Background:
QRNG prevalence has increased in the U.S., especially in gay men and in the West. Traditional diagnosis is based on culture susceptibility testing-which cannot be performed when nucleic acid amplification tests (NAAT) are used for NG diagnosis. We have developed direct NAAT probes for QRNG and other resistance determinants in NG.

Objective:
To test the feasibility and outcome of using a NAAT-based resistance assay in an STD clinic environment in Baltimore-an area not considered hyperendemic for QRNG.

Method:
We collected 716 NG clinical samples from March to October 2005 from patients attending Baltimore STD clinics. We analyzed for point mutations in the quinolone resistance-determining region of gyrA and parC, using polymerase chain reaction, Roche LightTyper^TM fluorescence melting curve analysis, and direct sequencing. On samples with mutations, minimum inhibitory concentrations (MIC) to ciprofloxacin (CIP) was determined by E-test.

Result:
38/716 (5.3%) of isolates contained mutations in gyrA, parC, or both. Of the 21/38 (55.3%) mutation containing strains with that could be re-cultured 5/21 (24%) were CIP-R (resistant; MIC≥ 1µg/mL), and 9/21(43%) were CIP-I (intermediate; MIC= 0.12-0.5µg/mL). In reviewing the clinical records, 40% of the cipR and 67% of CIP-I strains were isolated from patients not known to be part of a QRNG high-risk group.

Conclusion:
Molecular-based resistance testing surveillance found a much higher prevalence of mutations than was clinically suspected. A large proportion of QRNG did not have CDC-defined risk factors, indicating an early endemic pattern in an area with low QRNG by traditional surveillance.

Implications:
Optimizing and integrating real-time high throughput non-culture based molecular assays into surveillance and clinical care may better define the local epidemiology of resistant organisms and help guide appropriate therapeutic decisions, and are a potential solution to antimicrobial susceptibility testing in the NAAT era.