Site gating for urine
Urinary-only agents are graded when the specimen is urine and marked not applicable for every other site. The reverse also holds: agents that don't achieve useful urinary concentrations aren't offered for a urinary source.
Organism rules that change the urinary grid
- Proteus mirabilis / vulgaris are intrinsically resistant to nitrofurantoin and the tetracyclines, so a common first-line cystitis agent is removed for them.
- Klebsiella is intrinsically resistant to ampicillin.
- Pseudomonas aeruginosa removes most oral options, including TMP-SMX.
- Enterococcus is intrinsically resistant to cephalosporins.
Genes that matter most in urine
Beta-lactamase genes (CTX-M, KPC / SHV, AmpC), plasmid quinolone resistance (qnrA / qnrB, qnrS) and folate-pathway genes (dfrA, sul1 / sul2) move the common oral options. CORE-ABR applies each only to the organisms known to carry it.
Molecular detection does not replace urine culture or phenotypic susceptibility testing. Absence of a detected resistance gene does not establish susceptibility.
Pathogens on UTI panels
Acinetobacter baumanniiA non-fermenting gram-negative bacillus, notorious in healthcare settings for accumulating resistance.Gram-negative bacteria · UTI · Wound · STICitrobacter freundiiAn Enterobacterales species that carries a chromosomal AmpC beta-lactamase.Gram-negative bacteria · UTI · Wound · STIEnterobacter aerogenes / cloacaeEnterobacterales with chromosomal AmpC. E. aerogenes has been renamed Klebsiella aerogenes; many panels still report the…Gram-negative bacteria · UTI · Wound · STIEscherichia coliThe most common cause of urinary tract infection, and a frequent organism in wound and intra-abdominal specimens.Gram-negative bacteria · UTI · WoundHaemophilus influenzaeA small gram-negative coccobacillus, more familiar from the respiratory tract but detected on some wound and urinary pan…Gram-negative bacteria · UTI · WoundKlebsiella pneumoniae / oxytocaCommon uropathogens and a leading host of ESBL and KPC carbapenemase genes.Gram-negative bacteria · UTI · Wound · STIProteus mirabilis / vulgarisUrease-producing Enterobacterales associated with complicated UTI, catheters and stones.Gram-negative bacteria · UTI · WoundPseudomonas aeruginosaA non-fermenting gram-negative bacillus common in chronic wounds and complicated UTI, with a long list of intrinsic resi…Gram-negative bacteria · UTI · Wound · STIStaphylococcus aureusThe leading cause of skin and soft-tissue infection, and the organism most wound reports are built around.Gram-positive bacteria · UTI · Wound · STIStaphylococcus epidermidisA coagulase-negative staphylococcus that lives on normal skin. Usually a colonizer; sometimes the cause — particularly w…Gram-positive bacteria · UTI · WoundStreptococcus pyogenesGroup A streptococcus — a cause of cellulitis, erysipelas and necrotizing soft-tissue infection.Gram-positive bacteria · UTI · WoundStreptococcus agalactiaeGroup B streptococcus — found in urinary, genital and diabetic-foot specimens.Gram-positive bacteria · UTI · WoundEnterococcus speciesGram-positive cocci common in urinary and wound specimens. Many panels detect E. faecalis and E. faecium in one pooled w…Gram-positive bacteria · UTI · WoundMycoplasma hominis / genitaliumBacteria without a cell wall, found in genitourinary and occasionally wound specimens.Atypical and cell-wall-deficient bacteria · UTI · Wound · STIUreaplasma parvum / urealyticumCell-wall-deficient bacteria frequently present in the lower genitourinary tract, often without disease.Atypical and cell-wall-deficient bacteria · UTI · STIGardnerella vaginalisAn organism associated with bacterial vaginosis, commonly detected on combined UTI/STI panels.Atypical and cell-wall-deficient bacteria · UTI · STITreponema pallidumThe spirochete that causes syphilis.Atypical and cell-wall-deficient bacteria · UTI · STITrichomonas vaginalisA protozoan parasite and the most common curable non-viral STI.Protozoan · UTI · STICandida albicansThe most common Candida species — frequently a colonizer of skin, urine and mucosa, sometimes the cause.Fungus · UTI · Wound · STICandida glabrata / tropicalisNon-albicans Candida species. C. glabrata (now Nakaseomyces glabratus) often shows reduced susceptibility to fluconazole…Fungus · UTI · Wound · STIEnterovirusA genus of RNA viruses that includes the causes of hand, foot and mouth disease.Virus · UTI · Wound
Resistance genes relevant to UTI
mecA / mecCMethicillin resistance (MRSA, MRSE)2 organisms on panelvanA / vanBVancomycin resistance (VRE)1 organisms on paneltetB / tetMTetracycline resistance9 organisms on panelermB / ermCMLSb resistance7 organisms on paneldfrA1 / dfrA5Trimethoprim resistance6 organisms on panelsul1 / sul2Sulfonamide resistance6 organisms on panelqnrA / qnrBPlasmid-mediated quinolone resistance7 organisms on panelqnrSPlasmid-mediated quinolone resistance3 organisms on panelClass A beta-lactamase (CTX-M)Extended-spectrum beta-lactamase (ESBL) production6 organisms on panelClass A beta-lactamase (KPC / SHV)Carbapenemase (KPC) or ESBL (SHV variants) production5 organisms on panelClass C beta-lactamase (AmpC)AmpC cephalosporinase production5 organisms on panelClass D beta-lactamase (OXA)Oxacillinase production4 organisms on panelClass B metallo-beta-lactamase (IMP / VIM)Metallo-carbapenemase production5 organisms on panel
Decision support only. The treating clinician decides. Molecular genotype does not replace phenotypic susceptibility testing, culture, or public-health reporting. Absence of a detected resistance gene does not establish susceptibility. Organism targets vary by panel; CORE-ABR is configured to the assay each laboratory runs.