Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage.

Catarina Ferreira, Saria Otani, Frank Møller Aarestrup, Célia M Manaia
{"title":"Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage.","authors":"Catarina Ferreira,&nbsp;Saria Otani,&nbsp;Frank Møller Aarestrup,&nbsp;Célia M Manaia","doi":"10.1093/femsmc/xtad008","DOIUrl":null,"url":null,"abstract":"<p><p>The widespread occurrence of clinically relevant antibiotic resistance within humans, animals, and environment motivates the development of sensitive and accurate detection and quantification methods. Metagenomics and quantitative PCR (qPCR) are amongst the most used approaches. In this study, we aimed to evaluate and compare the performance of these methods to screen antibiotic resistance genes in animal faecal, wastewater, and water samples. Water and wastewater samples were from hospital effluent, different treatment stages of two treatment plants, and of the receiving river at the discharge point. The animal samples were from pig and chicken faeces. Antibiotic resistance gene coverage, sensitivity, and usefulness of the quantitative information were analyzed and discussed. While both methods were able to distinguish the resistome profiles and detect gradient stepwise mixtures of pig and chicken faeces, qPCR presented higher sensitivity for the detection of a few antibiotic resistance genes in water/wastewater. In addition, the comparison of predicted and observed antibiotic resistance gene quantifications unveiled the higher accuracy of qPCR. Metagenomics analyses, while less sensitive, provided a markedly higher coverage of antibiotic resistance genes compared to qPCR. The complementarity of both methods and the importance of selecting the best method according to the study purpose are discussed.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad008"},"PeriodicalIF":0.0000,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/62/d3/xtad008.PMC10117749.pdf","citationCount":"3","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"FEMS microbes","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/femsmc/xtad008","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 3

Abstract

The widespread occurrence of clinically relevant antibiotic resistance within humans, animals, and environment motivates the development of sensitive and accurate detection and quantification methods. Metagenomics and quantitative PCR (qPCR) are amongst the most used approaches. In this study, we aimed to evaluate and compare the performance of these methods to screen antibiotic resistance genes in animal faecal, wastewater, and water samples. Water and wastewater samples were from hospital effluent, different treatment stages of two treatment plants, and of the receiving river at the discharge point. The animal samples were from pig and chicken faeces. Antibiotic resistance gene coverage, sensitivity, and usefulness of the quantitative information were analyzed and discussed. While both methods were able to distinguish the resistome profiles and detect gradient stepwise mixtures of pig and chicken faeces, qPCR presented higher sensitivity for the detection of a few antibiotic resistance genes in water/wastewater. In addition, the comparison of predicted and observed antibiotic resistance gene quantifications unveiled the higher accuracy of qPCR. Metagenomics analyses, while less sensitive, provided a markedly higher coverage of antibiotic resistance genes compared to qPCR. The complementarity of both methods and the importance of selecting the best method according to the study purpose are discussed.

Abstract Image

Abstract Image

Abstract Image

定量PCR与宏基因组学监测抗生素耐药基因:平衡高灵敏度和广泛覆盖。
临床相关抗生素耐药性在人类、动物和环境中的广泛发生,促使人们发展敏感、准确的检测和定量方法。宏基因组学和定量PCR (qPCR)是最常用的方法。在本研究中,我们旨在评估和比较这些方法在动物粪便、废水和水样中筛选抗生素耐药基因的性能。水和废水样本来自医院废水、两个处理厂的不同处理阶段以及排放点的接收河流。动物样本来自猪和鸡的粪便。对抗生素耐药基因的覆盖、敏感性和定量信息的有效性进行了分析和讨论。两种方法均能区分猪粪和鸡粪的梯度逐步混合物,但qPCR对水/废水中少数抗生素耐药基因的检测灵敏度更高。此外,通过对预测和观察到的抗生素耐药基因定量的比较,发现qPCR具有更高的准确性。宏基因组分析虽然灵敏度较低,但与qPCR相比,提供了明显更高的抗生素耐药基因覆盖率。讨论了两种方法的互补性以及根据研究目的选择最佳方法的重要性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
CiteScore
3.30
自引率
0.00%
发文量
0
审稿时长
15 weeks
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信