Shigella sonnei and Shigella flexneri infection in Caenorhabditis elegans led to species-specific regulatory responses in the host and pathogen

Abstract

In recent decades, Shigella sonnei has surpassed Shigella flexneri as the leading cause of shigellosis, possibly due to species-specific differences in their transcriptomic responses. This study used dual RNA sequencing to analyse the transcriptomic responses of Caenorhabditis elegans and the two Shigella species at early (10 minutes) and late (24 hours) stages of infection. While the nematode defence response was downregulated during both Shigella infections, only infection by S. sonnei led to downregulation of sphingolipid metabolism, cadmium ion response and xenobiotic response in C. elegans. Furthermore, S. sonnei upregulates biofilm formation and energy generation/conservation during infection, acid resistance-related genes and biofilm regulators compared to S. flexneri. These findings highlight species-specific responses during C. elegans infection.

Keywords: Caenorhabditis elegans; Shigella flexneri; Shigella sonnei; dual-RNA sequencing; infection.

Fig. 1.. C. elegans–Shigella host–pathogen infection samples. (a) A total of five conditions were used to collect RNA for sequencing (S. sonnei in vitro, S. sonnei-infected C. elegans 10 mpi, S. sonnei-infected C. elegans 24 hpi, S. flexneri-infected C. elegans 10 mpi and S. flexneri-infected C. elegans 24 hpi). The number of differentially expressed genes (DEGs) (P-value<0.05, fold change >2) are labelled between the conditions compared (orange indicates DEGs by C. elegans; black indicates DEGs by Shigella). Boxes indicate the samples used in the three different parts of the analysis. (b) The principal component analysis (PCA) plot of C. elegans during S. sonnei or S. flexneri infection at 10 mpi and 24 hpi. (c) PCA plot of the S. sonnei or S. flexneri response during C. elegans infection at 10 mpi and 24 hpi.

Fig. 2.. C. elegans response during S. sonnei or S. flexneri infection at 10 mpi and 24 hpi. (a) Volcano plot of DEGs in C. elegans during S. sonnei infection. (b) Volcano plot of DEGs in C. elegans during S. flexneri infection. (c) The enriched gene ontology (GO) biological processes identified among the downregulated DEGs in S. sonnei-infected nematodes. (d) The enriched GO biological processes identified among the downregulated DEGs in S. flexneri-infected nematodes.

Fig. 3.. Enriched GO biological processes identified among the DEGs in S. sonnei during in vivo C. elegans infection at 10 mpi and 24 hpi. (a) Enriched within DEGs upregulated at 10 mpi. (b) Enriched within DEGs upregulated at 24 hpi. (c) Enriched within DEGs downregulated at 10 mpi. (d) Enriched within DEGs downregulated at 24 hpi. Red boxes indicate the common pathway enriched between two time points of infection.

Fig. 4.. Genomic and transcriptomic differences between S. sonnei ATCC 29930 and S. flexneri ATCC 12022 during C. elegans infection. (a) The number of orthologous genes between S. sonnei and S. flexneri was identified using ProteinOrtho. Black circles denote the genes with multiple orthologs in either strain, which are mostly hypothetical proteins. (b, c) Volcano plots of DEGs between S. sonnei and S. flexneri during (b) 10 mpi and (c) 24 hpi of C. elegans infection. (d) Heatmap of the 15 DEGs commonly identified from both analyses.