An amplification-free, 16S rRNA test for Neisseria gonorrhoeae in urine

An amplification-free, nanopore-based nucleic acid detection platform has been demonstrated for rapid, 16S rRNA sequence-specific detection of Neisseria gonorrhoeae at 10-100 CFU mL^-1 in human urine against background bacterial flora at 1000 CFU mL^-1. Gonorrhea is a very common notifiable communicable disease, antibiotic resistant strains have emerged, and the rate of reported gonococcal infections continues to increase. Since rapid clinical identification of bacterial pathogens in clinical samples is needed to guide proper antibiotic treatment and to control disease spread, it is important to engineer rapid, sensitive, selective, and inexpensive point-of-care (POC) diagnostic devices for pathogens such as N. gonorrhoeae. Our detector technology is based on straightforward conductometric detection of sustained blockage of a glass nanopore. Charge neutral, complementary peptide nucleic acid probes are conjugated to polystyrene beads to capture N. gonorrhoeae 16S rRNA selectively. In the presence of an electric field applied externally through a glass nanopore, the PNA-microbead conjugates that acquire substantial negative charge upon target hybridization are driven to the smaller diameter nanopore. At least partial blockage of the nanopore results in a sustained drop in ionic current that can be measured easily with simple electronics. The ability to detect N. gonorrhoeae over the range of 10 to 100 CFU mL^-1 spiked in human urine was demonstrated successfully with estimated sensitivity and specificity of ∼98% and ∼100%, respectively. No false positives were observed for the control group of representative background flora (E. coli, K. pneumoniae, and E. faecalis) at 1000 CFU mL^-1. Also, N. gonorrhoeae at 50 CFU mL^-1 was successfully detected against 1000 CFU mL^-1 of background flora in urine. These results suggest that this amplification-free technology may serve as the basis for rapid, inexpensive, low-power detection of pathogens in clinical samples at the POC.

Development of a Novel Test for Simultaneous Bacterial Identification and Antibiotic Susceptibility

Background. Elucidation of a pathogen's antimicrobial susceptibility requires subculture after the organism is first isolated. This takes several days, requiring patients to be treated with broad-spectrum antibiotics. This approach contributes to the development of bacterial resistance. Methods. Microtiter wells were coated with a polyclonal antibody targeting the pathogen of interest. Bacterial suspensions were added in the presence/absence of selected antibiotics. After washing, captured bacteria were detected. Findings. Group B streptococcus (GBS), Enterococcus faecalis, and Neisseria gonorrhoeae were each detected at 105 bacteria/mL following a 20-minute incubation period. Susceptibility to select antibiotics was discernable following a 6-hour incubation period (GBS and Enterococcus). Sensitivity was increased to 10-2 bacteria/mL for GBS, 10-1 bacteria/mL for E. faecalis, and 101 bacteria/mL for N. gonorrhoeae following 18-24-hour culture. Conclusion. This novel assay allows for the highly sensitive and specific identification of a pathogen and simultaneous determination of its antimicrobial susceptibility in a reduced time.

Purification of DNA eluates from the ProbeTec GC Q(x) assay on BD Viper™ XTR allows for further analysis and confirmation of gonorrhea

Low positive predictive values of Neisseria gonorrhoeae nucleic acid amplification tests in low-prevalence populations are a major challenge for accurate diagnostics. It is therefore necessary to verify all positive N. gonorrhoeae results with a different assay and target gene, preferably using the same sample. The BD ProbeTec™ Q(x) Collection Kit for Endocervical or Lesion Specimens, which is recommended for BD Viper™ XTR, is incompatible with other commercial platforms. Therefore, a confirmatory PCR has not been available for samples received on this transport medium. To be able to verify results from these samples with another assay, our objective was to establish a procedure for using the DNA eluates from BD Viper™ XTR for further analysis. DNA eluates from BD Viper™ XTR were collected and analyzed in two in-house confirmatory real-time PCRs targeting the porA pseudogene and the opa multicopy gene. BD Viper™ XTR DNA eluates were analyzed directly and also after purification with the nucleic acid extraction system NucliSENS® easyMag®. Purification of BD Viper™ XTR DNA eluates with the nucleic acid extraction system NucliSENS® easyMag® provided a sensitivity of the in-house PCR comparable to BD Viper™. With the inclusion of two target genes in the confirmatory PCR, specific and reliable verification of results were obtained. This study presents a simple, inexpensive procedure which allows for rapid verification of gonorrhea from samples received on the BD ProbeTec™ Q(x) Collection Kit for Endocervical or Lesion Specimens.

Process Evaluation of a Fully Automated Molecular Diagnostics System

Molecular diagnostics presents challenges to clinical laboratories that are under pressure to consolidate and automate. There is a need to evaluate molecular automation for process efficiency and suitability for high-throughput environments in core laboratories.

A fully automated molecular instrument platform (the BD Viper System with XTR Technology in extracted mode [BD Viper System with XTR]), was evaluated for automation efficiency, labor requirements, and system robustness. System productivity was predicted using time and motion studies as well as process simulation.

Preanalytical steps required 15 min of skilled operator time. The BD Viper System with XTR fully automated DNA extraction, amplification, and analysis of 368 specimens (736 results for Chlamydia and Gonorrhea). Time and motion studies estimated that the total hands-on full time employee (FTE) burden was approximately 35 min per run, of which 41% was high complexity, 29% medium complexity and 29% relatively unskilled labor. A skilled operator can easily operate four instruments for 8.5 h and generate data on 2944 results (four runs on each instrument for a total of 1472 clinical specimens) for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) analysis. Based on mean time between intervention data, the BD Viper System with XTR was estimated to be capable of operating for more than 1000 runs without system malfunction.

We determined that fully automated molecular analysis of GC and CT is possible in a core laboratory facility with significant throughput and minimal impact on labor demand using a fully automated and robust molecular diagnostics platform (such as the BD Viper System with XTR).