Gut microbiota signature of pathogen-dependent dysbiosis in viral gastroenteritis

Abstract

Acute gastroenteritis associated with diarrhea is considered a serious disease in Africa and South Asia. In this study, we examined the trends in the causative pathogens of diarrhea and the corresponding gut microbiota in Ghana using microbiome analysis performed on diarrheic stools via 16S rRNA sequencing. In total, 80 patients with diarrhea and 34 healthy adults as controls, from 2017 to 2018, were enrolled in the study. Among the patients with diarrhea, 39 were norovirus-positive and 18 were rotavirus-positive. The analysis of species richness (Chao1) was lower in patients with diarrhea than that in controls. Beta-diversity analysis revealed significant differences between the two groups. Several diarrhea-related pathogens (e.g., Escherichia-Shigella, Klebsiella and Campylobacter) were detected in patients with diarrhea. Furthermore, co-infection with these pathogens and enteroviruses (e.g., norovirus and rotavirus) was observed in several cases. Levels of both Erysipelotrichaceae and Staphylococcaceae family markedly differed between norovirus-positive and -negative diarrheic stools, and the 10 predicted metabolic pathways, including the carbohydrate metabolism pathway, showed significant differences between rotavirus-positive patients with diarrhea and controls. This comparative study of diarrheal pathogens in Ghana revealed specific trends in the gut microbiota signature associated with diarrhea and that pathogen-dependent dysbiosis occurred in viral gastroenteritis.

Role of Microbiota in Viral Infections and Pathological Progression

“…Furthermore, there are reports suggesting that microbiota inhibit the cell adhesion of noroviruses during in vitro experiments [ 31 , 32 ]. The diversity of the intestinal bacterial layer decreases after norovirus or rotavirus infection [ 33 ], and the composition of the microbiota is different in patients with diarrhea in Ghana [ 34 ]. These observations may be explained by the differences in interactions with the microbiota in viral infections.…”

Dynamic of the human gut microbiome under infectious diarrhea

“…This may suggest that viral infections lead to a less severe reductions in anaerobic gut commensals [ 35 , 36 ], possibly because most viruses (rotavirus, norovirus) infect cells lining the small intestine, instead of the colon [ 37 • , 38 ]. In mouse model, rotavirus infection resulted in increased Bacteroides and Akkermansia populations (both with mucin-degrading capability) only in the ileal microbiome [ 37 • ], but evidence for the overgrowth of these two taxa in human rotavirus infections has been inconclusive [ 21 , 26 , 34 , 39 ]. On the other hand, Giardia -induced diarrhea was consistently linked to a decrease in Gammaproteobacteria and an enrichment of Prevotella [ 40 ].…”

Diarrhea-Causing Bacteria and Their Antibiotic Resistance Patterns Among Diarrhea Patients From Ghana

“…Reports of over 40% of non-bacterial diarrhea in children being treated with antibiotics, easy accessibility to antibiotics through unapproved means in Ghana, and wrongful prescription of drugs are of grave concern ( Arhinful, 2009 ; Ahiabu et al, 2016 ). There are some studies implicating bacteria in diarrhea cases in Ghana ( Akuffo et al, 2017 ; Mizutani et al, 2021 ), with a prevalence of rate of 3% and high resistance to commonly abused drugs such as tetracycline ( Newman et al, 2011 ; Akuffo et al, 2017 ). This study aimed to isolate bacterial organisms associated with diarrhea in patients reporting to five health facilities in Ga West, Accra-Ghana, and determine the antimicrobial susceptibility profile of the isolates.…”