Escherichia coli soxS with mutation conferring antibiotic resistance

Download Sequences
Accession ARO:3003511
CARD Short NameEcol_soxS_MULT
DefinitionSoxS is a global regulator that up-regulates the expression of AcrAB efflux genes. It also reduces OmpF expression to decrease cell membrane permeability.
AMR Gene Familyresistance-nodulation-cell division (RND) antibiotic efflux pump, ATP-binding cassette (ABC) antibiotic efflux pump, major facilitator superfamily (MFS) antibiotic efflux pump, General Bacterial Porin with reduced permeability to beta-lactams
Drug Classtetracycline antibiotic, cephalosporin, phenicol antibiotic, glycylcycline, penam, fluoroquinolone antibiotic, disinfecting agents and antiseptics, rifamycin antibiotic, monobactam, cephamycin, carbapenem, penem
Resistance Mechanismantibiotic efflux, reduced permeability to antibiotic, antibiotic target alteration
Efflux Componentefflux pump complex or subunit conferring antibiotic resistance
Efflux Regulatorprotein(s) and two-component regulatory system modulating antibiotic efflux
Resistomes with Sequence VariantsCitrobacter amalonaticusg, Citrobacter freundiig, Citrobacter koserig, Citrobacter portucalensisg, Citrobacter werkmaniig, Citrobacter youngaeg, Escherichia albertiig, Escherichia colig+p, Escherichia fergusoniig, Escherichia marmotaeg, Klebsiella aerogenesg, Klebsiella oxytocap, Salmonella bongorig, Salmonella entericag, Shigella boydiig, Shigella dysenteriaeg, Shigella flexnerig, Shigella sonneig
Classification46 ontology terms | Show
+ process or component of antibiotic biology or chemistry
+ antibiotic molecule
+ beta-lactam antibiotic
+ mechanism of antibiotic resistance
+ determinant of antibiotic resistance
+ antibiotic efflux [Resistance Mechanism]
+ tetracycline antibiotic [Drug Class]
+ reduced permeability to antibiotic [Resistance Mechanism]
+ cephem
+ cephalosporin [Drug Class]
+ phenicol antibiotic [Drug Class]
+ glycylcycline [Drug Class]
+ protein modulating permeability to antibiotic
+ penam [Drug Class]
+ antibiotic target alteration [Resistance Mechanism]
+ fluoroquinolone antibiotic [Drug Class]
+ efflux pump complex or subunit conferring antibiotic resistance [Efflux Component]
+ disinfecting agents and antiseptics [Drug Class]
+ rifamycin antibiotic [Drug Class]
+ monobactam [Drug Class]
+ resistance-nodulation-cell division (RND) antibiotic efflux pump [AMR Gene Family]
+ norfloxacin [Antibiotic]
+ ciprofloxacin [Antibiotic]
+ rifampin [Antibiotic]
+ chloramphenicol [Antibiotic]
+ General Bacterial Porin (GBP)
+ cephamycin [Drug Class]
+ ATP-binding cassette (ABC) antibiotic efflux pump [AMR Gene Family]
+ cefalotin [Antibiotic]
+ tetracycline [Antibiotic]
+ carbapenem [Drug Class]
+ penem [Drug Class]
+ ampicillin [Antibiotic]
+ major facilitator superfamily (MFS) antibiotic efflux pump [AMR Gene Family]
+ tigecycline [Antibiotic]
+ mutation conferring antibiotic resistance
+ triclosan [Antibiotic]
+ General Bacterial Porin with reduced permeability to beta-lactams [AMR Gene Family]
+ PatA-PatB
+ AcrAB-TolC
+ protein(s) and two-component regulatory system modulating antibiotic efflux [Efflux Regulator]
+ QepA1
+ antibiotic resistant gene variant or mutant
+ soxRS
+ mutant efflux regulatory protein conferring antibiotic resistance
+ porin OmpF
Parent Term(s)4 ontology terms | Show
+ soxS
+ confers_resistance_to_antibiotic enrofloxacin [Antibiotic]
+ confers_resistance_to_antibiotic ciprofloxacin [Antibiotic]
+ confers_resistance_to_antibiotic chloramphenicol [Antibiotic]
Publications

Aly SA, et al. 2015. J. Antimicrob. Chemother. 70(8):2228-33 A novel alanine to serine substitution mutation in SoxS induces overexpression of efflux pumps and contributes to multidrug resistance in clinical Escherichia coli isolates. (PMID 25921515)
Resistomes

Prevalence of Escherichia coli soxS with mutation conferring antibiotic resistance among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 381 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 overexpression model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Citrobacter amalonaticus100%0%0%0%
Citrobacter freundii99.18%0%0%0%
Citrobacter koseri100%0%0%0%
Citrobacter portucalensis100%0%0%0%
Citrobacter werkmanii100%0%0%0%
Citrobacter youngae100%0%0%0%
Escherichia albertii100%0%0%0%
Escherichia coli67.77%0.02%0%0%
Escherichia fergusonii100%0%0%0%
Escherichia marmotae100%0%0%0%
Klebsiella aerogenes98%0%0%0%
Klebsiella oxytoca0%0.68%0%0%
Salmonella bongori100%0%0%0%
Salmonella enterica95.71%0%0%0%
Shigella boydii93.33%0%0%0%
Shigella dysenteriae100%0%0%0%
Shigella flexneri99%0%0%0%
Shigella sonnei97.56%0%0%0%
Show Perfect Only


Detection Models

Model Type: protein overexpression model

Model Definition: Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from 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 Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain 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 may or may not contain at least one curated mutation from amongst the mapped resistance variants.

Bit-score Cut-off (blastP): 200

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:


>gb|AAC77032.1|-|Escherichia coli soxS with mutation conferring antibiotic resistance [Escherichia coli str. K-12 substr. MG1655]
MSHQKIIQDLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLL
LAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTPSDYRHRL


>gb|U00096.3|-|4277060-4277383|Escherichia coli soxS with mutation conferring antibiotic resistance [Escherichia coli str. K-12 substr. MG1655]
ATGTCCCATCAGAAAATTATTCAGGATCTTATCGCATGGATTGACGAGCATATTGACCAGCCGCTTAACATTGATGTAGTCGCAAAAAAA
TCAGGCTATTCAAAGTGGTACTTGCAACGAATGTTCCGCACGGTGACGCATCAGACGCTTGGCGATTACATTCGCCAACGCCGCCTGTTA
CTGGCCGCCGTTGAGTTGCGCACCACCGAGCGTCCGATTTTTGATATCGCAATGGACCTGGGTTATGTCTCGCAGCAGACCTTCTCCCGC
GTTTTCCGTCGGCAGTTTGATCGCACTCCCAGCGATTATCGCCACCGCCTGTAA