Shigella flexneri parC conferring resistance to fluoroquinolones

Accession ARO:3003941
DefinitionPoint mutation in parC conferring resistance to fluoroquinolone antibiotics in Shigella flexneri,
AMR Gene Familyfluoroquinolone resistant parC
Drug Classfluoroquinolone antibiotic
Resistance Mechanismantibiotic target alteration
Classification11 ontology terms | Show
Parent Term(s)3 ontology terms | Show
+ fluoroquinolone resistant parC [AMR Gene Family]
+ confers_resistance_to_antibiotic nalidixic acid [Antibiotic]
+ confers_resistance_to_antibiotic norfloxacin [Antibiotic]
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 parC 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): 1400

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:

PMID: 27620866A85T D111H S129P

>gb|AAN44541.1|-|Shigella flexneri parC conferring resistance to fluoroquinolones [Shigella flexneri 2a str. 301]
MSDMAERLALHEFTENAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNASAKF
KKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRY
TESRLSKYSELLLSELGQGTADWVPNFDGTLQEPKMLPARLPNILLNGTTGIAVGMATDI
PPHNLREVAQAAIALIDQPKTTLDQLLDIVQGPDYPTEAEIITSRAEIRKIYENGRGSVR
MRAVWKKEDGAVVISALPHQVSGARVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIV
PRSNRVDMDQVMNHLFATTDLEKSYRINLNMIGLDGRPAVKNLLEILSEWLVFRRDTVRR
RLNYRLEKVLKRLHILEGLLVAFLNIDEVIEIIRNEDEPKPALMSRFGLTETQAEAILEL
KLRHLAKLEEMKIRGEQSELEKERDQLQGILASERKMNNLLKKELQADAQAYGDDRRSPL
QEREEAKAMSEHDMLPSEPVTIVLSQMGWVRSAKGHDIDAPGLNYKAGDSFKAAVKGKSN
QPVVFVDSTGRSYAIDPITLPSARGQGEPLTGKLTLPPGATVDHMLMESDDQKLLMASDA
GYGFVCTFNDLVARNRAGKALITLPENAHVMPPVVIEDASDMLLAITQAGRMLMFPVSDL
PQLSKGKGNKIINIPSAEAARGEDGLAQLYVLPPQSTLTIHVGKRKIKLRPEELQKVTGE
RGRRGTLMRGLQRIDRVEIDSPRRASSGDSEE



>gb|AE005674.2|-|3159155-3161413|Shigella flexneri parC conferring resistance to fluoroquinolones [Shigella flexneri 2a str. 301]
ATGAGCGATATGGCAGAGCGCCTTGCGCTACATGAATTTACGGAAAACGCCTACTTAAACTACTCCATGTACGTGATCATGGACCGTGCG
TTGCCGTTTATTGGTGATGGTCTGAAACCTGTTCAGCGCCGCATTGTGTATGCGATGTCTGAACTGGGCCTGAATGCCAGCGCCAAATTT
AAAAAATCGGCCCGTACCGTCGGTGACGTACTGGGTAAATACCATCCGCACGGCGATAGCGCCTGTTATGAAGCGATGGTCCTGATGGCG
CAGCCGTTCTCTTACCGTTATCCGCTGGTTGATGGTCAGGGGAACTGGGGCGCGCCGGACGATCCGAAATCGTTCGCGGCAATGCGTTAC
ACCGAATCCCGGTTGTCGAAATATTCCGAGCTGCTATTGAGCGAGCTGGGGCAGGGGACGGCTGACTGGGTGCCAAACTTCGACGGCACT
TTGCAGGAGCCGAAAATGCTACCTGCCCGTCTGCCAAACATTTTGCTTAACGGCACCACCGGTATTGCCGTCGGCATGGCGACCGATATT
CCACCGCATAACCTGCGTGAAGTAGCTCAGGCGGCAATCGCATTAATCGACCAGCCGAAAACTACGCTCGATCAGCTGCTGGATATCGTG
CAGGGGCCGGATTATCCGACTGAAGCGGAAATTATCACTTCGCGCGCCGAGATTCGTAAAATCTACGAGAACGGACGTGGTTCAGTGCGT
ATGCGCGCGGTGTGGAAGAAAGAAGATGGCGCGGTGGTTATCAGCGCATTACCGCATCAGGTTTCAGGTGCGCGCGTACTGGAGCAAATT
GCTGCGCAAATGCGCAACAAAAAGCTGCCGATGGTTGACGATCTGCGCGATGAATCTGACCACGAGAACCCGACCCGTCTGGTGATTGTG
CCGCGTTCCAACCGCGTGGATATGGATCAGGTGATGAACCACCTCTTCGCTACCACCGATCTGGAAAAGAGCTATCGCATTAACCTCAAT
ATGATCGGTCTGGATGGTCGTCCGGCGGTGAAAAACCTGCTGGAAATCCTCTCCGAATGGCTGGTGTTCCGTCGCGATACCGTGCGCCGC
CGACTGAACTATCGTCTGGAGAAAGTCCTCAAGCGCCTGCATATCCTGGAAGGTTTGCTGGTGGCGTTTCTCAACATCGACGAAGTGATT
GAGATCATTCGTAACGAAGATGAACCGAAACCGGCGCTGATGTCGCGGTTTGGCCTTACGGAAACCCAGGCGGAAGCGATCCTCGAACTG
AAACTGCGTCATCTTGCCAAACTGGAAGAGATGAAGATTCGCGGTGAGCAGAGTGAGCTGGAAAAAGAGCGCGACCAGTTGCAGGGCATT
TTGGCTTCCGAGCGTAAAATGAATAACCTGCTGAAGAAAGAACTGCAGGCAGACGCGCAAGCCTACGGTGACGATCGTCGTTCGCCGTTG
CAGGAACGCGAAGAAGCGAAAGCGATGAGCGAGCACGACATGCTGCCGTCTGAACCTGTCACCATTGTGCTGTCGCAGATGGGCTGGGTA
CGCAGCGCTAAAGGCCATGATATCGACGCGCCGGGCCTGAATTATAAAGCGGGTGATAGCTTCAAAGCGGCGGTGAAAGGTAAGAGTAAC
CAACCGGTAGTGTTTGTTGATTCCACCGGTCGTAGCTATGCCATCGACCCGATTACGCTGCCGTCGGCGCGTGGTCAGGGCGAACCACTC
ACCGGCAAATTAACGTTGCCGCCTGGGGCGACCGTTGACCATATGCTGATGGAAAGCGACGATCAGAAACTGCTGATGGCTTCCGATGCG
GGTTACGGTTTCGTCTGCACCTTTAACGATCTGGTAGCGCGTAACCGTGCGGGTAAGGCTTTGATCACCTTACCGGAAAATGCCCATGTT
ATGCCGCCGGTGGTGATTGAAGATGCTTCCGATATGCTGCTGGCAATCACTCAGGCAGGCCGTATGTTGATGTTCCCGGTAAGCGATCTG
CCGCAGCTGTCGAAGGGCAAAGGCAACAAGATTATCAACATTCCATCGGCAGAAGCCGCGCGTGGCGAGGATGGTCTGGCGCAACTGTAC
GTTCTGCCGCCGCAAAGCACGCTGACCATTCATGTTGGGAAACGCAAAATTAAACTGCGTCCGGAAGAGCTACAGAAAGTCACTGGCGAA
CGTGGACGCCGCGGTACGTTGATGCGCGGTTTGCAGCGTATCGATCGTGTTGAGATCGACTCTCCTCGCCGTGCCAGCAGCGGTGATAGC
GAAGAGTAA