Direct detection of Nocardia spp. in clinical samples by a rapid molecular method

We developed a 16S PCR-based assay for the rapid detection of Nocardia spp. directly from human clinical samples. The applicability of the assay was confirmed by using 18 samples from patients with nocardiosis as diagnosed by conventional cultures and 20 clinical samples from patients with confirmed tuberculosis used as negative controls.     

Evaluation of Legionella V-TesT for the detection of Legionella pneumophila antigen in urine samples

We evaluated a new immunochromatographic assay (Legionella V-TesT, Coris BioConcept, Gembloux, Belgium) for its ability to detect Legionella pneumophila serogroup 1 antigen in urine. Test devices were read at various time points to determine the optimum incubation time regarding performance. The results were compared with those obtained with the BinaxNOW urinary antigen test. The sensitivity and specificity were 82.2% and 98.6%, respectively, for the Legionella V-TesT and 83.9% and 100%, respectively, for the BinaxNOW urinary antigen test after 15 min of incubation. When tests were examined after 60 min, the sensitivity for both tests increased to 91.5%.     

New methods for detection of campylobacters in stool samples in comparison to culture

Campylobacter species, especially Campylobacter jejuni and Campylobacter coli, are a major cause of human bacterial enteritis. Current detection in stools is done essentially by culture on selective and nonselective media with filtration. These methods were compared to 2 molecular biology methods, an in-house real-time PCR and a multiplex PCR named Seeplex Diarrhea ACE Detection, and 3 immunoenzymatic methods, Premier Campy, RidaScreen Campylobacter, and ImmunoCard Stat!Campy. Out of 242 stool specimens tested, 23 (9.5%) fulfilled the positivity criteria, i.e., they were positive by one or both culture methods or, in case of a negative culture, by a positive molecular method and a positive immunoenzymatic method. The striking feature of this study is the low sensitivity of culture, in the range of 60%, in contrast to immunoenzymatic and molecular tests.     

Polymerase chain reaction for detection of Leptospira spp. in clinical samples.

A sensitive assay for Leptospira spp., the causative agent of leptospirosis, was developed on the basis of the polymerase chain reaction (PCR). A 331-bp sequence from the Leptospira interrogans serovar canicola rrs (16S) gene was amplified, and the PCR products were analyzed by DNA-DNA hybridization by using a 289-bp fragment internal to the amplified DNA. Specific PCR products also were obtained with DNA from the closely related nonpathogenic Leptospira biflexa but not with DNA from other spirochetes, such as Borrelia burgdorferi, Borrelia hermsii, Treponema denticola, Treponema pallidum, Spirochaeta aurantia, or more distant organisms such as Escherichia coli, Staphylococcus aureus, Mycobacterium tuberculosis, and Proteus mirabilis. The assay was able to detect as few as 10 bacteria. Leptospira DNA was detected in urine from experimentally infected mice. In addition, the test was found to be suitable for diagnosing leptospirosis in humans. Cerebrospinal fluid and urine from patients with leptospirosis were positive, whereas samples from control uninfected patients were negative.     

Evaluation of detection of Legionella spp. in water samples by fluorescence in situ hybridization,PCR amplification and bacterial culture

One hundred water samples (32 from clinical units and 68 from private households) were examined for Legionella by culture, fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR). Twenty-four samples were positive by culture (22 L. pneumophila; 2 non-pneumophila species), 36 by FISH (32 L. pneumophila; 4 non-pneumophila species) and 75 by PCR (41 positive for L. pneumophila; 26 positive for L. pneumophila and a non-pneumophila species; 8 positive for non-pneumophila species). PCR and FISH results were compared to bacterial culture as the "gold standard" method by calculating sensitivities and specificities, respectively: PCR assays, 96% and 47%; FISH assays, 67% and 72%, respectively. In comparison with FISH the lower specificity of PCR is probably caused by dead Legionella bacteria and/or free Legionella DNA in potable water, and the higher sensitivity of PCR may be explained by the detection limit of fluorescence microscopy. In conclusion, the relatively high specificity, sensitivity and quickness of the FISH assay offer significant advantages over conventional PCR and culture-based techniques.     

Real-time PCR for detection of Brucella spp. DNA in human serum samples

Presented here are the results of an evaluation of an in-house real-time PCR assay for the rapid and specific diagnosis of human brucellosis. The assay was based on direct amplification from serum samples of a 169-bp portion of bcsp31, a gene found in all Brucella species and biovars. Species specificity and selectivity of this real-time PCR assay were evaluated using genomic DNA from 15 Brucella strains and 42 non-Brucella strains, and the results were 100%. Among 17 culture-proven brucellosis patients, sera from 11 gave a positive amplification signal, corresponding to a sensitivity of 64.7%. In contrast, negative results were obtained for all sera from 60 control patients, corresponding to a specificity of 100%. The results indicate this test is well adapted for definite confirmation of brucellosis cases, when Brucella cultures remain sterile and serological tests demonstrate the presence of cross-reacting antibodies against Brucella sp. and Yersinia enterocolitica O:9 antigens.     

Identification of Burkholderia spp. in the clinical microbiology laboratory: comparison of conventional and molecular methods.

Cystic fibrosis (CF) predisposes patients to bacterial colonization and infection of the lower airways. Several species belonging to the genus Burkholderia are potential CF-related pathogens, but microbiological identification may be complicated. This situation is not in the least due to the poorly defined taxonomic status of these bacteria, and further validation of the available diagnostic assays is required. A total of 114 geographically diverse bacterial isolates, previously identified in reference laboratories as Burkholderia cepacia (n = 51), B. gladioli (n = 14), Ralstonia pickettii (n = 6), B. multivorans (n = 2), Stenotrophomonas maltophilia (n = 3), and Pseudomonas aeruginosa (n = 11), were collected from environmental, clinical, and reference sources. In addition, 27 clinical isolates putatively identified as Burkholderia spp. were recovered from the sputum of Dutch CF patients. All isolates were used to evaluate the accuracy of two selective growth media, four systems for biochemical identification (API 20NE, Vitek GNI, Vitek NFC, and MicroScan), and three different PCR-based assays. The PCR assays amplify different parts of the ribosomal DNA operon, either alone or in combination with cleavage by various restriction enzymes (PCR-restriction fragment length polymorphism [RFLP] analysis). The best system for the biochemical identification of B. cepacia appeared to be the API 20NE test. None of the biochemical assays successfully grouped the B. gladioli strains. The PCR-RFLP method appeared to be the optimal method for accurate nucleic acid-mediated identification of the different Burkholderia spp. With this method, B. gladioli was also reliably classified in a separate group. For the laboratory diagnosis of B. cepacia, we recommend parallel cultures on blood agar medium and selective agar plates. Further identification of colonies with a Burkholderia phenotype should be performed with the API 20NE test. For final confirmation of species identities, PCR amplification of the small-subunit rRNA gene followed by RFLP analysis with various enzymes is recommended.     

Evaluation of a novel PCR-based diagnostic assay for detection of Mycobacterium tuberculosis in sputum samples.

We report on a PCR-based assay we have developed for the detection of Mycobacterium tuberculosis in sputum samples. One hundred sputum specimens, which included 34 culture-positive and 66 culture-negative specimens, were evaluated with this system. Of the 34 culture-positive specimens, 31 were PCR positive, and 60 of the culture-negative specimens were PCR negative. An internal standard has been included in the assay system to monitor PCR inhibition and to confirm the reliability of the PCR assay.     

Application of polymerase chain reaction for detection of Legionella pneumophila in serum samples

Objective: To apply the polymerase chain reaction (PCR) to serum samples for the rapid diagnosis of Legionnaire's disease using the L5SL9 and L5SR93 primers designed to generate a 104-base-pair (bp) fragment from the 5S RNA gene of Legionella spp. The amplified product was detected by electrophoresis and by hybridization with the L5S–1-specific probe.
Methods: Single specimens of serum obtained from 24 patients with confirmed legionellosis, at different stages of their disease, were tested by PCR. Additionally, 10 serum samples from patients with no clinical symptoms of pneumonia and 10 samples from patients suffering from pneumonia caused by Mycoplasma pneumoniae, Coxiella bumetii or Chlamydia psittaci were also tested as controls in order to determine the specificity of the method.
Results: Of the 24 examined serum samples, the amplified products from 12 hybridized with the L5S–1 probe (sensitivity 50%). None of the negative controls was positive after PCR. No correlation was found between the day of illness and the positivity in the test.
Conclusions: The PCR technique could be applied as a diagnostic tool for the rapid diagnosis of legionellosis in serum samples after modification, mainly to improve its sensitivity.     

Multicenter comparison trial of DNA extraction methods and PCR assays for detection of Chlamydia pneumoniae in endarterectomy specimens

The reported rate of detection of Chlamydia pneumoniae DNA within atherosclerotic lesions by PCR varies between 0 and 100%. In this study, identical sets of coded experimental atheroma samples (n = 15) and spiked controls (n = 5) were analyzed by 16 test methods in nine centers by means of PCR. The positive controls were correctly identified to levels of 1, 0.1, and 0.01 inclusion bodies of C. pneumoniae/ml of tissue homogenate by 16 (100%), 11 (69%), and 3 (19%) of the test methods, respectively. Three out of 16 negative controls (19%) were rated positive. Positivity rates for atheroma samples varied between 0 and 60% for the different test methods, with the maximum concordant result for positivity being only 25% for one carotid artery sample. There was no consistent pattern of positive results among the various laboratories, and there was no correlation between the detection rates and the sensitivity of the assay used.     

Laboratory and clinical evaluation of a commercial DNA probe for the detection of Legionella spp.

We prospectively compared a commercially available Legionella DNA probe with culture and direct immunofluorescence. The analytical sensitivities of the DNA probe and direct immunofluorescence were equal. Both tests detected 4 X 10(3) CFU of Legionella pneumophila or Legionella micdadei per ml in the pulmonary secretions of experimentally infected guinea pigs. The diagnostic sensitivity of the reagent was evaluated by using 809 samples of respiratory secretions. Of 51 DNA probe-positive specimens, 31 came from patients with culture-confirmed legionellosis. Two culture-positive specimens had negative DNA probe tests. The sensitivity and specificity of the DNA probe were 93.9 and 97.4%, respectively. The sensitivity and specificity of direct immunofluorescence were 68.9 and 99.6%, respectively. The low specificity of the DNA probe resulted in an unacceptable positive predictive value (60.8%). False-positive DNA probe tests were not due to nonspecific binding of the probe or to technical problems but were associated with one lot of probe reagent. Most of the false-positive probe tests had values near the threshold value of greater than or equal to 4.0 suggested by the manufacturer. Raising the threshold value for a positive test to 7 lowered the sensitivity to 69.2% but raised the specificity to 99.2%. At this level, the performances of the DNA probe and direct fluorescent-antibody testing were equivalent. Respiratory secretions from patients receiving therapy for culture-confirmed Legionella infection remained DNA probe positive for up to 8 days, even though cultures and/or direct immunofluorescence tests often became negative. The DNA probe test is a satisfactory replacement for direct immunofluorescence but cannot replace culture for the laboratory diagnosis of Legionella infections.     

Development of antigen detection assay for diagnosis of tuberculosis using sputum samples

The rising incidence of tuberculosis worldwide means an increasing burden on diagnostic facilities, so tests simpler than Ziehl-Neelsen staining are needed. Such tests should be objective, reproducible, and have at least as good a detection limit as 10(4) bacteria/ml. A capture enzyme-linked immunosorbent assay (ELISA) was developed for detection of lipoarabinomannan (LAM) in human sputum samples. As a capture antibody, we used a murine monoclonal antibody against LAM, with rabbit antiserum against Mycobacterium tuberculosis as a source of detector antibodies. The sensitivity of the capture ELISA was evaluated by using purified LAM and M. tuberculosis whole cells. We were able to detect 1 ng of purified LAM/ml and 10(4) M. tuberculosis whole cells/ml. LAM could also be detected in culture filtrate of a 3-week-old culture of M. tuberculosis. The culture filtrate contained approximately 100 microgram of LAM/ml. The detection limit in sputum pretreated with N-acetyl-L-cysteine and proteinase K was 10(4) M. tuberculosis whole cells per ml. Thirty-one (91%) of 34 sputum samples from 18 Vietnamese patients with tuberculosis (32 smear positive and 2 smear negative) were positive in the LAM detection assay. In contrast, none of the 25 sputum samples from 21 nontuberculous patients was positive. This specific and sensitive assay for the detection of LAM in sputum is potentially useful for the diagnosis of tuberculosis.     

Multicenter quality assessment of PCR methods for detection of enteroviruses

We conducted a multicenter evaluation of commercial and in-house PCR methods for the detection of enteroviruses. Three coded panels of test and control RNA samples, artificial clinical specimens, and representative enterovirus serotypes were used to assess amplification methods, RNA extraction methods, and reactivities with different enterovirus serotypes. Despite several differences between PCR methods, there was good agreement, although some variation in sensitivity was observed. Most PCR methods were able to detect enterovirus RNA derived from 0.01 50% tissue culture infective dose (TCID50) and were able to detect at least 1 TCID50 of enterovirus in cerebrospinal fluid, stool, or throat swab specimens. Most were also able to detect a wide range of enterovirus serotypes, although serotypic identification was not possible. Some laboratories experienced false-positive results due to PCR contamination, which appeared to result mainly from cross-contamination of specimens during RNA extraction. Provided that this problem is overcome, these PCR methods will prove to be a sensitive and rapid alternative to cell culture for the diagnosis of enterovirus infection.     

Prospective comparison of direct immunofluorescence and conventional staining methods for detection of Giardia and Cryptosporidium spp. in human fecal specimens.

In a prospective comparative study, 2,696 consecutive fresh stool specimens over the course of 1 year were examined for Giardia lamblia and Cryptosporidium parvum by using a direct immunofluorescent-monoclonal antibody stain (for unspun specimens) and conventional staining methods (chlorazol black E for Giardia cysts and modified Kinyoun acid-fast for Cryptosporidium oocysts). The direct immunofluorescent-monoclonal antibody method resulted in a significantly increased detection rate for both giardia (118 versus 79 specimens, 49.4%; P = 0.006) and cryptosporidia (39 versus 23 specimens, 69.6%; P = 0.055).     

Real-time PCR assay targets the 23S-5S spacer for direct detection and differentiation of Legionella spp. and Legionella pneumophila

A real-time PCR for the ABI Prism 7000 system targeting the 23S-5S spacer of Legionella spp. was developed. Simultaneous detection and differentiation of Legionella spp. and Legionella pneumophila within 90 min and without post-PCR melting-curve analysis was achieved using two TaqMan probes. In sputum samples from 23 controls and 17 patients with legionellosis, defined by positive culture, urinary antigen testing, or seroconversion, 94% sensitivity and 100% specificity were observed.     

Assessment of rapid methods of pneumococcal antigen detection in routine sputum bacteriology.

Sputum specimens from 480 patients were examined for the presence of pneumococci by Gram film and culture and for pneumococcal antigen by counterimmunoelectrophoresis, coagglutination, and latex agglutination. Ninety six positive specimens were detected. Gram film and culture provided the most reliable techniques in well taken specimens collected early in the illness before antibiotic treatment had started. More than 70% of the specimens examined were submitted after starting antibiotics, however, and in these specimens, methods of antigen detection proved of greater value than either Gram film or culture. Counterimmunoelectrophoresis, coagglutination, and latex agglutination were similar in sensitivity and specificity, but coagglutination and latex agglutination were much easier to perform and to read.