Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-producing Enterobacterales carriage: a matched case–control study in infectious diseases department

Objective Little is known on the effect of gut microbial and Extended-Spectrum β-Lactamase-Producing Enterobacterales (ESBL-E) carriage, particularly in the general population. The aim of this study was to identify microbiota signatures uniquely correlated with ESBL-E carriage. Methods We conducted a case-control study among individuals seeking care at the Sexual Health Clinic or Department of Infectious and Tropical Diseases at Saint-Antoine Hospital, Paris, France. Using coarsened exact matching, 176 participants with ESBL-carriage (i.e., cases) were matched 1:1 to those without ESBL-carriage (i.e., controls) based on sexual group, ESBL-E prevalence of countries traveled in <12 months, number of sexual partners in <6 months, geographic origin, and any antibiotic use in <6 months. 16S rRNA gene amplicon sequencing was used to generate differential abundances at the genus level and measures of α- and β-diversity. Results Participants were mostly men (83.2%, n=293/352) and had a median age of 33 years (IQR=27-44). Nine genera were found associated with ESBL-E carriage (Figure 2C): Proteus (p<0.0001), Carnobacterium (p<0.0001), Enterorhabdus (p=0.0079), Catonella (p=0.017), Dermacoccus (p=0.017), Escherichia/Shigella (p=0.021), Kocuria (p=0.023), Bacillus (p=0.040), and Filifactor (p=0.043); however, differences were no longer significant after Benjamini-Hochberg correction (q>0.05). There were no differences between those with versus without ESBL-E carriage in measures of α-diversity (Shannon Diversity Index, p=0.49; Simpson Diversity Index, p=0.54; and Chao1 Richness Estimator, p=0.16) or β-diversity (Bray-Curtis dissimilarity index, p=0.42). Conclusion In this large carefully controlled study, there is lacking evidence that gut microbial composition and diversity is any different between individuals with and without ESBL-E carriage.