Indexed variation graphs for efficient and accurate resistome profiling

Bioinformatics
Will P M Rowe, Martyn D Winn

Abstract

Antimicrobial resistance (AMR) remains a major threat to global health. Profiling the collective AMR genes within a metagenome (the 'resistome') facilitates greater understanding of AMR gene diversity and dynamics. In turn, this can allow for gene surveillance, individualized treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools. Our method combines a variation graph representation of gene sets with a locality-sensitive hashing Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, graphing Resistance Out Of meTagenomes (GROOT), and show it to be both faster and more accurate than a current reference-dependent tool...Continue Reading

References

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Citations

Mar 20, 2019·Nature Reviews. Genetics·Manish BoolchandaniGautam Dantas
Jun 13, 2019·Omics : a Journal of Integrative Biology·Ilaria LaudadioClaudia Carissimi
May 27, 2020·Annual Review of Genomics and Human Genetics·Jordan M EizengaErik Garrison
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Mar 18, 2019·Microbiome·Will Pm RoweMartyn D Winn
Sep 26, 2019·Frontiers in Public Health·Rene S HendriksenPatrick F McDermott
Mar 12, 2020·Frontiers in Public Health·Ana Sofia Ribeiro DuarteTine Hald
Mar 3, 2020·Frontiers in Microbiology·Leonardo G Panunzi
Sep 12, 2019·Frontiers in Microbiology·Evgenii I OlekhnovichElena N Ilina
Feb 4, 2021·MBio·Emily CrossetteKrista Wigginton
Apr 24, 2021·Drug Discovery Today·Lubna MaryamGajendra P S Raghava
May 18, 2021·Access Microbiology·Arun Gonzales DecanoTim Downing

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Datasets Mentioned

BETA
PRJNA349463

Methods Mentioned

BETA
profilers
profiler
Illumina sequencing

Software Mentioned

OAP
VSEARCH
Bandage
Mykrobe
BLAST
Bioawk
GROOT
ARGS
AMRPlusPlus
Graphing Out Of meTagenomes ( GROOT

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