Staphylococcus aureus bacteremia in patients receiving pegylated interferon-alpha and ribavirin for chronic hepatitis C virus infection.

Bacteremia has rarely been reported in patients receiving treatment for hepatitis C virus (HCV) infection. We describe the features and investigation of four cases of Staphylococcus aureus bacteremia occurring between 3 November 2004 and 10 January 2005 in patients on therapy for chronic HCV infection. The unusual occurrence of S. aureus bacteremia in a series of patients led to an epidemiologic investigation and molecular typing methods were employed to assess the relatedness of cases. The mean time of bacteremia onset was week 10 of HCV treatment. No patient had neutropenia previously. The average duration of bacteremia was 2.6 days and complications included acute renal failure (2/4), disseminated intravascular coagulopathy (DIC) with sepsis syndrome (1/4), septic arthritis (1/4), spinal epidural abscess (1/4) and endocarditis (1/4). Two patients were in the same weight class for dosing, but no other epidemiologic links were found. One patient admitted to intravenous drug use (IVDU) and a second was suspected of IVDU. The two other patients were cirrhotic, but had no further identifiable risk factors. All bacterial isolates were methicillin-susceptible. By pulsed-field gel electrophoresis, two cases were found to have identical bacterial strains. However, fluorescent-based amplified fragment-length polymorphism analysis demonstrated distinct band patterns in all four cases. The epidemiologic data and molecular analysis of this cluster of S. aureus bacteremia cases among patients receiving combination therapy for treatment of chronic HCV infection suggest that these cases were not related. Additionally, IVDU and cirrhosis, but not neutropenia, are identified as potential risk factors for this uncommon complication of HCV therapy.

Evaluation of fluorescence-based amplified fragment length polymorphism analysis for molecular typing in hospital epidemiology: comparison with pulsed-field gel electrophoresis for typing strains of vancomycin-resistant Enterococcus faecium.

Fluorescence-based amplified fragment length polymorphism (fbAFLP) is a novel assay based on the fluorescent analysis of an amplified subset of restriction fragments. The fbAFLP assay involves the selective PCR amplification of restriction fragments from a total digest of genomic DNA. The ligation of adapters with primer-specific sites coupled with primers containing selective nucleotides allowed the full potential of PCR to be realized while maintaining the advantages of restriction endonuclease analysis. Fluorescence-based fragment analysis with polyacrylamide gel electrophoresis provides the accurate band sizing required for homology assessment. The large number of phylogenetically informative characters obtained by fbAFLP is well suited for cluster analysis and database development. The method demonstrated excellent reproducibility and ease of performance and interpretation. We typed 30 epidemiologically well-characterized isolates of vancomycin-resistant enterococci from an outbreak in a university hospital by fbAFLP. Clustering of fbAFLP data matched epidemiological, microbiological, and pulsed-field gel electrophoresis data. This study demonstrates the unprecedented utility of fbAFLP for epidemiological investigation. Future developments in standardization and automation will set fbAFLP as the "gold standard" for molecular typing in epidemiology.

Performance characteristics of the Becton Dickinson ProbeTec System for direct detection of Chlamydia trachomatis and Neisseria gonorrhoeae in male and female urine specimens in comparison with the Roche Cobas System.

OBJECTIVE: The Becton Dickinson BDProbeTec ET System is a new semiautomated system using strand displacement amplification technology that simultaneously amplifies and detects Chlamydia trachomatis and Neisseria gonorrhoeae DNA. The strand displacement amplification products are hybridized with a fluorescent detector probe and are captured by a chemiluminescent assay in a microwell format. An amplification control is also included to monitor assay inhibition. This study evaluated the performance of the BDProbTec ET system in detecting C trachomatis and N gonorrhoeae in male and female urine specimens, calculated its ability to process large volumes of specimens, and determined the inhibition rate. MATERIALS AND METHODS: Eight hundred twenty-five male and 399 female urine specimens were tested for both C trachomatis and N gonorrhoeae with the BDProbeTec ET system, and results were compared with those of the Roche Amplicor Cobas system. All urine specimens were processed on both assays on the same day they were received, according to the manufacturers' instructions. Discrepant results were resolved by in-house polymerase chain reaction assays. Internal or amplification controls were also used in each specimen assay to monitor inhibition. The throughput of the BDProbTec ET system was further tested with 150 urine specimens on an 8-hour shift for 2 days. RESULTS: The overall sensitivity, specificity, positive predicative value, and negative predicative value for for detection of chlamydia were 95.3%, 99.3%, 95.9%, and 99.2% for strand displacement amplification and 95.9%, 98.3%, 90.6%, and 99.3% for the Roche Amplicor system. For detection of gonorrhea, these values were 100%, 99.7%, 88.2%, and 100% and 96.7%, 98.9%, 69%, and 99.9%, respectively. The overall inhibition rates for both strand displacement amplification and Roche Amplicor were less than 3.5%. The BDProbTec ET system was able to produce 150 results each for chlamydia and gonorrhea and the internal control within the 8-hour shift. CONCLUSIONS: The performance characteristics of the BDProbeTec ET assay are similar to those of the Roche Amplicor polymerase chain reaction for detection of chlamydia and gonorrhea in male and female urine specimens. The system was able to produce 300 results in an 8-hour shift.

Comparison of the effectiveness of polymerase chain reaction and enzyme immunoassay in detecting Chlamydia trachomatis in different female genitourinary specimens.

BACKGROUND: In high-volume laboratories, enzyme immunoassay (EIA) is the most commonly used method of detecting Chlamydia trachomatis. The optimal specimen for detecting C trachomatis is a combined urethral and cervical swab. OBJECTIVE: To compare EIA with the combined urethral and cervical swab with polymerase chain reaction (PCR) on urine alone and urine mixed with cervical cells. PATIENTS AND METHODS: Phase 1 of the study included 752 sets of specimens used for comparison. In phase 2, another 212 samples of urine and urine plus cervical cells were added to the study for comparison of the 2 specimen types using PCR. RESULTS: In phase 1, 648 samples were negative and 76 were positive by all 3 methods and specimen combinations. Enzyme immunoassay was able to detect 81 positive samples (10.8%), whereas PCR on urine alone detected 97 positive samples (12.9%) and PCR on urine plus cervical cells detected 102 positive samples (13.6%), giving a sensitivity of 75%, 93.3%, and 98. 1% respectively. In phase 2, PCR on urine alone detected 119 positive samples (12.3%) and PCR on urine plus cervical cells detected 127 positive samples (13.1%), with a sensitivity of 92.2% and 98.5%, respectively. CONCLUSION: Polymerase chain reaction on urine alone or urine plus cervical cells is superior to EIA on combined cervical and urethral swabs. There is a slight advantage of adding cervical cells to the urine compared with the urine specimen alone when PCR is used as the assay for detection. The total inhibition rate in our female population is only 3.1% when PCR is used.

Detection of Bordetella pertussis in a clinical laboratory by culture, polymerase chain reaction, and direct fluorescent antibody staining; accuracy, and cost.

Control of Bordetella pertussis in the community is hampered by slow and insensitive diagnostic tests. We therefore examined the accuracy and cost of culture, direct fluorescent antibody (DFA) staining, and PCR in a routine clinical laboratory. Six hundred thirty seven nasopharyngeal swabs and aspirates in casamino acids transport medium were cultured, stained with polyclonal (Difco), and monoclonal (BL-5 and Accu-Mab) anti-B. pertussis reagents, and amplified by an IS481-specific PCR. PCR products were detected by a hybridization-enzyme immunoassay kit (Gen-eti-k DEIA, DiaSorin), with confirmation by a second PCR in a separate laboratory. Sensitivities and specificities of culture, polyclonal DFA, monoclonal DFA, and PCR were 36 and 100%, 11.4 and 94.6%, 8.3 and 98. 4%, and 95.0 and 99.3%, respectively, with a prevalence of 15.7%. The DFA tests were the most economical, and the PCR cost was 31% higher than culture. This study suggests that with minor improvements in economy, pertussis PCR can be implemented in a clinical laboratory with marked improvement in diagnostic accuracy.

Minimal inhibitory effect of male urine on detection of Chlamydia trachomatis by Roche Amplicor PCR.

A total of 1120 specimens of fresh urine from male patients was tested for Chlamydia trachomatis with the Roche Amplicor PCR Kit and an in-house PCR assay. The in-house PCR had an internal control to monitor inhibitory effects of clinical specimens on the PCR assay. All urine samples were processed within 24-48 h of collection and DNA was extracted on the same day that the assays were performed. Specimens that gave discrepant PCR results were tested by a reference laboratory with both the Roche Amplicor kit and their in-house PCR assay. Of the 1120 samples, 174 gave positive results in both assays and 942 gave negative results in both assays. Only one specimen showed an inhibitory effect on the in-house PCR assays, as indicated by failure to produce the internal control PCR product. This specimen gave negative results by both assays. There were four discrepant results in the two PCR assays. One was a false negative result obtained with the Roche Amplicor kit and the remaining three discrepant results could not be resolved because there was an insufficient quantity of specimen. This study demonstrated that the Roche Amplicor kit could effectively detect C. trachomatis in urine specimens from this population of male patients with negligible inhibition of PCR.

A feasibility study of the use of random amplified polymorphic DNA in the population genetics and systematics of grasshoppers.

Single, short primers of arbitrary nucleotide sequence were used in polymerase chain reactions to amplify regions of DNA isolated from several melanopline and oedipodine grasshoppers collected from local Saskatchewan populations. This represents one of the first applications of the method, called randomly amplified polymorphic DNA (or RAPD), to natural populations. Twenty-four different oligonucleotide primers, nine nucleotides in length, yielded clear and reproducible bands corresponding to amplified products and separable by agarose gel electrophoresis. On average, about 8.1 bands (range 0-17) were obtained per primer per individual. The mean percent similarity between band profiles of conspecific individuals was 51.2%, whereas the mean value for individuals representing different species or genera was 35.0%. Clearly, greater numbers of insects and primers will be required to achieve a satisfactory level of phylogenetic resolution. Given RAPDs technical advantages and ease of execution, however, this should not be problematic to the molecular systematist.