Performance of the Abbott RealTime CT/NG for detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

A multicenter clinical study was conducted to evaluate the performance characteristics of the Abbott RealTime CT/NG assay, a multiplex real-time PCR assay, for simultaneous detection of Chlamydia trachomatis and Neisseria gonorrhoeae. The specimens were collected from a total of 3,832 male and female subjects at 16 geographically diverse sites. Specimens included male and female urine samples, male urethral swabs, female endocervical swabs, and self-collected and clinician-collected vaginal swabs. Specimens were tested with the automated Abbott RealTime CT/NG assay, Aptima Combo 2 assay (Gen-Probe), ProbeTec ET CT/GC assay (Becton Dickinson), and culture for N. gonorrhoeae. The Aptima Combo 2 assay, the ProbeTec assay, and the N. gonorrhoeae culture were used as the reference assays. For each subject, a patient infected status (PIS) was determined based on the combined results from the reference assays. The overall prevalence in female subjects was 8.9% for C. trachomatis and 3.8% for N. gonorrhoeae. The overall male prevalence was 18.2% for C. trachomatis and 16.7% for N. gonorrhoeae. The overall sensitivity and specificity of the Abbott RealTime CT/NG assay were 92.4% and 99.2% for C. trachomatis and 96.9% and 99.7% for N. gonorrhoeae, respectively. In comparison, the sensitivity and specificity, respectively, for the Aptima Combo 2 assay were 94.5% and 99.0% for C. trachomatis and 96.1% and 99.5% for N. gonorrhoeae, and those for the ProbeTec ET assay were 90.3% and 99.5% for C. trachomatis and 92.0% and 97.3% for N. gonorrhoeae in this study. The Abbott RealTime CT/NG assay offers C. trachomatis and N. gonorrhoeae dual detection with high sensitivity and specificity. The automated assay provides a useful alternative nucleic acid amplification assay for clinical laboratories and clinicians.

Characteristics of the m2000 automated sample preparation and multiplex real-time PCR system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

We evaluated a new real-time PCR-based prototype assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae developed by Abbott Molecular Inc. This assay is designed to be performed on an Abbott m2000 real-time instrument system, which consists of an m2000sp instrument for sample preparation and an m2000rt instrument for real-time PCR amplification and detection. The limit of detection of this prototype assay was determined to be 20 copies of target DNA for both C. trachomatis and N. gonorrhoeae, using serially diluted linearized plasmids. No cross-reactivity could be detected when 55 nongonococcal Neisseria isolates and 3 non-C. trachomatis Chlamydia isolates were tested at 1 million genome equivalents per reaction. Concordance with the Roche Amplicor, BDProbeTec ET, and Gen-Probe APTIMA Combo 2 tests was assessed using unlinked/deidentified surplus clinical specimens previously analyzed with these tests. For C. trachomatis, concordance for positive results ranged from 93.7% to 100%, while concordance for negative results ranged from 98.2% to 100%. For N. gonorrhoeae, concordance for positive and negative results ranged from 91.4% to 100% and 99.3% to 100%, respectively. A workflow analysis of the prototype assay was conducted to obtain information on throughput under laboratory conditions. At 48 samples/run, the time to first result for both C. trachomatis and N. gonorrhoeae was 4.5 h. A total of 135 patient specimens could be analyzed in 8.9 h, with 75 min of hands-on time. This study demonstrated the technical and clinical feasibility of the new Abbott real-time PCR C. trachomatis/N. gonorrhoeae assay.

Evaluation of an automated liquid-handling system (Tecan Genesis RSP 100) in the Abbott LCx assay for Chlamydia trachomatis.

The present study investigated the feasibility of automating the specimen-pipetting component of sample preparation in the LCx Chlamydia assay (LCx-CT assay; Abbott Laboratories, Chicago, Ill.) by using a commercially available liquid-handling system (Tecan Genesis RSP100; Tecan Inc., Research Triangle Park, N.C.). The Tecan instrument proved to be comparable in both precision and accuracy to a manual multipipettor (Eppendorf model 4850; Eppendorf Scientific, Westbury, N.Y.). The Tecan instrument was extensively checked for evidence of specimen-to-specimen transfer, and no level of contamination sufficient to generate a signal above the background in the LCx-CT assay was detected. Finally, pipetting speed was significantly improved by using the Tecan instrument. A mean time of 2.5 min was required to pipette a complete LCx-CT assay carousel (20 samples and 4 controls) with the Tecan instrument, whereas 8.4 min was required to pipette a comparable number of samples manually (P < 0.001).

Use of an enzyme immunoassay does not eliminate the need to analyze multiple stool specimens for sensitive detection of Giardia lamblia.

The relative sensitivities of a commercially available enzyme immunoassay (EIA) (ProSpecT Giardia; Alexon-Trend Inc., Ramsey, Minn.) and conventional ovum-and-parasite (O&P) examination for the detection of Giardia lamblia in preserved stool specimens were determined. Paired stool samples collected independently within a 7-day period from 103 patients were analyzed by both methods. A total of 54 specimens from 30 patients (18 asymptomatically infected with G. lamblia and 12 with symptoms consistent with intestinal giardiasis) were determined to be positive for G. lamblia, of which 48 (88.9%) were positive by microscopy and 52 (96.3%) were positive by EIA. Both specimens submitted were positive for G. lamblia by O&P examination for 66.7% (20 of 30) of the positive patients; for 26.7% (8 of 30) a single specimen was positive by O&P examination, and for 6.7% (2 of 30) of those determined to be infected with G. lamblia, both samples were negative by microscopy. The sensitivity of conventional O&P examination was somewhat higher in symptomatically infected individuals, with 75% (9 of 12) of patients in this category having G. lamblia detected in both samples, compared with 61% (11 of 18) of asymptomatic patients. A total of 24 positive patients (80%) had G. lamblia antigen detected by EIA in both submitted samples, 4 positive patients (13.3%) had one specimen positive by EIA, and the EIA was negative in both specimens from 2 infected individuals (6.5%), the sensitivity of EIA was substantially equivalent in asymptomatic and symptomatic individuals (77 versus 83% of patients with positive results on both specimens). Although the sensitivity of EIA for the detection of G. lamblia on a single stool specimen was somewhat higher than that of conventional O&P examination in symptomatic patients (83 versus 75%), in asymptomatic patients (77 versus 61%), and overall (80 versus 67%), examination of two specimens by either EIA or microscopy was necessary to achieve a diagnostic sensitivity of greater than 90%.

Pharmacogenetics: the Dx perspective.

The promise of the rapidly developing field of pharmacogenetics is that genetically determined propensities of individual patients to respond favorably or adversely to a given pharmacologic agent will be able to be determined prior to administration of that drug. The realization of that promise, however, is predicated on a number of developments in the capabilities of diagnostic laboratories. These developments include the introduction of automated technologies for efficiently and accurately detecting, quantifying and decoding specific nucleic acid sequences and the concomitant availability of information technology-based applications for rapidly analyzing, interpreting and then communicating complex genetic data to healthcare providers. This article will review currently available and developmental molecular diagnostic technology and in addition, describe the current status and speculate on the future of pharmacogenetic testing in the clinical laboratory.

Performance of para-Pak Ultra ECOFIX compared with Para-Pak Ultra formalin/mercuric chloride-based polyvinyl alcohol for concentration and permanent stained smears of stool parasites.

ECOFIX is a mercury and formalin-free fecal preservative that can be used for concentration of stool specimens and preparation of permanently-stained slides. In this study, the standard two-vial ParaPak Ultra system was compared with ECOFIX Ultra for the detection of intestinal parasites. A total of 261 specimens in 92 sets (77 with 3 specimens, 15 with 2 specimens) were collected in ECOFIX, formalin, and low viscosity polyvinyl alcohol (LV-PVA). Concentrations were performed from ECOFIX using Hemo-De and saline and from formalin using ethyl acetate and formalin. To prepare permanently-stained smears, ECOSTAIN (a modification of Wheatley's trichrome stain) was used on ECOFIX material and Wheatley's trichrome stain was used on specimens preserved in PVA. A total of 157 protozoa and helminths were detected; 132 (84.1%) were recovered in formalin/PVA and 129 (82.2%) in ECOFIX. In permanently-stained smears, 139 protozoa were observed, 116 (83.5%) in PVA-preserved material and 117 (84.2%) in ECOFIX. Fecal concentration yielded 111 parasites (103 protozoa and 8 helminths), of which 98 (88.3%) were detected in formalin-fixed stool and 48 (43.2%) in ECOFIX. Significantly fewer ECOFIX-preserved concentrates were positive for Blastocystis hominis (35 versus 15, p-value <0.001) and Endolimax nana (19 versus 2, p-value <0.001). In conclusion, use of the ECOFIX Ultra collection device in combination with ECOSTAIN resulted in largely comparable recovery of enteric parasites to the conventional two-vial ParaPak Ultra system when both sedimentation-concentration and permanently stained smears were performed, and 2-3 specimens per patient were evaluated.

Identification of nocardia species by restriction endonuclease analysis of an amplified portion of the 16S rRNA gene.

Identification of clinical isolates of Nocardia to the species level is important for defining the spectrum of disease produced by each species and for predicting antimicrobial susceptibility. We evaluated the usefulness of PCR amplification of a portion of the Nocardia 16S rRNA gene and subsequent restriction endonuclease analysis (REA) for species identification. Unique restriction fragment length polymorphism (RFLP) patterns were found for Nocardia sp. type strains (except for the N. asteroides type strain) and representative isolates of the drug pattern types of Nocardia asteroides (except for N. asteroides drug pattern type IV, which gave inconsistent amplification). A variant RFLP pattern for Nocardia nova was also observed. Twenty-eight clinical isolates were evaluated both by traditional biochemical identification and by amplification and REA of portions of the 16S rRNA gene and the 65-kDa heat shock protein (HSP) gene. There was complete agreement among the three methods on identification of 24 of these isolates. One isolate gave a 16S rRNA RFLP pattern consistent with the biochemical identification but was not identifiable by its HSP gene RFLP patterns. Three isolates gave 16S rRNA RFLP patterns which were inconsistent with the identification obtained by both biochemical tests and HSP gene RFLP; sequence analysis suggested that two of these isolates may belong to undefined species. The PCR and REA technique described appears useful both for the identification of clinical isolates of Nocardia and for the detection of new or unusual species.

Utility of multiple-stool-specimen ova and parasite examinations in a high-prevalence setting.

A retrospective analysis of the results of 2,704 ova and parasite (O & P) examinations performed on stool specimens collected from 1,374 patients between October 1996 and September 1997 was performed to evaluate the utility of performing O & P examinations on multiple, independently collected stool specimens in a high-prevalence setting. A total of 995 specimens (36.8%) examined during the study contained parasites; 546 (20.2%) contained pathogenic organisms. The positivity rate (54.5%) for the patients from whom three specimens were examined was significantly higher than for the patients from whom either two specimens (33.3%) or a single specimen (19.8%) was submitted for examination. For the group of patients from whom at least 3 specimens were submitted for O & P examination, 373 independent opportunities for diagnosing infection with intestinal parasites could be analyzed. The first stool specimen collected proved to be adequate in only 75.9% (283 of 373) of evaluated cases; however, examination of two specimens increased the sensitivity of O & P detection to 92% (343 of 373). The third specimen collected provided additional information on only 30 of 373 occasions (8%). These data indicate that in populations with a high prevalence of intestinal parasitic infections, two independently collected stool specimens should be subjected to O & P examination to ensure adequate diagnostic sensitivity.

Comparison of simple and rapid methods for identifying enterococci intrinsically resistant to vancomycin.

Three different methodologies, reduction of litmus milk (LM) and acidification of arabinose (ARA), acidification of methyl-alpha-D-glucopyranoside (MGP), and rapid motility (RM), for differentiating isolates of Enterococcus casseliflavus and Enterococcus gallinarum (intrinsically vancomycin-resistant enterococci [IVRE]) from Enterococcus faecalis and Enterococcus faecium were evaluated. All 33 isolates of E. faecalis tested reduced LM within 4 h and were negative in all other tests, while the 53 isolates of E. faecium were ARA positive only. In contrast, 45 of 46 (98%) IVRE isolates examined (26 E. casseliflavus and 20 E. gallinarum isolates) acidified MGP, 41 of 46 (89%) were LM and ARA positive, and 45 of 46 (98%) were RM positive. Acidification of MGP was therefore the single most useful test for differentiating IVRE from vancomycin-resistant E. faecium and E. faecalis; however, a combination of LM-ARA and RM testing enabled the correct designation of organisms without the need for overnight incubation.

Comparison of algorithms for selective use of nucleic-acid probes for identification of Mycobacterium tuberculosis from BACTEC 12B bottles.

We retrospectively compared the sensitivity of two approaches, a time-to-detection algorithm and the presence of serpentine cords of acid-fast bacilli, for discriminating between BACTEC 12B cultures containing either Mycobacterium tuberculosis complex (MTB) or Mycobacterium avium complex (MAC). From January 1996 through March 1997 a total of 217 of 2089 respiratory specimens received in our laboratory were positive in the BACTEC 12B radiometric culture system for either MTB (120 specimens) or MAC (97 specimens). Use of a previously published time-to-positivity algorithm would have resulted in the correct use of the MTB probe on 109 of 120 cultures (91% sensitivity), and the MAC probe on 52 of 97 cultures (54% sensitivity). The presence of serpentine cords was detected in 58 of 120 cultures containing MTB (48%), and in 3 of 97 (3%) cultures containing MAC. Using a combination of time to positivity and cord formation to determine initial probe selection would have resulted in first use of the MTB probe in 116 of 120 (97%) instances in which MTB was present in the culture. In only 49 of 97 (51%) cultures, however, from which MAC was recovered would the correct probe have been selected. These results indicate that limiting the initial use of the MTB probe to those cultures that are either identified by the time-to-detection algorithm or demonstrate serpentine cords on acid-fast smear would eliminate a considerable amount of unnecessary probe use without compromising the efficiency of identification of isolates of MTB.

Value of examining multiple sputum specimens in the diagnosis of pulmonary tuberculosis.

To objectively assess the value of examining multiple sputum specimens in maximizing the sensitivity of detection of Mycobacterium tuberculosis, we retrospectively reviewed the acid-fast bacillus smear and culture results of patients diagnosed with culture-proven pulmonary tuberculosis (TB) at Hennepin County Medical Center between 1986 and 1996. Two hundred and forty six persons were diagnosed with pulmonary TB in the time period analyzed. In 93% of these cases (229 of 246) the laboratory diagnosis was made by detection of M. tuberculosis in sputum specimens; however, only 52% (120 of 229) of these patients had at least three sputum specimens submitted to the laboratory at the time of diagnosis. Of the patients from whom at least three specimens were collected, 47% (56 of 120) had at least one smear-positive specimen; the third or later specimen submitted was the first smear-positive specimen for 13% (7 of 56) of these persons but was the first culture-positive specimen for only 7% (4 of 56). Of the 64 patients with smear-negative specimens, for only 5% (3 of 64) was the third or subsequent specimen submitted the first from which M. tuberculosis was recovered. This data indicates that, in our institution, the overwhelming majority of culture-proven pulmonary TB cases are diagnosed from the first or second sputum specimen submitted to the laboratory and that only rarely is a third specimen of diagnostic value.

Comparison of PCR-based approaches to molecular epidemiologic analysis of Clostridium difficile.

Representative isolates of the 10 serogroups of Clostridium difficile and 39 clinical isolates (30 toxigenic and 9 nontoxigenic), including 5 isolates from a confirmed nosocomial outbreak, were analyzed by using two previously described arbitrary-primer PCR (AP-PCR) molecular typing methodologies (AP-PG05 and AP-ARB11) and PCR ribotyping. The two AP-PCR methods investigated gave comparable results; AP-PG05 and AP-ARB11 identified 8 and 7 groups among the serogroup isolates and classified the clinical isolates into 21 and 20 distinct groups, respectively. PCR ribotyping also identified 8 unique groups among the serogroup isolates but classified the clinical isolates into 23 groups. In addition, when results obtained by the PCR methods were compared with typing data generated by pulsed-field gel electrophoresis (PFGE), PCR ribotyping and PFGE were found to be in agreement for 83% (29 of 35) of isolates typeable by both techniques while AP-PG05 was in agreement with PFGE for 60% (20 of 33) and AP-ARB11 was in agreement with PFGE for only 44% (17 of 36). These results indicate that PCR ribotyping is a more discriminatory approach than AP-PCR for typing C. difficile and, furthermore, that this technique generates results that are in higher concordance with those obtained by using an established method for differentiating isolates of this organism on a molecular level than are results generated by using AP-PCR.

Identification of microsporidia in stool specimens by using PCR and restriction endonucleases.

We report the development of a PCR-based assay for the detection of microsporidia in clinical specimens. A single primer pair complementary to conserved sequences of the small-subunit rRNA enabled amplification of DNA from the four major microsporidian pathogens of humans: Encephalitozoon cuniculi, Encephalitozoon hellem, Enterocytozoon bieneusi, and Septata intestinalis. The extraction method allowed PCR amplification of E. bieneusi and S. intestinalis DNA from sodium hypochlorite-treated stool specimens. Differentiation of the microsporidian gastrointestinal pathogens E. bieneusi and S. intestinalis could be accomplished by restriction endonuclease digestion of PCR products using PstI and HaeIII.

Comparison of pigment production and motility tests with PCR for reliable identification of intrinsically vancomycin-resistant enterococci.

Forty-eight clinical isolates identified as either Enterococcus faecium or Enterococcus faecalis with the MicroScan system (Dade International, MicroScan Inc., West Sacramento, Calif.) were further characterized by two supplementary biochemical tests (pigment production and motility). Twenty isolates (42%), all initially identified as E. faecium, were motile. Of these 20, 8 isolates (17%) produced yellow pigment and were identified as Enterococcus casseliflavus and the remaining 12 (25%) were nonpigmented and were identified as Enterococcus gallinarum. Identical identification results were obtained when PCR amplification of regions of the vanC gene was used as a technique for differentiating these organisms. The results of this study indicate that motility and pigment production tests together with commercial test systems are sufficient for reliable identifications of E. faecium, E. casseliflavus, and E. gallinarum.

PCR amplification of rRNA intergenic spacer regions as a method for epidemiologic typing of Clostridium difficile.

From January to March 1993, a suspected outbreak of antibiotic-associated diarrhea occurred on a pediatric oncology ward of the Clinical Center Hospital at the National Institutes of Health. Isolates of Clostridium difficile obtained from six patients implicated in this outbreak were typed by both PCR amplification of rRNA intergenic spacer regions (PCR ribotyping) and restriction endonuclease analysis of genomic DNA. Comparable results were obtained with both methods; five of the six patients were infected with the same strain of C. difficile. Subsequent analysis of 102 C. difficile isolates obtained from symptomatic patients throughout the Clinical Center revealed the existence of 41 distinct and reproducible PCR ribotypes. These data suggest that PCR ribotyping provides a discriminatory, reproducible, and simple alternative to conventional molecular approaches for typing strains of C. difficile.

Development and evaluation of a rapid and simple procedure for detection of Pneumocystis carinii by PCR.

We report the development of a simplified PCR-based assay for the detection of Pneumocystis carinii DNA in clinical specimens. The adoption of a rapid DNA extraction procedure and the introduction of a type of enzyme-linked immunosorbent assay for PCR product detection enabled this procedure to be carried out in a single working day in a clinical microbiology laboratory. The PCR assay was prospectively compared with an immunofluorescent-antibody (FA) staining method for the detection of P. carinii in induced sputum and bronchoalveolar lavage (BAL) specimens. The results of the study showed that, for induced sputum specimens, FA staining had a sensitivity of 78% (32 of 41 specimens) and a specificity of 100% (166 of 166 specimens); PCR was 100% (41 of 41 specimens) sensitive and 98% (162 of 166 specimens) specific. For BAL specimens, FA staining was 100% sensitive (21 of 21 specimens) and 100% specific (133 of 133 specimens), and PCR had a sensitivity of 100% (21 of 21 specimens) and a specificity of 99% (132 of 133 specimens). These results strongly suggest that use of our PCR-based assay could effect clinically useful improvements in the sensitivity of induced sputum specimens for the detection of P. carinii.

Improved enrichment broth for cultivation of fastidious organisms.

An enrichment broth developed in our laboratory, fastidious broth (FB), was compared with two commercially available broth media, supplemented thioglycolate broth and enriched eugonic broth. FB supported the growth of a number of organisms that were not cultivatable in either of the other two media, including Corynebacterium jeikeium, Haemophilus influenzae, Neisseria gonorrhoeae, and Streptococcus pneumoniae. In addition, for several organisms that were able to grow in all three broths, including Neisseria meningitidis, Nocardia asteroides, and Actinomyces spp., both the time of incubation and the starting inoculum necessary to enable detection of growth were decreased significantly by using FB.

Use of beta-lactamase as a secreted reporter of promoter function in yeast.

K1 preprotoxin is the 316 residue precursor of the K1 killer toxin secreted by the yeast Saccharomyces cerevisiae. The SP beta la reporter consists of the mature, secreted form of beta-lactamase (beta la) fused to S and P, two fragments of preprotoxin. S is the N-terminal 34 residues, including the secretion signal. P, a 67 residue 'processing' segment with three sites for N-glycosylation, terminates in a Lys Arg site for cleavage by the Kex2 protease. Expression of SP beta 1a in yeast results in efficient secretion, processing by signal peptidase and glycosylation in the endoplasmic reticulum, producing pro beta la. Kex2 cleavage of pro beta la in the lumen of a late Golgi compartment releases beta la, which accumulates stably in culture media buffered at pH 5.8-7. The half-life of secretion is 11 min at 30 degrees C; 10-12% of the total activity in exponential-phase cells is intracellular, mostly in the form of pro beta la, indicating that transit from the endoplasmic reticulum to the Golgi is rate limiting. We have used SP beta la expression in single- and multi-copy vectors to compare the PGK, GAL1, GAL10, PHO5 and CUP1 promoters under varying nutritional conditions. In exponential-phase cells, secretion of beta la over a 40-fold range and up to several micrograms/ml was proportional to transcript level, demonstrating that SP beta la can be employed as a convenient secreted reporter of promoter function in yeast.