Shigella flexneri gyrA conferring resistance to fluoroquinolones

Accession ARO:3003940
CARD Short NameSfle_gyrA_FLO
DefinitionPoint mutations in Shigella flexneri gyrA observed to confer resistance to fluoroquinolone antibiotics.
AMR Gene Familyfluoroquinolone resistant gyrA
Drug Classfluoroquinolone antibiotic
Resistance Mechanismantibiotic target alteration
Classification11 ontology terms | Show
Parent Term(s)3 ontology terms | Show
+ confers_resistance_to_antibiotic nalidixic acid [Antibiotic]
+ confers_resistance_to_antibiotic norfloxacin [Antibiotic]
+ fluoroquinolone resistant gyrA [AMR Gene Family]
Publications

Qin T, et al. 2016. Eur. J. Clin. Microbiol. Infect. Dis. : Novel mutations in quinolone resistance-determining regions of gyrA, gyrB, parC and parE in Shigella flexneri clinical isolates from eastern Chinese populations between 2001 and 2011. (PMID 27620866)

Resistomes

Prevalence of Shigella flexneri gyrA 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

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
No prevalence data


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): 1500

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:

PMID: 27620866N57K H80P

>gb|AAN43827.1|-|Shigella flexneri gyrA conferring resistance to fluoroquinolones [Shigella flexneri 2a str. 301]
MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWN
KAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAM
RYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMAT
NIPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKV
YIRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDG
MRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRRE
VVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNV
AAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKE
LLDQIAELLRILGSADRLMEVIREELELVREQFGDKRRTEITANSADINLEDLITQEDVV
VTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSRGRVY
SMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTVKKTVL
TEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMGCNTTG
VRGIRLGEGDKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERN
GLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRVA
EPVDEEDLDTIDGSAAEGDDEIAPEVDVDDEPEEE



>gb|AE005674.2|-|2352232-2354859|Shigella flexneri gyrA conferring resistance to fluoroquinolones [Shigella flexneri 2a str. 301]
ATGAGCGACCTTGCGAGAGAAATTACACCGGTCAACATTGAGGAAGAGCTAAAGAGCTCCTATCTGGATTATGCGATGTCGGTCATTGTT
GGCCGTGCGCTGCCAGATGTCCGAGATGGCCTGAAGCCGGTACACCGTCGCGTACTTTACGCCATGAACGTACTAGGCAATGACTGGAAC
AAAGCCTATAAAAAATCTGCCCGTGTCGTTGGTGACGTAATCGGTAAATACCATCCCCATGGTGACTCGGCGGTTTATGACACGATCGTC
CGTATGGCGCAGCCATTCTCGCTGCGTTACATGCTGGTAGACGGTCAGGGTAACTTCGGTTCCATCGACGGCGACTCTGCGGCGGCAATG
CGTTATACGGAAATCCGTCTGGCGAAAATTGCCCATGAACTGATGGCCGATCTCGAAAAAGAGACGGTCGATTTCGTTGATAACTATGAC
GGCACGGAAAAAATTCCCGACGTCATGCCAACCAAAATTCCTAACCTGCTGGTGAACGGTTCTTCCGGTATCGCCGTAGGTATGGCAACC
AACATCCCGCCGCACAACCTGACGGAAGTCATCAACGGTTGTCTGGCGTATATCGATGATGAAGACATCAGCATTGAAGGGCTGATGGAA
CACATCCCGGGGCCGGACTTCCCGACGGCGGCAATCATTAACGGTCGTCGCGGTATTGAAGAAGCTTACCGTACCGGTCGCGGCAAGGTA
TATATCCGCGCCCGTGCTGAAGTGGAAGTTGACGCCAAAACCGGACGTGAAACCATTATCGTCCACGAAATTCCGTATCAGGTAAACAAA
GCGCGCCTGATCGAGAAGATTGCGGAACTGGTAAAAGAAAAACGCGTGGAAGGCATCAGCGCGCTGCGTGACGAGTCTGACAAAGACGGT
ATGCGCATCGTGATTGAAGTGAAACGCGATGCGGTCGGTGAAGTTGTGCTCAACAACCTCTACTCCCAGACCCAGTTGCAGGTTTCTTTC
GGTATCAACATGGTGGCATTGCACCATGGTCAGCCGAAGATCATGAACCTGAAAGACATCATCGCGGCGTTTGTTCGTCACCGCCGTGAA
GTGGTGACCCGTCGTACTATTTTCGAACTGCGTAAAGCTCGCGATCGTGCTCATATCCTTGAAGCATTAGCCGTGGCGCTGGCGAACATT
GACCCGATCATCGAACTGATCCGTCATGCGCCGACGCCTGCAGAAGCGAAAACTGCGCTGGTTGCTAATCCGTGGCAGCTGGGCAACGTT
GCCGCCATGTTGGAACGTGCTGGCGACGATGCTGCGCGTCCGGAATGGCTGGAGCCAGAGTTCGGCGTGCGTGATGGTCTGTACTACCTG
ACCGAACAGCAAGCTCAGGCGATTCTGGATCTGCGTTTGCAGAAACTGACCGGCCTTGAGCACGAAAAACTGCTCGACGAATACAAAGAG
CTGCTGGATCAGATCGCGGAACTGTTGCGTATTCTTGGTAGCGCCGATCGTCTGATGGAAGTGATCCGCGAAGAGCTGGAGCTGGTTCGT
GAACAGTTCGGTGACAAACGTCGTACTGAAATCACCGCCAACAGCGCAGACATCAACCTGGAAGATCTGATCACCCAGGAAGATGTGGTC
GTGACGCTCTCTCACCAGGGCTACGTTAAATATCAGCCGCTTTCTGAATACGAAGCGCAGCGTCGTGGCGGGAAAGGTAAATCTGCCGCA
CGTATTAAAGAAGAAGACTTTATCGACCGACTGCTGGTGGCGAACACGCACGACCATATTCTGTGCTTCTCCAGCCGTGGTCGCGTCTAT
TCGATGAAAGTTTACCAGTTGCCGGAAGCCACTCGTGGCGCGCGCGGTCGTCCGATCGTCAACCTGCTACCGCTGGAACAGGACGAACGT
ATCACCGCGATCCTGCCGGTGACCGAGTTTGAAGAAGGCGTGAAAGTCTTCATGGCGACCGCTAACGGTACTGTGAAGAAAACCGTCCTC
ACCGAATTCAACCGTCTGCGTACCGCCGGTAAAGTGGCGATCAAACTGGTTGACGGCGATGAGCTGATCGGCGTTGATCTGACCAGTGGC
GAAGATGAAGTAATGCTGTTCTCCGCCGAAGGTAAAGTGGTGCGCTTTAAAGAGTCTTCTGTCCGTGCGATGGGCTGCAATACCACTGGT
GTGCGCGGTATTCGCTTAGGTGAAGGCGATAAAGTCGTCTCTCTGATCGTGCCTCGTGGCGATGGCGCAATCCTCACCGCAACGCAAAAC
GGTTACGGTAAACGTACTGCAGTGGCGGAATACCCAACCAAGTCGCGTGCGACGAAAGGGGTTATCTCCATCAAGGTTACCGAACGTAAC
GGTTTAGTGGTTGGCGCGGTGCAGGTAGATGACTGCGACCAGATCATGATGATCACCGATGCCGGTACGCTGGTACGTACTCGCGTTTCA
GAAATCAGCATCGTGGGCCGTAACACCCAGGGCGTGATCCTCATCCGTACTGCGGAAGATGAAAACGTAGTGGGTCTGCAGCGTGTTGCT
GAACCGGTTGACGAGGAAGATCTGGATACCATCGACGGCAGTGCCGCGGAAGGGGATGATGAAATTGCTCCGGAAGTGGACGTTGACGAC
GAGCCAGAAGAAGAATAA