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

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

doi:10.3390/molecules24010163

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

Molecules. 2019 Jan 3;24(1):163. doi: 10.3390/molecules24010163.

Authors

Hassan Waseem^{1

2

3}, Sana Jameel⁴, Jafar Ali⁵, Hamza Saleem Ur Rehman⁶, Isfahan Tauseef⁷, Uzma Farooq⁸, Asif Jamal⁹, Muhammad Ishtiaq Ali¹⁰

Affiliations

¹ Department of Environmental Engineering, Michigan State University, East Lansing, MI 48823, USA. waseemh1@msu.edu.
² Department of Biotechnology, University of Sialkot, Punjab 51310, Pakistan. waseemh1@msu.edu.
³ Environmental Microbiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan. waseemh1@msu.edu.
⁴ Department of Biotechnology, University of Sialkot, Punjab 51310, Pakistan. jameels@msu.edu.
⁵ key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China. Jafarali_st@rcees.ac.cn.
⁶ Department of Biotechnology, University of Sialkot, Punjab 51310, Pakistan. h.s.rehman15@gmail.com.
⁷ Department of Microbiology, University of Hazara, Mansehra 21300, Pakistan. isfahantauseef@yahoo.com.
⁸ Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan. uzma.ishi@gmail.com.
⁹ Environmental Microbiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan. asifjamall@yahoo.com.
¹⁰ Environmental Microbiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan. ishimrl@qau.edu.pk.

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. WaferGen^TM 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.

Keywords: AMR; ARGs; MGEs; gut microbiome; high throughput qPCR.

Publication types

Meta-Analysis
Review

MeSH terms

Anti-Infective Agents / pharmacology*
Computational Biology / methods
Data Analysis
Drug Resistance, Microbial*
Environmental Microbiology*
Gastrointestinal Microbiome
Genes, Bacterial
High-Throughput Screening Assays*
Humans
Metagenome
Metagenomics / methods
Quality Control
Real-Time Polymerase Chain Reaction*

Substances

Anti-Infective Agents