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COBAS AMPLICOR N. gonorrhoeae PCR positive results should always be confirmed with an alternate nucleic acid amplification test when low prevalence populations or genital specimens are tested.

Comparison of COBAS AMPLICOR N. gonorrhoeae PCR, including confirmation with N. gonorrhoeae-specific 16S rRNA PCR, with traditional culture.
Luijt DS, Bos PAJ, van Zwet AA, van Voorst Vader PC, Schirm J.
Journal of Clinical Microbiology 2005;43:1445-47
 
Summary:

Question

What are the performances of culture and of the COBAS AMPLICOR PCR assay with confirmation of positives by a 16S rRNA PCR for the detection of N. gonorrhoeae in clinical specimens from a low prevalence population?

Design

Detection of N. gonorrhoeae in clinical specimens using culture and the COBAS AMPLICOR (CA) PCR assay, with and without confirmation by a 16S rRNA PCR, was determined after resolution of specimens with discrepant culture and PCR results using a ligase chain reaction (LCR) assay.

Participants

Six hundred eight men and 2415 women seen by general practitioners, general hospitals, or venereal disease clinics were tested. The majority was symptomatic and 75% were between 15 and 35 years old. Specimens collected included urogenital swabs (95%) and rectal, throat, or eye swabs (5%).

Description of Tests and Diagnostic Standard

Swabs for PCR and culture were collected in 2-sucrose-phosphate medium and charcoal transport medium, respectively. The specimens for culture were inoculated on chocolate agar and chocolate agar with vancomycin-trimethoprim-colistin-sulfate-amphotericin and incubated for 2 days. Suspected colonies were examined by an oxidase test and Gram staining. The CA and 16S rRNA N. gonorrhoeae PCR assays (Roche Diagnostics) were performed from separate DNA extracts according to the manufacturer's instructions. The 16S rRNA PCR included hybridization with an N. gonorrhoeae specific probe added to microwell plates. Specimens were considered CA PCR negative for N. gonorrhoeae if the optical density (OD) was <0.200 and the OD of the inhibition control was >0.200.CA N. gonorrhoeae positive specimens were retested by the CA assay. Specimens N. gonorrhoeae positive in both CA assays were tested using the 16S rRNA assay. Discordant specimens that were N. gonorrhoeae PCR positive (repeatedly CA PCR positive and 16S rRNA PCR positive) and culture negative were tested using N. gonorrhoeae LCR (Abbott Laboratories).A true N. gonorrhoeae positive specimen was defined as positive by culture or positive by repeat CA PCR, 16S rRNA PCR, and LCR.

Main Outcome Measures

The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of culture, CA PCR, and CA PCR confirmed by 16S rRNA PCR for the detection of N. gonorrhoeae in clinical specimens as determined by true positive results defined above were calculated.

Main Results

The number of N. gonorrhoeae positive specimens detected by each assay is shown in Table 1.One specimen was positive by culture and negative by PCR. The performances of culture, CA PCR, and CA PCR confirmed by 16S rRNA PCR for the detection of N. gonorrhoeae in clinical specimens as determined by true positive results are shown in Table 2.Of the 70 CA PCR false positive specimens, 30 (42.9%) were not genital specimens. The PPV of the CA PCR was 65.8% for genital specimens and 21.2% for nongenital specimens.

Table 1.Number of N. gonorrhoeae positive specimens detected by different methods

*One culture positive specimen was negative by PCR

Table 2.Performance of culture and PCR for detection of N. gonorrhoeae

Authors' Conclusions

Due to its high sensitivity, N. gonorrhoeae PCR, or another nucleic acid amplification test, should replace culture, especially when asymptomatic patients are tested. CA PCR is a very useful screening assay due to its semiautomatic platform.

Source of funding: None given

For correspondence: Jurjen Schirm, Regional Public Health Laboratory, van Ketwich Verschuurlaan 92, 9721 SW Groningen, The Netherlands. E-mail address: j.schirm@slgd.nl

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