Shigella flexneri gyrA conferring resistance to fluoroquinolones

Accession ARO:3003940
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 for 88 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, 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 WGS
No prevalence data


Detection Models

Model Type: protein variant model

Model Definition: The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: strict and loose. A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.

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