Dual RNA-seq identifies proteins and pathways modulated duringClostridioides difficilecolonisation

Abstract

AbstractThe gastrointestinal pathogen,Clostridioides difficile, is the most common cause of hospital-acquired diarrhoea. Bacterial interactions with the gut mucosa are crucial for colonisation and establishment ofC. difficileinfection, however, key infection events like bacterial attachment and gut penetration are still poorly defined. To better understand the initial events that occur when this anaerobic pathogen interacts with human gut epithelial cells, we employed a dual RNA-sequencing approach to study the bacterial and host transcriptomic profiles duringC. difficileinfection in a dual-environmentin vitrohuman gut model. Temporal changes in gene expression during infection were studied in the bacterium and the host cells over the course of 3-24 hours. While there were several common differentially expressed bacterial genes across the different times after infection, mammalian transcriptional profiles were quite distinct with little overlap. Interestingly, an induction of colonic receptors forC. difficiletoxins was observed, along with the expression downregulation of genes encoding immune response markers. Several cell wall associated proteins were downregulated inC. difficilewhen in association with host cells, includingslpA, which encodes the main S-layer protein. Gene function and pathway enrichment analyses revealed a potential modulation of the purine/pyrimidine synthesis pathways both in the mammalian and the bacterial cells. We observed that proline-proline endopeptidase, a secreted metalloprotease responsible for cell surface protein cleavage, is downregulated during infection, and a mutant lacking this enzyme demonstrated enhanced adhesion to epithelial cells during infection. This study provides new insight into the host and bacterial pathways based on gene expression modulation during the initial contact ofC. difficilewith gut cells.ImportanceThe initial interactions between the colonic epithelium and the bacterium are likely critical in the establishment ofClostridioides difficileinfection, one of the major causes of hospital acquired diarrhoea worldwide. Molecular interactions betweenC. difficileand human gut cells have not been well defined mainly due to the technical challenges of studying cellular host-pathogen interactions with this anaerobe. Here we have examined transcriptional changes occurring in the pathogen and host cells during the initial 24 hours of infection. Our data indicate several changes in metabolic pathways and virulence-associated factors during the initial bacterium-host cell contact and early stages of infection. We describe canonical pathways enriched based on the expression profiles of a dual RNAseq in the host and the bacterium, and functions of bacterial factors modulated during infection. This study provides insight into the early infection process at a molecular level.