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