Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens

Title: Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens
Authors: Leggett, RM
Alcon-Giner, C
Heavens, D
Caim, S
Brook, TC
Kujawska, M
Martin, S
Peel, N
Acford-Palmer, H
Hoyles, L
Clarke, P
Hall, LJ
Clark, MD
Item Type: Journal Article
Abstract: The MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used the MinION platform coupled to the NanoOK RT software package to perform shotgun metagenomic sequencing and profile mock communities and faecal samples from healthy and ill preterm infants. Using Nanopore data, we reliably classified a 20-species mock community and captured the diversity of the immature gut microbiota over time and in response to interventions such as probiotic supplementation, antibiotic treatment or episodes of suspected sepsis. We also performed rapid real-time runs to assess gut-associated microbial communities in critically ill and healthy infants, facilitated by NanoOK RT software package, which analysed sequences as they were generated. Our pipeline reliably identified pathogenic bacteria (that is, Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance gene profiles within as little as 1 h of sequencing. Results were confirmed using pathogen isolation, whole-genome sequencing and antibiotic susceptibility testing, as well as mock communities and clinical samples with known antimicrobial resistance genes. Our results demonstrate that MinION (including cost-effective Flongle flow cells) with NanoOK RT can process metagenomic samples to a rich dataset in < 5 h, which creates a platform for future studies aimed at developing these tools and approaches in clinical settings with a focus on providing tailored patient antimicrobial treatment options.
Issue Date: 1-Mar-2020
Date of Acceptance: 1-Nov-2019
URI: http://hdl.handle.net/10044/1/87329
DOI: 10.1038/s41564-019-0626-z
ISSN: 2058-5276
Publisher: Nature Research
Start Page: 430
End Page: 442
Journal / Book Title: Nature Microbiology
Volume: 5
Issue: 3
Copyright Statement: © The Author(s), 2019. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Sponsor/Funder: Medical Research Council (MRC)
Medical Research Council (MRC)
Funder's Grant Number: MR/L01632X/1
MR/L01632X/1
Keywords: Science & Technology
Life Sciences & Biomedicine
Microbiology
ENTEROBACTER-CLOACAE
NANOPORE
ALIGNMENT
IDENTIFICATION
Anti-Bacterial Agents
Bacteria
Computational Biology
DNA, Bacterial
Drug Resistance, Bacterial
Enterobacter cloacae
Gastrointestinal Microbiome
Infant, Premature
Klebsiella pneumoniae
Metagenome
Microbial Sensitivity Tests
Microbiota
Nanopores
Sequence Analysis, DNA
Software
Whole Genome Sequencing
Bacteria
Enterobacter cloacae
Klebsiella pneumoniae
DNA, Bacterial
Anti-Bacterial Agents
Microbial Sensitivity Tests
Sequence Analysis, DNA
Computational Biology
Drug Resistance, Bacterial
Software
Infant, Premature
Metagenome
Nanopores
Microbiota
Gastrointestinal Microbiome
Whole Genome Sequencing
Science & Technology
Life Sciences & Biomedicine
Microbiology
ENTEROBACTER-CLOACAE
NANOPORE
ALIGNMENT
IDENTIFICATION
0605 Microbiology
1108 Medical Microbiology
Publication Status: Published
Online Publication Date: 2019-12-16
Appears in Collections:Department of Surgery and Cancer



This item is licensed under a Creative Commons License Creative Commons