Helicobacter pylori gyrB conferring resistance to fluoroquinolones

Accession ARO:3007053
CARD Short NameHpyl_gyrB_FLO
DefinitionPoint mutations in Helicobacter pylori conferring resistance to fluoroquinolone antibiotics.
AMR Gene Familyfluoroquinolone resistant gyrB
Drug Classfluoroquinolone antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsHelicobacter pylorig+wgs
Classification11 ontology terms | Show
Parent Term(s)3 ontology terms | Show
+ confers_resistance_to_antibiotic levofloxacin [Antibiotic]
+ confers_resistance_to_antibiotic norfloxacin [Antibiotic]
+ fluoroquinolone resistant gyrB [AMR Gene Family]
Publications

Chung JW, et al. 2012. J Gastroenterol Hepatol 27(3):493-7 Resistance of Helicobacter pylori strains to antibiotics in Korea with a focus on fluoroquinolone resistance. (PMID 21793912)

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

Rimbara E, et al. 2012. Helicobacter 17(1):36-42 Fluoroquinolone resistance in Helicobacter pylori: role of mutations at position 87 and 91 of GyrA on the level of resistance and identification of a resistance conferring mutation in GyrB. (PMID 22221614)

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)

Resistomes

Prevalence of Helicobacter pylori gyrB conferring resistance to fluoroquinolones among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 377 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 GI
Helicobacter pylori0.26%0%0.11%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): 1200

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:

PMID: 2500370745612,D91G,V199I+ 45613,D481E 45612,D91N+45613,D481E,D484K 45612,D91N,V199I+45613,D481E,D484K 45612,N87K+45613,F438S 45612,N87K,V199A+45613,D481E,R484K 45612,N87K,V199I+45613,D484K
PMID: 22221614E463K
PMID: 3077440045612,A129T+45613,S479G 45612,D91N+45613,R484K 45612,D91N,A129T+45613,S479G 45612,N87Y+45613,R484K

>gb|WP_001182024.1|+|Helicobacter pylori gyrB conferring resistance to fluoroquinolones [Helicobacter pylori]
MQNYQSHSIKVLKGLEGVRKRPGMYIGDTNVGGLHHMVYEVVDNAVDESMAGFCDTINIT
LTDEGSCIVEDNGRGIPVDIHPTEKIPACTVVLTILHAGGKFDNDTYKVSGGLHGVGVSV
VNALSKRLIMTIKKEGQIYRQEFEKGIPTSELEIIGKTKSAKESGTTIEFFPDESVMEVV
EFQAGILQKRFKEMAYLNDGLKISFKEEKTQLQETYFYEDGLKQFVKDSAKKELLTPIIS
FKSMDEETRTSIEVALAYADDYNENTLSFVNNIKTSEGGTHEAGFKMGLSKAILQYIGNN
IKTKESRPISEDIKEGLIAVVSLKMSEPLFEGQTKSKLGSSYARALVSKLVYDKIHQFLE
ENPNEAKIIANKALLAAKAREASKKARELTRKKDNLSVGTLPGKLADCQSKDPLESEIFL
VEGDSAGGSAKQGRDRVFQAILPLKGKILNVEKSHLSKILKSEEIKNMITAFGCGIQESF
DIERLRYHKIIIMTDADVDGSHIQTLLMTFFYRYLRPLIEQGHVYIAQAPLYKYKKGKTE
IYLKDSVALDHFLIEHGINSVDIEGIGKNDLMNLLKVARHYRYALLELEKRYNLLEILRF
LIETKDALSLDMKVLEKSILEKLEGLNYQILRSFATEESLHLHTQTPKGLVEFNLDDNLF
KEVLFEEANYTYQKLMEYNLDFLENKDILAFLEEVENHAKKGANIQRYKGLGEMNPNDLW
ETTMHKENRSLIKLKIEDLEKTDAVFSLCMGDEVEPRRAFIQAHAKDVKQLDV



>gb|NC_000915.1|+|527686-530007|Helicobacter pylori gyrB conferring resistance to fluoroquinolones [Helicobacter pylori]
ATGCAAAATTACCAGAGCCATAGTATTAAGGTTTTAAAAGGCTTAGAGGGGGTTAGGAAACGCCCTGGAATGTATATTGGTGATACCAAT
GTGGGTGGGTTGCACCACATGGTGTATGAAGTCGTGGATAACGCTGTAGATGAGAGCATGGCGGGTTTTTGCGATACGATTAATATCACT
TTGACCGATGAGGGTTCATGCATCGTAGAAGATAACGGGCGAGGCATTCCTGTAGATATTCACCCCACGGAAAAAATCCCCGCTTGCACC
GTGGTTTTAACGATTTTGCATGCGGGGGGCAAGTTTGATAACGATACTTATAAAGTTTCAGGCGGTTTGCATGGCGTGGGCGTTTCGGTT
GTGAACGCTTTGAGCAAACGCTTGATTATGACCATTAAAAAAGAGGGTCAAATTTATCGCCAAGAGTTTGAAAAGGGTATTCCTACTAGC
GAGCTTGAAATCATTGGCAAAACCAAAAGCGCTAAAGAAAGCGGCACGACTATTGAATTTTTCCCTGATGAAAGCGTGATGGAAGTCGTT
GAATTTCAAGCGGGTATTTTACAAAAACGCTTTAAAGAAATGGCGTATCTTAACGATGGCTTAAAAATTTCTTTCAAAGAAGAAAAAACC
CAACTGCAAGAGACTTATTTCTATGAAGACGGCTTGAAACAATTCGTTAAAGACAGCGCTAAAAAAGAATTGCTCACCCCCATTATTTCG
TTTAAAAGCATGGATGAAGAAACGCGCACTTCTATAGAAGTCGCTCTAGCGTATGCTGATGATTATAATGAAAACACTTTAAGCTTTGTG
AATAACATTAAAACTTCTGAAGGTGGCACGCATGAGGCGGGCTTTAAAATGGGCTTGTCTAAAGCAATTTTGCAATATATTGGCAATAAT
ATTAAAACCAAAGAGTCACGCCCCATCTCTGAAGATATTAAAGAGGGGTTGATCGCTGTTGTGAGCTTGAAAATGAGCGAGCCTTTGTTT
GAAGGGCAGACTAAATCCAAACTCGGCAGTTCGTATGCGCGCGCGTTGGTTTCAAAATTAGTCTATGATAAAATCCATCAATTTTTAGAA
GAAAACCCTAACGAAGCCAAAATCATTGCCAATAAAGCCCTACTAGCTGCAAAAGCCAGAGAAGCCAGTAAGAAAGCCAGAGAGCTTACA
AGGAAAAAAGATAATTTGAGTGTCGGCACTTTGCCTGGAAAATTAGCCGATTGCCAGAGTAAAGACCCCTTAGAGAGTGAAATCTTTTTA
GTGGAGGGCGATAGTGCGGGCGGGAGCGCTAAACAAGGGCGCGATAGGGTTTTCCAAGCGATCTTGCCCCTAAAAGGTAAGATTTTAAAT
GTGGAAAAAAGCCATTTATCAAAAATCCTAAAATCAGAAGAAATTAAAAACATGATCACGGCTTTTGGGTGCGGCATTCAAGAGAGTTTT
GATATAGAAAGATTGCGCTATCATAAAATCATTATCATGACCGATGCTGATGTGGATGGGAGCCATATCCAAACCTTGCTGATGACTTTT
TTCTATCGTTATTTGCGCCCGCTGATTGAACAAGGGCATGTTTATATCGCTCAAGCCCCTCTTTACAAATACAAGAAGGGCAAGACAGAA
ATTTATCTTAAAGACAGCGTCGCTTTGGATCATTTTTTAATTGAGCATGGCATCAATTCGGTGGATATTGAAGGGATTGGCAAGAACGAT
TTGATGAACTTGTTAAAAGTGGCACGCCATTACCGCTATGCGCTTTTGGAATTAGAAAAACGCTACAATTTGCTAGAAATTTTACGCTTT
CTCATTGAAACTAAGGACGCCTTAAGCCTTGATATGAAAGTTTTAGAAAAAAGCATTTTAGAAAAATTAGAGGGCTTGAATTATCAGATC
TTACGCTCTTTTGCCACTGAAGAAAGCTTACATTTGCACACGCAAACCCCTAAAGGCTTGGTGGAATTTAACCTAGATGACAATCTCTTT
AAAGAAGTGTTGTTTGAAGAAGCGAATTACACTTACCAAAAGCTTATGGAGTATAATTTAGACTTCTTAGAAAATAAGGATATTTTGGCG
TTTTTAGAAGAAGTGGAAAATCACGCTAAAAAGGGAGCGAATATCCAGCGCTATAAGGGGCTAGGCGAGATGAACCCTAATGATTTGTGG
GAAACGACCATGCATAAAGAAAACCGCAGCTTGATCAAACTCAAAATTGAAGATTTAGAAAAAACCGATGCAGTCTTTTCGCTTTGCATG
GGCGATGAAGTAGAGCCTAGAAGAGCCTTTATCCAAGCGCATGCTAAAGATGTGAAACAACTAGATGTGTAA