Rapid detection and identification of Mycobacterium avium by amplification of 16S rRNA sequences

Differentiating host-associated variants of Mycobacterium avium by PCR for detection of large sequence polymorphisms

The Mycobacterium avium species consists of a group of organisms that are genetically related but phenotypically diverse, with certain variants presenting clear differences in terms of their host association and disease manifestations. The ability to distinguish between these subtypes is of relevance for accurate diagnosis and for control programs. Using a comparative genomics approach, we have uncovered large sequence polymorphisms that are, respectively, absent from bird-type M. avium isolates and from cattle types and sheep types of M. avium subsp. paratuberculosis. By evaluating the distribution of these genomic polymorphisms across a panel of strains, we were able to assign unique genomic signatures to these host-associated variants. We propose a simple PCR-based strategy based on these polymorphisms that can rapidly type M. avium isolates into these subgroups.

Genetic diversity of the dnaJ gene in the Mycobacterium avium complex

The Mycobacterium avium complex (MAC) is associated with various diseases in humans as a zoonosis. The dnaJ gene was partially sequenced in Schaefer's 28 reference strains of MAC, 14 human MAC isolates and 22 veterinary isolates. From substitutions affecting 21-32 nucleotides, all strains could be classified into 14 groups. Most nucleotide substitutions did not alter amino acid sequences. Approximately 8 % genetic diversity was seen in these strains, which divided into two clusters: cluster I (0.8 % genetic diversity), comprising the reference strain serotypes 1-6, 8-11 and 21 and all isolates; and cluster II (7 % genetic diversity), comprising the remaining reference strains. Analysis of the dnaJ gene in MAC may be useful in epidemiological studies.

Relationship between IS901 in the Mycobacterium avium complex strains isolated from birds, animals, humans, and the environment and virulence for poultry

A total of 738 strains of Mycobacterium avium complex (MAC) were examined in biological experiments on poultry by use of PCR methods with primers for detection of the insertion sequence IS901. Serotype strains of MAC from all known 28 serotypes were examined. Further strains were isolated from human immunodeficiency virus (HIV)-negative and HIV-positive patients, 6 animal species, 17 bird species, and the environment. Of 165 strains virulent for poultry, characterized by generalized tuberculosis, 164 strains contained IS901, a result which is statistically highly significant (P, 0.01). The remaining 573 strains were nonvirulent; however, IS901 was present in 24 strains. From among 20 strains of serotypes 1, 2, and 3, IS901 was found in 15 strains, only 5 of which were virulent for poultry. The remaining 111 strains, of serotypes 4 to 28, were nonvirulent and did not incorporate IS901. None of the 152 strains isolated from humans was virulent for poultry, including 12 strains which were IS901 positive.

Rapid detection and identification of mycobacteria by combined method of polymerase chain reaction and hybridization protection assay

A new method for the rapid detection and identification of mycobacteria, combining polymerase chain reaction (PCR) with DNA probe, was developed. The mycobacterial 16S rRNA encoding gene was amplified by nested PCR, and the PCR product was identified by hybridization protection assay using acridinium ester labelled DNA probe. The optimum temperature for hybridization of PCR product and DNA probe was estimated as 55 degrees C. The specificity of the combined method was excellent in the detection and identification of Mycobacterium tuberculosis and Mycobacterium avium-intracellulare complex (MAC). The detection limit was 10 fg DNA for M. tuberculosis, and 100 fg DNA for MAC. Results of preliminary clinical investigation of this method using 207 clinical specimens demonstrated an efficient detection and identification of M. tuberculosis and MAC. These results indicate that the new combined method may be a useful test for the rapid detection and identification of M. tuberculosis and MAC in clinical specimens.

Rapid differentiation of Mycobacterium avium and M. paratuberculosis by PCR and restriction enzyme analysis

Mycobacterium avium subsp. avium (M. avium) and M. avium subsp. paratuberculosis (M. paratuberculosis), intracellular bacteria that can cause chronic granulomatous enteritis in cattle, are difficult to distinguish on the basis of growth and biochemical characteristics. We report the development of a PCR-based strategy for the rapid differentiation of isolates of M. avium from isolates of M. paratuberculosis. Restriction fragment length polymorphism was identified by PCR amplification and subsequent restriction enzyme digestion with PstI of a 960-bp fragment of the 65-kDa heat shock protein (hsp65) from 21 clinical isolates of M. paratuberculosis and 14 isolates of M. avium. These results indicate that a restriction fragment length polymorphism in the hsp65 gene can be used for the rapid differentiation of clinical isolates of M. paratuberculosis and M. avium.

Genetic and serovar typing of clinical isolates of the Mycobacterium avium-intracellulare complex

SETTING

One hundred and thirty-four Mycobacterium avium-intracellulare complex (MAC) isolates were obtained from 121 patients in the UK.

OBJECTIVE

To compare serotyping and genetic analysis for species identification of MAC isolates from patients with and without the acquired immunodeficiency syndrome (AIDS).

DESIGN

Clinical MAC isolates were cultured and analyzed by serotyping, the commercially available Accuprobe kit, hybridization with genes coding for the 19 kDa and 38 kDa antigens of M. tuberculosis and fingerprinting with the pMB22 probe derived from M. paratuberculosis.

RESULTS

Species classification on the basis of genetic analysis was similar to serovar typing, with only exceptional discrepancies. Serovar prevalence was different in the two groups of patients, and different from those reported in other countries. MAC isolates from AIDS patients were exclusively M. avium, whereas patients without AIDS had MAC infections with M. avium and M. intracellulare in about equal proportion. M. intracellulare clinical isolates were genetically more heterogeneous than M. avium. Only M. intracellulare hybridized with the 38 kDa gene probe.

CONCLUSIONS

Serovars are strongly linked with species in clinical MAC isolates, confirming results previously obtained with reference strains. M. intracellulare can be easily identified by the presence of a 38 kDa gene.

Identification of Mycobacterium tuberculosis complex, Mycobacterium avium and Mycobacterium intracellulare by selective nested polymerase chain reaction

A nested polymerase chain reaction (PCR) procedure was devised for identification of mycobacteria. The outer reaction exploiting genus-specific sequences on the 16S rRNA gene was able to amplify specifically strains of the genus Mycobacterium. The identification of Mycobacterium tuberculosis complex, Mycobacterium avium and Mycobacterium intracellulare was accomplished by selective reamplification of the outer PCR product in three distinct inner amplifications exploiting species-specific primers mapping to a hypervariable region of mycobacterial 16S rRNA. Detection of mycobacteria, other than those for which species-specific primers were used, was accomplished by adding a supplementary genus-specific upper primer to one of the inner reactions. Specificity of amplification was confirmed for clinical isolates and reference strains of different mycobacterial species with the exception of a M. intracellulare type 7 strain which was recognized as M. avium. The amplification protocol presented thus provides a reliable and cost-effective way for identification of clinically relevant mycobacteria.

Detection of Pseudomonas (Burkholderia) cepacia using PCR

Pseudomonas cepacia colonization of the lung is associated with increased morbidity and mortality for cystic fibrosis (CF) patients. The lack of a sensitive detection method for Pseudomonas cepacia in CF sputum has resulted in controversy regarding its epidemiology. We designed a PCR method to detect P. cepacia using P. cepacia 16 S rRNA sequences as the amplification target region. The PCR amplification with purified DNA as template yielded the expected 209-bp products from P. cepacia, but not from related Pseudomonas species of medical importance or other bacteria which have been reported to colonize CF patients. In serial dilution experiments as few as 10(2) P. cepacia CFU were detectable. When sputum samples from three CF patients chronically colonized with P. cepacia and P. aeruginosa were analyzed, P. cepacia was detected in all three specimens by PCR, but only in two when selective culture was performed. Our data support the potential role of PCR technology in the rapid, sensitive, and definitive detection of P. cepacia in CF sputum samples, even in the context of concomitant P. aeruginosa colonization.