding phenotypes of a therapeutic monoclonal antibody against the E. coli ST131 specific O-antigen were defined. This method can be used in the future to evaluate Salmonella serovar specific O-antigen monoclonal antibodies