Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq)

Genome Medicine
Romain GuérillotBenjamin P Howden

Abstract

Mutation acquisition is a major mechanism of bacterial antibiotic resistance that remains insufficiently characterised. Here we present RM-seq, a new amplicon-based deep sequencing workflow based on a molecular barcoding technique adapted from Low Error Amplicon sequencing (LEA-seq). RM-seq allows detection and functional assessment of mutational resistance at high throughput from mixed bacterial populations. The sensitive detection of very low-frequency resistant sub-populations permits characterisation of antibiotic-linked mutational repertoires in vitro and detection of rare resistant populations during infections. Accurate quantification of resistance mutations enables phenotypic screening of mutations conferring pleiotropic phenotypes such as in vivo persistence, collateral sensitivity or cross-resistance. RM-seq will facilitate comprehensive detection, characterisation and surveillance of resistant bacterial populations ( https://github.com/rguerillot/RM-seq ).

References

Mar 13, 1999·Journal of Clinical Microbiology·G PozziG Orefici
May 29, 2000·Trends in Genetics : TIG·P RiceA Bleasby
May 1, 2001·The Journal of Antimicrobial Chemotherapy·A J O'NeillI Chopra
Jan 20, 2004·Journal of Medical Microbiology·Srinivas V RamaswamyEdward A Graviss
Mar 4, 2005·The Journal of Antimicrobial Chemotherapy·Jun YuJagath L Kadurugamuwa
May 23, 2007·Proceedings of the National Academy of Sciences of the United States of America·Michael M MwangiAlexander Tomasz
Aug 31, 2007·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·F DrobniewskiUNKNOWN Subcommittee on Antimicrobial Susceptibility Testing of Mycobacterium tuberculosis of the European Committee for Antimicrobi
Oct 4, 2008·Nucleic Acids Research·Bo Liu, Mihai Pop
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 13, 2010·Clinical Microbiology Reviews·Graeme N Forrest, Kimberly Tamura
Sep 15, 2010·Antimicrobial Agents and Chemotherapy·Longzhu CuiKeiichi Hiramatsu
Aug 26, 2011·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·David R CameronAnton Y Peleg
Nov 17, 2011·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·Y SmaniJ Pachón
Nov 22, 2011·Nature Methods·Teemu KiviojaJussi Taipale
Jan 14, 2012·Nucleic Acids Research·Yongwei ZhangWinfried Edelmann
Mar 6, 2012·Enfermedades infecciosas y microbiología clínica·Alejandro BeceiroGermán Bou
Oct 13, 2012·Bioinformatics·Limin FuWeizhong Li
Oct 24, 2012·Antimicrobial Agents and Chemotherapy·Migla Miskinyte, Isabel Gordo
Mar 15, 2013·Journal of Clinical Microbiology·Alex van Belkum, W Michael Dunne
Apr 5, 2013·Clinical Microbiology Reviews·Alejandro BeceiroGermán Bou
Apr 10, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Benjamin P HowdenTimothy P Stinear
May 8, 2013·Antimicrobial Agents and Chemotherapy·Andrew G McArthurGerard D Wright
Jul 6, 2013·Science·Jeremiah J FaithJeffrey I Gordon
Sep 27, 2013·Science Translational Medicine·Lejla Imamovic, Morten O A Sommer
Oct 22, 2013·Bioinformatics·Jiajie ZhangAlexandros Stamatakis
Apr 2, 2014·Antimicrobial Agents and Chemotherapy·Brandon EilertsonTimothy R Sterling
May 21, 2014·Antimicrobial Agents and Chemotherapy·Nadine HändelBenno H ter Kuile
Aug 7, 2014·Trends in Genetics : TIG·Claudio U KöserSharon J Peacock
Dec 17, 2014·Current Protocols in Bioinformatics·Fabian Sievers, Desmond G Higgins
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Jan 15, 2015·Nucleic Acids Research·Melanie SchirmerChristopher Quince
Mar 31, 2015·Trends in Microbiology·Csaba PálViktória Lázár

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Citations

Sep 19, 2019·Proceedings of the National Academy of Sciences of the United States of America·Romain GuérillotBenjamin P Howden
May 16, 2018·Bioinformatics·Will P M Rowe, Martyn D Winn
Jan 9, 2020·Microbial Genomics·Stefano G GiulieriDeborah A Williamson
Feb 15, 2020·Nature Reviews. Microbiology·Alex van BelkumWilliam Michael Dunne
Jul 2, 2020·The Journal of Biological Chemistry·Maiken MellergaardSøren Skov
Mar 9, 2019·Journal of Microbiological Methods·Alexander LimAkhilesh Ramachandran
Apr 24, 2021·Drug Discovery Today·Lubna MaryamGajendra P S Raghava
Jul 3, 2021·Annals of the New York Academy of Sciences·Meilin ZhuPaul C Blainey

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Datasets Mentioned

BETA
PRJNA399605
PRJNA360176

Methods Mentioned

BETA
scraping
PCR
Assay
Illumina sequencing
amplicon sequencing

Software Mentioned

GNU
bwa
EMBOSS
DESeq2
Miseq
mem aligner
Snippy
R DESeq2
GeneXpert
CD

Related Concepts

Related Feeds

Antimicrobial Resistance (ASM)

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.

Antimicrobial Resistance

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.