Multiprimer PCR system for differential identification of mycobacteria in clinical samples

First case of systemic fatal mycobacteriosis caused by Mycobacterium goodii in a pet Kenyan sand boa (Eryx colubrinus loveridgei)

BACKGROUND

Environmental nontuberculous mycobacteria species that are not members of the M. tuberculosis complex, are ordinary inhabitants of a wide variety of environmental reservoirs and their role in human and animal diseases has been fully recognized. Even if spontaneous mycobacterial infections have been reported in a wide variety of reptiles, this is the first report of systemic fatal mycobacteriosis sustained by Mycobacterium goodii in a pet reptile.  CASE PRESENTATION: An adult, wild caught (WC), male Kenyan sand boa (Eryx colubrinus loveridgei) age unknown, was presented for clinical examination due to decreased activity level, decreased appetite and diarrhea. Blood tests showed unreliable results. Coprologic exam showed a moderate to severe presence of flagellates. X rays and ultrasound showed moderate presence of air and faeces in the large intestine. The snake was hospitalized and oral metronidazole was chosen as antiprotozoal agent in association with subcutaneous warm fluids. The snake was discharged after 2 weeks therapy in good clinical condition. Faecal exam resulted negative. One month after, the snake was quickly hospitalized again because of a recrudescence of symptoms. Biochemistry showed severe increase of AST, ALT and biliary acids. Severe leucocytosis and moderate to severe anemia were highlighted. Ultrasound examination revealed a severe diffused alteration of the liver parenchyma and a fine needle aspiration was performed. The cytological diagnosis was mixed inflammation, with a numerous of unstained rod-shaped bacteria both inside macrophages and free in the sample. The snake's condition rapidly deteriorated and euthanasia was performed. The histology of the coelomic organs confirmed a systemic mycobacteriosis. Real-time PCR identified the mycobacteria as Mycobacterium goodii.

CONCLUSIONS

Species from the genus Mycobacterium are among the most important micro-organism including the causative agents of tuberculosis. Even if the general incidence of disease in reptiles due to mycobacteria is comparatively low, they can serve as reservoirs of many ubiquitous mycobacteria species. Mycobacterium goodii is a rapidly growing non-tuberculous mycobacterium that has recently been associated with severe infections in animals and humans. Although in this case the pathogenesis was not completely clear, we highlight the zoonotic risk of mycobacteriosis in exotic animals especially in WC specimens.

Zoonotic pathogens survey in free-living long-tailed macaques in Thailand

Long-tailed macaques (Macaca fascicularis) are known to harbour a variety of infectious pathogens, including zoonotic species. Long-tailed macaques and humans coexist in Thailand, which creates potential for interspecies pathogen transmission. This study was conducted to assess the presence of B virus, Mycobacterium spp., simian foamy virus (SFV), hepatitis B virus (HBV), and Plasmodium spp. in 649 free-living Thai long-tailed macaques through polymerase-chain reaction. DNA of SFV (56.5%), HBV (0.3%), and Plasmodium spp. (2.2%) was detected in these macaques, whereas DNA of B virus and Mycobacterium spp. was absent. SFV infection in long-tailed macaques is broadly distributed in Thailand and is correlated with age. The HBV sequences in this study were similar to HBV sequences from orangutans. Plasmodium spp. DNA was identified as P. inui. Collectively, our results indicate that macaques can carry zoonotic pathogens, which have a public health impact. Surveillance and awareness of pathogen transmission between monkeys and humans are important.

Frontiers Approaches to the Diagnosis of Thrips (Thysanoptera): How Effective Are the Molecular and Electronic Detection Platforms?

Simple Summary

Thrips are important agricultural and forest pests. They cause damage by sucking plant sap and transmitting several plant viruses. Correct identification is the key for epidemiological studies and formulating appropriate management strategies. The application of molecular and electronic detection platforms has improved the morphological character-based diagnosis of thrips species. This article reviews research on molecular and automated identification of thrips species and discusses future research strategies for rapid and high throughput thrips diagnosis.

Abstract

Thrips are insect pests of economically important agricultural, horticultural, and forest crops. They cause damage by sucking plant sap and by transmitting several tospoviruses, ilarviruses, carmoviruses, sobemoviruses, and machlomoviruses. Accurate and timely identification is the key to successful management of thrips species. However, their small size, cryptic nature, presence of color and reproductive morphs, and intraspecies genetic variability make the identification of thrips species challenging. The use of molecular and electronic detection platforms has made thrips identification rapid, precise, sensitive, high throughput, and independent of developmental stages. Multi-locus phylogeny based on mitochondrial, nuclear, and other markers has resolved ambiguities in morphologically indistinguishable thrips species. Microsatellite, RFLP, RAPD, AFLP, and CAPS markers have helped to explain population structure, gene flow, and intraspecies heterogeneity. Recent techniques such as LAMP and RPA have been employed for sensitive and on-site identification of thrips. Artificial neural networks and high throughput diagnostics facilitate automated identification. This review also discusses the potential of pyrosequencing, microarrays, high throughput sequencing, and electronic sensors in delimiting thrips species.

Nested Polymerase Chain Reaction and Cutaneous Tuberculosis

The role of Mycobacterium tuberculosis in the etiology and pathogenesis of cutaneous tuberculosis is controversial because of the difficulties associated with demonstrating the presence of these mycobacteria in tuberculid cutaneous lesions by routinely available microbiological and histological techniques. In this study, we aimed to demonstrate the presence of M. tuberculosis in cutaneous tuberculosis. Multiple polymerase chain reaction (PCR) followed by nested PCR was used to amplify genomic fragments from 3 different mycobacteria species. DNA was isolated from 30 paraffin-embedded skin biopsies. Samples were selected randomly from patients with a clinical and histopathological diagnosis of the most frequent groups of cutaneous tuberculosis in Mexico as follows: 5 cases of scrofuloderma tuberculosis; 2 cases of lupus vulgaris tuberculosis; and 5 cases of tuberculosis verrucosa cutis. The other cases denominated tuberculids in some countries such as Mexico and included the following: 7 cases of rosacea-like tuberculosis; one case of papulonecrotic tuberculosis; and 10 cases of erythema induratum of Bazin. Four normal skin biopsies were included as controls. M. tuberculosis DNA was amplified successfully by nested PCR in 80% of the samples (24 of the 30 samples) assayed. Mycobacterial DNA was not detected in the normal skin biopsies used as controls. Detection of M. tuberculosis DNA in 80% of cutaneous tuberculosis analyzed implicates this mycobacterium in the pathogenesis of multiple clinical forms of cutaneous tuberculosis.

Performance of nested multiplex PCR assay targeting MTP40 and IS6110 gene sequences for the diagnosis of tubercular lymphadenitis

The conventional methods for diagnosis of tubercular lymphadenitis (TBLN) such as - fine needle aspiration cytology, Ziehl-Neelsen staining and culture have limitations of low sensitivity and/or specificity. So, it becomes essential to develop a rapid, sensitive, and specific method for an early diagnosis of TBLN. Therefore, the present study was conducted to evaluate nested multiplex polymerase chain reaction (nMPCR) targeting MTP40 and IS6110 gene sequences of Mycobacterium tuberculosis and Mycobacterium tuberculosis complex, respectively in 48 successive patients of TBLN and 20 random patients with non-tubercular lymph node lesions. Out of the 48 cases of TBLN, 14 (29.2%) were found to be positive by Ziehl-Neelsen staining, 15 (31.2%) were positive by culture and 43 (89.6%) cases were positive after first round of PCR while 48 (100%) cases were positive by nMPCR assay. The sensitivity and specificity of nMPCR was found to be 100% for the diagnosis of TBLN. The results thus obtained indicate that nMPCR assay is a highly sensitive and specific tool for the diagnosis of TBLN.

Identification of Mycobacterium tuberculosis in the cerebrospinal fluid of patients with meningitis using nested PCR

Tuberculous meningitis (TBM) is the most severe form of tuberculosis. It is caused by Mycobacterium tuberculosis (M. tuberculosis; MT) and it is very difficult to diagnose. The symptoms are similar to other infectious neurological diseases, such as neurocysticercosis, neuroborreliosis, or herpes viral infection. The aim of this study was to identify tuberculosis (TB) in cases of meningitis with clinical and laboratory evidence suggestive of TBM, and to confirm our findings with molecular tests for TB infection. We recruited patients with neurological symptoms who were examined at the neurology services of Hospitals of Instituto Mexicano del Seguro Social (IMSS) in Mexico City. A total of 144 consecutive patients with suggestive infectious meningitis were initially included; 94 cases of meningitis with clinical and laboratory evidence suggestive of TBM were included, but only 50 of these cases fulfilled the criteria for probable TBM. As the controls, we included 50 cases of meningitis with clinical and laboratory evidence suggestive of non-TBM. Cerebrospinal fluid (CSF) was collected from all 100 patients (cases and controls) and tested for TB by multiplex and nested PCR analyses. Nested PCR detected 0.1 fg of M. tuberculosis DNA. TB infection was confirmed with molecular tests in 49 patients from the 50 cases suggestive of TBM and in 1 of the 50 non-TBM cases. The analysis exhibited a sensitivity of 98.0%, a specificity of 92.0%, a positive predictive value of 88.0% and a negative predictive value of 98.0%. The use CSF for the analyses proved to be effective for the rapid diagnosis of TBM using a developed system of multiplex and nested PCR analyses in patients presenting neurological symptoms.

Diagnostic Molecular Mycobacteriology in Regions With Low Tuberculosis Endemicity: Combining Real-time PCR Assays for Detection of Multiple Mycobacterial Pathogens With Line Probe Assays for Identification of Resistance Mutations

Molecular assays have not yet been able to replace time-consuming culture-based methods in clinical mycobacteriology.

Using 6875 clinical samples and a study period of 35 months we evaluated the use of PCR-based assays to establish a diagnostic workflow with a fast time-to-result of 1–2 days, for 1. detection of Mycobacterium tuberculosis complex (MTB), 2. detection and identification of nontuberculous mycobacteria (NTM), and 3. identification of drug susceptible MTB.

MTB molecular-based detection and culture gave concordant results for 97.7% of the specimens. NTM PCR-based detection and culture gave concordant results for 97.0% of the specimens. Defining specimens on the basis of combined laboratory data as true positives or negatives with discrepant results resolved by clinical chart reviews, we calculated sensitivity, specificity, PPV and NPV for PCR-based MTB detection as 84.7%, 100%, 100%, and 98.7%; the corresponding values for culture-based MTB detection were 86.3%, 100%, 100%, and 98.8%. PCR-based detection of NTM had a sensitivity of 84.7% compared to 78.0% of that of culture-based NTM detection. Molecular drug susceptibility testing (DST) by line-probe assay was found to predict phenotypic DST results in MTB with excellent accuracy.

Our findings suggest a diagnostic algorithm to largely replace lengthy culture-based techniques by rapid molecular-based methods.

•

Molecular assays have not yet been able to replace time-consuming culture-based methods in the mycobacteriology laboratory.

•

We have evaluated genetic tests for: i) detection of MTB, ii) detection of NTM, and iii) identification of susceptible MTB.

•

Our findings suggest a diagnostic algorithm to replace lengthy culture-based techniques by rapid molecular-based methods.

There are > 700 reports on molecular detection of tuberculosis in respiratory and non-respiratory specimens. Limited published data exist on molecular tests for detection of nontuberculous mycobacteria (NTM) and tuberculosis drug susceptibility in clinical samples. We demonstrate an excellent accuracy of molecular-based detection of tuberculosis and NTM in conjunction with molecular-based rapid recognition of drug-susceptible and drug-resistant tuberculosis. The diagnostic algorithm developed in this work allows the rapid recognition of clinically relevant mycobacterial infections and tuberculosis drug resistance.

Differentiation of Mycobacterium tuberculosis complex from non-tubercular mycobacteria by nested multiplex PCR targeting IS6110, MTP40 and 32kD alpha antigen encoding gene fragments

Background

Control of the global burden of tuberculosis is obstructed due to lack of simple, rapid and cost effective diagnostic techniques that can be used in resource poor-settings.

To facilitate the early diagnosis of TB directly from clinical specimens, we have standardized and validated the use of nested multiplex PCR, targeting gene fragments IS6110, MTP40 and 32kD α-antigen encoding genes specific for Mycobacterium tuberculosis complex and non-tubercular mycobacteria (NTM), in comparison to smear microscopy, solid culture and single step multiplex PCR. The results were evaluated in comparison to a composite reference standard (CRS) comprising of microbiological results (smear and culture), clinical, radiological and cytopathological findings, clinical treatment and response to anti-tubercular therapy.

Methods

The nested multiplex PCR (nMPCR) assay was evaluated to test its utility in 600 (535 pulmonary and 65 extra-pulmonary specimens) clinically suspected TB cases. All specimens were processed for smear, culture, single step multiplex PCR and nested multiplex PCR testing.

Results

Out of 535 screened pulmonary and 65 extra-pulmonary specimens, 329 (61.5 %) and 19 (29.2 %) cases were culture positive for M. tuberculosis. Based on CRS, 450 patients had “clinical TB” (definitive-TB, probable-TB and possible-TB). Remaining 150 were confirmed “non-TB” cases. For culture, the sensitivity was low, 79.3 % for pulmonary and 54.3 % for extra-pulmonary cases. The sensitivity and specificity results for nMPCR test were evaluated taken composite reference standard as a gold standard. The sensitivity of the nMPCR assay was 97.1 % for pulmonary and 91.4 % for extra-pulmonary TB cases with specificity of 100 % and 93.3 % respectively.

Conclusion

Nested multiplex PCR using three gene primers is a rapid, reliable and highly sensitive and specific diagnostic technique for the detection and differentiation of M. tuberculosis complex from NTM genome and will be useful in diagnosing paucibacillary samples. Nested multiplex PCR assay was found to be better than single step multiplex PCR for assessing the diagnosis of TB.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-1450-1) contains supplementary material, which is available to authorized users.

Use of endo-ovarian tissue biopsy and pelvic aspirated fluid for the diagnosis of female genital tuberculosis by conventional versus molecular methods

BACKGROUND

Til date, none of the diagnostic techniques available for the detection of female genital tuberculosis (FGTB) are 100% accurate. We therefore, proposed to use the endometrial tissue biopsies (ETBs), ovarian tissue biopsies (OTBs) and pelvic aspirated fluids (PAFs) for the diagnosis of FGTB among infertile women by conventional versus molecular methods.

METHODOLOGY/PRINCIPAL FINDINGS

A total of 302 specimens were collected both from 202 infertile women highly suspected of having FGTB on laparoscopy examination and 100 control women of reproductive age. Out of 302 specimens, 150 (49.67%) were ETBs, 95 (31.46%) were OTBs and 57 (18.87%) were PAFs. All specimens were tested by conventional techniques, later compared with multi-gene PCR for the detection of Mycobacterium tuberculosis (MTB) and correlated with laparoscopic findings. The presence of MTB DNA was observed in 49.5% of ETBs, 33.17% of OTBs and 5.44% of PAF specimens collected from highly suspected FGTB patients. All women of control group were confirmed as negative for tuberculosis. The conventional methods showed 99% to 100% specificity with a low sensitivity, ranging from 21.78% to 42.08% while hematoxylin and eosin staining showed a sensitivity of 51.48%. Multi-gene PCR was found to have much higher sensitivity of 70.29% with MTB64 gene, 86.63% with 19 kDa antigen gene at species and TRC4 element at regional MTB complex and 88.12% with 32 kDa protein gene at genus level. The specificity of multi-gene PCR was 100%. Compared with culturing and Ziehl-Neelsen's staining, multi-gene PCR demonstrated improvement in the detection of FGTB (χ2 = 214.612, 1 df, McNemar's test value <0.0001).

CONCLUSIONS SIGNIFICANCE

We suggest site specific sampling, irrespective of sample type and amplification of the 19 kDa antigen gene in combination with TRC4 element as a successful multi-gene PCR for the diagnosis of FGTB and differentiation of mycobacterial infection among endo-ovarian tissue biopsies and PAFs taken from infertile women.

Abundance of Mycobacterium avium ssp. hominissuis in soil and dust in Germany - implications for the infection route

The nontuberculous mycobacteria (NTM) are a heterogeneous group of bacteria found in soil, water and dust. The spread of NTM infection depends on the exposure to reservoirs with high proportions of mycobacteria, the virulence of the NTM strains, the enhanced sensitivity to infections such as those of immune-compromised hosts and patient risk factors such as Cystic Fibrosis. Since several decades, NTM lung disease has been increasingly observed in slender postmenopausal women. The most important NTM in Germany is Mycobacterium avium ssp. hominissuis (MAH). The routes of MAH infection are in almost all cases unknown, but water is often suspected as source of infection. We wanted to examine this hypothesis by determining the frequency of MAH in environmental samples of water, biofilms, soil and dust originating from Germany. We found MAH in 33% of the dust samples and 20% of the soil samples. No MAH could be isolated from water and biofilm. Dust and soil clearly presented more abundance of MAH in comparison with water and biofilms. Therefore, more attention should be paid to soil and dust in Germany as an important source of Myco. avium infections.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study was conducted to investigate the ecological abundance of the most prominent clinical nontuberculous mycobacteria (NTM) in Germany, the Mycobacterium avium ssp. hominissuis (MAH). Examination of soil, water, dust and biofilm samples revealed that MAH in Germany was predominant in soil and dust. No MAH was identified in water and biofilms. Our finding contributes to the identification of the environmental niche of this opportunistic pathogen and proposes soil and dust as sources of MAH infection in Germany.

Absence of the genetic marker IS6110 from a strain of Mycobacterium tuberculosis isolated in Ontario

A 35-year-old female patient from Waterloo, Ontario was diagnosed with pulmonary tuberculosis in June 1995. Records indicated that the patient had emigrated from Laos circa 1990. A culture grown from a bronchoalveolar lavage specimen was identified as Mycobacterium tuberculosis by standard biochemical methods. Drug-susceptibility testing indicated the strain was resistant to pyrazinamide (PZA), and a mutation was detected within pncA, a gene associated with PZA resistance. Sequence data from the 16S rRNA gene and the 16S/23S rRNA gene spacer confirmed that the strain was a member of the M tuberculosis complex, and analysis of the mpcA and pncA genes supported the identification of the strain as M tuberculosis rather than Mycobacterium bovis. However, the insertion element IS6110, which is used for epidemiological tracing of M tuberculosis, was not detected in this strain by either restriction fragment length polymorphism analysis or by polymerase chain reaction. Two other genetic markers associated with the M tuberculosis complex, IS1081 and the direct repeat element, were present. The arrival of immigrants with tuberculosis from southeast Asia, where most strains of M tuberculosis lacking IS6110 have been traced, has important implications for epidemiological studies of tuberculosis in North America.

Application of molecular techniques to identification of three plusiine species, Autographa nigrisigna, Macdunnoughia confusa, and Thysanoplusia intermixta (Lepidoptera: Noctuidae), found in integrated pest management lettuce fields in Japan

Three plusiine species, Autographa nigrisigna, Macdunnoughia confusa, and Thysanoplusia intermixta (Lepidoptera: Noctuidae), are commonly found together in lettuce, Lactuca sativa L., fields in Japan. Given the marked morphological similarities between these species and the difficulty associated with discriminating between them using only visual cues, we used multiplex polymerase chain reaction (PCR) assay to distinguish between the three target species. Multiplex PCR uses four primers to simultaneously amplify a specific region of the mitochondrial DNA and produce species-specific banding patterns. The stringency of the method was tested using specimens of different sex, location, and developmental stage, and consistent results were obtained for all samples. Indeed, our method has the potential to clarify the species structure of plusiine species in lettuce fields.

Validation and standardization of IS900 and F57 real-time quantitative PCR assays for the specific detection and quantification ofMycobacterium aviumsubsp.paratuberculosis

Mycobacterium avium subsp. paratuberculosis (Map) is the causative agent of Johne’s disease and may contribute to the onset and development of Crohn’s disease in humans. Rapid detection of Map is fundamental because of its reported isolation from pasteurized milk and its potential for transmission through environmental sources. In this study, we developed two independent real-time quantitative PCR assays targeting the IS900 genetic insertion sequence and the F57 sequence, which proved capable of detecting and quantifying Map DNA. Validation and standardization of the developed methods were performed by evaluating diagnostic trueness, precision, and accuracy of the techniques. Specificity of the IS900 and F57 methods was verified in both in silico and experimental studies. The assays were found to be very accurate and precise with high repeatability and reproducibility. Moreover, the two real-time assays were very specific for Map, discriminating most of mycobacterial and nonmycobacterial species.

The impact of the 2007 ATS/IDSA diagnostic criteria for nontuberculous mycobacterial disease on the diagnosis of nontuberculous mycobacterial lung disease

BACKGROUND

In 2007, the American Thoracic Society (ATS) and Infectious Disease Society of America (IDSA) published new diagnostic guidelines for nontuberculous mycobacterial (NTM) disease. Bacteriological criteria have become simpler compared to the 1997 ATS diagnostic criteria.

OBJECTIVE

For assessing the impact of the 2007 ATS/IDSA diagnostic criteria, we compared the diagnosis rate and time to diagnosis of NTM lung disease using the 1997 and 2007 ATS guidelines.

METHODS

Sixty-four patients who had excreted Mycobacterium intracellulare, M. avium, M. abscessus or M. kansasii at least one time in their respiratory specimens at Chonnam National University Hospital were reviewed. The 1997 ATS and 2007 ATS/IDSA guidelines were applied to these patients.

RESULTS

Thirty-seven of 64 patients (57.8%) were diagnosed with NTM lung disease by the 1997 ATS criteria. When the 2007 ATS/IDSA criteria were applied, 6 patients were newly diagnosed with NTM lung disease. The diagnosis rate significantly increased from 57.8 to 67.2% (p < 0.001). The time to diagnosis in the 1997 ATS and 2007 ATS/IDSA guidelines was 46.4 ± 53.0 and 36.2 ± 38.5 days, respectively (p = 0.002).

CONCLUSION

These data suggest that we can shorten the time to diagnose NTM lung disease and diagnose more simply by using the 2007 ATS/IDSA guidelines. Further study will be needed to assess that these changes affect the management of NTM disease.

[Differentiation of micobacteria by multiplex PCR]

This study aimed to optimize a method based on the polymerase chain reaction - multiplex PCR - for differentiation of mycobacteria species of interest for public health. The multiplex PCR was based on simultaneous amplification of the hsp65 gene, which is present in all species of the Mycobacterium genus, the dnaJ gene, which is present only in Mycobacterium tuberculosis and Mycobacterium avium and the IS6110 insertion sequence, which is present in the Mycobacterium tuberculosis complex, generating amplicons of 165 bp, 365 bp and 541 bp, respectively. The detection limit was 1 fg for the hsp65 target, 100 pg for dnaJ and 0.1 fg for IS6110. The multiplex PCR detected down to 100 pg of DNA of Mycobacterium tuberculosis. The system was shown to be specific and sensitive for detection of Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium avium and Mycobacterium smegmatis. The results obtained using reference strains of mycobacteria showed that multiplex PCR may be a fast, sensitive and specific tool for differentiation of mycobacteria.

Is tuberculous lymphadenitis over-diagnosed in Ethiopia? Comparative performance of diagnostic tests for mycobacterial lymphadenitis in a high-burden country

Ethiopia reports the third highest number of extrapulmonary TB cases globally, most of which are lymph node TB (TBLN). We investigated the performance of the available diagnostic tests for TBLN. Fine needle aspirate (FNA) and excision biopsy samples from affected lymph nodes were collected from 150 consenting patients with suspected TBLN visiting regional hospitals in Ethiopia. The sensitivity, specificity, positive (PPV) and negative predictive value (NPV) of histopathology against culture as reference was 92%, 88%, 97% and 77% and of FNA cytology (FNAC) 76%, 88%, 100% and 55%, respectively. Naked eye examination of FNA had 67% sensitivity and 64% specificity. HIV coinfection did not diminish the performance of macroscopic examination, Ziehl-Neelsen stain, histology or cytology examinations. When any positive result in ZN, histopathology or culture was considered confirmatory, clinical diagnosis could be confirmed in 85% of the patients, suggesting that TBLN is over-diagnosed in up to 15% of cases. With combined criteria as reference standard, the sensitivity, specificity, PPV and NPV of FNAC was 72%, 100%, 100% and 55%, respectively. FNAC is a practical tool that can improve the diagnosis of TBLN in high-burden settings. Over-diagnosis alone cannot explain the high burden of LNTB in Ethiopia.

Development and evaluation of a molecular assay for detection of nontuberculous mycobacteria by use of the cobas amplicor platform

We have developed and evaluated a semiautomated assay for detection of nontuberculous mycobacteria (NTM) from clinical samples based on the Cobas Amplicor Mycobacterium tuberculosis test (Roche Diagnostics, Switzerland). A capture probe, specific for mycobacteria at the genus level, was linked to magnetic beads and used for the detection of amplification products obtained by the Cobas Amplicor M. tuberculosis assay. We demonstrate that the analytical sensitivity of the genus assay is similar to that of Cobas Amplicor M. tuberculosis detection. Four hundred sixteen clinical specimens were evaluated for the presence of NTM DNA. Sensitivities for smear-positive and smear-negative specimens were found to be 100% and 47.9%, respectively. Specificity was 97.7%, the positive predictive value 84.6%, and the negative predictive value 93.1%. The genus assay is easy to perform, produces reliable results, and was found to be a valuable diagnostic tool for rapid diagnosis of infections with NTM. The genus assay has the potential to detect NTM not routinely recovered by culture and to discover new mycobacterial species.

TUBERCULOSE BOVINA: ALTERNATIVAS PARA O DIAGNÓSTICO

RESUMO A tuberculose é uma das principais preocupações da Organização Mundial da Saúde, especialmente após o surgimento da AIDS e do aumento da multidroga resistência, sendo considerada a principal causa de morte por um único agente. Além do Mycobaterium tuberculosis, principal responsável pela doença em humanos, outra manifestação de importância epidemiológica é a infecção causada pelo Mycobaterium bovis, devido à transmissão ao homem, especialmente, pela ingestão de alimentos contaminados, e à escassez de dados relacionados a sua prevalência na população. Em várias partes do mundo existem programas de controle da doença nos bovinos, fundamentados na identificação por teste tuberculínico e na eliminação dos animais positivos. As lesões encontradas em exames post-mortem podem ser confirmadas através do isolamento e identificação do agente, porém esse procedimento pode demandar meses para a sua conclusão, razão pela qual, para reduzir o tempo de diagnóstico, novos métodos moleculares são propostos. Para proporcionar uma visão atualizada sobre os esforços no combate da tuberculose bovina, sobre os resultados das campanhas de controle e erradicação e sobre os métodos recentes disponíveis para diagnóstico da tuberculose bovina, como o PCR, neste trabalho é apresentada uma revisão bibliográfica, ressaltando as vantagens e dificuldades para o emprego dos ensaios para diagnóstico e a possibilidade de sua utilização em escala. Concluímos que apesar dos avanços alcançados, ainda não se tem disponível, para a rotina laboratorial, um ensaio sensível, reprodutível e rápido para o diagnóstico da tuberculose em bovinos, sendo essencial esforço e investimento em pesquisas para a solução desse ponto crítico no combate à enfermidade.

Microscopic-observation drug-susceptibility assay for the diagnosis of TB

BACKGROUND

New diagnostic tools are urgently needed to interrupt the transmission of tuberculosis and multidrug-resistant tuberculosis. Rapid, sensitive detection of tuberculosis and multidrug-resistant tuberculosis in sputum has been demonstrated in proof-of-principle studies of the microscopic-observation drug-susceptibility (MODS) assay, in which broth cultures are examined microscopically to detect characteristic growth.

METHODS

In an operational setting in Peru, we investigated the performance of the MODS assay for culture and drug-susceptibility testing in three target groups: unselected patients with suspected tuberculosis, prescreened patients at high risk for tuberculosis or multidrug-resistant tuberculosis, and unselected hospitalized patients infected with the human immunodeficiency virus. We compared the MODS assay head-to-head with two reference methods: automated mycobacterial culture and culture on Löwenstein-Jensen medium with the proportion method.

RESULTS

Of 3760 sputum samples, 401 (10.7%) yielded cultures positive for Mycobacterium tuberculosis. Sensitivity of detection was 97.8% for MODS culture, 89.0% for automated mycobacterial culture, and 84.0% for Löwenstein-Jensen culture (P<0.001); the median time to culture positivity was 7 days, 13 days, and 26 days, respectively (P<0.001), and the median time to the results of susceptibility tests was 7 days, 22 days, and 68 days, respectively. The incremental benefit of a second MODS culture was minimal, particularly in patients at high risk for tuberculosis or multidrug-resistant tuberculosis. Agreement between MODS and the reference standard for susceptibility was 100% for rifampin, 97% for isoniazid, 99% for rifampin and isoniazid (combined results for multidrug resistance), 95% for ethambutol, and 92% for streptomycin (kappa values, 1.0, 0.89, 0.93, 0.71, and 0.72, respectively).

CONCLUSIONS

A single MODS culture of a sputum sample offers more rapid and sensitive detection of tuberculosis and multidrug-resistant tuberculosis than the existing gold-standard methods used.

Differentiation of Mycobacterial species by hsp65 duplex PCR followed by duplex-PCR-based restriction analysis and direct sequencing

Here we describe a novel duplex PCR method which can differentiate Mycobacterium tuberculosis and nontuberculosis mycobacteria (NTM) strains by amplifying hsp65 DNAs of different sizes (195 and 515 bp, respectively). The devised technique was applied to 54 reference and 170 clinical isolates and differentiated all strains into their respective groups with 100% sensitivity and specificity. Furthermore, a duplex PCR-restriction analysis (duplex PRA) and a direct sequencing protocol were developed to differentiate NTM strains at the species and subspecies levels based on previously reported hsp65 DNA sequences (H. Kim et al., Int. J. Syst. Evol. Microbiol. 55:1649-1656, 2005) and then applied to 105 NTM clinical isolates. All NTM isolates were clearly differentiated at the species and subspecies levels by subsequent procedures (PRA or direct sequencing) targeting 515-bp NTM duplex PCR amplicons. Our results suggest that novel duplex PCR-based methods are sensitive and specific for identifying mycobacterial culture isolates at the species level.

In-house nucleic acid amplification tests for the detection of Mycobacterium tuberculosis in sputum specimens: meta-analysis and meta-regression

BACKGROUND

More than 200 studies related to nucleic acid amplification (NAA) tests to detect Mycobacterium tuberculosis directly from clinical specimens have appeared in the world literature since this technology was first introduced. NAA tests come as either commercial kits or as tests designed by the reporting investigators themselves (in-house tests). In-house tests vary widely in their accuracy, and factors that contribute to heterogeneity in test accuracy are not well characterized. Here, we used meta-analytical methods, including meta-regression, to identify factors related to study design and assay protocols that affect test accuracy in order to identify those factors associated with high estimates of accuracy.

RESULTS

By searching multiple databases and sources, we identified 2520 potentially relevant citations, and analyzed 84 separate studies from 65 publications that dealt with in-house NAA tests to detect M. tuberculosis in sputum samples. Sources of heterogeneity in test accuracy estimates were determined by subgroup and meta-regression analyses. Among 84 studies analyzed, the sensitivity and specificity estimates varied widely; sensitivity varied from 9.4% to 100%, and specificity estimates ranged from 5.6% to 100%. In the meta-regression analysis, the use of IS6110 as a target, and the use of nested PCR methods appeared to be significantly associated with higher diagnostic accuracy.

CONCLUSION

Estimates of accuracy of in-house NAA tests for tuberculosis are highly heterogeneous. The use of IS6110 as an amplification target, and the use of nested PCR methods appeared to be associated with higher diagnostic accuracy. However, the substantial heterogeneity in both sensitivity and specificity of the in-house NAA tests rendered clinically useful estimates of test accuracy difficult. Future development of NAA-based tests to detect M. tuberculosis from sputum specimens should take into consideration these findings in improving accuracy of in-house NAA tests.

A pncA polymorphism to differentiate between Mycobacterium bovis and Mycobacterium tuberculosis

The pyrazinamidase gene coding for the enzyme that activates the bactericidal drug pyrazinamide contains a polymorphic site that is preserved in Mycobacterium bovis. We synthesized two sets of primers, one encompassing a 180 bp fragment, and the second spanning a 726 bp fragment including the full pncA gene. Following PCR of Mycobacterium tuberculosis and M. bovis samples, it is possible to discriminate by this polymorphism between these species by digestion with Eco065 I. Digestion of the 180 bp fragment results in two fragments of 101 and 79 bp, specific for M. tuberculosis. Alternatively, digestion of the 726 bp fragment yields three fragments of 452, 165 and 109 bp for M. tuberculosis, but only two fragments of 561 and 165 bp for M. bovis.

Severe combined immunodeficiency syndrome associated with colonic stenosis

BACKGROUND

This is the first report in Mexico of a case of severe combined immunodeficiency syndrome (SCID) associated with colonic stenosis. The patient was an 8-month-old Mexican female who died at this age. She suffered infections due to microorganisms such as Mycobacterium tuberculosis, bacille Calmette-Guérin (BCG), Candida sp., and Pneumocystis carinii; and had frequent diarrhea. She was HIV-negative without familial history of immunodeficiency. The aim of the work was to analyze the immunologic status of this patient.

METHODS

Peripheral blood from the patient and from a healthy matched control were analyzed by flow cytometry to determine peripheral leukocytes and production of cytokines and their receptors in T-lymphocytes and monocytes. Immunohistochemical analysis was performed in spleen and lymph node sections from the patient and control samples to assess alterations in architectural and cellular distribution within these lymphoid tissues.

RESULTS

Peripheral blood analysis demonstrated reduced numbers of both T and B cells and defective expression of cytokines by activated T cells. Postmortem analysis revealed very small T and B cell zones in spleen and lymph nodes, absence of germinal centers and follicular dendritic cell networks, and two zones of stenosis at level of colon sigmoides.

CONCLUSIONS

As a whole, these data are consistent with severe combined immunodeficiency (SCID) syndrome; thus, we conclude that this patient may have had a variant of SCID syndrome associated with intestinal stenosis.

Use of the hupB gene encoding a histone-like protein of Mycobacterium tuberculosis as a target for detection and differentiation of M. tuberculosis and M. bovis

The gene for histone-like protein (hupB [Rv2986c]) of Mycobacterium tuberculosis has been identified as a singular target which allows differentiation of two closely related mycobacterial species, namely, M. tuberculosis and M. bovis of the MTB complex, by a PCR assay. The N and S primer-generated PCR amplicons differed in M. tuberculosis and M. bovis; these amplicons were determined to be 645 and 618 bp, respectively. This difference was localized to the C-terminal part of the gene by using primers M and S. The C-terminal PCR amplicons of M. tuberculosis and M. bovis were determined to be 318 and 291 bp, respectively. The differences in the C-terminal portion of the gene were confirmed by restriction fragment length polymorphism analysis and sequencing. Sequence analysis indicated that in M. bovis there was a deletion of 27 bp (9 amino acids) in frame after codon 128 in the C-terminal part of the hupB gene. In the present study 104 mycobacterial strains and 11 nonmycobacterial species were analyzed for hupB gene sequences. Of the 104 mycobacterial strains included, 62 belonged to the MTB complex and 42 were non-MTB complex strains and species. Neither the hupB gene-specific primers (N and S) nor the C-terminal primers (M and S) amplify DNA from any other mycobacteria, making the assay suitable for distinguishing members of the MTB complex from other mycobacterial species, as well as for differentiating between members of the MTB complex, namely, M. tuberculosis and M. bovis.

A multiplex polymerase chain reaction assay for genus-, group- and species-specific detection of mycobacteria

We developed and evaluated a single-step, multiplex polymerase chain reaction (PCR) assay for distinguishing (1) between the Mycobacterium tuberculosis complex (MTBC) and mycobacteria other than tuberculosis (MOTT) and (2) between M. tuberculosis and M. bovis species. The assay targeted the 16S and the 23S rDNA to distinguish between MTBC and MOTT species, and the oxyR gene to distinguish between M. tuberculosis and M. bovis strains. Clinical samples and reference strains (N = 156) comprised 93 strains of M. tuberculosis, 44 of M. bovis, 1 M. africanum strain, and 18 strains representing 9 different species of MOTTs. MOTTs generated only a single PCR product of about 2.5 kilobase; however, all of the MTBC strains produced a 118 base pair (bp) fragment and an additional 270 bp fragment was obtained for M. tuberculosis and M. africanum when the primer pair oxyRTB-2.1/oxyRMT-1 was used. When oxyRTB-2.1/oxyRMB-1 primers were used, the 270 bp fragment was obtained for only M. bovis. The assay needed as little as 1 pg of purified genomic DNA to make a positive identification.

Differential identification of Mycobacterium tuberculosis complex and nontuberculous mycobacteria by duplex PCR assay using the RNA polymerase gene (rpoB)

A novel duplex PCR method that can amplify the 235- and 136-bp rpoB DNAs of Mycobacterium tuberculosis complex and nontuberculous mycobacteria (NTM), respectively, with two different sets of primers was used to differentially identify 44 reference strains and 379 clinical isolates of mycobacteria in a single-step assay. Showing 100% sensitivity and specificity, the duplex PCR method could clearly differentiate M. tuberculosis complex and NTM strains. In addition, restriction fragment length polymorphism analysis and direct sequencing of the amplicon of NTM could be used to supplement species identification.

The mtp40 gene is not present in Mycobacterium bovis

The mtp40 gene was initially reported to be lacking in classical Mycobacterium bovis strains, while being specific to classical M. tuberculosis strains. Later two clinical isolates reported to be M. bovis were shown to possess the mtp40 gene (A. Weil, B.B. Plikaytis, W.R. Butler, C.L. Woodley and T.M. Shinnik, J Clin Microbiol 1996; 34: 2309-2311). The two strains were, however, not fully characterized biochemically or genotypically. By PCR amplification of whole cell lysates and subsequent spoligotyping, which classifies isolates within the M. tuberculosis complex, the two strains were found to possess the spacers 40-43 which typically are lacking in classicalM. bovis, but had a spoligotyping pattern compatible with M. africanum. We conclude that the two strains, previously designated M. bovis, should be designated M. africanum. This reinvestigation has implications for the phylogenetic classification of M. bovis.

Mtp-40 and alpha antigen gene fragment amplification for the detection of Mycobacterium tuberculosis in Colombian clinical specimens

In this study, the use of Mtp-40 and alpha antigen polymerase chain reaction (PCR) amplification fragments for the precise tuberculosis (TB) diagnosis was evaluated. One hundred and ninety two different samples were obtained from 113 patients with suspected TB. Mtp-40 and alpha antigen protein genes were amplified by the PCR technique and compared to both the "gold standard" (culture) test, as well as the clinical parameters (including a clinical record and X-ray film exam in 113 patients). Thirty-eight of the 113 patients had a presumptive clinical diagnosis of TB; 74% being detected by PCR technique, 58% by culture and 44% by direct microscopic visualization. Weconclude that it is possible to use PCR as a suitable technique for the detection of any mycobacteria by means of the alpha antigen product, or the specific infection of Mycobacterium tuberculosis by means of the mtp-40 gene. This might be a good supporting tool in difficult clinical TB diagnosis and pauci-bacillary cases.

Identification of the causative organism of tuberculous lymphadenitis in ethiopia by PCR

Tuberculous lymphadenitis (TBLN) is a common form of extrapulmonary tuberculosis with multiple differential diagnoses. Demonstration of the etiologic agent by smear microscopy or culture of fine needle aspirate (FNA) specimens is often unsuccessful. FNA specimens from 40 patients presenting at a rural health center in South Ethiopia and diagnosed as positive for TBLN on the basis of clinical and cytological criteria were analyzed for mycobacterial DNA by PCR. Thirty (75%) had cervical lymphadenitis and 11 (27.5%) were seropositive for human immunodeficiency virus (HIV). Three primer sets were initially used to identify the causative agent at the genus (antigen 85 complex), complex (IS6110 insertion sequence), and species (pncA gene and allelic variation) levels. Among the forty TBLN cases, 35 (87.5%) were positive by PCR at the genus and complex levels. Based on PCR for detection of allelic variation at position 169, 24 (68.6%) of the 35 were positive for Mycobacterium tuberculosis and 6 (17.1%) were positive for M. bovis. These six were positive in additional PCR assays using the JB21-JB22 primer set, which is highly specific for M. bovis. Five (14.1%) showed amplification for both M. tuberculosis and M. bovis with the allele-specific primer set. Cooccurrence of pyrazinamide (PZA)-sensitive and -resistant M. tuberculosis in those five cases was indicated, since all were negative in assays with the JB21-JB22 primer set. This feature was seen in 3 of 11 HIV-positive and 2 of 29 HIV-negative individuals (P < 0.001).

CONCLUSION

among 35 PCR-positive cases of TBLN from southern Ethiopia, 29 (82.9%) were caused by M. tuberculosis and six (17.1%) were caused by M. bovis.

Assessment of mycobacterial, propionibacterial, and human herpesvirus 8 DNA in tissues of greek patients with sarcoidosis

The causes of sarcoidosis are unknown. In this study, we report the presence of Mycobacterium tuberculosis complex and Propionibacterium granulosum DNA in a significant proportion of Greek patients with sarcoidosis. Human herpesvirus 8 DNA was not detected in sarcoid tissues from Greek patients. Our findings are discussed.

Specificities and functions of the recA and pps1 intein genes of Mycobacterium tuberculosis and application for diagnosis of tuberculosis

The worldwide recrudescence of tuberculosis and the widespread appearance of antibiotic resistance have strengthened the need for rapid and specific diagnostic tools. The prevailing microbiological identification of Mycobacterium tuberculosis, the causative agent of tuberculosis, which implies the use of in vitro cultures and acid-fast staining microscopy, is time-consuming. Detection of M. tuberculosis directly in clinical samples through PCR amplification of mycobacterium-specific genes, designed to shorten diagnostic delay, demonstrated reliability and high sensitivity. However, the quality of the diagnosis depends on the specificity of the target sequence for M. tuberculosis complex strains. In the present study, we demonstrated the specificity of recA and pps1 inteins for this complex and thus the feasibility of using intein-coding sequences as a new target for PCR diagnosis. Indeed, the recA and pps1 genes of 36 clinical isolates of M. tuberculosis and 10 field strains of M. bovis were found to be interrupted by an intein sequence at the RecA-a and Pps1-b sites, respectively, while a large number of nontuberculous mycobacterial species failed to demonstrate these insertions. Besides, the MtuPps1, which was cloned and expressed in Escherichia coli, was shown to possess an endonuclease activity. The intein cleaves the 40-bp sequence spanning the intein insertion site Pps1-b in the inteinless pps1 gene. In addition to the PCR amplification of recA and pps1 intein genes as a tool for diagnosis, the specific endonuclease activity could represent a new molecular approach to identify M. tuberculosis.

Development and application of quantitative polymerase chain reaction assay based on the ABI 7700 system (TaqMan) for detection and quantification of Mycobacterium avium subsp. paratuberculosis

Numerous reports have described diagnostic methods based on the polymerase chain reaction (PCR) used to detect Mycobacterium avium subsp. paratuberculosis, the causative agent of Johne's disease. The result of conventional PCR tests has been only qualitative, either positive or negative; it does not present any quantitative information about the number of the agents in the specimen. A quantitative PCR method (IS900 TaqMan) was developed to measure the number of M. a. paratuberculosis organisms present in field and clinical samples. The sensitivity of IS900 TaqMan was 1 colony-forming unit (CFU) for M. a. paratuberculosis ATCC 19698. The specificity of the method was determined by testing 14 mycobacterial species (M. abscessus, M. asiaticum, M. avium subsp. avium, M. bovis, M. fortuitum subsp. fortuitum, M. intracellulare, M. kansasii, M. marinum, M. phlei, M. scrofulaceum, M. simiae, M. smegmatis, M. terrae, and M. ulcerans) and 9 nonmycobacterial species (Borrelia burgdorferi, Chlamydia psittaci, Ehrlichia canis, E. equi, E. risticii, Escherichia coli, E. coli O157:H7, Streptococcus equi, and S. zooepidemicus). Even at high cell numbers (10(5) CFU/reaction), most of the organisms tested negative for the IS900 insertion element except M. marinum and M. scrofulaceum. This finding for M. scrofulaceum was consistent with previous reports that several M. scrofulaceum-like isolates were positive for IS900. Those isolates had 71-79% homology with M. a. paratuberculosis in the region of IS900. When used in conjunction with the new liquid medium-based ESP culture system II for bovine clinical fecal samples, IS900 TaqMan confirmed that the ESP II-positive samples contained 10(5)-10(6) CFU/ml of M. a. paratuberculosis. All of the 222 ESP II-positive and acid-fast bacilli-positive samples tested in this study were positive by IS900 TaqMan. IS900 TaqMan was also useful in the study of growth characteristics of 3 groups of M. a. paratuberculosis strains in bovine fecal samples from 3 shedding levels (heavy, medium, and low) based on cell numbers measured by Herrold egg yolk (HEY) agar culture. When cultured in ESP medium, M. a. paratuberculosis reached 10(5)-10(6) CFU/ml within 2 weeks for heavy shedders, 3-4 weeks for medium, and 6-8 weeks for low shedders. No significant growth was observed after up to 5 weeks of incubation for some of low shedders. No or extremely slow growth characteristic of low shedders might be a possible explanation for frequent false-negative results by HEY. The detection time was dependent on the inoculum size and the growth rate of M. a. paratuberculosis. Generation times were inversely proportional to the shedding level: 1-2 days for medium and heavy shedders and >4 days for low shedders. IS900 TaqMan could be a useful tool for determining viable cell counts by measuring changes in cell numbers over the incubation period.

Characterization of a Mycobacterium intracellulare variant strain by molecular techniques

This paper describes a Mycobacterium intracellulare variant strain causing an unusual infection. Several isolates obtained from an immunocompromised patient were identified as members of the Mycobacterium avium complex (MAC) by the commercial AccuProbe system and biochemical standard identification. Further molecular approaches were undertaken for a more accurate characterization of the bacteria. Up to seven different genomic sequences were analyzed, ranging from conserved mycobacterial genes such as 16S ribosomal DNA to MAC-specific genes such as mig (macrophage-induced gene). The results obtained identify the isolates as a variant of M. intracellulare, an example of the internal variability described for members of the MAC, particularly within that species. The application of other molecular approaches is recommended for more accurate identification of bacteria described as MAC members.

Identification of substrains of BCG vaccine using multiplex PCR

Current methods for determining the identity of substrains of Mycobacterium bovis BCG (BCG) vaccine are labour intensive, or provide only limited substrain differentiation. In this paper we describe a multiplex PCR that distinguishes between M. tuberculosis (TB) and M. bovis and the non-pathogenic BCG strain, and also subdivides the BCG vaccine substrains investigated into seven distinct fingerprints based on six target regions in the DNA. This test is specific, rapid, reproducible and portable and is proposed as a novel test for BCG vaccine control. It offers substantial advantages over the methods currently in use. Using this test we have characterised a number of commercial BCG vaccines.

Duplex PCR for differential identification of Mycobacterium bovis, M. avium, and M. avium subsp. paratuberculosis in formalin- fixed paraffin-embedded tissues from cattle

We previously isolated and sequenced two genomic segments of Mycobacterium avium subsp. paratuberculosis, namely, f57, a species-specific sequence, and the p34 gene, coding for a 34-kDa antigenic protein. Comparison of sequences upstream of the p34 open reading frame (us-p34) from M. avium subsp. paratuberculosis and M. tuberculosis showed a 79-base deletion in M. tuberculosis. Sequence analysis of the p34 genes in another two species, M. bovis (strain BCG) and M. avium (strain D4), confirmed the differences observed between tuberculous and nontuberculous species. A duplex diagnostic PCR strategy based on coamplification of nonhomologous us-p34 and species-specific f57 sequences was therefore developed. Duplex PCR yielded three different patterns, specific either for tuberculous bacilli (M. tuberculosis, M. bovis, and M. africanum), for both nontuberculous mycobacteria M. avium and M. intracellulare, or for M. avium subsp. paratuberculosis. The specificity of this single-step DNA-based assay was assessed on DNA from cultured mycobacterial strains, as well as on a panel of formalin-fixed and paraffin-embedded tissues from cattle. Molecular assay results from tissular DNA were compared to conventional bacteriological and histological test results, including those obtained by Ziehl-Neelsen staining on tissue biopsy specimens. Molecular discrimination was successful and confirmed the value of duplex us-p34 and f57 sequence amplification for differential diagnosis of tuberculosis, paratuberculosis, or infections caused by other members of the M. avium complex.

Identification of non-tuberculous mycobacteria: 16S rRNA gene sequence analysis vs. conventional methods

In a retrospective study, 45 clinical isolates of non-tuberculous mycobacteria were identified to the species level by biochemical profile, gas liquid chromatography and partial sequence analysis of 16S rRNA, and were found to represent 13 different species. The results of sequence analysis showed 100% identity with conventional tests for 34 isolates (76%) and could identify species such as M. bohemicum which are difficult to characterise with conventional methods. Most of the discrepant results for the remaining 11 isolates resulted in species of the same group of mycobacteria. Based on these findings. we concluded that direct sequence analysis of amplified 16S rRNA gene is a promising rapid and accurate method for species determination of non-tuberculous mycobacteria.

Identification of Mycobacterium species by PCR-restriction fragment length polymorphism analyses using fluorescence capillary electrophoresis

We developed a scheme for the rapid identification of Mycobacterium species based upon PCR amplification of polymorphic genetic regions with fluorescent primers followed by restriction and analysis by fluorescence capillary electrophoresis. Mycobacterium species were identified by restriction enzyme analysis of a 439-bp segment of the 65-kDa heat shock protein gene (labeled [both strands] at the 5' end with 4,7,2',7'-tetrachloro-6-carboxyfluorescein) using HaeIII and BstEII and of a 475-bp hypervariable region of the 16S rRNA gene (labeled [both strands] at the 5' end with 6-carboxyfluorescein) using HaeIII and CfoI. Samples were analyzed on an automated fluorescence capillary electrophoresis instrument, and labeled fragments were sized by comparison with an internal standard. DNA templates were prepared with pure cultures of type strains. In all, we analyzed 180 strains, representing 22 Mycobacterium species, and obtained distinctive restriction fragment length polymorphism (RFLP) patterns for 19 species. Three members of the Mycobacterium tuberculosis complex had a common RFLP pattern. A computerized algorithm which eliminates subjectivity from pattern interpretation and which is capable of identifying the species within a sample was developed. The convenience and short preparatory time of this assay make it comparable to conventional methodologies such as high-performance liquid chromatography and hybridization assays for identification of mycobacteria.

Differentiation between Mycobacterium tuberculosis and Mycobacterium avium by amplification of the 16S-23S ribosomal DNA spacer

Differentiation between Mycobacterium tuberculosis and M. avium is helpful for the treatment of disseminated mycobacterial infection in AIDS patients. This can traditionally be done by time-consuming biochemical tests or with Accuprobe. Previously, PCR restriction enzyme analysis (PCR-REA) of the 16S-23S rRNA gene spacer was shown to be able to identify a limited number of strains of Mycobacterium. In this study the method was improved by using more specific primers and was tested with 50 clinical isolates of M. tuberculosis and 65 clinical isolates of M. avium complex. Probes specific to the spacers of M. tuberculosis and M. avium were also tested. Both M. tuberculosis and M. avium could be reliably identified either by PCR-REA or by PCR-hybridization, with the results completely agreeing with those obtained by biochemical tests and with the Accuprobe, respectively. The method may therefore be useful as an alternative in-house method for identification of the bacteria.

Identification of a new DNA region specific for members of Mycobacterium tuberculosis complex

The successful use of DNA amplification for the detection of tuberculous mycobacteria crucially depends on the choice of the target sequence, which ideally should be present in all tuberculous mycobacteria and absent from all other bacteria. In the present study we developed a PCR procedure based on the intergenic region (IR) separating two genes encoding a recently identified mycobacterial two-component system named SenX3-RegX3. The senX3-regX3 IR is composed of a novel type of repetitive sequence, called mycobacterial interspersed repetitive units (MIRUs). In a survey of 116 Mycobacterium tuberculosis strains characterized by different IS6110 restriction fragment length polymorphisms, 2 Mycobacterium africanum strains, 3 Mycobacterium bovis strains (including 2 BCG strains), and 1 Mycobacterium microti strain, a specific PCR fragment was amplified in all cases. This collection included M. tuberculosis strains that lack IS6110 or mtp40, two target sequences that have previously been used for the detection of M. tuberculosis. No PCR fragment was amplified when DNA from other organisms was used, giving a sensitivity of 100% and a specificity of 100% in the confidence limit of this study. The numbers of MIRUs were found to vary among strains, resulting in six different groups of strains on the basis of the size of the amplified PCR fragment. However, the vast majority of the strains (approximately 90%) fell within the same group, containing two 77-bp MIRUs followed by one 53-bp MIRU.

Detection of Mycobacterium tuberculosis in preserved tuberculous lymph nodes by polymerase chain reaction

We evaluated the usefulness of three types of polymerase chain reaction (PCR) targeting 16S rRNA, protein antigen b and IS6110 in detecting Mycobacterium tuberculosis in preserved tuberculous lymph nodes. The detection limit of all PCR methods was 100 colony forming unit (CFU) of M. tuberculosis in tissue. The test samples included eight paraffin-embedded tuberculous lymph nodes containing microscopical epithelioid cell granuloma with caseous necrosis and Langhans giant cells. Although acid-fast stained organisms in lymph node tissue were not detected in any sample, all three types of PCR tests were positive in four of eight lymph nodes. Our results suggest that PCR is not only a rapid and sensitive diagnostic method for tuberculous lymphadenitis, but also clinically significant in retrospective study for detecting M. tuberculosis even in some preserved lymph node tissues without evidence of acid-fast stained organisms.

The mtp40 gene is not present in all strains of Mycobacterium tuberculosis

A multiple PCR-based assay that targets IS6110 and the mtp40 gene was evaluated for the rapid differentiation of Mycobacterium bovis and M. tuberculosis, two of the causative agents of tuberculosis. The IS6110 target is present in both species, whereas the mtp40 gene was thought to be specific for M.tuberculosis (P. Del Portillo, L.A. Murillo, and M.E. Patarroyo, J. Clin. Microbiol. 29:2163-2168, 1991). However, the mtp-40 gene is not present in all M. tuberculosis strains and, hence, is not useful for differentiating M.tuberculosis and M.bovis.