CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment

Author:

Hackenberger Dirk,Imtiaz Hamna,Raphenya Amogelang R.,Alcock Brian P.,Poinar Hendrik N.,Wright Gerard D.,McArthur Andrew G.

Abstract

AbstractBetter interrogation of antimicrobial resistance requires new approaches to detect the associated genes in metagenomic samples. Targeted enrichment is an ideal method for their sequencing and characterization. However, no open-source, up-to-date hybridization probe set targeting antimicrobial resistance genes exists. Here we describe CARPDM, a probe design software package made to run alongside all future Comprehensive Antibiotic Resistance Database releases. To test its efficacy, we have created and validated two separate probe sets: AllCARD, which enriches all genes encoded in the Comprehensive Antibiotic Resistance Database’s protein homolog models (n = 4,661), and clinicalCARD, which focuses on a clinically relevant subset of resistance genes (n = 323). We demonstrate that allCARD increases the number of reads mapping to resistance genes by up to 594-fold. ClinicalCARD performs similarly when clinically relevant genes are present, increasing the number of resistance-gene mapping reads by up to 598-fold. In parallel with this development, we have established a protocol to synthesize any probe set in-house, saving up to 350 dollars per reaction. Together, these probe sets, their associated design program CARPDM, and the protocol for in-house synthesis will democratize metagenomic resistome analyses, allowing researchers access to a cost-effective and efficient means to explore the antibiotic resistome.

Publisher

Cold Spring Harbor Laboratory

Reference60 articles.

1. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis;The Lancet,2022

2. O’Neill, J. (2014) Antimicrobial Resistance: Tackling a crisis for the health and wealth of nations. The Review on Antimicrobial Resistance. London.

3. Waglechner, N. , Culp, E.J. and Wright, G.D . (2021) Ancient Antibiotics, Ancient Resistance. EcoSal Plus, 9.

4. Phylogenetic reconciliation reveals the natural history of glycopeptide antibiotic biosynthesis and resistance;Nature Microbiology 2019 4:11,2019

5. Evolution of the serine β-lactamases: past, present and future

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3