Helicobacter pylori gyrA conferring resistance to fluoroquinolones

Download Sequences
Accession ARO:3007052
CARD Short NameHpyl_gyrA_FLO
DefinitionPoint mutations in the quinolone resistance-determining regions of Helicobacter pylori observed to confer resistance to fluoroquinolone antibiotics.
AMR Gene Familyfluoroquinolone resistant gyrA
Drug Classfluoroquinolone antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsHelicobacter pylorig+wgs
Classification11 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ confers_resistance_to_antibiotic levofloxacin [Antibiotic]
+ fluoroquinolone resistant gyrA [AMR Gene Family]
Publications

Lee JW, et al. 2011. Helicobacter 16(4):301-10 Mutations of Helicobacter pylori associated with fluoroquinolone resistance in Korea. (PMID 21762270)

Chang WL, et al. 2012. Helicobacter 17(3):210-5 Gemifloxacin can partially overcome quinolone resistance of H. pylori with gyrA mutation in Taiwan. (PMID 22515359)

Garcia M, et al. 2012. Antimicrob Agents Chemother 56(1):550-1 Distribution of spontaneous gyrA mutations in 97 fluoroquinolone-resistant Helicobacter pylori isolates collected in France. (PMID 22064536)

Phan TN, et al. 2015. Int J Antimicrob Agents 45(3):244-8 High rate of levofloxacin resistance in a background of clarithromycin- and metronidazole-resistant Helicobacter pylori in Vietnam. (PMID 25499186)

Miftahussurur M, et al. 2016. BMC Microbiol 16(1):256 Emerging Helicobacter pylori levofloxacin resistance and novel genetic mutation in Nepal. (PMID 27809767)

Hanafi A, et al. 2016. Front Microbiol 7:2015 Molecular and Proteomic Analysis of Levofloxacin and Metronidazole Resistant Helicobacter pylori. (PMID 28018334)

Miftahussurur M, et al. 2016. PLoS One 11(12):e0166199 Surveillance of Helicobacter pylori Antibiotic Susceptibility in Indonesia: Different Resistance Types among Regions and with Novel Genetic Mutations. (PMID 27906990)

Rhie SY, et al. 2020. Antibiotics (Basel) 9(6): Discovery of a Novel Mutation in DNA Gyrase and Changes in the Fluoroquinolone Resistance of Helicobacter pylori over a 14-Year Period: A Single Center Study in Korea. (PMID 32471292)

Wei W, et al. 2023. Front Cell Infect Microbiol 13:1294379 Antibiotic resistance of Helicobacter pylori in Nanjing, China: a cross-section study from 2018 to 2023. (PMID 38089809)

Miftahussurur M, et al. 2019. Infect Drug Resist 12:345-358 Alternative eradication regimens for Helicobacter pylori infection in Indonesian regions with high metronidazole and levofloxacin resistance. (PMID 30774400)

Teh X, et al. 2014. PLoS One 9(7):e101481 Functional and molecular surveillance of Helicobacter pylori antibiotic resistance in Kuala Lumpur. (PMID 25003707)
Resistomes

Prevalence of Helicobacter pylori gyrA conferring resistance to fluoroquinolones among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 414 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, genome islands, or whole-genome shotgun assemblies that have at least one hit to the AMR detection model. Default view includes percentages calculated based on Perfect plus Strict RGI hits. Select the checkbox to view percentages based on only Perfect matches to AMR reference sequences curated in CARD (note: this excludes resistance via mutation as references in protein variant models are often wild-type, sensitive sequences).

Prevalence: protein variant model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GIGRDI-AMR2
Helicobacter pylori16.41%0%23.25%0%0%
Show Perfect Only


Detection Models

Model Type: protein variant model

Model Definition: Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.

Bit-score Cut-off (blastP): 1400

PubMed: mutation data hand curated from the scientific literature, evaluated as conferring resistance (R). CRyPTIC: mutation data acquired from the CRyPTIC catalog, evaluated as resistant (R), susceptible (S), or undetermined (U). ReSeqTB: mutation data acquired from the ReSeqTB catalog, evaluated as conferring resistance (Minimal, Moderate, High), not conferring resistance (None), or Indeterminate. WHO: mutation data acquired from the WHO 2023 catalog, evaluated as resistant (R), susceptible (S), or undetermined (U).

MutationMutation typePubMed
D34Nsingle resistance variantPMID:27906990
D34Y,R140Kmultiple resistance variantsPMID:27906990
S63P,R130Kmultiple resistance variantsPMID:27809767
S63P,D91Nmultiple resistance variantsPMID:27809767
S63P,N87K,P188Smultiple resistance variantsPMID:27809767
G85Csingle resistance variantPMID:32471292
N87Ysingle resistance variantPMID:21762270
N87K,H57Ymultiple resistance variantsPMID:22515359
N87K,D91N,V172Imultiple resistance variantsPMID:27809767
D87Gsingle resistance variantPMID:38089809
N87Ksingle resistance variantPMID:21762270
N87A,A88N,V65Imultiple resistance variantsPMID:25499186
T87Isingle resistance variantPMID:22064536
N87Isingle resistance variantPMID:21762270
A88Psingle resistance variantPMID:22064536
D91Y,A97Vmultiple resistance variantsPMID:21762270
D91N,V77Amultiple resistance variantsPMID:22515359
D91Ysingle resistance variantPMID:21762270
D91Gsingle resistance variantPMID:21762270
D91N,R130Kmultiple resistance variantsPMID:27809767
D91Nsingle resistance variantPMID:21762270
D91Hsingle resistance variantPMID:22064536
D91G,D161Nmultiple resistance variantsPMID:27906990
D91N,A97Vmultiple resistance variantsPMID:22515359
D99Vsingle resistance variantPMID:27809767
R140K,D192Nmultiple resistance variantsPMID:27906990
V172Isingle resistance variantPMID:28018334
45612,A129T+45613,S479Gco-dependent single resistance variantPMID:30774400
45612,N87K,V199I+45613,D484Kco-dependent single resistance variantPMID:25003707
45612,N87K,V199A+45613,D481E,R484Kco-dependent single resistance variantPMID:25003707
45612,D91N+45613,D481E,D484Kco-dependent single resistance variantPMID:25003707
45612,D91N+45613,R484Kco-dependent single resistance variantPMID:30774400
45612,N87K+45613,F438Sco-dependent single resistance variantPMID:25003707
45612,D91N,A129T+45613,S479Gco-dependent single resistance variantPMID:30774400
45612,D91N,V199I+45613,D481E,D484Kco-dependent single resistance variantPMID:25003707
45612,N87Y+45613,R484Kco-dependent single resistance variantPMID:30774400
45612,D91G,V199I+45613,D481Eco-dependent single resistance variantPMID:25003707

>gb|WP_001153763.1|+|Helicobacter pylori gyrA conferring resistance to fluoroquinolones [Helicobacter pylori]
MQDNSVNETKNIVEVGIDSSIEESYLAYSMSVIIGRALPDARDGLKPVHRRILYAMHELG
LTSKVAYKKSARIVGDVIGKYHPHGDNAVYDALVRMAQDFSMRLELVDGQGNFGSIDGDN
AAAMRYTEARMTKASEEILRDIDKDTIDFVPNYDDTLKEPDILPSRLPNLLVNGANGIAV
GMATSIPPHRMDEIIDALVHVLENPNAGLDEILEFVKGPDFPTGGIIYGKAGIIEAYKTG
RGRVKVRAKVHVEKTKNKEIIVLDEMPFQTNKAKLVEQISDLAREKQIEGISEVRDESDR
EGIRVVIELKRDAMSEIVLNHLYKLTTMETTFSIILLAIYNKEPKIFTLLELLHLFLNHR
KTIIIRRTIFELEKAKARAHILEGYLIALDNIDEIVRLIKTSQSPEAAKNALMERFTLSE
IQSKAILEMRLQRLTGLERDKIKEEYQNLLELIDDLNGILKSEDRLNGVVKTELLEVKEQ
FSSPRRTEIQESYENIDIEDLIANEPMVVSMSYKGYVKRVDLKAYEKQNRGGKGKLSGST
YEDDFIENFFVANTHDILLFITNKGQLYHLKVYKIPEASRIAMGKAIVNLISLAPDEKIM
ATLSTKDFSDERSLAFFTKNGVVKRTNLSEFESNRSCGIRAIVLDEGDELVSAKVVDKNA
KHLLIASHLGIFIKFPLEEVREIGRTTRGVIGIKLNENDFVVGAVVISDDGNKLLSVSEN
GLGKQTLAEAYRGQSRGGKGVIGMKLTQKTGNLVGVISVDDENLDLMILTASAKMIRVSI
KDIRETGRNASGVKLINTADKVMYVNSCPKEEEPENLETSSAQNLFE


>gb|NC_000915.1|+|752512-754995|Helicobacter pylori gyrA conferring resistance to fluoroquinolones [Helicobacter pylori]
ATGCAAGATAATTCAGTCAATGAAACAAAAAATATTGTAGAAGTGGGGATTGATTCTTCTATTGAAGAGAGCTATTTAGCTTATTCCATG
AGCGTGATCATAGGGCGCGCTTTACCGGACGCTAGAGATGGCTTAAAGCCCGTGCATAGGCGTATTTTGTATGCGATGCATGAATTAGGC
CTTACTTCAAAAGTCGCTTACAAAAAAAGCGCTAGGATCGTGGGTGATGTGATTGGTAAATACCACCCCCATGGCGATAATGCGGTTTAT
GATGCGCTAGTGAGAATGGCGCAAGATTTTTCCATGCGTTTGGAATTAGTGGATGGGCAGGGCAACTTTGGCTCTATTGATGGCGATAAC
GCCGCAGCGATGCGTTACACTGAAGCCAGAATGACTAAGGCGAGTGAAGAAATTTTAAGGGATATTGATAAAGACACCATTGATTTTGTG
CCTAATTATGACGATACCTTAAAAGAGCCAGATATTTTACCAAGCCGTCTGCCTAACCTTTTAGTCAATGGGGCTAATGGGATCGCTGTG
GGGATGGCGACTTCTATCCCCCCTCACAGGATGGATGAAATCATAGACGCTTTAGTGCATGTCTTAGAAAACCCTAACGCTGGATTAGAT
GAAATCTTAGAATTTGTCAAAGGGCCTGATTTTCCCACTGGTGGGATCATTTATGGCAAGGCGGGTATTATTGAAGCCTATAAAACGGGG
CGAGGACGCGTGAAAGTGCGGGCCAAAGTGCATGTGGAAAAAACAAAAAATAAAGAAATCATCGTTTTAGATGAAATGCCTTTTCAAACC
AATAAAGCCAAATTAGTGGAACAAATCAGCGATTTAGCGCGAGAAAAGCAAATTGAAGGCATTAGTGAAGTGCGCGATGAGAGCGATAGA
GAGGGCATTAGAGTGGTGATTGAATTAAAAAGAGACGCGATGAGTGAAATTGTCTTAAACCACCTCTACAAACTCACCACTATGGAAACC
ACTTTTAGCATCATTTTACTCGCTATTTACAATAAAGAGCCTAAGATTTTCACGCTTTTAGAGTTGTTGCACCTTTTCTTAAACCACAGA
AAAACCATTATTATAAGACGCACGATTTTTGAATTAGAAAAGGCTAAGGCCAGAGCGCATATTTTAGAGGGCTATTTGATCGCACTAGAC
AATATTGATGAAATCGTGCGACTCATTAAAACAAGCCAAAGCCCAGAAGCGGCTAAAAACGCCTTAATGGAGCGTTTCACTTTGAGCGAG
ATTCAAAGCAAGGCCATTTTAGAAATGCGTTTGCAACGCTTAACAGGCCTTGAAAGGGATAAGATCAAAGAAGAATACCAAAACTTGTTG
GAGCTTATTGATGATCTCAATGGCATTTTAAAGAGCGAAGATCGCTTGAATGGAGTCGTCAAAACAGAGCTTTTAGAAGTCAAAGAGCAA
TTTTCTTCTCCAAGGCGCACTGAAATTCAAGAATCTTATGAAAATATTGACATAGAAGATTTGATCGCTAATGAGCCTATGGTAGTGAGC
ATGAGTTATAAAGGCTATGTGAAAAGAGTGGATTTAAAAGCTTATGAAAAGCAAAATCGTGGTGGTAAAGGCAAGCTTTCAGGCAGCACT
TATGAAGACGATTTCATTGAAAACTTTTTTGTGGCTAACACGCATGATATTTTGCTCTTTATCACCAATAAGGGGCAATTGTATCATTTG
AAAGTCTATAAAATCCCAGAAGCGAGCCGGATCGCTATGGGTAAAGCCATTGTAAATTTAATCTCGCTCGCTCCGGATGAAAAGATCATG
GCGACTCTAAGCACCAAAGACTTTAGCGATGAACGCTCTTTGGCCTTCTTCACGAAAAATGGCGTGGTGAAGCGCACCAATTTGAGCGAA
TTTGAAAGCAACAGGAGTTGTGGTATCAGAGCGATTGTTTTAGATGAAGGCGATGAATTAGTGAGCGCAAAAGTTGTGGATAAAAACGCT
AAGCATTTGCTCATCGCATCGCATTTGGGCATTTTCATTAAATTCCCTTTAGAAGAGGTGCGCGAGATCGGAAGAACTACTCGTGGGGTT
ATAGGCATCAAGCTGAATGAAAACGATTTTGTTGTCGGTGCGGTCGTTATTAGCGATGATGGCAACAAGCTTTTGAGCGTGAGTGAAAAC
GGGCTTGGCAAGCAAACTTTAGCCGAAGCGTATAGAGGGCAATCTCGTGGAGGTAAGGGGGTCATTGGCATGAAGCTCACTCAAAAAACC
GGCAATCTAGTGGGCGTTATCAGCGTGGATGATGAAAATTTGGATTTGATGATCCTTACTGCAAGCGCAAAAATGATCAGAGTTTCTATT
AAAGATATTAGAGAAACCGGAAGAAACGCTAGTGGGGTAAAGCTCATAAACACCGCCGATAAAGTCATGTATGTCAATTCTTGCCCTAAA
GAAGAAGAGCCAGAAAATTTAGAAACCTCTTCGGCACAAAATTTGTTTGAGTGA

Curator Acknowledgements
Curator Description Most Recent Edit