Comparative transcriptional profiling of the early host response to infection by typhoidal and non-typhoidal Salmonella serovars in human intestinal organoids

Abstract

Salmonella enterica represents over 2500 serovars associated with a wide-ranging spectrum of disease; from self-limiting gastroenteritis to invasive infections caused by non-typhoidal serovars (NTS) and typhoidal serovars, respectively. Host factors strongly influence infection outcome as malnourished or immunocompromised individuals can develop invasive infections from NTS, however, comparative analyses of serovar-specific host responses have been constrained by reliance on limited model systems. Here we used human intestinal organoids (HIOs), a three-dimensional “gut-like” in vitro system derived from human embryonic stem cells, to elucidate similarities and differences in host responses to NTS and typhoidal serovars. HIOs discriminated between the two most prevalent NTS, Salmonella enterica serovar Typhimurium (STM) and Salmonella enterica serovar Enteritidis (SE), and typhoidal serovar Salmonella enterica serovar Typhi (ST) in epithelial cell invasion, replication and transcriptional responses. Pro-inflammatory signaling and cytokine output was reduced in ST-infected HIOs compared to NTS infections, consistent with early stages of NTS and typhoidal diseases. While we predicted that ST would induce a distinct transcriptional profile from the NTS strains, more nuanced expression profiles emerged. Notably, pathways involved in cell cycle, metabolism and mitochondrial functions were downregulated in STM-infected HIOs and upregulated in SE-infected HIOs. These results correlated with suppression of cellular proliferation and induction of host cell death in STM-infected HIOs and in contrast, elevated levels of reactive oxygen species production in SE-infected HIOs. Collectively, these results suggest that the HIO model is well suited to reveal host transcriptional programming specific to infection by individual Salmonella serovars, and that individual NTS may provoke unique host epithelial responses during intestinal stages of infection.

Neutrophils prime unique transcriptional responses in intestinal organoids during infection with nontyphoidal Salmonella enterica serovars

“…SE and STM share high levels of gene homology but accessory genes unique to SE contribute to its pathogenesis in a mouse model of infection (28)(29)(30). We also found that these serovars elicit unique responses by human intestinal epithelium (8). Consistent with this earlier finding, we observed clustering of SE-infected PMN-HIOs away from STMinfected PMN-HIOs via principal component analysis (PC2) (Fig.…”

“…HIOs are derived from human pluripotent stem cells and self-organize to form a 3dimensional polarized epithelium with differentiated epithelial cells and an underlying mesenchyme (9). Bacteria, including Salmonella, are able to replicate and stimulate robust inflammatory responses in HIOs (6)(7)(8)(10)(11)(12). Although the HIO model and other tissue culture models have been invaluable in revealing human-specific responses to Salmonella infection (6)(7)(8)(13)(14)(15), key features missing from these models are known to shape the outcome of infection, including immune cells.…”

“…Notably, disease progression caused by Salmonella is often different in mice compared to humans, including the fact that mice rarely develop diarrhea during these infections (5). To better understand human infection, human-derived cells including human intestinal organoids (HIOs) have been used to define human-specific host responses to Salmonella (6)(7)(8). HIOs are derived from human pluripotent stem cells and self-organize to form a 3dimensional polarized epithelium with differentiated epithelial cells and an underlying mesenchyme (9).…”

Cross-Talk Between the Intestinal Epithelium and Salmonella Typhimurium

“…For example, secretory cell hyperplasia (goblet, paneth, and tuft cells), mucus, and AMP production such as Reg3γ and DEFA1 were induced in response to STm infection ( Lu et al, 2020 ). In addition, similar results indicating an inhibition of the cell turnover at the intestinal epithelium and intestinal epithelial secretion induced by STm infection in susceptible mice ( Santos et al, 2016 ) were also observed using human intestinal organoids microinjected with STm to model the bacterial infection at the apical side ( Abuaita et al, 2021 ). Interestingly, organoids from juvenile inflammatory bowel patient failed to control STm growth and highlight the role of IL22 and IL10RB gene in antimicrobial defense against STm ( Forbester et al, 2018 ).…”

Whole Genome Sequencing, Antibiotic Resistance, and Epidemiology Features of Nontyphoidal Salmonella Isolated From Diarrheic Children: Evidence From North China

“…Children under 5 years old bear the burden of the major disease, especially in low-income regions (Havelaar et al, 2015 ; GBD 2017 Non-Typhoidal Salmonella invasive disease collaborators , 2019 ; Gilchrist and MacLennan, 2019 ). NTS generally causes self-limiting diarrheal illness, but may typically lead to severe invasive NTS for children's lack of immunity (Abuaita et al, 2021 ; Rana et al, 2021 ). Infection with different NTS serovars can present various epidemiological and clinical manifestations.…”