A degenerate PCR-based strategy as a means of identifying homologues of aminoglycoside and β-lactam resistance genes in the gut microbiota

Fouhy, Fiona; Ross, R. Paul; Fitzgerald, Gerald F.; Stanton, Catherine; Cotter, Paul D.

doi:10.1186/1471-2180-14-25

Cited by 18 publications

(13 citation statements)

References 61 publications

(59 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The dysbioses brought about by antibiotics bear the added disadvantage of enriching the microbiota in resistant organisms. The human gut microbiota has been established as a significant reservoir of antibiotic resistances ( Salyers et al, 2004 ; Seville et al, 2009 ; Sommer et al, 2009 ; Ghosh et al, 2013 ; Moore et al, 2013 ; Pehrsson et al, 2013 ; Card et al, 2014 ; Fouhy et al, 2014a , b ; Hu et al, 2014 ; Lu et al, 2014 ; von Wintersdorff et al, 2014 ; Clemente et al, 2015 ; Field and Hershberg, 2015 ). The scale of the problem can be gaged by the fact that an analysis of 252 fecal metagenomes from different countries identified resistance genes for 50 out of the 68 antibiotic classes and subclasses that were being screened for, with an average of 21 per sample ( Forslund et al, 2013 ).…”

Section: The Gut Microbiota As Reservoir Of Antibiotic Resistancesmentioning

confidence: 99%

Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances

2016

View full text Add to dashboard Cite

The human microbiome is overly exposed to antibiotics, due, not only to their medical use, but also to their utilization in farm animals and crops. Microbiome composition can be rapidly altered by exposure to antibiotics, with potential immediate effects on health, for instance through the selection of resistant opportunistic pathogens that can cause acute disease. Microbiome alterations induced by antibiotics can also indirectly affect health in the long-term. The mutualistic microbes in the human body interact with many physiological processes, and participate in the regulation of immune and metabolic homeostasis. Therefore, antibiotic exposure can alter many basic physiological equilibria, promoting long-term disease. In addition, excessive antibiotic use fosters bacterial resistance, and the overly exposed human microbiome has become a significant reservoir of resistance genes, contributing to the increasing difficulty in controlling bacterial infections. Here, the complex relationships between antibiotics and the human microbiome are reviewed, with focus on the intestinal microbiota, addressing (1) the effects of antibiotic use on the composition and function of the gut microbiota, (2) the impact of antibiotic-induced microbiota alterations on immunity, metabolism, and health, and (3) the role of the gut microbiota as a reservoir of antibiotic resistances.

show abstract

Section: The Gut Microbiota As Reservoir Of Antibiotic Resistancesmentioning

confidence: 99%

Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances

2016

View full text Add to dashboard Cite

show abstract

“…To ensure that the primers cover all the sequence variations, we incorporated degenerate bases during primer design, which have been a common practice in microbial studies [49], such as microbial population taxonomy [50], diversity of functional genes related to antibiotic or arsenite resistance, etc. [51, 52].…”

Section: Resultsmentioning

confidence: 99%

Application of qPCR assays based on haloacids transporter gene dehp2 for discrimination of Burkholderia and Paraburkholderia

Shi

et al. 2019

BMC Microbiol

View full text Add to dashboard Cite

BackgroundA major facilitator superfamily transporter Dehp2 was recently shown to be playing an important role in transport and biodegradation of haloacids in Paraburkholderia caribensis MBA4, and Dehp2 is phylogenetically conserved in Burkholderia sensu lato.ResultsWe designed both Burkholderia sensu stricto-specific and Paraburkholderia-specific qPCR assays based on dehp2 and 16S rRNA, and validated the qPCR assays in 12 bacterial strains. The qPCR assays could detect single species of Burkholderia sensu stricto or Paraburkholderia with high sensitivity and discriminate them in mixtures with high specificity over a wide dynamic range of relative concentrations. At relatively lower cost compared with sequencing-based approach, the qPCR assays will facilitate discrimination of Burkholderia sensu stricto and Paraburkholderia in a large number of samples.ConclusionsFor the first time, we report the utilization of a haloacids transporter gene for discriminative purpose in Burkholderia sensu lato. This enables not only quick decision on proper handling of putative pathogenic samples in Burkholderia sensu stricto group but also future exploitation of relevant species in Paraburkholderia group for haloacids biodegradation purposes.Electronic supplementary materialThe online version of this article (10.1186/s12866-019-1411-0) contains supplementary material, which is available to authorized users.

show abstract

“…As mentioned earlier, antibiotic resistance genes are vertically transferred from one generation to another and favor the survival of resistant microbes (Schjørring and Krogfelt, 2011; Penders et al, 2013; Verraes et al, 2013; Allen and Stanton, 2014; Fouhy et al, 2014; Hu et al, 2014; Card et al, 2015; van Schaik, 2015). However, it is the ability of microbes to conduct horizontal gene transfer that somehow complements the rampant human antibiotic applications in hastening the development of antibiotic-resistant strains.…”

Section: Antibiotic Resistancementioning

confidence: 99%

Addressing the Antibiotic Resistance Problem with Probiotics: Reducing the Risk of Its Double-Edged Sword Effect

2016

View full text Add to dashboard Cite

Antibiotic resistance is a global public health problem that requires our attention. Indiscriminate antibiotic use is a major contributor in the introduction of selective pressures in our natural environments that have significantly contributed in the rapid emergence of antibiotic-resistant microbial strains. The use of probiotics in lieu of antibiotic therapy to address certain health conditions in both animals and humans may alleviate these antibiotic-mediated selective pressures. Probiotic use is defined as the actual application of live beneficial microbes to obtain a desired outcome by preventing diseased state or improving general health. Multiple studies have confirmed the beneficial effects of probiotic use in the health of both livestock and humans. As such, probiotics consumption is gaining popularity worldwide. However, concerns have been raised in the use of some probiotics strains that carry antibiotic resistance genes themselves, as they have the potential to pass the antibiotic resistance genes to pathogenic bacteria through horizontal gene transfer. Therefore, with the current public health concern on antibiotic resistance globally, in this review, we underscore the need to screen probiotic strains that are used in both livestock and human applications to assure their safety and mitigate their potential in significantly contributing to the spread of antibiotic resistance genes in our natural environments.

show abstract

A degenerate PCR-based strategy as a means of identifying homologues of aminoglycoside and β-lactam resistance genes in the gut microbiota

Cited by 18 publications

References 61 publications

Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances

Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances

Application of qPCR assays based on haloacids transporter gene dehp2 for discrimination of Burkholderia and Paraburkholderia

Addressing the Antibiotic Resistance Problem with Probiotics: Reducing the Risk of Its Double-Edged Sword Effect

Contact Info

Product

Resources

About