Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580

Abstract

Salmonella Typhimurium sequence type (ST) 313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV ⁺, malarial, or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580 and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in 16 infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium, SalComD23580: http://bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl. We discovered that the ablation of melibiose utilization was caused by three independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolize this carbon source has been negatively selected during ST313 evolution. The data revealed a novel, to our knowledge, plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multicondition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

Abstract

Comparative transcriptomic analysis of two contrasting Salmonella enterica Typhimurium isolates across 16 in vitro conditions and within macrophages reveals the mechanism of African Salmonella metabolic defect and a novel bacterial plasmid maintenance system.

Author summary

Invasive nontyphoidal Salmonella (iNTS) is associated with a major and largely unreported tropical disease that is responsible for hundreds of thousands of deaths per year in Africa. The main causative agent is a pathovariant of Salmonella Typhimurium called ST313, which is closely related to the well-characterized ST19 sequence type of Salmonella that causes gastroenteritis globally. ST313 and ST19 vary by just 856 core genome single-nucleotide polymorphisms (SNPs). To understand how genetic changes generate phenotypic and mechanistic differences between African and global Salmonella, we used functional transcriptomic and proteomic approaches. By investigating the transcriptome of African and global S. Typhimurium in 17 growth conditions, we discovered that 677 genes and small RNAs were differentially expressed between strains D23580 (ST313) and 4/74 (ST19). A parallel proteomic approach linked gene expression differences to alterations at the protein level. We also identified differentially expressed genes during the actual infection of murine macrophages. Our data revealed the genetic basis of the loss of a carbon source utilization in African Salmonella and the discovery of a new mechanism for maintaining a plasmid in a bacterial population involving a plasmid-encoded essential bacterial gene.