Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes

Microbiome

卷:10

Research

Mattia Prosperi¹  Christina Boucher²  Jonathen K. Settle²  Marco Oliva²  Ilya B. Slizovskiy³  Noelle R. Noyes³  Lidiya V. Zyskina⁴ 

[1] Data Intelligence Systems Lab, Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA;

[2] Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA;

[3] Food-Centric Corridor, Infectious Disease Laboratory, Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA;

[4] Program in Human-Computer Interaction, College of Information Studies, University of Maryland, College Park, MD, USA;

关键词: Metagenomics;    Microbiome;    Long-read sequencing;    Antimicrobial resistance;    Resistome;    Public health;    Mobile genetic elements;   

DOI  :  10.1186/s40168-022-01368-y

 received in 2021-12-31, accepted in 2022-09-02,  发布年份 2022

来源: Springer

【 摘 要 】

BackgroundMetagenomic data can be used to profile high-importance genes within microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct partial or full genomes, particularly those in low abundance. These limitations preclude colocalization analysis, i.e., characterizing the genomic context of genes and functions within a metagenomic sample. Genomic context is especially crucial for functions associated with horizontal gene transfer (HGT) via mobile genetic elements (MGEs), for example antimicrobial resistance (AMR). To overcome this current limitation of metagenomics, we present a method for comprehensive and accurate reconstruction of antimicrobial resistance genes (ARGs) and MGEs from metagenomic DNA, termed target-enriched long-read sequencing (TELSeq).ResultsUsing technical replicates of diverse sample types, we compared TELSeq performance to that of non-enriched PacBio and short-read Illumina sequencing. TELSeq achieved much higher ARG recovery (>1,000-fold) and sensitivity than the other methods across diverse metagenomes, revealing an extensive resistome profile comprising many low-abundance ARGs, including some with public health importance. Using the long reads generated by TELSeq, we identified numerous MGEs and cargo genes flanking the low-abundance ARGs, indicating that these ARGs could be transferred across bacterial taxa via HGT.ConclusionsTELSeq can provide a nuanced view of the genomic context of microbial resistomes and thus has wide-ranging applications in public, animal, and human health, as well as environmental surveillance and monitoring of AMR. Thus, this technique represents a fundamental advancement for microbiome research and application.6X1EiwfAnJZFh2ohemyba9Video abstract

【 授权许可】

CC BY   
© The Author(s) 2022

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