Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AAC
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • AAC Podcast
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Antimicrobial Agents and Chemotherapy
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AAC
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • AAC Podcast
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
Mechanisms of Resistance

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

Sushim Kumar Gupta, Babu Roshan Padmanabhan, Seydina M. Diene, Rafael Lopez-Rojas, Marie Kempf, Luce Landraud, Jean-Marc Rolain
Sushim Kumar Gupta
aUnité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278—IRD 198 IHU, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Babu Roshan Padmanabhan
aUnité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278—IRD 198 IHU, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Seydina M. Diene
aUnité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278—IRD 198 IHU, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Rafael Lopez-Rojas
bServicio de Enfermedades Infecciosas, Hospitales Universitarios Virgen del Rocıo, Seville, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marie Kempf
cLaboratoire de Bacteriologie, Institut de Biologie en santé-PHB, CHU, Angers, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Luce Landraud
dINSERM U895, Nice, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jean-Marc Rolain
aUnité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278—IRD 198 IHU, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/AAC.01310-13
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Additional Files
  • FIG 1
    • Open in new tab
    • Download powerpoint
    FIG 1

    ARG-ANNOT database browser on Bio-Edit. (A) Paste the query sequences and select type of database, select the different parameters, and search. (B) BLAST output.

  • FIG 2
    • Open in new tab
    • Download powerpoint
    FIG 2

    (A) Topographical representation of BLAST results for rmtF after curing it from the database. (B) BLAST analysis of rmtF gene using ARG-ANNOT.

Tables

  • Figures
  • Additional Files
  • TABLE 1

    Position of the mutation in the reference gene which leads to antibiotic resistance in different chromosomal genes

    GeneaMutational point(s)Reference sequence (5′–3′)b
    rpoBC1564(64)A:A1565(65)T:A1565(65)G:G1573(73)T:A1574(74)T:C1603(103)G:C1603(103)T:A1604(104)T:C1619(119)A:C1619(119)T:C1696(196)T:A1741(241)T1501(1):TTGATTAATGCAAAACCAGTTGCTGCTGCAATCAAAGAATTCTTTGGTTCAAGCCAGTTATCTCAGTTTATGGACCAAAACAACCCACTATCTGAGATTACACATAAACGTCGTGTATCTGCGCTTGGTCCTGGTGGTTTAACACGTGAACGTGCGGGCTTCGAAGTACGTGACGTACACCAAACTCACTATGGTCGTGTTTGTCCAATTGAAACTCCTGAAGGTCCAAACATTGGTTTGATCAACTCGCTTTCTGTATACGCAAAAGCGAATGACTTCGGTTTCTTGGAAACTCCATAC:1800(300)
    gyrA1T175(175)A:G224(224)C:C198(198)T:G259(259)T:G259(259)A1(1):ATGAGCGACCTTGCGAGAGAAATTACACCGGTCAACATTGAGGAAGAGCTGAAGAGCTCCTATCTGGATTATGCGATGTCGGTCATTGTTGGCCGTGCGCTGCCAGATGTCCGAGATGGCCTGAAGCCGGTACACCGTCGCGTACTTTACGCCATGAACGTACTAGGCAATGACTGGAACAAAGCCTATAAAAAATCTGCCCGTGTCGTTGGTGACGTAATCGGTAAATACCATCCCCATGGTGACTCGGCGGTCTATGACACGATCGTCCGCATGGCGCAGCCATTCTCGCTGCGTTAT:300(300)
    gyrA2G2599(299)T2301(1):GACGAAAGGGGTTATCTCCATCAAGGTTACCGAACGTAACGGTTTAGTTGTTGGCGCGGTACAGGTAGATGACTGCGACCAGATCATGATGATCACCGATGCCGGTACGCTGGTACGTACTCGCGTTTCGGAAATCAGCATCGTGGGCCGTAACACCCAGGGCGTGATCCTCATCCGTACTGCGGAAGATGAAAACGTAGTGGGTCTGCAACGTGTTGCTGAACCGGTTGACGAGGAAGATCTGGATACCATCGACGGCAGTGCCGCGGAAGGGGACGATGAAATCGCTCCGGAAGTGGA:2600(300)
    parCG233(33)A:A238(38)C:G239(39)T:C240(40)A:G250(50)A: A682(482)G:G757(557)A201(1):CGGTGACGTACTGGGTAAATACCATCCGCACGGCGATAGCGCCTGTTATGAAGCGATGGTCCTGATGGCGCAACCGTTCTCTTACCGTTATCCGCTGGTTGATGGTCAGGGGAACTGGGGCGCGCCGGACGATCCGAAATCGTTCGCGGCAATGCGTTACACCGAATCCCGGTTGTCGAAATATTCCGAGCTGCTATTGAGCGAGCTGGGGCAGGGGACGGCTGACTGGGTGCCAAACTTCGACGGCACTTTGCAGGAGCCGAAAATGCTACCTGCCCGTCTGCCAAACATTTTGCTTAACGGCACCACCGGTATTGCCGTCGGCATGGCGACCGATATTCCACCGCATAACCTGCGTGAAGTGGCTCAGGCGGCAATCGCATTAATCGACCAGCCGAAAACCACGCTCGATCAGCTGCTGGATATCGTGCAGGGGCCGGATTATCCGACTGAAGCGGAAATTATCACTTCGCGCGCCGAGATCCGTAAAATCTACGAGAACGGACGTGGTTCAGTGCGTATGCGCGCGGTGTGGAAGAAAGAAGATGGCGCGGTGGTTATCAGCGCATTGCCGCATCAGGTTTCAGGTGCGCGCGTACT:800(600)
    16S rRNAT1406(206)A:A1408(208)G:C1409(209)T:G1491(291)T1201(1):ATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAA:1500(300)
    23S rRNAA2058(8)G:A2059(9)G:C2611(561)T2051(1):AAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCTTGACTGCGAGCGTGACGGCGCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAACTGAGGGGGGCTGCT:2650(300)
    katGG871(171)A:G900(200)C:G944(244)C:G985(285)GG701(1):GGCCGAACGGCAACCCGGACCCCATGGCCGCGGCGGTCGACATTCGCGAGACGTTTCGGCGCATGGCCATGAACGACGTCGAAACAGCGGCGCTGATCGTCGGCGGTCACACTTTCGGTAAGACCCATGGCGCCGGCCCGGCCGATCTGGTCGGCCCCGAACCCGAGGCTGCTCCGCTGGAGCAGATGGGCTTGGGCTGGAAGAGCTCGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCG:1000(300)
    pncAA139(39)G:T192(92)TA1(1):ATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCTCGTCGTGGCCACCGCATTGCGTCAGCGGTACTCCCGGCGCGGACTTCCATCCCAGTCTGGACACGTCGGCAATCGAGGCGGTGTTCTACAAGGGTGCCTACACC:300(300)
    embBA916(16)G:A916(16)C:G918(18)T:G918(18)A:G918(18)C901(1):GGCTACATCCTGGGCATGGCCCGAGTCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGAGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAAC:1200(300)
    rpsLA128(128)G:A263(263)G1(1):ATGGCAACAGTTAACCAGCTGGTACGCAAACCACGTGCTCGCAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGCCGTGTTCGTCTGACTAACGGTTTCGAAGTGACTTCCTACATCGGTGGTGAAGGTCACAACCTGCAGGAGCACTCCGTGATCCTGATCCGTGGCGGTCGTGTTAAAGACCTCCCGGGTGTTCGTTACCACACCGTACGTGGT:300(300)
    pmrAG305(155)A151(1):GAGTTGCTTGCCCGTATTCATGCCTTACTACGCCGTAGTGGAGTAGAAGCTCAACTTGCGAGTCAAGATCAACTATTAGAAAGTGGTGATCTGGTTTTAAATGTTGAACAGCATATTGCGACGTTTAAAGGCCAACGCATTGATTTATCAAATCGTGAATGGGCAATCTTTYKAATTCCACTTATGACTCACCCAAATAAAATCTTTTCTAAAGCCAACTTAGAAGATAAGTTATATGATTTTGATAGTGATGTGACCAGTAATACTATTGAAGTATATGTTCACCATTTAAGAGCGAAG:450(300)
    pmrB1C38(38)A:C41(41)T:G261(261)C:G261(261)T1(1):GTGCATTATTCATTAAAAAAACGACTGATTTGGGGCACCTCAATTTTCAGTGTCATCTTAGGTTGTATTTTAATTTTTAGTGCTTATAAGGTTGCACTTCAAGAAGTCGATGAAATTCTAGATACTCAAATGAAGTATTTAGCGGAAAGAACAGCTGAGCACCCTTTAAAAACTGTAAGCAGTAAGTTTGATTTTCATAAAACTTACCACGAAGAAGATCTGTTTATCGATATCTGGGCTTATAAGGATCAGGCCCATTTGTCTCATCATTTACATTTGCTGGTTCCACCTGTTGAGCAA:300(300)
    pmrB2T434(14)A:C680(260)T:C697(277)T:C697(277)A:G784(364)C321(1):CTTGCGGGCAGTATGTTTATTCCGTATTTAATTATTTTACCTTTTGCAATATTTGCCTTAGCAGCCATTATTCGTCGTGGTTTAAAACCAATAGATGATTTTAAAAATGAGTTAAAAGAACGCGATTCCGAAGAACTCACACCAATTGAAGTACATGATTATCCTCAAGAGCTTTTACCTACTATTGACGAAATGAACCGTCTTTTTGAGCGCATTTCTAAAGCGCAAAATGAACAGAAGCAATTTATTGCCGATGCTGCTCATGAATTACGAACACCTGTGACTGCATTGAACTTACAAACCAAGATTTTGCTAAGCCAGTTTCCTGAGCATGAATCATTGCAAAACTTAAGCAAGGGTTTGGCGCGTATTCAGCATTT:700(380)
    pmrB3T1057(7)A:T1160(110)A:C1208(158)T1051(1):GTTATTAATATTTCAGTTTATACCGATCCAGATCACTACGCATGTATTCAAATTGAAGATAGCGGTGCAGGAATAGACCCTGAAAATTACGATAAAGTCCTTAAGCGTTTTTATCGCGTGCATCACCATCTTGAGGTGGGAAGTGGTCTAGGTTTATCTATTGTAGATCGTGCAACTCAAAGGCTTGGTGGGACTTTAACTCTCGATAAGAGCTTAGAGCTTGGCGGTCTTTCTGTATTAGTGAAATTAC:1300(250)
    • ↵a The nucleotide sequences for gyrA, parC, rpsL, 16s rRNA, and 23s rRNA were obtained from Escherichia coli sp. strain K-12 substrain MG1655; for rpoB, pmrA, and pmrB genes from Acinetobacter baumannii 17978; and for katG, pncA, and embB genes from Mycobacterium tuberculosis H37Rv.

    • ↵b The first number and the second number in parentheses represent the nucleotide position of the reference gene in NCBI GenBank and the nucleotide position in the table, respectively.

  • TABLE 2

    BLAST analyses to validate the system under different stringent conditions using gene fragments of different percentages of lengtha

    % length e-valueParameterValue(s) for gene fragment of length:
    100%70%50%25%10%5%
    XYXYXYXYXYXY
    1E-100Sp (%)100096 (4)090 (10)074 (26)NoNoNoNoNo
    Sn (%)0100010001000NoNoNoNoNo
    1E-50Sp (%)100095 (5)089 (11)086 (14)081 (19)NoNoNo
    Sn (%)01000100010001000NoNoNo
    1E-25Sp (%)100094 (6)089 (11)086 (14)077 (23)066 (34)No
    Sn (%)010001000100010001000No
    1E-10Sp (%)100094 (6)089 (11)086 (14)081 (19)077 (23)0
    Sn (%)010001000100010001000100
    1E-5Sp (%)100094 (6)089 (11)084 (16)076 (24)074 (26)0
    Sn (%)010001000100010001000100
    • ↵a The table shows the specificity and sensitivity analysis of 100 randomly selected sequences (1.0E-100 to 1.0E-5). The e-values represent the different stringent conditions. X, randomly selected antibiotic resistance gene sequences from the database (see Fig. S8 in the supplemental material); Y, randomly selected gene sequences (no antibiotic resistance gene) from Escherichia coli, Acinetobacter baumannii, and Staphylococcus aureus genomes; Sp, specificity; Sn, sensitivity; No, no output. Values in parentheses show the numbers of specific hits at the group level.

Additional Files

  • Figures
  • Tables
  • Supplemental material

    Files in this Data Supplement:

    • Supplemental file 1 -

      Supplemental material.

      PDF, 232K

PreviousNext
Back to top
Download PDF
Citation Tools
ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes
Sushim Kumar Gupta, Babu Roshan Padmanabhan, Seydina M. Diene, Rafael Lopez-Rojas, Marie Kempf, Luce Landraud, Jean-Marc Rolain
Antimicrobial Agents and Chemotherapy Dec 2013, 58 (1) 212-220; DOI: 10.1128/AAC.01310-13

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print

Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Antimicrobial Agents and Chemotherapy article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes
(Your Name) has forwarded a page to you from Antimicrobial Agents and Chemotherapy
(Your Name) thought you would be interested in this article in Antimicrobial Agents and Chemotherapy.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes
Sushim Kumar Gupta, Babu Roshan Padmanabhan, Seydina M. Diene, Rafael Lopez-Rojas, Marie Kempf, Luce Landraud, Jean-Marc Rolain
Antimicrobial Agents and Chemotherapy Dec 2013, 58 (1) 212-220; DOI: 10.1128/AAC.01310-13
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • INTRODUCTION
    • MATERIALS AND METHODS
    • RESULTS
    • DISCUSSION
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About AAC
  • Editor in Chief
  • Editorial Board
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • AAC Podcast
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Ethics
  • Contact Us

Follow #AACJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Print ISSN: 0066-4804; Online ISSN: 1098-6596