Mobilome and Resistome Reconstruction from Genomes Belonging to Members of the Bifidobacterium Genus.

Walter Mancino,Gabriele Andrea Lugli,Marco Ventura,Douwe Van Sinderen,Francesca Turroni

doi:10.3390/microorganisms7120638

Walter Mancino, Gabriele Andrea Lugli + Show 3 more

Open Access

https://doi.org/10.3390/microorganisms7120638

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Abstract

Specific members of the genus Bifidobacterium are among the first colonizers of the human/animal gut, where they act as important intestinal commensals associated with host health. As part of the gut microbiota, bifidobacteria may be exposed to antibiotics, used in particular for intrapartum prophylaxis, especially to prevent Streptococcus infections, or in the very early stages of life after the birth. In the current study, we reconstructed the in silico resistome of the Bifidobacterium genus, analyzing a database composed of 625 bifidobacterial genomes, including partial assembled strains with less than 100 genomic sequences. Furthermore, we screened bifidobacterial genomes for mobile genetic elements, such as transposases and prophage-like elements, in order to investigate the correlation between the bifido-mobilome and the bifido-resistome, also identifying genetic insertion hotspots that appear to be prone to horizontal gene transfer (HGT) events. These insertion hotspots were shown to be widely distributed among analyzed bifidobacterial genomes, and suggest the acquisition of antibiotic resistance genes through HGT events. These data were further corroborated by growth experiments directed to evaluate bacitracin A resistance in Bifidobacterium spp., a property that was predicted by in silico analyses to be part of the HGT-acquired resistome.

Highlights

Bifidobacteria are gram-positive, anaerobic, non-motile, and non-spore-forming bacteria with a high G + C genomic content [1]
In order to investigate the genetic antibiotic resistance (AR) arsenal carried by members of the Bifidobacterium genus, we investigated the resistome of 625 bifidobacterial genomes
The AR genetic arsenal of the Bifidobacterium genus seems to be less complex compared to the resistome of other gram-positive bacteria, such as members of the Lactobacillus genus, or other species included in food supplements and used as probiotics, such as members of the Bacillus genus [54,56,65,66,85,86]

Summary

Introduction

Bifidobacteria are gram-positive, anaerobic, non-motile, and non-spore-forming bacteria with a high G + C genomic content [1]. They represent one of the dominant microbial groups inhabiting the gastrointestinal tract (GIT) of humans and animals, including mammals, birds, and social insects [2,3,4]. The extensive use of antibiotics can promote the development of antibiotic resistance in members of the microbiota and in the selection of antibiotic-resistant microorganisms [11] In this context, the collective genetic arsenal responsible for conferring antibiotic resistance (AR) through inactivation and/or removal of antibiotics is commonly referred to as the resistome [14,15,16]. The presence of AR genes in mobile genetic elements (MGEs) or near transposable elements, in pathogenic and non-pathogenic microorganisms, may be the cause for the relatively frequent transfer of such elements to human/animal pathogens or to other non-resident microorganisms of the gastrointestinal tract [19,20]

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