Abstract
Hospitalized patients are at increased risk for acquiring healthcare-associated infections (HAIs) and inadequate nutrition. The human intestinal microbiota plays vital functions in nutrient supply and protection from pathogens, yet characterization of the microbiota of hospitalized patients is lacking. We used 16S rRNA amplicon sequencing to characterize the global pattern of microbial composition of fecal samples from 196 hospitalized patients with suspected infectious diarrhea in comparison to healthy, non-hospitalized subjects (n = 881), and to traditional culture results. We show that hospitalized patients have a significant rise in α-diversity (richness within sample) from birth to <4 years of age, which continues up to the second decade of life. Additionally, we noted a profoundly significant increase in taxa from Proteobacteria phylum in comparison to healthy subjects. Finally, although more than 60% of hospitalized samples had a greater than 10% abundance of Proteobacteria, there were only 19/196 (10%) positive cultures for Campylobacter, Salmonella, or Shigella entero-pathogens in traditional culturing methods. As hospitalized patients have increased risk for HAIs and inadequate nutrition, our data support the consideration of nutritional and/or microbial modification in this population.
Highlights
Hospitalized patients are at increased risk for acquiring healthcare-associated infections (HAIs) and inadequate nutrition
Our study focused on characterizing the gut microbiome composition and diversity of hospitalized patients suspected to have infectious diarrhea across all ages in comparison to the healthy population in Israel
Proteobacteria taxa that were highly enriched in hospitalized patients included Actinetobater[25], Bilophila[26], Citrobacter, Escherichia, and Sutterella compared to the healthy population
Summary
Hospitalized patients are at increased risk for acquiring healthcare-associated infections (HAIs) and inadequate nutrition. We used 16S rRNA amplicon sequencing to characterize the global pattern of microbial composition of fecal samples from 196 hospitalized patients with suspected infectious diarrhea in comparison to healthy, non-hospitalized subjects (n = 881), and to traditional culture results. Number of participants (n) Mean(SD) Age(years) Male gender (%) Culture result (n) Negative Campylobacter Campylobacter & Salmonella Salmonella Shigella to capture the overall microbial composition of the culturable and non-culturable taxa These techniques have already had a substantial impact on our understanding of the epidemiology of many diarrhea-associated bacteria including the discovery that horizontal gene exchange facilitated the emergence of a novel, highly virulent strain of Shiga toxin-producing Escherichia coli (STEC) during the European outbreak of hemolytic-uremic syndrome in 201113. In support of this concept is a recent study that showed that a mixture containing Lactobacillus GG and micronutrients reduced the incidence of HAI15
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