PCR vs. Culture: Why Testing for DNA Directly Is More Accurate
For decades, the standard way to find an infection was to culture it: put the sample on a growth medium and wait to see whether bacteria grow. Today, molecular tests such as PCR (polymerase chain reaction), part of the broader family of nucleic acid amplification tests (NAATs), look for the organism's DNA directly. For sexually transmitted infections, and for organisms that are hard to grow, the difference in accuracy and speed is large.
How culture works, and where it falls short
A culture only turns positive if the organism is still alive when it reaches the lab, and if it grows on the medium the lab uses. That creates several problems:
- Organisms die in transit. Bacteria in a urine sample keep changing after collection. Unpreserved urine left at room temperature for 24 hours or more shows significant overgrowth, which is why culture labs use boric-acid "C&S" (culture and sensitivity) tubes. Even with that preservative, the manufacturer rates the specimen as stable for up to 48 hours at room temperature.4,5 A kit that sits in the mail longer than that may no longer give a reliable culture.
- Some organisms barely grow at all. Mycoplasma genitalium can take up to six months to grow in culture, and that capacity exists only in research labs.2 Mycoplasma hominis and Ureaplasma need special media and take two to five days.6 Routine urine cultures are not set up to grow them.
- Culture misses infections. For trichomoniasis, the CDC lists culture sensitivity at 44%–75%, compared with 95.3%–100% for a nucleic acid amplification test.1 For gonorrhea at throat and rectal sites, culture caught 41%–43% of infections while NAATs caught 72%–93%, and switching to NAAT more than doubled the number of infections found in one study.3
- Culture is slow. Growing, identifying and confirming organisms takes days. PCR for Mycoplasma and Ureaplasma can produce a result in about three hours of instrument time.6
How PCR works
PCR copies a short, unique stretch of an organism's DNA millions of times, so even a very small amount can be detected. Because it looks for genetic material rather than living cells, the organism does not need to survive shipping or grow in the lab. That is why the CDC recommends NAATs for chlamydia and gonorrhea, and why NAAT is the diagnostic method for Mycoplasma genitalium.2,3
PCR also tells organisms apart that culture cannot easily separate. For example, it distinguishes Ureaplasma urealyticum from Ureaplasma parvum.6 And a single sample can be tested for several infections at once.
PCR vs. culture at a glance
| Culture | PCR / NAAT | |
|---|---|---|
| What it detects | Living organisms that grow on the lab's medium | The organism's DNA or RNA |
| Sample must stay alive | Yes; boric-acid urine tubes are rated for up to 48 hours | No; DNA is detected whether or not the organism survives |
| Trichomoniasis sensitivity | 44%–75% | 95.3%–100% |
| Mycoplasma genitalium | Up to 6 months; research labs only | Standard diagnostic method |
| Mycoplasma hominis / Ureaplasma | 2–5 days on special media | Hours of lab time |
| Several infections from one sample | Limited | Yes |
Culture's remaining strength is antibiotic susceptibility testing, such as Kirby-Bauer disk diffusion, which shows which antibiotics work against a specific bacterial strain. It is used, for example, when gonorrhea persists after treatment.3 But susceptibility results are only as good as the culture behind them: if a sample sat in the mail past its preservative's limit, what grows in the lab may not be what is causing the symptoms. For finding out whether an infection is there, molecular testing is the more sensitive choice.
What sets Genome-Based Diagnostics apart
- Molecular testing, not culture. Our urine and swab tests detect the organism's DNA directly using nucleic acid amplification such as PCR.
- Sample preparation developed in-house. Before any test runs, DNA has to be released and purified from the urine. We developed and validated our own process for this step, specifically for urine samples.
- Our own CLIA-certified, high-complexity laboratory. Samples are tested in our lab in Carlsbad, California, not sent out to another lab.
- First-catch urine. Collection is simple and non-invasive. For men, the CDC calls first-catch urine the recommended sample for chlamydia and gonorrhea NAAT, equivalent to a urethral swab.3
- Controls on every run and outside proficiency testing. Each test run includes controls, and the lab takes part in external proficiency testing, where unknown samples are graded against other labs. See our 2024 performance.
- Fast results. Most tests are completed within 1–3 days of the sample arriving at the lab, with results delivered through a secure, HIPAA-compliant patient portal.
See all at-home test kits or read more about Mycoplasma and Ureaplasma testing. Our M. hominis, U. urealyticum & U. parvum urine test kit is also available on Amazon.
References
- Centers for Disease Control and Prevention. Trichomoniasis. Sexually Transmitted Infections Treatment Guidelines, 2021. cdc.gov
- Centers for Disease Control and Prevention. Mycoplasma genitalium. Sexually Transmitted Infections Treatment Guidelines, 2021. cdc.gov
- Papp JR, Schachter J, Gaydos CA, Van Der Pol B. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae, 2014. MMWR Recomm Rep. 2014;63(RR-02):1–19. cdc.gov
- Eisinger SW, Schwartz M, Dam L, Riedel S. Evaluation of the BD Vacutainer Plus Urine C&S Preservative Tubes compared with nonpreservative urine samples stored at 4°C and room temperature. Am J Clin Pathol. 2013;140(3):306–313. PubMed
- BD. BD Vacutainer Plus C&S Preservative Tube, product information. bd.com
- Cunningham SA, Mandrekar JN, Rosenblatt JE, Patel R. Rapid PCR detection of Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum. Int J Bacteriol. 2013;2013:168742. PMC
This article is for general information and is not medical advice. Talk with a healthcare provider about your symptoms and results.
Check Out Our Latest Posts:
- Mycoplasma and Ureaplasma Explained: Testing, Technology, and Accuracy
- Benefits of Preventive Testing for Health
- Advanced Non-Invasive NAAT Testing: Revolutionizing Diagnostics
- HPV Testing vs Pap Smears: Key Differences, Accuracy, and Benefits
- NATs vs Antigen and Antibody Tests
