MultiSeq-AMR: a modular amplicon-sequencing workflow for rapid detection of bloodstream infection and antimicrobial resistance markers
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (Rapid Reviews Infectious Diseases)
Abstract
Bloodstream infections (BSIs) represent a significant global health challenge, and traditional diagnostic methods are suboptimal for timely guiding targeted antibiotic therapy. We introduce MultiSeq-AMR, a rapid and modular nanopore amplicon-sequencing workflow to identify bacterial and fungal species and a comprehensive set of antimicrobial resistance (AMR) genes ( n =91) from various types of infection sources. We initially benchmarked MultiSeq-AMR using DNA from 16 bacterial and 5 fungal reference strains and accurately identified all species. AMR gene identification exhibited 99.4% categorical agreement (CA: 153/154 prediction) with whole-genome sequencing. Further validation with 33 BACT/ALERT positive samples from suspected BSI cases revealed 100% accuracy for genus and 96.7% for species identification, with 97.4% CA (151/155) for AMR gene prediction. To accelerate microbiological diagnosis, a 6 h culture enrichment step was tested with MultiSeq-AMR using 15 clinically important bacterial species. Of 13 species selected for sequencing, 11 were correctly identified, with 96% CA (59/61 predictions) for AMR gene identification. With only 2 Mbp yield, sequencing identified 93.7% of species and 89.8% AMR genes initially detected with 20–50 Mbp yield/sample. MultiSeq-AMR holds promise for BSI diagnosis, as species/AMR genes could be identified under 5 h of BACT/ALERT positivity and potentially <11 h of sample collection (rapid-enrichment) for a large set of bacterial species. MultiSeq-AMR gene targets can be modified/increased indefinitely to suit user needs. Further research is required to clinically validate MultiSeq-AMR, especially the rapid enrichment method, to assess its utility in a medical setup and in improving patient outcomes in BSI.
Article activity feed
-
Ariya Chindamporn, Nutapong Lengsiri
Review 6: "MultiSeq-AMR: A Modular Amplicon-Sequencing Workflow for Rapid Detection of Bloodstream Infection and Antimicrobial Resistance Markers"
Reviewers acknowledge the potential of MultiSeq-AMR for rapid diagnosis but highlight limitations, including small sample sizes, insufficient validation of all AMR primer pools, concerns about primer specificity and false positives and its clinical relevance.
-
-
Steven Foley
Review 5: "MultiSeq-AMR: A Modular Amplicon-Sequencing Workflow for Rapid Detection of Bloodstream Infection and Antimicrobial Resistance Markers"
Reviewers acknowledge the potential of MultiSeq-AMR for rapid diagnosis but highlight limitations, including small sample sizes, insufficient validation of all AMR primer pools, concerns about primer specificity and false positives and its clinical relevance.
-
Yu Xia
Review 4: "MultiSeq-AMR: A Modular Amplicon-Sequencing Workflow for Rapid Detection of Bloodstream Infection and Antimicrobial Resistance Markers"
Reviewers acknowledge the potential of MultiSeq-AMR for rapid diagnosis but highlight limitations, including small sample sizes, insufficient validation of all AMR primer pools, concerns about primer specificity and false positives and its clinical relevance.
-
Mato Lagator
Review 3: "MultiSeq-AMR: A Modular Amplicon-Sequencing Workflow for Rapid Detection of Bloodstream Infection and Antimicrobial Resistance Markers"
Reviewers acknowledge the potential of MultiSeq-AMR for rapid diagnosis but highlight limitations, including small sample sizes, insufficient validation of all AMR primer pools, concerns about primer specificity and false positives and its clinical relevance.
-
Timothy Read
Review 2: "MultiSeq-AMR: A Modular Amplicon-Sequencing Workflow for Rapid Detection of Bloodstream Infection and Antimicrobial Resistance Markers"
Reviewers acknowledge the potential of MultiSeq-AMR for rapid diagnosis but highlight limitations, including small sample sizes, insufficient validation of all AMR primer pools, concerns about primer specificity and false positives and its clinical relevance.
-
Yu-Chieh Liao
Review 1: "MultiSeq-AMR: A Modular Amplicon-Sequencing Workflow for Rapid Detection of Bloodstream Infection and Antimicrobial Resistance Markers"
Reviewers acknowledge the potential of MultiSeq-AMR for rapid diagnosis but highlight limitations, including small sample sizes, insufficient validation of all AMR primer pools, concerns about primer specificity and false positives and its clinical relevance.
-
Strength of evidence
Reviewers: Y Liao (National Health Research Institutes)|📒📒📒 ◻️◻️
T Read (Emory University)|📗📗📗📗◻️
M Lagator (The University of Manchester)|📗📗📗📗◻️
Y Xia (SUSTech) |📘📘📘📘📘
S Foley (FDA)|📗📗📗📗◻️
A Chindamporn & N Lengsiri (Chulalongkorn University)|📙📙 ◻️◻️◻️ -
