Limitations of Standard Urine Culture in Detection of Polymicrobial UTI Infections

Margo Lee, Ph.D.

Standard urine culture (SUC) is a laboratory test first standardized in the 1950s to diagnose urinary tract infections.¹ The test is performed by using a urine specimen from a patient and placing it in a culture environment with nutrients and hormones to help promote bacteria growth. If a pathogen is present using these supportive conditions, bacteria, viruses, and yeast will be able to grow outside the body and can be identified using many different techniques, such as gram staining, direct fluorescence antibody (DFA), and direct microscopy.²


There are many limitations when using standard urine culture (SUC) to detect UTI pathogens. Pathogen growth in vitro is time intensive and can take 2-3 days to identify any growth present.³ Typically, empiric therapy will begin before a patient specimen is collected, and grown in culture, with results available, contributing to antibiotic resistance in a patient.⁴ Traditional laboratory culturing supports the growth of one or two pathogens per test, thus limiting the identification of 3+ pathogens in complex polymicrobial infections.^5,6 In these cases, a standard urine culture will produce a mixed flora or contaminated result, which will not give providers the diagnostic information to treat their patients effectively.

New molecular laboratory techniques, such as multiplex polymerase chain reaction (M-PCR), identify pathogens rapidly and with high sensitivity, specificity, and accuracy levels.⁷ Since specimens do not need to be grown in culture using this technology, patient results are delivered in less than one day upon receipt at the laboratory. Numerous pathogenic nucleic acid sequences can be detected accurately in one test, making it easy to detect many pathogens simultaneously without the limitations of a culture test.⁸ Using molecular probes, M-PCR can also help detect antibiotic resistance (ABR) genes, which cannot be performed using a standard urine culture test (SUC).

The limitations of standard urine culture, such as long growth times, collection of specimens, processing, and providing results, have been drivers for applying molecular techniques for pathogen detection.⁹ Pathogenic organisms and any antibiotic-resistance genes in monomicrobial and polymicrobial UTI infections can both be detected by utilizing PCR which amplifies genetic material. Some limitations of PCR are that it amplifies both live and nonviable organisms’ genetic material and does not measure phenotypic susceptibility, with a study showing 40% discordance between them, leading to potentially inappropriate antibiotic selection.¹⁰ So far, research studies are lacking that show a significant association between UTI PCR results alone and improved patient outcomes.¹¹ Guidance^® UTI has six clinical studies identifying reductions in critical adverse outcomes, healthcare resource utilization, and cost for complicated UTIs (cUTI). By addressing these diagnostic limitations in using standard urine culture and PCR in UTI diagnostics, Guidance^® UTI can help reduce empiric treatment and improve patient antibiotic stewardship.

Laboratory culture techniques can deliver phenotypic results from monomicrobial infections. Since many reoccurring, chronic UTIs are both monomicrobial and polymicrobial, new alternatives are needed to provide this type of information for polymicrobial infections. Guidance^® UTI testing forms this bridge to provide phenotypic information on polymicrobial infections to deliver the best solution for complicated UTIs.

Pathnostics’ Guidance^® UTI testing combines M-PCR testing and our unique patented Pooled Antibiotic Susceptibility Test (P-AST™) to help identify treatment options for complicated, recurrent, or persistent UTIs and elevated-risk patients.¹² Our P-AST™ testing determines the pooled antibiotic susceptibility obtained from a patient sample in the presence of 19 antibiotics. P-AST™ test results are combined with the molecular detection of 27 pathogens, three bacterial groups, two phenotypes (ESBL, MRSA), and 32 antibiotic-resistance genes. Our comprehensive patient reports are available in less than one day upon specimen receipt at our laboratory to help providers with complicated, reoccurring infections quickly, with high sensitivity/specificity, and comprehensively.

1 Kass EH. Asymptomatic infections of the urinary tract. 1956. J Urol. 2002 Feb;167(2 Pt 2):1016-9; discussion 1019-21. doi: 10.1016/s0022-5347(02)80328-7. PMID: 11905871.
2 Lynne S. Garcia Editor in Chief, Third Edition and 2007 Update, Henry D. Isenberg Editor in Chief, Original and Second Editions (Deceased), First published:1 August 2010 Online ISBN:9781683674054 |DOI:10.1128/9781555817435
3 Neopane, Puja & Nypaver, Jerome & Beqaj, S & Shrestha, Rojeet. (2022). Rapid Detection of Uropathogens and Antibiotic-resistant Genes Using Open Array Multiplex PCR Technology. American Journal of Clinical Pathology. 158. S143-S144. 10.1093/ajcp/aqac126.305.
4 Waller TA, Pantin SAL, Yenior AL, Pujalte GGA. Urinary Tract Infection Antibiotic Resistance in the United States. Prim Care. 2018 Sep;45(3):455-466. doi: 10.1016/j.pop.2018.05.005. Epub 2018 Jul 9. PMID: 30115334.
5 Sathiananthamoorthy S, Malone-Lee J, Gill K, Tymon A, Nguyen TK, Gurung S, Collins L, Kupelian AS, Swamy S, Khasriya R, Spratt DA, Rohn JL. Reassessment of Routine Midstream Culture in Diagnosis of Urinary Tract Infection. J Clin Microbiol. 2019 Feb 27;57(3):e01452-18. doi: 10.1128/JCM.01452-18. PMID: 30541935; PMCID: PMC6425166.
6 Nityadarshini, Neha & Mohapatra, Sarita & Gautam, Hitender & Jain, Vishesh & Chaudhry, Rama & Kapil, Arti. (2022). Polymicrobial growth in standard urine culture: Time to Act or Ignore?. Tropical Doctor. 52. 004947552210769. 10.1177/00494755221076909.
7 P Neopane, J Nypaver, S S Beqaj, R Shrestha, Rapid Detection of Uropathogens and Antibiotic-resistant Genes Using Open Array Multiplex PCR Technology, American Journal of Clinical Pathology, Volume 158, Issue Supplement_1, November 2022, Pages S143–S144, https://doi.org/10.1093/ajcp/aqac126.305
8 Sun Z, Liu W, Zhang J, Wang S, Yang F, Fang Y, Jiang W, Ding L, Zhao H, Zhang Y. The Direct Semi-Quantitative Detection of 18 Pathogens and Simultaneous Screening for Nine Resistance Genes in Clinical Urine Samples by a High-Throughput Multiplex Genetic Detection System. Front Cell Infect Microbiol. 2021 Apr 12;11:660461. doi: 10.3389/fcimb.2021.660461. PMID: 33912478; PMCID: PMC8072482.
9 Davenport M, Mach KE, Shortliffe LMD, Banaei N, Wang TH, Liao JC. New and developing diagnostic technologies for urinary tract infections. Nat Rev Urol. 2017 May;14(5):296-310. doi: 10.1038/nrurol.2017.20. Epub 2017 Mar 1. PMID: 28248946; PMCID: PMC5473291.
10 Baunoch D, Luke N, Wang D, Vollstedt A, Zhao X, Ko DSC, Huang S, Cacdac P, Sirls LT. Concordance Between Antibiotic Resistance Genes and Susceptibility in Symptomatic Urinary Tract Infections. Infect Drug Resist. 2021 Aug 19;14:3275-3286. doi: 10.2147/IDR.S323095. PMID: 34447256; PMCID: PMC8382965.
11 Baunoch D, Luke N, Wang D, Vollstedt A, Zhao X, Ko DSC, Huang S, Cacdac P, Sirls LT. Concordance Between Antibiotic Resistance Genes and Susceptibility in Symptomatic Urinary Tract Infections. Infect Drug Resist. 2021 Aug 19;14:3275-3286. doi: 10.2147/IDR.S323095. PMID: 34447256; PMCID: PMC8382965.
12 Baunoch D, Luke N, Wang D, Vollstedt A, Zhao X, Ko DSC, Huang S, Cacdac P, Sirls LT. Concordance Between Antibiotic Resistance Genes and Susceptibility in Symptomatic Urinary Tract Infections. Infect Drug Resist. 2021 Aug 19;14:3275-3286. doi: 10.2147/IDR.S323095. PMID: 34447256; PMCID: PMC8382965.