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About Guidance® UTI Testing Methodology


The Guidance® UTI Assay is made up of two components:

1. The extraction of DNA from the patient’s urine sample followed by semi-quantitative multiplex polymerase chain reaction (M-PCR) for the detection of UTI relevant bacteria, fungi, and antibiotic resistance genes.

2. Pooled Antibiotic Susceptibility Testing (P-AST™) is a proprietary method to determine the antibiotic susceptibility for multiple antibiotics against the pool of organisms in the urine sample and is reported in those samples that are positive by M-PCR for non-fastidious bacteria.

Clinical Significance

The combination of PCR and P-AST™ is backed by clinical evidence in multiple peer reviewed publications and allows for more informed treatment decisions.  Multiple clinical trials evaluating Guidance® UTI have demonstrated the improved detection of uropathogens and improved outcomes in presumed UTI cases as compared to standard urine culture.1-9

Organisms Tested:

If detected, targets are reported semi-quantitatively as cells per milliliter in the following ranges:

  • <10,000 cells/mL
  • 10,000-49,999 cells/mL
  • 50,000-99,999 cells/mL
  • >100,000 cells/mL

Identifies 27 individual organisms and 3 bacterial groups.

  • Acinetobacter baumannii
  • Actinotignum schaalii
  • Aerococcus urinae
  • Alloscardovia omnicolens
  • Candida albicans
  • Candida auris
  • Candida glabrata
  • Candida parapsilosis
  • Citrobacter freundii
  • Citrobacter koseri
  • Corynebacterium riegelii
  • Enterococcus faecalis
  • Enterococcus faecium
  • Escherichia coli
  • Gardnerella vaginalis
  • Klebsiella oxytoca
  • Klebsiella pneumoniae
  • Morganella morganii
  • Mycoplasma hominis
  • Pantoea agglomerans
  • Proteus mirabilis
  • Providencia stuartii
  • Pseudomonas aeruginosa
  • Serratia marcescens
  • Staphylococcus aureus
  • Streptococcus agalactiae
  • Ureaplasma urealyticum
  • Coagulase-negative staphylococci*
  • Viridans group streptococci†
  • Enterobacter group‡

ESBL phenotypic assay will be performed when E. coli, Klebsiella, Enterocobacter, Citrobacter, Proteus, Acinetobacter, or Pseudomonas are detected and is a chromatographic assay that detects the presence of active B-lactamase enzyme, a protein produced by bacteria that is responsible for degrading beta-lactam antibiotic, thereby renders them ineffective.

MRSA phenotypic assay will be performed when selected and Staphylococcus aureus and the mecA gene are detected.

*Coagulase-negative staphylococci: Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus lugdunenesis, Staphylococcus saprophyticus
Viridans group streptococci: Streptococcus anginosus, Streptococcus oralis, Streptococcus pasteuranus
‡Enterobacter group: Klebsiella aerogenes (formally known as Enterobacter aerogenes), Enterobacter cloacae

Resistance Genes:

Guidance® UTI tests for 32 resistance genes from six different classes of antibiotics.  When detected, resistance genes detected (RGD) will be indicated on the table of the report.

Ampicillin resistance genes: AmpC, FOX, ACC, DHA, MOX/CMY, BIL/LAT/CMY
Extended-spectrum beta-lactamases (ESBL) resistance genes: CTX-M group 1, CTX-M group 2, CTX-M group 8/25, CTX-M group 9, OXA-1, SHV, TEM, VEB, GES, PER-1, PER-2
Methicillin resistance genes: mecA
Quinolone and fluoroquinolone resistance genes: QnrA, QnrS
Vancomycin resistance genes: vanA1, vnA2, vanB
Carbapenems resistance genes: IMP-1 group, KPC, OXA-23, OXA-40, blaOXA-48, VIM, IMP-7, IMP-16 OXA-72

Pooled Antibiotic Sensitivity Testing:

P-AST™ is not performed when only the following are detected:

  • Fastidious or slow growing organisms: Gardnerella vaginalis, Ureaplasma urealyticum, Actinobaculum schaalii, Aerococcus urinae, Alloscardovia omnicolens. Corynebacterium riegelii, Mycoplasma hominis, and Enterococcus faecium.
  • Yeast: Candida albicans, Candida auris, Candida glabrata, and Candida parapsilosis.
  • Viridans group streptococci (Streptococcus anginosus, Streptococcus oralis, Streptococcus pasteuranus)

In addition to providing both the presence of resistance genes (RGD) and pooled antibiotic susceptibility patterns (S for sensitive, R for resistance), we also include a table of antibiotics that have shown strong supportive evidence for use in the treatment of UTI.

The checkmarks indicate situations for which

  • The FDA shows the antibiotic is efficacious for the indicated organisms
  • In vitro data shows MIC levels equal to or less than the susceptibility breakpoints
  • CLSI breakpoints are reported for urine culture
  • Or there is sufficient literature supporting the use of the efficacious use antibiotic for the organism listed.

Appropriate medical judgement should be exercised by the health care provider before prescribing a course of treatment. Further treatment or workup may be necessary if clinically indicated.

White boxes with checkmarks indicate situations where the pool of organisms was susceptible to an antibiotic and there is supportive evidence for the organisms listed. There may be changes in research showing changes in antibiotic susceptibility. Although we attempt to update the report with new data promptly, we cannot prevent delays.

Candida auris:

Candida auris is an emerging fungus that presents a serious global health threat and can be the cause of bloodstream infections, wound infections, and ear infections. It also has been isolated from respiratory and urine specimens. Click here for guidance on C. auris.


We do not perform antifungal susceptibility testing.


This test was developed, and its performance characteristics determined by Pathnostics. It has not been cleared or approved by the US Food and Drug Administration. The FDA has determined that such clearance or approvals is not necessary. This test is used for clinical purposes. It should not be regarded as investigational or for research. This laboratory is certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA-88) as qualified to perform high complexity clinical testing. Urine specimens received greater than 5 days post collection may give unreliable cells/mL counts due to overgrowth of microorganism(s).


  1. Wojno KJ, Baunoch D, Luke N. Multiplex PCR Based Urinary Tract Infection (UTI) Analysis Compared to Traditional Urine Culture in Identifying Significant Pathogens in Symptomatic Patients. Urology. 2019;136:119-126.
  2. Vollstedt A, Baunoch D, Wojno KJ, et al. Multisite Prospective Comparison of Multiplex Polymerase Chain Reaction Testing with Urine Culture for Diagnosis of Urinary Tract Infections in Symptomatic Patients. J Sur Urology . 2020;JSU-102. DOI: 10.29011/ JSU-102.100002.
  3. Vollstedt A, Baunoch D, Wolfe A, et al. Bacterial Interactions as Detected by Pooled Antibiotic Susceptibility Testing (P-AST) in Polymicrobial Urine Specimens. J Sur Urology. 2020;JSU-101. DOI: 10.29011/JSU-101.100001.
  4. Daly A, Baunoch D, Rehling K, et al. Utilization of M-PCR and P-AST for Diagnosis and Management of Urinary Tract Infections in Home-Based Primary Care. JOJ Urology & Nephrology. 2020;7(2),555707. DOI: 10.19080/JOJUN.2020.07.555707.
  5. Luke N, Baunoch D. After 180 Years, Is it Time for Something Better for Diagnosing UTIs? JOJ Urology & Nephrology. 2020;7(2):555714. DOI: 10.19080/JOJUN.2020.07.555714.
  6. Baunoch D, Luke N, Wang D, et al. Concordance Between Antibiotic Resistance Genes and Susceptibility in Symptomatic Urinary Tract Infections. Infection and Drug Resistance. 2021;14:3275-3286. DOI: 10.2147/IDR.S323095.
  7. Korman A, Ramanathan S, Shen N, et al. The Diagnosis of Urinary Tract Infections Using a Novel At-home Testing Protocol to Enhance Telemedicine: A Retrospective Analysis. Ambulatory, Office-based, and Geriatric Urology. 2023;127:26-31. DOI: 10.1016/j.urology.2022.12.023.
  8. Korman HJ, Baunoch D, Luke N, et al. A Diagnostic Test Combining Molecular Testing with Phenotypic Pooled Antibiotic Susceptibility Improved the Clinical Outcomes of Patients with Non-E. coli or Polymicrobial Complicated Urinary Tract Infections. Res Rep Urol. 2023;15:141-147. DOI: 10.2147/RRU.S404260.
  9. Korman HJ, Mathur M, Luke N, et al. Multiplex Polymerase Chain Reaction/Pooled Antibiotic Susceptibility Testing Was Not Associated with Increased Antibiotic Resistance in Management of Complicated Urinary Tract Infections. Infect Drug Resist. 2023;16:2841-2848. DOI: 10.2147/IDR.S406745.
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