Composition of the intestinal microbiota in extended-spectrum β-lactamase-producing Enterobacteriaceae carriers and non-carriers in Thailand

Abstract

There is increasing recognition that the intestinal microbiota govern human well-being and prevent diseases. Intestinal colonization by antibiotic-resistant pathogens, however, can lead to the spread of resistance as well as serious infections. Extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E) represent particularly dangerous pathogens, which are known to asymptomatically colonized the intestinal tract in the community. Here, we performed a 16s rRNA metagenomics sequence analysis to analyze differences in the microbiota composition between ESBL-E carriers and non-carriers in Thailand, where ESBL-E carriage rates are notoriously high. The most notable difference we detected was that the phylum Bacteroidetes, and in particular, the species Bacteroides uniformis, were significantly more abundant in ESBL-E non-carriers than carriers. The Shannon diversity index in non-carriers (5.10 ± 0.69) was also lower than that in ESBL-E carriers (5.39 ± 0.48) without statistical significance (p = 0.13). The overall beta diversity difference of the intestinal microbiota of ESBL-E carriers as compared to non-carriers was statistically significant (Adonis on weighted unifrac: R2=0.14, P =0.005). Furthermore, ESBL-E carriage was significantly lower in farmers than other occupations. Our findings suggest that a dynamic interaction exists between microbiota diversity and ESBL-E carriage, which is possibly driven by dietary composition and may be exploited using probiotic approaches to control the spread of ESBL-E.

Colonization With Multidrug-Resistant Organisms Among Healthy Adults in the Community Setting: Prevalence, Risk Factors, and Composition of Gut Microbiome

“…In this study, 27.4% of healthy adults carried ESBL-producing E. coli or K. pneumoniae . The results are concordant with the high prevalence of ESBL-producing Enterobacteriaceae colonization reported among healthy individuals in Southeast Asia ( Karanika et al, 2016 ; Piewngam et al, 2019 ). However, a study conducted in Southern Taiwan reported a low (1.9%) prevalence of ESBL-producing E. coli fecal carriage among healthy adults ( Wu et al, 2019 ).…”

“…How commensal gut microbiota react with colonization by specific pathogens remains unclear. To date, only two studies in rural areas have investigated the composition of gut microbiota in participants with or without colonization by ESBL-producing Enterobacteriaceae (Gosalbes et al, 2015;Piewngam et al, 2019), and both studies included fewer cases than did our study. We showed that the gut microbiota of 3GC-R Enterobacteriaceae carriers was characterized by an increased FIGURE 3 | (A) Box plot of the alpha-diversity index measured based on the Shannon diversity index for third-generation cephalosporin-resistant (3GC-R) E. coli or K. pneumoniae carriers (blue) and non-carriers (red).…”

Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases

“…The enrichment in some species, such as Barnesiella have been reported to provide a colonization resistance against vancomycin resistant Enterococcus but the interactions within bacterial communities conferring resistance to colonization are not yet fully understood [10,11]. Two 16S rRNA based studies identified specific taxonomic profiles associated with resistance to ESBL-E colonization in humans and a recent experimental work highlighted the role of short chain fatty acids (SCFA) mediated inhibition of ESBL-E [12][13][14]. To date, such observations have not been confirmed in humans.…”

Gut microbiome signatures of nursing home residents carrying Enterobacteria Producing Extended-spectrum β-lactamases

“…The enrichment in some species, such as Barnesiella have been reported to provide a colonization resistance against vancomycin resistant Enterococcus but the interactions within bacterial communities conferring resistance to colonization are not yet fully understood (10,11). Two 16S rRNA based studies identified specific taxonomic profiles associated with resistance to ESBL-E colonization in humans and a recent experimental work highlighted the role of short chain fatty acids (SCFA) mediated inhibition of ESBL-E (12)(13)(14) To date, bacterial species and functional pathways involved in the colonization resistance in the human gut microbiome have not been explored using metagenomics. Here, we assessed architectural, taxonomical and functional characteristics of the gut microbiome in ESBL-E carriers and non-carriers from nursing home.…”