Abstract
Background: Diarrheagenic Escherichia coli (DEC) strains are a major cause of diarrhea in children under 5 years of age worldwide. DEC pathogenicity relies on the interaction of bacteria with environmental factors, including the host's resident gut microbiota. Previous reports have shown changes in the gut microbiota's composition during episodes of diarrhea, which may increase the pathogenicity of DEC strains. More intense and detailed identification of microbiota strains specifically associated with DEC infections and disease is needed to pinpoint their role in DEC pathogenicity.Aim: To identify resident indicative bacterial taxa in DEC-positive diarrhea stool samples of Chilean children.Methods: We analyzed 63 diarrheal stool samples from children 1–5 years of age by FilmArray® GI in order to identify a potential pathogen and to group diarrhea episodes into those caused by DEC as sole pathogen (DEC group, 32 samples) and those caused by an enteric virus as sole pathogen (viral group, 31 samples). In addition, 30 stool samples from healthy children, negative for enteric pathogens, were evaluated (healthy group). The 16S rRNA gene was amplified and sequenced using 454 pyrosequencing. Sequences were clustered into operational taxonomic units (OTUs) at 99% identity and their representatives were used to assign them to operational phylogenetic units (OPUs) using a phylogenetic inference approach.Results: Taxa assignment using the OPU approach resulted in a lower number of units but with higher accuracy compared to the OTU approach. Data analysis indicated an increase in sequences belonging to the phylum Proteobacteria in the DEC group compared to the viral and healthy groups. Samples displayed a statistically different community structure by sample grouping by redundancy analysis and ANOVA. Escherichia albertii (p = 0.001), Citrobacter werkmanii (p = 0.001), Yersinia enterocolitica, subsp. paleartica (p = 0.048), and Haemophilus sputorum (p = 0.028) were indicative species for the DEC group as compared to the viral and healthy groups.Conclusion: Gut microbiota in Chilean children with DEC-positive diarrhea differed from microbiota associated with enteric virus and healthy children. Indicative species found in this study may prove relevant in advancing our understanding of the relationship between resident gut microbiota and DEC leading to the occurrence of disease.
Highlights
According to the World Health Organization (WHO), there are nearly 1.7 billion cases of diarrheal disease every year, and 760,000 deaths, representing the second cause of death in children under 5 years of age (World Health Organization, 2014)
Several groups have focused on the role components of the gut microbiota and its association with diarrheal disease caused by enteric pathogens, including Diarrheagenic Escherichia coli (DEC) strains (Nelson et al, 2012; Curtis et al, 2014; Iversen et al, 2015; Lindsay et al, 2015)
We identified eight indicative Operational Phylogenetic Units (OPUs) for the DEC group compared to the viral and healthy groups, all of which belonged to phylum Proteobacteria
Summary
According to the World Health Organization (WHO), there are nearly 1.7 billion cases of diarrheal disease every year, and 760,000 deaths, representing the second cause of death in children under 5 years of age (World Health Organization, 2014). The expression of specific virulence genes and the ability to efficiently utilize nutrient in the intestinal milieu are key events for the successfully colonization of DEC to intestinal epithelia This phenomenon is not completely understood for DEC, as most studies have focused on molecular mechanism occurring inside the bacteria, with only a few evaluating environmental factors, such as, gut microbiota (Pacheco and Sperandio, 2015; Singh et al, 2015). Several groups have focused on the role components of the gut microbiota and its association with diarrheal disease caused by enteric pathogens, including DEC strains (Nelson et al, 2012; Curtis et al, 2014; Iversen et al, 2015; Lindsay et al, 2015). More intense and detailed identification of microbiota strains associated with DEC infections and disease is needed to pinpoint their role in DEC pathogenicity
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