Onychomycosis, the most common nail disorder encountered in clinical practice, may cause pain and decreased quality of life.¹ Since about half of nail conditions are not onychomycosis, diagnosis is essential before initiating treatments that may be costly or cause side effects.² Unlike potassium hydroxide with microscopy and histopathology, culture and polymerase chain reaction (PCR) can identify the causative pathogen¹; however, real-world data comparing these techniques’ utility are lacking. We aimed to compare culture and PCR for onychomycosis diagnosis and potential impact on patient outcomes.

A retrospective analysis was conducted on Weill Cornell Dermatology patients with onychodystrophies (4/20/2017-6/22/2023) with both PCR and fungal culture performed. Accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of PCR were calculated using culture as the standard. Discordant results were compared with histopathology data. χ² tests compared PCR versus culture in identifying dermatophytes and nondermatophytes (α < 0.05).

Three-hundred-six patients were included; mean age was 53.3 years (range: 8-89) and 63.4% were male (Supplementary Table I, available via Mendeley at https://data.mendeley.com/datasets/9v6bb7dv9f/1). Percent positivity for PCR (vs culture) was higher for dermatophytes (42.8% vs 14.7%, P < .01) and similar for nondermatophytes (12.4% vs 9.2%, P = .193) (Table I). Culture and PCR results agreed in 218 (71.2%) instances for dermatophytes and 280 (93.3%) instances for nondermatophytes. For dermatophytes, PCR’s sensitivity and specificity were 97.8% and 66.7%; for nondermatophytes, PCR’s sensitivity and specificity were 71.4% and 93.5%.

In 87 patients, dermatophytes were detected by PCR but not culture (Table II), with histopathology identifying hyphae in 84 (96.6%). Among 87 patients with dermatophyte PCR-positive/culture-negative testing, 77 received treatment; of those, 47 completed follow-up, 37 (78.8%) of whom improved. Findings were similar among 18 patients with nondermatophyte PCR-positive/culture-negative testing. In 44 PCR-positive/culture-positive dematophyte cases there was agreement in 40 cases (Table I).

We showed that PCR more often diagnosed dermatophytes and nondermatophytes from nail samples than fungal culture, corroborating prior smaller studies. In a retrospective study of 121 patients with toenail onychodystrophy, diagnosis of onychomycosis was made more often using PCR (52.1%) versus culture (33.1%, P < .001).³ In a prospective study of 177 nail samples from patients with onychodystrophies, onychomycosis diagnosis was more often positive using PCR (78/177, 44%) than with culture (59/177, 34%, no P value reported).⁴ In a retrospective study of 35,257 fungal nail cultures, only half were positive, and the proportion of nondermatophytes exceeded dermatophytes, which might suggest potential contaminants.⁵ Of the 105 cases (34.3%) in our study where PCR was positive for fungal organism but culture was negative, strong concordance with histopathological findings and clinical improvement with treatment suggest that these are true onychomycosis cases (rather than colonization) that were missed by culture. Theoretically, these patients would not have been treated had they been evaluated using culture alone.

Limitations include small sample size and singlecenter/physician/retrospective design. Antifungal resistance was not assessed. Microscopy was not performed.

Our findings suggest culture may be inadequate for diagnosing onychomycosis. Although costlier than culture and potentially less accessible, PCR might help improve diagnosis and treatment outcomes. Larger prospective trials are needed to validate these findings.