Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review

Waseem, Hassan; Jameel, Sana; Ali, Jafar; Rehman, Hamza Saleem ur; Tauseef, Isfahan; Farooq, Umar; Jamal, A. Rahman A.; Ali, Muhammad Ishtiaq

doi:10.3390/molecules24010163

Cited by 99 publications

(54 citation statements)

References 96 publications

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“…Sequencing-based approaches (i.e., PCR-based assays, microarray-based assays, and in-solution targeted capture) and quantitative PCR (qPCR) methods offer selective and sensitive means to identify a larger contingent of antibiotic resistance genes than other methods but can be (or are designed to be) heavily biased or selective. While PCR is highly sensitive, many panels for AMR genes target only a range of between 200 and 400 genes (42). As we have shown here, probe-based hybridization methods enable the detection of over 2,000 ARGs in a single assay.…”

Section: Discussionmentioning

confidence: 84%

Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes

Guitor

Raphenya

Klunk

et al. 2019

Antimicrob Agents Chemother

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Identification of the nucleotide sequences encoding antibiotic resistance elements and determination of their association with antibiotic resistance are critical to improve surveillance and monitor trends in antibiotic resistance. Current methods to study antibiotic resistance in various environments rely on extensive deep sequencing or laborious culturing of fastidious organisms, both of which are heavily time-consuming operations. An accurate and sensitive method to identify both rare and common resistance elements in complex metagenomic samples is needed. Referencing the sequences in the Comprehensive Antibiotic Resistance Database, we designed a set of 37,826 probes to specifically target over 2,000 nucleotide sequences associated with antibiotic resistance in clinically relevant bacteria. Testing of this probe set on DNA libraries generated from multidrug-resistant bacteria to selectively capture resistance genes reproducibly produced higher numbers of reads on target at a greater length of coverage than shotgun sequencing. We also identified additional resistance gene sequences from human gut microbiome samples that sequencing alone was not able to detect. Our method to capture the resistome enables a sensitive means of gene detection in diverse environments where genes encoding antibiotic resistance represent less than 0.1% of the metagenome.

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Section: Discussionmentioning

confidence: 84%

Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes

Guitor

Raphenya

Klunk

et al. 2019

Antimicrob Agents Chemother

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“…Other enzymes along with nitrate reductase have been studied for further possibilities of heavy metal remediation. Microbe metal interaction and the importance of their enzymes still required further investigation [140]. The studies of these microbial interactions at the genetic level may provide new genetic tools for bioremediation.…”

Section: Future Scenariosmentioning

confidence: 99%

<strong>Role of Nanoscience in Agriculture</strong>

Kumar¹

2020

Preprint

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Nanoparticles are widely used in the agricultural sector because of their distinctive properties. Studies have shown the influence of nanoparticles on plant growth and production. Nanoparticles act as effective carriers in the delivery of agrochemicals to plants. They provide site targeted delivery of nutrients and thus, prevents wastage of nutrients applied for plant growth and productivity. Bioremediation of pollutants is an emerging technology that provides bio-nano materials for the protection of agriculture from pollution. The aim of this review is to present and focus on the latest techniques used for the reduction of environmental pollution and improved agricultural production. This review speculates about the biosynthesis of nanomaterials from different sources like plants, fungi, and bacteria along with chemical and organic synthesis from carbon, silver, and gold. The role of nanoscience in detecting plant diseases and the removal of heavy metals. Application of Nanoscience in storing, production, processing, and transport of agricultural materials. It is also emphasized that Nanoscience may transform agriculture through the innovation of new techniques like Precision farming, improvement of plants to engross nutrients, targeted use of inputs, detection and control of diseases and withstand environmental pressures. Further, efforts have been made in describing that nanoparticles may act as a better substitute for agricultural plant growth and nutrition improvement by lowering the content of pollutants and pre-detection of diseases in plants. The biosynthetic route of nanomaterial synthesis could emerge as a better and safer option for environmental pollution reduction. Thus, nanoscience may increase agricultural production to feed a huge population in near future.

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“…HT-qPCR has the advantage of being more sensitive and requiring less DNA input than metagenomics, although ARG of interest need to be known prior to analyses for primer design. In contrast, metagenomics have the advantage of analyzing unknown sequences that may be related to novel ARG-associated genes or mutations of known genes (Waseem et al, 2019). Databases such as CARD are good resources to detect ARG and potentially novel ARG from metagenomic surveys (Jia et al, 2017).…”

Section: Framework To Fill Knowledge Gaps Surrounding Unconventional mentioning

confidence: 99%

Unconventional Oil and Gas Energy Systems: An Unidentified Hotspot of Antimicrobial Resistance?

et al. 2019

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Biocides used in unconventional oil and gas (UOG) practices, such as hydraulic fracturing, control microbial growth. Unwanted microbial growth can cause gas souring, pipeline clogging, and microbial-induced corrosion of equipment and transportation pipes. However, optimizing biocide use has not been a priority. Moreover, biocide efficacy has been questioned because microbial surveys show an active microbial community in hydraulic fracturing produced and flowback water. Hydraulic fracturing produced and flowback water increases risks to surface aquifers and rivers/lakes near the UOG operations compared with conventional oil and gas operations. While some biocides and biocide degradation products have been highlighted as chemicals of concern because of their toxicity to humans and the environment, the selective antimicrobial pressure they cause has not been considered seriously. This perspective article aims to promote research to determine if antimicrobial pressure in these systems is cause for concern. UOG practices could potentially create antimicrobial resistance hotspots under-appreciated in the literature, practice, and regulation arena, hotspots that should not be ignored. The article is distinctive in discussing antimicrobial resistance risks associated with UOG biocides from a biological risk, not a chemical toxicology, perspective. We outline potential risks and highlight important knowledge gaps that need to be addressed to properly incorporate antimicrobial resistance emergence and selection into UOG environmental and health risk assessments.

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Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review

Cited by 99 publications

References 96 publications

Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes

Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes

<strong>Role of Nanoscience in Agriculture</strong>

Unconventional Oil and Gas Energy Systems: An Unidentified Hotspot of Antimicrobial Resistance?

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