Rapid detection and identification of mycobacterial DNA by PCR

We have developed a highly sensitive and rapid PCR assay for detection and identification of mycobacterial species. Two sets of PCR primers were prepared; one was for the 19 kDa antigen gene and the other for the dna J gene. The PCR for 19 kDa antigen gene was found to be specific to the M. tuberculosis complex; M. tuberculosis, M. bovis and M. africanum. On the other hand, the PCR for the dna J gene was able to detect a broad spectrum of mycobacterial species including M. tuberculosis, M. avium, M. intracellulare and M. kansasii. The sensitivity of PCR was similar to that of the culture method for precultured M. tuberculosis whereas PCR was much more sensitive than the culture for clinical samples. The procedure of decontamination by sodium hydroxide for clinical samples could reduce the viability of M. tuberculosis while it did not affect mycobacterial DNA. The nucleotide sequence homologies among major mycobacteria were also determined following PCR for the dna J gene. This allowed us to make restriction maps for each mycobacterium. We have demonstrated that the PCR-RFLP for the dna J gene will be a useful laboratory test for rapid identification of tuberculous and nontuberculous mycobacterial species.     

A simple method for isolation of DNA from formalin-fixed paraffin-embedded samples for PCR.

A simple method of processing formalin-fixed, paraffin-embedded tissue sections for DNA amplification by polymerase chain reaction (PCR) is described. In this procedure, deparaffinized sections are readily subjected to DNA isolation simply by boiling and the released DNA can be directly employed for PCR. The method allows analysis of single-copy genes or viral sequences at least up to 300 base pairs long in one working day. This method is particularly useful in analysing retrospective materials when the simplicity and low cost of the assay are preferable. Furthermore, the simplicity of the procedure reduces the risk of contamination.     

Rapid detection of Klebsiella pneumoniae from blood culture bottles by real-time PCR

A LightCycler real-time PCR hybridization probe-based assay which detects a partial Klebsiella pneumoniae 16S rRNA gene was developed for the rapid identification of K. pneumoniae directly from growth-positive blood culture bottles (BACTEC 9240 system) within 2 h. No cross-reactivity was observed with 65 negative-control blood cultures that grew bacteria other than K. pneumoniae and 48 negative blood cultures from double-blind experiments, thus demonstrating 100% specificity when compared to results of conventional biochemical characterization. The assay also showed 100% sensitivity, as it correctly identified all 142 positive-control blood cultures and 4 from double-blind trials.     

Detection and identification of mycobacteria by amplification of RNA and DNA in pretreated blood and bone marrow aspirates by a simple lysis method.

A sodium dodecyl (lauryl) sulfate method was evaluated for the preparation of blood specimens and bone marrow aspirates for use in two amplification procedures (Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test [AMTDT] and Roche Amplicor M. avium/M. intracellulare [MAI] Test) for the detection and identification of Mycobacterium tuberculosis and M. avium and M. intracellulare, respectively. The AMTDT is based on amplification of rRNA, whereas the Amplicor MAI Test amplifies a specific DNA region of the 16S rRNA gene. The results of amplification techniques were compared with those of standard culture and culture in BACTEC 13A and BACTEC 12B liquid media. A total of 121 blood specimens and 15 bone marrow aspirates were collected from 136 AIDS patients. Mycobacterial growth was recovered for 103 specimens; 35 yielded M. tuberculosis, 62 yielded M. avium, 5 yielded M. genavense, and 1 yielded M. kansasii. The values of sensitivity and specificity in pretreated specimens for detection of M. tuberculosis by the AMTDT were 94.3 and 100%, respectively, and those for detection of M. avium by the Amplicor MAI Test were 91.9 and 100%, respectively. The simple lysis method described in the present work allows the recovery of mycobacteria from blood specimens and bone marrow aspirates and may be used in combination with the AMTDT and the Amplicor MAI Test to detect and identify different members of the genus Mycobacterium. This method might also be applicable for the identification of mycobacteria from blood culture fluids with acridinium-ester-labeled DNA probes.     

Rapid and simple method for preparation of genomic DNA from easily obtainable clotted blood.

A method was developed for the preparation of genomic DNA from clotted blood that is usually discarded after extraction, for other laboratory tests. The method, which involves proteinase K digestion, salt/chloroform extraction and 90% ethanol precipitation of DNA from clotted blood, is rapid, simple, and easy because it does not impose an extra burden on the patient.     

Rapid detection of methicillin-resistant staphylococci by real-time PCR directly from positive blood culture bottles

For the rapid detection of methicillin-resistant staphylococci directly from blood cultures containing gram-positive cocci in clusters, we implemented a real-time (LightCycler) polymerase chain reaction (PCR) specific for the Staphylococcus aureus nuc gene encoding nuclease and the mecA gene encoding methicillin resistance. For the 475 positive blood cultures tested, the assay turned out to have 100% sensitivity and 100% specificity for the identification of methicillin-susceptible (n = 108) and methicillin-resistant (n = 34) S. aureus. When coagulase-negative staphylococci (CoNS) were included, the overall sensitivity for the detection of methicillin resistance was 93% and the specificity was 99%. Real-time PCR for nuc and mecA from blood culture bottles with staphylococci yields therefore a rapid (2–3 h) identification of S. aureus and CoNS including methicillin resistance.     

Improved detection of mycobacterial DNA by PCR in formalin-fixed, paraffin-embedded tissues using thin sections

PCR is a unique methodology allowing for the sensitive detection of mycobacterial DNA-sequences in cases in which no fresh material can be obtained for classic analyses. Despite the limitations of this technique, for example the less satisfactory quality of DNA from paraffin-embedded specimens and the high effort necessary to control contamination, PCR still represents a useful additional tool for routine diagnostic examinations of mycobacterial infections. Fragmentation of the DNA extracted from formalin-fixed, paraffin-embedded samples on the one hand and the rigid cell wall of mycobacteria on the other hand are obstacles to detecting the DNA of these microorganisms by PCR. Here, we describe a simple mechanical procedure that allows us to improve the detection of mycobacterial DNA with the use of thin (1 microm) sections instead of thicker sections. This could be explained by a gentle, mechanical opening of the acid fast mycobacterial cell wall. Thus, even the application of heat/cold shock treatments is not necessary. This inexpensive fast procedure can also be used for the detection of other infectious agents.     

Use of the real-time PCR assay in conjunction with MagNA Pure for the detection of mycobacterial DNA from fixed specimens.

Tuberculosis in immunocompromised patients is often caused by Mycobacterial species other than Mycobacterium tuberculosis. Thus, detection of and differentiation between M. tuberculosis and nontuberculosis species is necessary for diagnosis of disease in these patients. Furthermore, when tissue changes show granulomatous inflammation, quick confirmation testing for mycobacterial infection is needed for conclusive diagnosis. The aim of this study was to validate the utility of a real-time polymerase chain reaction (PCR) assay in conjunction with the MagNA Pure LC automated extraction system for the detection of mycobacterial DNA from formalin-fixed, paraffin-embedded specimens. A total of 46 archived, paraffin-embedded, fixed specimens showing granulomatous inflammation were studied for mycobacterial infection by real-time PCR. Bacterial DNA was extracted and isolated using the MagNA Pure extraction system. Real-time PCR was performed on the LightCycler using the Artus Real Art Mycob Diff ASR kit from Qiagen. Thirteen of the 46 patient specimens were positive for mycobacterial infection by acid-fast bacilli (AFB) stain. Of the13 reported positive by AFB stain, 12 where positive by real-time PCR. All 13 specimens reported positive by AFB were sent for culture confirmation. Eleven of 13 were returned positive by culture. Specimens reported as negative by culture and positive by real-time PCR were confirmed positive by a second PCR method from another reference laboratory. We believe that these studies are beneficial in the differential diagnosis of mycobacterial infection from fixed tissue specimens where tuberculosis might not have been clinically initially suspected and when specimens are not suitable for microbiologic examination.     

Rapid detection of methicillin-resistant staphylococci from blood culture bottles by using a multiplex PCR assay

Rapid detection and accurate identification of methicillin-resistant staphylococci are critical for the effective management of infections caused by these organisms. We describe a multiplex PCR-based assay for the direct detection of methicillin-resistant staphylococci from blood culture bottles (BacT/Alert; Organon-Teknika, Durham, N.C.). A simple lysis method followed by a multiplex PCR assay designed to detect the nuc, mecA, and bacterial 16S rRNA genes was performed. A total of 306 blood culture specimens were collected over a period of 10 months from June 1998 to April 1999, consisting of 236 blood cultures growing staphylococci (including 124 methicillin-resistant Staphylococcus spp.), 50 positive blood cultures which grew organisms other than staphylococci, and 20 blood cultures that were negative for bacterial and fungal pathogens after 5 days of incubation and terminal subculture. DNA extraction, PCR, and detection could be completed in 2.5 h. Of the positive blood cultures with staphylococci, the multiplex PCR assay had a sensitivity and specificity of 99.2% and 100%, respectively. Our results show that rapid, direct detection of methicillin-resistant staphylococci is possible, allowing clinicians to make prompt and effective decisions for the management of patients with staphylococcal bacteremia.     

Comparison between plasma and whole blood specimens for detection of Aspergillus DNA by PCR

Ninety-six plasma and whole blood specimens from nine selected patients were analyzed for the presence of Aspergillus DNA. Nineteen specimens from three patients with proven aspergillosis were PCR positive in both materials, whereas an additional 22 were PCR positive in whole blood only. All 36 samples from six patients without signs of aspergillosis were negative in both assays. We conclude that although plasma and whole blood spiked with Aspergillus conidia showed an identical lower detection limit (10 CFU), the sensitivity of plasma PCR was lower than that of PCR performed on whole blood samples.     

Evaluation of in-house optimized semi-nested PCR and EIA for direct detection of mycobacterial DNA in CSF

A rapid and correct diagnosis of mycobacterial infections is important for effective patient treatment. Semi-nested-PCR with Fl-16 SOL, 16SOR and 16SNSR primers based on the 16S rRNA gene, under optimized conditions, can detect 499 bp amplified products from all tested mycobacteria. The assay could detect as little as 100 fg of mycobacterial DNA except for rapid growing mycobacteria, whose detection limits ranged from 1 ng to 10 pg. The specificities of the capture probes were assessed with 96 mycobacterial strains (22 species) and 33 nonmycobacterial strains (30 species). The specificities of pAll1, pTbc1 and pMar1 were 94%, 93% and 82%, respectively, and that of pAvi1, pInt1, pChe1 and pFor1 were 100%. The pTbc1 and pAvi1 were tested with DNA from 108 CSF samples, and the sensitivity and specificity of the detection method were 56% and 84% compared to culture and patient histories. The assay should be used for rapid detection and concurrent identification of slow growing mycobacteria without parallel conventional culture verification.     

Specific detection of Brucella DNA by PCR.

A PCR assay with primers derived from the 16S rRNA sequence of Brucella abortus was developed. Nine different combinations between six primers were tested. One pair of primers, which amplified a 905-bp fragment, was selected. As little as 80 fg of Brucella DNA was detected by this method. DNAs from all of the representative strains of the species and biovars of Brucella and from 23 different Brucella isolates were analyzed and yielded exclusively the 905-bp fragment. No amplification was detected with DNAs from 10 strains phylogenetically related to Brucella spp., 5 gram-negative bacteria showing serological cross-reactions with Brucella spp., and 36 different clinical isolates of non-Brucella species. Only Ochrobactrum anthropi biotype D yielded a PCR product of 905 bp, suggesting a closer relationship between Brucella spp. and O. anthropi biotype D. The specificity and high sensitivity of the PCR assay may provide a valuable tool for the diagnosis of brucellosis.     

Clinical evaluation of PCR method for detection of cytomegalovirus DNA

Polymerase chain reaction (PCR) to detect Cytomegalovirus (CMV)-DNA from the clinical specimens is useful to diagnose CMV infection. Eighty-one specimens of 31 patients including peripheral blood, bronchioalveolar lavage fluid, biopsy tissues, feces, urine, sputum and etc. and normal peripheral blood from 59 volunteers were used in this study. After DNA extraction each samples was amplified by the seminested PCR using primers recognizing sequences in the Immediate-early gene of CMV. This PCR method specifically detected more than 10 virus copies even in the presence of the genomic DNA. CMV-DNA was detected in only one of 59 normal peripheral bloods (1.7%). Six of 31 patients were clinically diagnosed as CMV infection by anti-CMV therapy. These 6 patients were positive in the peripheral blood by PCR for CMV, and 5 of them were positive in other samples. However, 3, 5 and 1 of 25 patients, who were clinically diagnosed as not having CMV infection, were also positive in peripheral blood, in the other samples and in both, respectively. The PCR method was able to examine any clinical samples. To examine both the peripheral blood and the samples from infected organs is helpful for the diagnosis of CMV infection.     

Detection of Mycobacterium tuberculosis DNA in clinical samples by using a simple lysis method and polymerase chain reaction.

We have evaluated the polymerase chain reaction for detection of Mycobacterium tuberculosis in clinical samples from patients with tuberculous infection. Two simple methods for mycobacterial DNA release have been compared: sonication and lysis with nonionic detergents and proteinase K. The more effective method was the enzymatic technique. By using this protocol with 75 specimens we detected M. tuberculosis DNA in all of the samples, whereas only 48 and 71 samples were positive by acid-fast staining and culture, respectively.     

A simple, rapid ELISA method for the detection of DNA antibodies.

Employing an enzyme-linked immunosorbent assay (ELISA) technique the serum antibodies against native (double stranded) and denatured (single stranded) deoxyribonucleic acid (DNA) have been measured in various disease groups and a group of blood donor sera. The ELISA method has been compared with a radioimmunoassay method using native (double stranded) DNA is substrate antigen and a latex-fixation technique using particles coated with soluble deoxyribonucleoprotein (SNP). It is concluded that ELISA offers an economic and reliable alternative to isotope techniques for the assessment of antibody content in systemic lupus erythematosus (SLE) and related disease states for the clinical laboratory.     

PCR扩增孕妇外周血DNA进行胎儿性别诊断

采用密度梯度离心技术对40例孕妇外用血中胎儿细胞进行富集,并用PCR技术扩增了Y染色体特异重复序列,以产前基因诊断胎儿性别,结果38例胎儿性别诊断准确,证明此技术可作为无创伤性方法用于X连锁遗传病的产前诊断.     

Detection of Haemophilus influenzae and Streptococcus pneumoniae DNA in blood culture by a single PCR assay.

A multiplex PCR assay was developed to screen blood cultures from children in The Gambia with suspected pneumonia for the simultaneous detection of Haemophilus influenzae type b and Streptococcus pneumoniae isolates. Analysis of 295 blood cultures showed that PCR detected the organisms in all samples positive by culture in two samples infected with H. influenzae type b and four samples infected with S. pneumoniae that were culture negative, indicating that this method is sensitive for detecting these organisms in blood cultures.