Smith, Thomas F.

SUMMARY Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.

ABSTRACT Specimens submitted in M5 medium for cell culture detection of Chlamydia trachomatis were tested by nucleic acid amplification testing (NAAT) and in cell cultures. Of 35 (genital) and 26 (nongenital) specimens positive for C. trachomatis , 21 and 14 specimens, respectively, were detected exclusively by NAAT. NAAT is significantly ( P < 0.0001) more sensitive than cell culture and should be considered the new “gold standard” for the laboratory diagnosis of C. trachomatis infections.

ABSTRACT DNA from 101 specimens containing herpes simplex virus (HSV) produced atypical intermediate melting curves compared with those expected for HSV type 1 or HSV type 2 subsequent to real-time PCR. Nucleic acid sequence analysis of amplified target DNA revealed 1- or 3-bp polymorphisms in the probe region which allowed designation of these viruses as HSV genotype 1 or HSV genotype 2. These two subpopulations of HSV were also identified as HSV genotype 1 or HSV genotype 2 using another commercially available PCR method. Amplified HSV target DNA producing intermediate melting curves could be designated as HSV genotype 1 or HSV genotype 2 without performing sequencing or another PCR method with 96/101 (95%) specimens by adding known intermediate HSV DNA characteristic for the two subpopulations as controls.

ABSTRACT A total of 563 specimens (234 dermal and 329 genital swabs) from patients suspected of having herpes simplex virus (HSV) infections were processed using two different extraction methods (the MagNA Pure LC system and the swab extraction tube system [SETS]); HSV DNA was amplified by LightCycler PCR. HSV DNA was detected in 157 of 563 specimens (27.9%) processed by the MagNA Pure LC system and in 179 of 563 specimens (31.8%) processed by SETS ( P < 0.0001). There was no specimen processed by the MagNA Pure LC extraction method that was positive only for HSV DNA. Of 157 specimens positive by both methods, HSV DNA copy levels were higher (using cycle crossover points [cycle threshold { C T }]) with SETS (mean C T , 25.9 cycles) than with the MagNA Pure LC system (mean C T , 32.0 cycles) ( P < 0.0001). The time to process 32 samples was longer with the MagNA Pure LC extraction system (90 min) than with SETS (35 min). HSV DNA extraction using SETS is faster, less expensive, and more sensitive than the MagNA Pure LC system and could replace the latter for the laboratory diagnosis of HSV infections using LightCycler PCR.

ABSTRACT The TRUGENE HCV 5′NC genotyping kit (GeneLibrarian modules 3.1.1 and 3.1.2) and VERSANT HCV genotyping assay were compared by using 96 hepatitis C virus (HCV) RNA-positive patient specimens, including HCV genotypes 1, 2, 3, 4, 5, 6, and 10. The TRUGENE HCV 5 ′ NC genotyping kit (GeneLibrarian module 3.1.2) yielded the most accurate genotyping results.

ABSTRACT Three enzyme immunoassays, Borrelia DotBlot G (GenBio, San Diego, Calif.), MarDx EIA (MarDx Diagnostics, Inc., Carlsbad, Calif.), and VIDAS (bioMérieux, St. Louis, Mo.) were compared for their ability to detect immunoglobulin G antibodies to Borrelia burgdorferi in 100 human serum samples. The “gold standard” positive result for each of these samples was determined by Western immunoblot analysis (MarDx Marblot Test System) ( n = 99) or clinical signs and symptoms suggestive of Lyme disease with other laboratory results positive for B. burgdorferi ( n = 1). Based on these criteria for a gold standard positive result, 29 of the 100 samples tested were considered true positives and 71 were considered true negatives. The following sensitivities and specificities were noted, respectively, for each method: Borrelia DotBlot G, 93 and 90%; MarDx, 100 and 35%; and VIDAS, 100 and 92%. Because of high sensitivity and specificity and ease of use, the VIDAS test is an appealing method, especially for laboratories that perform high volumes of tests. The high sensitivity but low specificity of the MarDx method compared to the VIDAS and Borrelia DotBlot G methods requires that Western blot confirmatory tests be performed frequently. The Borrelia DotBlot G method has acceptable specificity but appears to lack sensitivity when compared to the VIDAS and MarDx methods.

ABSTRACT Anthrax is a zoonotic disease that is also well recognized as a potential agent of bioterrorism. Routine culture and biochemical testing methods are useful for the identification of Bacillus anthracis , but a definitive identification may take 24 to 48 h or longer and may require that specimens be referred to another laboratory. Virulent isolates of B. anthracis contain two plasmids (pX01 and pX02) with unique targets that allow the rapid and specific identification of B. anthracis by PCR. We developed a rapid-cycle real-time PCR detection assay for B. anthracis that utilizes the LightCycler instrument (LightCycler Bacillus anthracis kit; Roche Applied Science, Indianapolis, Ind.). PCR primers and probes were designed to identify gene sequences specific for both the protective antigen (plasmid pX01) and the encapsulation B protein (plasmid pX02). The assays (amplification and probe confirmation) can be completed in less than 1 h. The gene encoding the protective antigen ( pagA ) was detected in 29 of 29 virulent B. anthracis strains, and the gene encoding the capsular protein B ( capB ) was detected in 28 of 29 of the same strains. Three avirulent strains containing only pX01 or pX02, and therefore only pagA or pagB genes, could be detected and differentiated from virulent strains. The assays were specific for B. anthracis : the results were negative for 57 bacterial strains representing a broad range of organisms, including Bacillus species other than anthracis ( n = 31) and other non- Bacillus species ( n = 26). The analytical sensitivity demonstrated with target DNA cloned into control plasmids was 1 copy per μl of sample. The LightCycler Bacillus anthracis assay appears to be a suitable method for rapid identification of cultured isolates of B. anthracis . Additional clinical studies are required to determine the usefulness of this test for the rapid identification of B. anthracis directly from human specimens.