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

Hassan Waseem,Muhammad Ishtiaq Ali,Asif Jamal,Hamza Saleem Ur Rehman,Sana Jameel,Jafar Ali,Isfahan Tauseef,Uzma Farooq

doi:10.3390/molecules24010163

Abstract

Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGenTM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.

Highlights

Antimicrobial resistance (AMR) is a major public health safety issue and is not a new phenomenon in health and agricultural settings [1,2]
For analyzing the role of high throughput qPCR (HT-qPCR) in the field of antimicrobial resistance, we have used the Web of Knowledge database to collect publications
Our study has provided an effective assessment of the contributions made by HT-qPCR technology in the field of antimicrobial resistance

Summary

Introduction

Antimicrobial resistance (AMR) is a major public health safety issue and is not a new phenomenon in health and agricultural settings [1,2]. AMR has gained more attention due to ever increasing discharge of pollutants (including antibiotics) into environmental matrices [3,4,5]. Detection of bacterial resistance by conventional methods is time consuming and laborious. Molecular techniques can detect antimicrobial resistance genes (ARGs) in a rapid and sensitive manner. ARGs encode the ability in bacteria to resist and grow in the presence of antibiotics. ARGs presence inside bacteria pose a serious threat but their existence in environmental matrices is of equal concern because

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