Imperial College London
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Professor Lesley Hoyles

Faculty of Medicine, Department of Surgery & Cancer

Visiting Professor
 
 
 
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Contact

 

lesley.hoyles11 Website

 
 
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Location

 

Norfolk PlaceSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Leggett:2020:10.1038/s41564-019-0626-z,
author = {Leggett, RM and Alcon-Giner, C and Heavens, D and Caim, S and Brook, TC and Kujawska, M and Martin, S and Peel, N and Acford-Palmer, H and Hoyles, L and Clarke, P and Hall, LJ and Clark, MD},
doi = {10.1038/s41564-019-0626-z},
journal = {Nature Microbiology},
pages = {430--442},
title = {Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens},
url = {http://dx.doi.org/10.1038/s41564-019-0626-z},
volume = {5},
year = {2020}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - 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.
AU  - Leggett,RM
AU  - Alcon-Giner,C
AU  - Heavens,D
AU  - Caim,S
AU  - Brook,TC
AU  - Kujawska,M
AU  - Martin,S
AU  - Peel,N
AU  - Acford-Palmer,H
AU  - Hoyles,L
AU  - Clarke,P
AU  - Hall,LJ
AU  - Clark,MD
DO  - 10.1038/s41564-019-0626-z
EP  - 442
PY  - 2020///
SN  - 2058-5276
SP  - 430
TI  - Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens
T2  - Nature Microbiology
UR  - http://dx.doi.org/10.1038/s41564-019-0626-z
UR  - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000516654000006&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
UR  - https://www.nature.com/articles/s41564-019-0626-z
UR  - http://hdl.handle.net/10044/1/87329
VL  - 5
ER  -
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