DNA probes for mycobacteria. I. Isolation of DNA probes for the identification of Mycobacterium tuberculosis complex and for mycobacteria other than tuberculosis (MOTT)

Standing of nucleic acid testing strategies in veterinary diagnosis laboratories to uncover Mycobacterium tuberculosis complex members

Nucleic acid testing (NAT) designate any molecular approach used for the detection, identification, and characterization of pathogenic microorganisms, enabling the rapid, specific, and sensitive diagnostic of infectious diseases, such as tuberculosis. These assays have been widely used since the 90s of the last century in human clinical laboratories and, subsequently, also in veterinary diagnostics. Most NAT strategies are based in the polymerase chain reaction (PCR) and its several enhancements and variations. From the conventional PCR, real-time PCR and its combinations, isothermal DNA amplification, to the nanotechnologies, here we review how the NAT assays have been applied to decipher if and which member of the Mycobacterium tuberculosis complex is present in a clinical sample. Recent advances in DNA sequencing also brought new challenges and have made possible to generate rapidly and at a low cost, large amounts of sequence data. This revolution with the high-throughput sequencing (HTS) technologies makes whole genome sequencing (WGS) and metagenomics the trendiest NAT strategies, today. The ranking of NAT techniques in the field of clinical diagnostics is rising, and we provide a SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis with our view of the use of molecular diagnostics for detecting tuberculosis in veterinary laboratories, notwithstanding the gold standard being still the classical culture of the agent. The complementary use of both classical and molecular diagnostics approaches is recommended to speed the diagnostic, enabling a fast decision by competent authorities and rapid tackling of the disease.

Microbial Utilization of Free and Clay-Bound Insecticidal Toxins from Bacillus thuringiensis and Their Retention of Insecticidal Activity after Incubation with Microbes

The insecticidal toxins produced by Bacillus thuringiensis subspp. kurstaki and tenebrionis were resistant when bound on clays, but not when free, to utilization by pure and mixed cultures of microbes as sources of carbon and carbon plus nitrogen, and their availability as a nitrogen source was reduced. The bound toxins retained insecticidal activity both before and after exposure to microbes or pronase. The insecticidal activity of the toxins persisted for 40 days (the longest time evaluated) in nonsterile soil continuously maintained at the -33-kPa water tension and room temperature, alternately air dried and rewetted to the -33-kPa water tension, or alternately frozen and thawed, although alternate drying and wetting reduced the activity.

Establishment and evaluation of a multiplex polymerase chain reaction for detection of mycobacteria and specific identification of Mycobacterium tuberculosis complex

OBJECTIVE

To establish a multiplex polymerase chain reaction for detection of mycobacteria and specific identification of Mycobacterium tuberculosis complex and to evaluate the test in the diagnosis of tuberculosis.

DESIGN

Three sets of primers were used to amplify 383 bp, 240 bp and 131 bp DNA fragments from the genes encoding the 65 kDa, MPB64 and the 19 kDa proteins of M. tuberculosis in a single reaction tube. Reaction conditions were optimized with respect to the requirement of DMSO, concentration of MgCl2, annealing and denaturation temperatures and number of amplification cycles. Inhibitory activity in clinical samples was identified by amplifying a 500 bp DNA fragment of the phage lambda along with the mycobacterial targets within the same reaction tube. The multiplex PCR was evaluated in differentiating M. tuberculosis complex from other mycobacteria and in the diagnosis of tuberculosis by testing clinical specimens.

RESULTS

Amplification of the 383 bp DNA fragments was specific to the genus Mycobacterium. The 240 bp DNA fragment was amplified from M. tuberculosis complex and M. fortuitum and the 131 bp DNA fragment was amplified from the mycobacteria of M. tuberculosis complex and M. scrofulaceum. All the three bands were amplified only from M. tuberculosis complex. Applicability of the multiplex PCR is demonstrated in differentiating M. tuberculosis complex from other mycobacteria by using standard strains and clinical isolates. The multiplex PCR was also useful in the detection of inhibitory activity and in the identification of M. tuberculosis complex directly in clinical samples.

CONCLUSION

The multiplex PCR established in this study could differentiate M. tuberculosis complex from other mycobacteria. This test may also be helpful in the early and specific diagnosis of tuberculosis.

The molecular diagnosis of cutaneous infection

Molecular biologic techniques are having an impact on many different aspects of medicine. In the realm of infectious agents, they are enhancing our diagnostic capabilities, allowing earlier detection of infection, avoiding the need of culturing infectious agents for the purpose of diagnosis, and broadening our concepts to include the presence of infection in the absence of a culturable agent or serologic evidence of infection. As one might expect, the applicability of these techniques varies with the type of infectious agent being considered. For example, in most bacterial infections the infectious agent can be cultured and accurately identified within 48 hours. It is therefore unlikely that molecular diagnostic techniques will replace the "gold standard" of culture in instances of bacterial infection. Mycobacterial and spirochetal agents, by contrast, do not fall into this category. Although the rapid growers (Mycobacterium fortuitum and Mycobacterium chelonae) pose little problem because they can be cultured within 1 week, M. tuberculosis, M. leprae and the slow growing mycobacteriae require long intervals to culture and/or identify. These organisms may in the future be identified with molecular diagnostic techniques. In the group of spirochetal pathogens, Treponema pallidum infection is, for the most part, easily diagnosed with serologic studies. In early seronegative cases, spirochetes can be detected in primary inoculation lesions by darkfield microscopy or in tissue sections with appropriate stains. Conversely, detection of Borrelia burgdorferi is currently fraught with difficulties. Tissue sections stained for these spirochetes are difficult to interpret, and serologic studies have shown widely variable results. The polymerase chain reaction has already been applied to the study of Borrelia infection with encouraging early results.(ABSTRACT TRUNCATED AT 250 WORDS)

The Mycobacterium avium complex

Mycobacterium avium complex (MAC) disease emerged early in the epidemic of AIDS as one of the common opportunistic infections afflicting human immunodeficiency virus-infected patients. However, only over the past few years has a consensus developed about its significance to the morbidity and mortality of AIDS. M. avium was well known to mycobacteriologists decades before AIDS, and the MAC was known to cause disease, albeit uncommon, in humans and animals. The early interest in the MAC provided a basis for an explosion of studies over the past 10 years largely in response to the role of the MAC in AIDS opportunistic infection. Molecular techniques have been applied to the epidemiology of MAC disease as well as to a better understanding of the genetics of antimicrobial resistance. The interaction of the MAC with the immune system is complex, and putative MAC virulence factors appear to have a direct effect on the components of cellular immunity, including the regulation of cytokine expression and function. There now is compelling evidence that disseminated MAC disease in humans contributes to both a decrease in the quality of life and survival. Disseminated disease most commonly develops late in the course of AIDS as the CD4 cells are depleted below a critical threshold, but new therapies for prophylaxis and treatment offer considerable promise. These new therapeutic modalities are likely to be useful in the treatment of other forms of MAC disease in patients without AIDS. The laboratory diagnosis of MAC disease has focused on the detection of mycobacteria in the blood and tissues, and although the existing methods are largely adequate, there is need for improvement. Indeed, the successful treatment of MAC disease clearly will require an early and rapid detection of the MAC in clinical specimens long before the establishment of the characteristic overwhelming infection of bone marrow, liver, spleen, and other tissue. Also, a standard method of susceptibility testing is of increasing interest and importance as new effective antimicrobial agents are identified and evaluated. Antimicrobial resistance has already emerged as an important problem, and methods for circumventing resistance that use combination therapies are now being studied.

Characterization of a DNA probe for detection of Mycobacterium tuberculosis complex in clinical samples by polymerase chain reaction

We cloned and sequenced a DNA fragment from Mycobacterium tuberculosis for use in the identification of members of the M. tuberculosis complex. The DNA probe for culture confirmation had a sensitivity and a specificity of 100%. By using primers developed from this probe, the polymerase chain reaction detected 20 mycobacteria by ethidium bromide staining. This polymerase chain reaction system demonstrated 98% sensitivity and 100% specificity for detection of the M. tuberculosis complex in 200 sputum specimens.

The detection of Mycobacterium tuberculosis in uncultured clinical specimens using the polymerase chain reaction and a non-radioactive DNA probe

A Sal I-Hin dIII restriction fragment from Mycobacterium tuberculosis was found to hybridize specifically with genomic DNA from M. tuberculosis. Primers were designed from the sequence of this fragment and used to amplify uniquely M. tuberculosis-group DNA in a polymerase chain reaction. It is suggested that a combination of these primers and an acetylaminofluorene-labelled probe will prove to be a useful tool for the early diagnosis of tuberculous infections.

Genus- and species-specific DNA probes to identify mycobacteria using the polymerase chain reaction

Differential diagnosis of Mycobacterium tuberculosis, M. avium, and other mycobacteria remains a lengthy process. Recently, the use of DNA probes has been proposed as a new approach for a more specific and rapid diagnosis. Here, we report the cloning and sequencing of a genus-specific probe for Mycobacterium and a species-specific M. avium probe. The genus-specific probe hybridizes with DNA from nine ATCC type strains and 13 isolates of mycobacteria but not to non-mycobacterial DNA. In addition, the cloned fragment could also be amplified by polymerase chain reaction (PCR) in DNa of ten different mycobacterial type strains. The M. avium specific probe hybridizes strongly to sequences amplified in M. avium but not other mycobacterial or non-mycobacterial DNA. Amplification of the target sequence by PCR allowed the detection of 1 fg of all mycobacterial DNA tested for the genus-specific probe and 1 fg of M. avium DNA for the species-specific probe.

Isolation of a species-specific DNA probe for Neisseria gonorrhoeae using a novel technique particularly suitable for use with closely related species displaying high levels of DNA homology

The use of nucleic acid probes has become an increasingly common method for detecting pathogenic micro-organisms in clinical specimens. In the course of our efforts to isolate species-specific DNA probes for bacterial pathogens, we encountered a special problem with regard to Neisseria gonorrhoeae. As a consequence of the high degree of DNA homology that this organism displays with its nearest relative, Neisseria meningitidis, the isolation of such probes could not be readily achieved. We therefore developed a novel method of probe isolation which overcomes this problem. This methodology relies upon the application of a 'sandwich' hybridization assay to screen an M13 'shotgun' library derived from N. gonorrhoeae genomic DNA. For this, genomic DNA from N. gonorrhoeae and N. meningitidis was immobilized on nitrocellulose filters and probed with recombinant phage DNA from candidate clones. Those clones which had hybridized to target sequences were then detected using labelled vector sequences in a second hybridization step. By this means we obtained a numerical assessment of the degree of specificity of candidate clones for the target organism as compared to one or more related species. Using this technique we have isolated three DNA probes which are highly specific for N. gonorrhoeae and which display no cross-reactivity with N. meningitidis or other members of the Neisseriaceae. This paper presents the basis of the methodology and describes the isolation and characterization of three N. gonorrhoeae-like specific probes.

Speciation of organisms within the Mycobacterium avium-Mycobacterium intracellulare-Mycobacterium scrofulaceum (MAIS) complex based on restriction fragment length polymorphisms

A DNA probe which hybridizes to all pathogenic species of slow-growing mycobacteria has been used to identify restriction-fragment-length-polymorphisms (RFLPs) in Bam Hl digests of chromosomal DNA from members of the Mycobacterium avium-Mycobacterium intracellulare-Mycobacterium scrofulaceum complex. The RFLP patterns so produced were found to fall into distinct categories which were representative of each of the three species. Except for two doubtful isolates, strains of M. avium were found to fall into two related RFLP-types, one of which contained the vast majority of the strains tested. In contrast, M. intracellulare strains were found to be more heterogeneous. For these strains, we found one major RFLP-type and one subsidiary type which appears to be a sub-set of the first. We also found two further RFLP-types which contained serovars 7 and 18 respectively. We conclude from this that M. avium, M. intracellulare and M. scrofulaceum are three distinct species and that serovars belonging to the 'intermediate group' of Meissner and Anz belong to the species M. avium. Utilizing these criteria, we examined a number of isolates from the 'ambiguous' serovar 9 and found that of eight strains tested, six typed as M. avium and two typed as M. intracellulare.