Genomic and Transcriptomic Comparison Between Invasive Non-Typhoidal Salmonella and Non-Invasive Isolates

Invasive non-typhoidal Salmonella (iNTS) poses a significant threat to global public health. Salmonella enterica Enteritidis and Typhimurium are the primary serovars responsible for both invasive diseases and gastroenteritis. This study aims to investigate the genomic and transcriptomic differences between isolates associated with these contrasting clinical presentations. We retrieved genomes of Salmonella Enteritidis and Salmonella Typhimurium from Enterobase, utilizing blood and stool isolates as representatives for iNTS and non-iNTS, respectively. An indistinguishable phylogenetic relationship was revealed between the blood and stool isolates for both serovars. Few genes were specifically identified in iNTS. Random forest and principal coordinates analysis permitted moderate discrimination between the two sources of isolates based on overall genome content. Notably, the blood isolates of Salmonella Typhimurium displayed an elevated level of antimicrobial resistance and genome degradation compared to stool isolates. Meanwhile, transcriptome sequencing identified few genes that were differentially expressed between blood and stool isolates. Hierarchical clustering and principal component analysis did not effectively differentiate the expression profile of iNTS from non-iNTS. In summary, few genes could serve as reliable biomarkers to distinguish iNTS and non-iNTS at either the genomic or transcriptomic level. Nevertheless, iNTS has indeed accumulated subtle genomic differences from non-iNTS, which might contribute to invasiveness.