Microbiota that affect risk for shigellosis in children in low-income countries

Abstract

Pathogens in the gastrointestinal tract exist within a vast population of microbes. We examined associations between pathogens and composition of gut microbiota as they relate to Shigella spp./enteroinvasive Escherichia coli infection. We analyzed 3,035 stool specimens (1,735 nondiarrheal and 1,300 moderate-to-severe diarrheal) from the Global Enteric Multicenter Study for 9 enteropathogens. Diarrheal specimens had a higher number of enteropathogens (diarrheal mean 1.4, nondiarrheal mean 0.95; p<0.0001). Rotavirus showed a negative association with Shigella spp. in cases of diarrhea (odds ratio 0.31, 95% CI 0.17-0.55) and had a large combined effect on moderate-to-severe diarrhea (odds ratio 29, 95% CI 3.8-220). In 4 Lactobacillus taxa identified by 16S rRNA gene sequencing, the association between pathogen and disease was decreased, which is consistent with the possibility that Lactobacillus spp. are protective against Shigella spp.-induced diarrhea. Bacterial diversity of gut microbiota was associated with diarrhea status, not high levels of the Shigella spp. ipaH gene.

Figure 1

Association of co-occurring pathogens with high levels of ipaH gene of Shigella spp. in stool specimens of children with diarrhea (cases) and children without diarrhea (controls) in low-income countries. Dark circles indicate means, and error bars indicate 95% CIs. tEPEC, typical enteropathogenic Escherichia coli; EAEC, enteroaggregative E. coli; ETEC, enterotoxigenic E. coli.

Figure 2

Departure from additivity between level of ipaH gene and presence of Lactobacillus taxon TSK G32-2 on odds of moderate-to-severe diarrhea in children in low-income countries. The reference group is TSK G32-2 negative, low level of ipaH. The observed combined joint effect of a high level of the ipaH gene and TSK G32-2 was lower than the expected additive effect. Gray bars indicate effect of TSK G32-2; black bars indicate effect of high levels of ipaH; and white bar indicates observed joint effect of TSK G32-2 and high levels of ipaH. Neg, negative; Pos, positive; Exp, expected; Obs, observed.

Figure 3

Overall 16S rRNA gene–based bacterial community profiles (proportional abundance) of diarrheal samples with high levels of ipaH gene (n = 277), diarrheal samples with low levels of ipaH gene (n = 1,023), nondiarrheal samples with high levels of ipaH gene (n = 127), and nondiarrheal samples with low levels of ipaH gene (n = 1,608) from children in low-income countries. Other indicates sequences that were not identified as 1 of the 9 most abundant taxa or did not have good (>100 bp exact match, >97% identity) matches with isolate sequences from the Ribosomal Database Project (19).

Figure 4

Shannon diversity index for diarrheal and nondiarrheal samples with high (A) and low (B) levels of Shigella spp. ipaH gene stratified by age group for children in low-income countries. Box and whisker plot indicates distribution of diversity index for each group. The upper whisker extends from the 75th percentile to the highest value that is ≤1.5× the interquartile range (IQR) of the hinge (upper end) or the distance between the first and third quartiles. The lower whisker extends from the hinge (lower end) to the lowest values 1.5× the IQR of the hinge. Diamonds indicate means and horizontal lines indicate medians. Points outside the ends of the whiskers are outliers beyond 1.5× the IQR of the hinge.