Molecular Survey of Viral and Bacterial Causes of Childhood Diarrhea in Khartoum State, Sudan

Abstract

Diarrheal disease is a major public health problem for children in developing countries. Knowledge of etiology that causes diarrheal illness is essential to implement public health measures to prevent and control this disease. Published studies regarding the situation of childhood diarrhea in Sudan is scanty. This study aims to investigate viral and bacterial etiology and related clinical and epidemiological factors in children with acute diarrhea in Khartoum State, Sudan. A total of 437 fecal samples were collected from hospitalized children <5 years old with acute diarrhea, viral and bacterial pathogens were investigated by using two-tube multiplex RT-PCR. The genotypes of adenovirus and bocavirus were determined by sequencing. Viral diarrhea was identified in 79 cases (62 single and 17 co-infections) (18%), and bacterial diarrhea in 49 cases (37 single and 12 co-infections) (11.2%). Mixed infections in both groups totaled 19 samples (4.3%) with more than one pathogen, they were viral co-infections (n = 7, 36.8%) bacterial co-infections (n = 2, 10.5%) and viral bacterial co-infection (n = 10, 52.6%). Rotavirus (10.2%) was predominantly detected, followed by norovirus G2 (4.0%), adenovirus (1.6%), bocavirus (1%), and norovirus G1 (0.9%). Infection with astrovirus was not detected in this study. The Shigella –Enteroinvasive E.coli (EIEC) (8.9%) was the predominantly found bacterial pathogen, followed by Vibrio parahaemolyticus (0.9%), enterohaemorrhagic E.coli (EHEC) –Enteropathogenic E. coli (EPEC) (0.6%) and Salmonella enteritidis (0.6%). V. cholerae, Yersinia enterocolitica and Campylobacter jejuni were not detected in this study. The phylogenetic tree identified adenovirus belonged to genotype 41 and bocavirus belonged to two different clades within human bocavirus 1. Our findings represent the first report that adenovirus 41 is a cause of diarrhea in Sudan and that human bocavirus 1 is the principal bocavirus strain circulating in Sudan. In conclusion, this is the first comprehensive report to elaborate the pathogen spectrum associated with childhood diarrhea in Khartoum State, Sudan. The results obtained in the present study highlighted the current epidemic situation, the diverse pathogens related to childhood diarrhea, and the importance and the urgency of taking appropriate intervention measures in Khartoum State, Sudan.

vAetiology of Diarrhoea in Children Under Five in Zambia Detected Using Luminex xTAG Gastrointestinal Pathogen Panel

“…The high prevalence of single Adenovirus infection, only next to rotavirus, in our study tallies with the GEMS re-analysis study where, when assessed with PCR-based methods, Adenovirus incidence was five times more than previously reported using microbiological methods [17,22], shifting this enteropathogen to become among the top six diarrhoea attributable pathogens [23,24]. However, our study did not find attributable cases of moderate-to-severe diarrhoea due to Adenovirus.…”

A Pilot Study: Changes of Intestinal Microbiota of Patients With Non-small Cell Lung Cancer in Response to Osimertinib Therapy

“…Secondly, we explored the differences of alpha and beta diversity of intestinal microbiota from NSCLC patients in response to osimertinib therapy. In previous study, Zhuang et al (2019) found that there was no significant reduction in alpha diversity of intestinal microbiota in lung cancer patients compared to healthy individuals. In line with it, our results indicated that there were almost no significant differences in richness, phylogenetic diversity, and Shannon diversity between NSCLC patients and healthy individuals (P > 0.05, Supplementary Table S4).…”

“…Moreover, no significant difference was observed in the richness and Shannon diversity of intestinal microbiota in NSCLC patients between pre-therapy (T1) and post-therapy (T2, T3, T4, T5, T6, T7, T8, T9, T10) ( P > 0.05, Supplementary Table S4 ), indicating that osimertinib therapy did not play great roles in alpha diversity of intestinal microbiota. However, we found that there was significantly different in beta diversity between pre-therapy and post-therapy in NSCLC patients based on the dissimilar test ( P < 0.05, Supplementary Table S5 ), suggesting that osimertinib therapy has made the intestinal microbial community composition changed from the whole ( Zhuang et al, 2019 ). At the same time, there was a little separation among NSCLC samples with different treatment cycles, and between healthy individuals and NSCLC patients ( Figure 4 ).…”

“…Significant differences are found in bacterial community composition between healthy and diseased lungs (Garzoni et al, 2013;Dickson et al, 2014). An increasing number of studies have revealed the close relationship between the intestinal microbial composition and lung diseases, known as the gut-lung axis (Budden et al, 2017;Zhuang et al, 2019). For example, an increase in the abundance of Bacteroides fragilis and total anaerobes, as well as a decrease in the relative abundance of Faecalibacterium spp., Veillonella spp., Rothia spp., and Lachnospira spp.…”

“…in early life were associated with increased risk of asthma ( Vael et al, 2008 ; Arrieta et al, 2015 ). Recently, Strickertsson et al (2013) , Amarnani and Rapose (2017) , and Zhuang et al (2019) found that patients with lung cancer in fecal microbiome showed elevated levels of Enterococcus, which could lead to increased DNA mismatch rate that indirectly promote rectal cancer. However, there were no significant differences in intestinal microbiota between NSCLC patients and healthy individuals and between pre-therapy and post-therapy at the phylum, family, and genus level in our pilot study ( P > 0.05, Supplementary Tables S1–S3 ).…”