Salmonella enterica gyrA conferring resistance to fluoroquinolones

Accession ARO:3003926
CARD Short NameSent_gyrA_FLO
DefinitionPoint mutations in Salmonella gyrA that confer resistance to Nalidixic acid, a fluoroquinolone antibiotic. These mutations have also been shown to reduce susceptibility to ciprofloxacin.
AMR Gene Familyfluoroquinolone resistant gyrA
Drug Classfluoroquinolone antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsCitrobacter amalonaticusg, Citrobacter freundiig+wgs, Citrobacter koseriwgs, Citrobacter youngaewgs, Enterobacter asburiaewgs, Enterobacter cloacaeg+wgs, Enterobacter hormaecheig+wgs, Enterobacter kobeig+wgs, Enterobacter roggenkampiig+wgs, Klebsiella aerogenesg+wgs, Klebsiella michiganensiswgs, Klebsiella oxytocawgs, Klebsiella pneumoniaeg+wgs, Klebsiella quasipneumoniaeg+wgs, Salmonella entericag+wgs
Classification11 ontology terms | Show
Parent Term(s)3 ontology terms | Show
+ confers_resistance_to_antibiotic ciprofloxacin [Antibiotic]
+ confers_resistance_to_antibiotic nalidixic acid [Antibiotic]
+ fluoroquinolone resistant gyrA [AMR Gene Family]
Publications

Campioni F, et al. 2016. Microb. Drug Resist. : Prevalence of gyrA Mutations in Nalidixic Acid-Resistant Strains of Salmonella Enteritidis Isolated from Humans, Food, Chickens, and the Farm Environment in Brazil. (PMID 27559761)

Gopal M, et al. 2016. J Clin Diagn Res 10(7):DC14-8 GyrA ser83 and ParC trp106 Mutations in Salmonella enterica Serovar Typhi Isolated from Typhoid Fever Patients in Tertiary Care Hospital. (PMID 27630841)

Resistomes

Prevalence of Salmonella enterica gyrA conferring resistance to fluoroquinolones among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 263 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
Citrobacter amalonaticus10%0%0%0%
Citrobacter freundii4.62%0%1.77%0%
Citrobacter koseri0%0%3.33%0%
Citrobacter youngae0%0%7.14%0%
Enterobacter asburiae0%0%1.39%0%
Enterobacter cloacae6.82%0%4.09%0%
Enterobacter hormaechei11.9%0%15.75%0%
Enterobacter kobei16.67%0%6.56%0%
Enterobacter roggenkampii3.85%0%0.61%0%
Klebsiella aerogenes2.5%0%2.52%0%
Klebsiella michiganensis0%0%0.97%0%
Klebsiella oxytoca0%0%1.84%0%
Klebsiella pneumoniae11.73%0%14.43%0%
Klebsiella quasipneumoniae3.06%0%0.9%0%
Salmonella enterica11.71%0%10.08%0%
Show Perfect Only


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: 27559761S83F D87N D87Y S97P

>gb|AAL21173.1|-|Salmonella enterica gyrA conferring resistance to fluoroquinolones [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWN
KAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAM
RYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMAT
NIPPHNLTEVINGCLAYIDNEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKV
YIRARAEVEADAKTGRETIIVHEIPYQVNKARLIEKIAELVKDKRVEGISALRDESDKDG
MRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIISAFVRHRRE
VVTRRTIFELRKARDRAHILEALAIALANIDPIIELIRRAPTPAEAKAALISRPWDLGNV
AAMLERAGDDAARPEWLEPEFGVRDGQYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKE
LLEQIAELLHILGSADRLMEVIREEMELIRDQFGDERRTEITANSADINIEDLISQEDVV
VTLSHQGYVKYQPLTDYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDTILCFSSRGRLY
WMKVYQLPEASRGARGRPIVNLLPLEANERITAILPVREYEEGVNVFMATASGTVKKTAL
TEFSRPRSAGIIAVNLNDGDELIGVDLTSGSDEVMLFSAAGKVVRFKEDAVRAMGRTATG
VRGIKLAGDDKVVSLIIPRGEGAILTVTQNGYGKRTAADEYPTKSRATQGVISIKVTERN
GSVVGAVQVDDCDQIMMITDAGTLVRTRVSEISVVGRNTQGVILIRTAEDENVVGLQRVA
EPVDDEELDAIDGSVAEGDEDIAPEAESDDDVADDADE



>gb|AE006468.2|-|2373710-2376346|Salmonella enterica gyrA conferring resistance to fluoroquinolones [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
ATGAGCGACCTTGCGAGAGAAATTACACCGGTCAACATTGAGGAGGAGCTGAAGAGCTCCTATCTGGATTATGCGATGTCGGTCATTGTT
GGCCGTGCGCTGCCGGATGTCCGAGATGGCCTGAAGCCGGTACACCGTCGCGTACTTTACGCCATGAACGTATTGGGCAATGACTGGAAC
AAAGCCTATAAAAAATCTGCCCGTGTCGTTGGTGACGTAATCGGTAAATACCATCCCCACGGCGATTCCGCAGTGTATGACACCATCGTT
CGTATGGCGCAGCCATTCTCGCTGCGTTACATGCTGGTGGATGGTCAGGGTAACTTCGGTTCTATTGACGGCGACTCCGCGGCGGCAATG
CGTTATACGGAGATCCGTCTGGCGAAAATCGCCCACGAACTGATGGCCGATCTCGAAAAAGAGACGGTGGATTTCGTGGATAACTATGAC
GGTACGGAAAAAATTCCGGACGTCATGCCGACCAAAATTCCGAATCTGCTGGTGAACGGTTCTTCCGGTATCGCAGTAGGTATGGCGACG
AATATCCCGCCGCACAACCTGACGGAAGTGATTAACGGCTGCCTGGCGTATATCGACAACGAAGACATCAGCATTGAAGGGCTGATGGAA
CATATTCCGGGGCCGGACTTCCCGACCGCCGCGATCATCAACGGTCGTCGTGGTATCGAAGAAGCCTACCGCACCGGTCGTGGCAAAGTG
TACATTCGCGCCCGCGCGGAAGTTGAAGCTGACGCCAAAACGGGCCGTGAAACCATCATCGTCCATGAAATTCCCTATCAGGTGAACAAA
GCGCGCCTGATCGAGAAAATCGCCGAGCTGGTGAAAGATAAACGCGTGGAAGGCATCAGCGCGCTGCGTGACGAATCCGACAAAGACGGG
ATGCGCATCGTGATTGAAGTGAAACGCGATGCGGTGGGCGAGGTGGTGCTTAATAATCTCTACTCCCAGACCCAGCTACAGGTTTCCTTC
GGTATTAACATGGTGGCGCTGCATCACGGCCAGCCGAAGATCATGAACCTGAAAGATATCATTTCAGCGTTCGTGCGCCACCGCCGTGAA
GTGGTGACGCGTCGGACTATTTTTGAACTGCGTAAAGCCCGTGACCGTGCGCATATCCTTGAAGCTCTGGCGATTGCGCTGGCCAACATC
GACCCGATTATCGAACTGATTCGCCGCGCGCCAACGCCGGCGGAAGCAAAAGCGGCGCTGATTTCGCGTCCGTGGGATCTGGGCAACGTT
GCTGCGATGCTGGAGCGCGCTGGTGATGACGCCGCGCGTCCGGAATGGCTGGAGCCAGAATTTGGCGTGCGTGACGGTCAGTACTACCTG
ACTGAACAGCAGGCGCAGGCGATTCTGGATCTGCGTTTGCAGAAACTGACCGGCCTGGAGCATGAAAAACTGCTCGACGAATACAAAGAG
CTGCTGGAGCAGATTGCTGAATTGCTGCACATTCTGGGCAGCGCCGATCGCCTGATGGAAGTGATCCGCGAAGAGATGGAGTTAATTCGC
GATCAGTTCGGCGATGAGCGTCGTACCGAAATCACCGCCAACAGCGCCGATATTAATATCGAAGATCTGATTAGCCAGGAAGATGTTGTC
GTGACGCTGTCTCACCAGGGTTACGTCAAATATCAACCGCTGACAGATTACGAAGCGCAACGTCGTGGTGGGAAAGGTAAATCTGCCGCG
CGTATTAAAGAAGAAGACTTTATCGACCGCCTGCTGGTGGCTAACACCCATGACACCATCCTCTGCTTCTCCAGCCGGGGCCGTCTGTAC
TGGATGAAGGTCTATCAGCTGCCGGAAGCCAGCCGCGGCGCGCGCGGTCGTCCGATCGTCAACCTGCTGCCGCTGGAAGCCAACGAACGT
ATCACCGCGATTCTGCCGGTTCGTGAGTATGAAGAAGGCGTCAACGTCTTTATGGCGACCGCCAGCGGTACCGTGAAGAAAACGGCGCTG
ACCGAATTCAGCCGTCCGCGTTCCGCCGGTATTATCGCGGTGAACCTCAACGACGGCGACGAGCTGATTGGCGTTGACCTGACTTCTGGT
TCTGACGAAGTCATGCTGTTCTCGGCCGCGGGTAAAGTGGTGCGCTTCAAAGAAGACGCCGTCCGTGCGATGGGGCGTACCGCGACCGGT
GTGCGCGGTATTAAGCTGGCGGGAGACGATAAAGTCGTCTCTCTGATCATCCCACGCGGCGAAGGCGCTATTCTGACCGTAACGCAAAAC
GGCTACGGGAAGCGTACCGCAGCGGACGAGTACCCGACCAAGTCTCGTGCGACGCAGGGCGTTATCTCTATCAAAGTGACCGAGCGCAAC
GGTTCCGTTGTCGGTGCGGTACAGGTAGACGATTGCGACCAGATCATGATGATCACGGATGCCGGTACTCTGGTGCGTACCCGTGTGTCC
GAGATCAGCGTAGTGGGACGTAATACCCAGGGCGTTATCCTTATCCGCACGGCGGAAGATGAAAACGTGGTGGGTCTGCAACGCGTTGCT
GAACCGGTAGATGACGAAGAACTCGACGCTATCGACGGCAGCGTGGCGGAAGGGGATGAGGATATCGCCCCGGAAGCGGAAAGCGATGAC
GACGTTGCGGATGACGCTGACGAGTAA