Escherichia coli soxS with mutation conferring antibiotic resistance

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 Familymajor facilitator superfamily (MFS) antibiotic efflux pump, ATP-binding cassette (ABC) antibiotic efflux pump, resistance-nodulation-cell division (RND) antibiotic efflux pump, General Bacterial Porin with reduced permeability to beta-lactams
Drug Classtetracycline antibiotic, disinfecting agents and antiseptics, phenicol antibiotic, fluoroquinolone antibiotic, glycylcycline, penam, cephalosporin, rifamycin antibiotic, monobactam, cephamycin, carbapenem, penem
Resistance Mechanismreduced permeability to antibiotic, antibiotic efflux, 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+wgs, Citrobacter freundiig+wgs, Citrobacter koserig+wgs, Citrobacter portucalensisg+wgs, Citrobacter werkmaniig+wgs, Citrobacter youngaeg+wgs, Enterobacter cloacaewgs, Enterobacter hormaecheiwgs, Escherichia albertiig+wgs, Escherichia colig+p+wgs, Escherichia fergusoniig+wgs, Escherichia marmotaeg+wgs, Klebsiella aerogenesg+wgs, Klebsiella oxytocap, Klebsiella pneumoniaewgs, Salmonella entericag+wgs, Shigella boydiig+wgs, Shigella dysenteriaeg+wgs, Shigella flexnerig+wgs, Shigella sonneig+wgs
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
+ cephem
+ reduced permeability to antibiotic [Resistance Mechanism]
+ antibiotic efflux [Resistance Mechanism]
+ tetracycline antibiotic [Drug Class]
+ disinfecting agents and antiseptics [Drug Class]
+ efflux pump complex or subunit conferring antibiotic resistance [Efflux Component]
+ phenicol antibiotic [Drug Class]
+ fluoroquinolone antibiotic [Drug Class]
+ glycylcycline [Drug Class]
+ penam [Drug Class]
+ cephalosporin [Drug Class]
+ rifamycin antibiotic [Drug Class]
+ protein modulating permeability to antibiotic
+ antibiotic target alteration [Resistance Mechanism]
+ mutation conferring antibiotic resistance
+ tigecycline [Antibiotic]
+ monobactam [Drug Class]
+ cephamycin [Drug Class]
+ ciprofloxacin [Antibiotic]
+ chloramphenicol [Antibiotic]
+ norfloxacin [Antibiotic]
+ cefalotin [Antibiotic]
+ major facilitator superfamily (MFS) antibiotic efflux pump [AMR Gene Family]
+ ATP-binding cassette (ABC) antibiotic efflux pump [AMR Gene Family]
+ tetracycline [Antibiotic]
+ carbapenem [Drug Class]
+ rifampin [Antibiotic]
+ triclosan [Antibiotic]
+ resistance-nodulation-cell division (RND) antibiotic efflux pump [AMR Gene Family]
+ General Bacterial Porin (GBP)
+ penem [Drug Class]
+ ampicillin [Antibiotic]
+ antibiotic resistant gene variant or mutant
+ protein(s) and two-component regulatory system modulating antibiotic efflux [Efflux Regulator]
+ QepA1
+ PatA-PatB
+ General Bacterial Porin with reduced permeability to beta-lactams [AMR Gene Family]
+ AcrAB-TolC
+ mutant efflux regulatory protein conferring antibiotic resistance
+ soxRS
+ porin OmpF
Parent Term(s)1 ontology terms | Show
+ soxS

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)


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 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 overexpression model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Citrobacter amalonaticus100%0%87.5%0%
Citrobacter freundii99.23%0%57.72%0%
Citrobacter koseri100%0%46.67%0%
Citrobacter portucalensis100%0%86%0%
Citrobacter werkmanii100%0%100%0%
Citrobacter youngae100%0%100%0%
Enterobacter cloacae0%0%0.91%0%
Enterobacter hormaechei0%0%0.24%0%
Escherichia albertii100%0%97.7%0%
Escherichia coli61.46%0.03%74.67%0%
Escherichia fergusonii100%0%44.62%0%
Escherichia marmotae100%0%69.05%0%
Klebsiella aerogenes97.5%0%76.73%0%
Klebsiella oxytoca0%0.95%0%0%
Klebsiella pneumoniae0%0%0.09%0%
Salmonella enterica94.6%0%89.22%0%
Shigella boydii92.86%0%94.62%0%
Shigella dysenteriae90.91%0%100%0%
Shigella flexneri94.74%0%83.33%0%
Shigella sonnei100%0%95.34%0%
Show Perfect Only

Detection Models

Model Type: protein overexpression model

Model Definition: This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).

Bit-score Cut-off (blastP): 200


  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB

Published Variants:

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

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