In Silico Assigned Resistance Genes Confer Bifidobacterium with Partial Resistance to Aminoglycosides but Not to Β-Lactams

Fiona Fouhy,R Paul Ross,Mary O’Connell Motherway,Gerald F Fitzgerald,Catherine Stanton,Douwe Van Sinderen,Paul D Cotter

doi:10.1371/journal.pone.0082653

Abstract

Bifidobacteria have received significant attention due to their contribution to human gut health and the use of specific strains as probiotics. It is thus not surprising that there has also been significant interest with respect to their antibiotic resistance profile. Numerous culture-based studies have demonstrated that bifidobacteria are resistant to the majority of aminoglycosides, but are sensitive to β-lactams. However, limited research exists with respect to the genetic basis for the resistance of bifidobacteria to aminoglycosides. Here we performed an in-depth in silico analysis of putative Bifidobacterium-encoded aminoglycoside resistance proteins and β-lactamases and assess the contribution of these proteins to antibiotic resistance. The in silico-based screen detected putative aminoglycoside and β-lactam resistance proteins across the Bifidobacterium genus. Laboratory-based investigations of a number of representative bifidobacteria strains confirmed that despite containing putative β-lactamases, these strains were sensitive to β-lactams. In contrast, all strains were resistant to the aminoglycosides tested. To assess the contribution of genes encoding putative aminoglycoside resistance proteins in Bifidobacterium sp. two genes, namely Bbr_0651 and Bbr_1586, were targeted for insertional inactivation in B. breve UCC2003. As compared to the wild-type, the UCC2003 insertion mutant strains exhibited decreased resistance to gentamycin, kanamycin and streptomycin. This study highlights the associated risks of relying on the in silico assignment of gene function. Although several putative β-lactam resistance proteins are located in bifidobacteria, their presence does not coincide with resistance to these antibiotics. In contrast however, this approach has resulted in the identification of two loci that contribute to the aminoglycoside resistance of B. breve UCC2003 and, potentially, many other bifidobacteria.

Highlights

Following the discovery of penicillin by Alexander Fleming [1], exponential antibiotic discovery and development occurred which revolutionized medicine
It has more recently been postulated that this complex microbial population is a sizeable reservoir for antibiotic resistance genes [53,54], and that microbes containing such genes can become dominant in the human gastrointestinal tract following antibiotic exposure [36,55,56]
There is a risk that such genes could be transferred to other microbes, including those passing through the gastrointestinal tract, and could contribute to the dissemination of antibiotic resistance genes [53]

Summary

Introduction

Following the discovery of penicillin by Alexander Fleming [1], exponential antibiotic discovery and development occurred which revolutionized medicine. During this same period, target bacteria developed sophisticated mechanisms of resistance against many of the most commonly prescribed antibiotics [2]. Aminoglycosides are a family of broad spectrum antibiotics that were first reported in 1944 [5], whose bactericidal activity results from their binding to the 30S subunit of the prokaryotic ribosome and the subsequent impairment of protein synthesis [5,6]. Aminoglycoside resistance genes have been classified based on the enzymatic modification mechanism used by the resultant protein and the chemical position at which the aminoglycoside is modified [8]

Methods

Results

Conclusion