Detection of Mycobacterium tuberculosis complex in formalin-fixed, paraffin-embedded tissue specimens with necrotizing granulomatous inflammation by strand displacement amplification

Utility of anti-Mycobacterium tuberculosis antibody (ab905) for detection of mycobacterial antigens in formalin-fixed paraffin-embedded tissues from clinically and histologically suggestive extrapulmonary tuberculosis cases

Background

The detection of acid-fast bacilli in extrapulmonary tissue samples is challenging due to its paucibacillary nature. The present study assessed the utility of immunohistochemistry (IHC) using anti-Mycobacterium tuberculosis antibody (ab905) for detecting the presence of mycobacterial antigens in archived formalin-fixed paraffin-embedded (FFPE) tissues.

Methods

FFPE tissues [surgical biopsies (n = 32) and post-mortem tissues (n = 8)] from clinically and histologically suggestive extrapulmonary tuberculosis (EPTB) cases at the Korle Bu Teaching Hospital, Accra, Ghana from 2015 to 2020 were stained with IHC (anti-Mycobacterium tuberculosis antibody) and Ziehl-Neelsen (ZN) stain. The staining outcomes of IHC and ZN were compared, and their sensitivity and specificity determined against histopathology as reference standard.

Results

Lymph nodes were about 40% (16/40) of the samples analyzed. IHC stained positive in 43.8% (7/16) biopsies and 87.5% (4/5) post-mortem samples ranging from 43.8% (7/16) in lymph nodes to 80% (4/5) in gastrointestinal organs. The overall sensitivity for IHC was 52.50% (95% CI: 36.13%-68.49%) and 0% (95% CI: 0.00%-8.81%) for ZN. Specificity was 72.50% (95% CI: 56.11%-85.40%) and 75% (95% CI: 58.80-87.31%) for IHC and ZN respectively.

Conclusions

IHC using anti-Mycobacterium tuberculosis antibody (ab905) can detect mycobacterial antigens in diverse range of paucibacillary extrapulmonary tissue sections. It is potentially a useful tool for the diagnosis of EPTB in FFPE tissues in a routine pathology laboratory.

Development of a Highly Specific, Selective, and Sensitive Fluorescent Probe for Detection of Mycobacteria in Human Tissues

Tuberculosis (TB), including extrapulmonary TB, is responsible for more than one million deaths in a year worldwide. Existing methods of mycobacteria detection have poor sensitivity, selectivity, and specificity, especially in human tissues. Herein, the synthesis of a cholic acid-derived fluorescent probe (P4) that can specifically stain the mycobacterium species is presented. It is shown that P4 probe specifically binds with mycobacterial lipids, trehalose monomycolate, and phosphatidylinositol mannoside 6. P4 probe can detect mycobacteria in polymicrobial planktonic cultures and biofilms with high specificity, selectivity, and sensitivity. Moreover, it can detect a single mycobacterium in the presence of 10 000 other bacilli. Unlike the probes that depend on active mycobacterial enzymes, the membrane-specific P4 probe can detect mycobacteria even in formalin-fixed paraffin-embedded mice and human tissue sections. Therefore, the ability of the P4 probe to detect mycobacteria in different biological milieu makes it a potential candidate for diagnostic and prognostic applications in clinical settings.

Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M

Microbiome samples with low microbial biomass or severe DNA degradation remain challenging for amplicon-based or whole-metagenome sequencing approaches. Here, we introduce 2bRAD-M, a highly reduced and cost-effective strategy which only sequences ~ 1% of metagenome and can simultaneously produce species-level bacterial, archaeal, and fungal profiles. 2bRAD-M can accurately generate species-level taxonomic profiles for otherwise hard-to-sequence samples with merely 1 pg of total DNA, high host DNA contamination, or severely fragmented DNA from degraded samples. Tests of 2bRAD-M on various stool, skin, environmental, and clinical FFPE samples suggest a successful reconstruction of comprehensive, high-resolution microbial profiles.

Agreement Test of Histopathology in the Diagnosis of Extrapulmonary Tuberculosis with Gold Standard Polymerase Chain Reaction Technique: A Step to Overcome False Diagnosis

BACKGROUND: Tuberculosis (TB) is global health problem which is caused by Mycobacterium tuberculosis (M. tuberculosis) bacteria. One-quarter of the world’s populations is infected by M. tuberculosis and only 10–15% of those develop the disease, while the remaining 85–95% of the population are carrying the bacteria and cannot transmit the disease to the others. M. tuberculosis bacteria affects the lungs, but any organ in the body can be affected by the bacteria. About 15% of M. tuberculosis infections are of in the extrapulmonary type. The diagnosis of extrapulmonary TB (EPTB) is very challenging because most sites are inaccessible and paucibacillary nature of the bacteria in these sites. The need for rapid and more sensitive and specific tests for the diagnosis of EPTB in comparison to culture and histopathology is increasing. The molecular methods for the detection of M. tuberculosis gene(s) in the provided sample are now promising. PATIENT AND METHODS: A cross-sectional descriptive study at AL-Kindy Teaching Hospital at Al-Resaffa part of Baghdad city, Iraq. Data collection has been done in three months duration (July, August, and September) 2015. A total of 74 formalin-fixed paraffin-embedded samples from suspected EPTB cases was collected, both Polymerase Chain reaction test for M. tuberculosis and histopathological examination was done for each sample. RESULTS: A total of 74 patients (18 males, 56 females), mean age 29.72 suspected to had extrapulmonary TB underwent biopsies from different tissue types. The biopsies from the 74 patients were taken from different tissues according to the site of lesion, 49 (66.2%) biopsies were taken from lymph node, 12 biopsies (16.2%) was taken from mass in the axilla, 6 (8.1%) from abscess, 4 (5.4%) from the intestine, 3 (4.1%) from fistula. Of the 74 studied patients 57 (77%) showed positive polymerase chain reaction (PCR) and 17 (23%) showed negative PCR results. Regarding to the histopathological reports of the biopsies, there were 54 (73%) patients had positive histopathological (granuloma) result and 20 (27%) patients had negative results (nongranuloma). The sensitivity of histopathological examination of the biopsies was 91.02%, the specificity 88.2%, and the kappa was 0.748 (p = 0.00) which is mean good agreement between histopathological examination of the biopsies and the polymerase chain reaction test. CONCLUSIONS: The sensitivity, specificity, and the positive predictive value of histopathology examination of biopsies were 91.02%, 88.2%, and 96%, respectively. The kappa was 0.748 (p = 0.00) which is mean good agreement between histopathological examination of the biopsies and the polymerase chain reaction test.

DNA isolated from formalin-fixed paraffin-embedded healthy tissue after 30 years of storage can be used for forensic studies

Tissue formalin fixation and paraffin embedding (FFPE) is a standard method for long-term preservation and morphological and molecular analysis. The aim of this study was to analyze the effect of storage time on the integrity of DNA isolated from three different healthy FFPE tissues. DNA was isolated from FFPE heart, liver and brain tissues obtained from autopsy and archived from 1988 to 2017 using two different methods of DNA isolation: phenol-chloroform-isoamyl alcohol (PCI) and PureLink Genomic DNA Kit. The quantification and purity of DNA was measured spectrophotometrically at 260 nm and 280 nm. The quality of isolated DNA was evaluated by PCR amplification of GPD1 (150 bp), ACTB (262 bp) and RPL4 (407 bp) genes. The histomorphological characteristics of FFPE tissues were not significantly changed during 30 years of storage. Higher yield (272.9 ± 10.3 µg) and purity (A260/280 = 2.05) of DNA was obtained using the PCI method for DNA isolation from FFPE liver tissue. The PCI extraction method showed reproducible and consistent results in PCR amplification of all of three examined genes. The GPD1 gene can be amplified up to 30 years, the ACTB gene in the same samples up to 26 years and the RPL4 gene up to 6 years of storage in FFPE blocks. Although the best yield and purity of isolated DNA (using both isolation methods) was obtained from FFPE liver tissue, the DNA with the most preserved integrity was obtained from brain tissue archived up to 30 years. This is the first report using long-term archived healthy FFPE tissues (up to 30 years) that shows that the DNA isolated from these tissues is of preserved integrity and can be used in molecular autopsy.

Delays in the Diagnosis and Treatment of Tuberculous Lymphadenitis in Low-Incidence Countries: A Systematic Review

Early detection and treatment of tuberculosis (TB) is essential to achieve the goals appointed in the WHO End TB Strategy. Tuberculous lymphadenitis (TBLA) is the most common manifestation of extrapulmonary TB, but the diagnosis can be challenging in low-incidence countries due to sparse and inconsistent clinical features, resulting in delay. We aimed to summarize and discuss the current literature on patient delay, health care delay, and total delay (i.e., time to first health care contact, diagnosis, and treatment) in patients with TBLA in TB low-incidence countries. A systematic review using PubMed was conducted, searching for studies set in TB low-incidence countries (defined as <20 per 100,000 citizens) that reported on health care seeking behaviour, patient delay, health care delay, and/or total delay. Studies were categorized by type of delay and compared. We identified 11 heterogeneous studies with highly variable observations. Mean patient delay varied from 55 to 154 days (range, 14-1,461), mean health care delay from 44 to 94 days (range, 7-224) and median total delay from 77.5 to 122 days (range, 0-2,820). Evidently, more comprehensive insights into the diagnostic pathway and delay in TBLA patients are warranted.

Potential Value of Qiagen and PrepIT•MAX Kits in Extraction of Mycobacterial DNA From Presumptive Tuberculosis Archived Formalin-Fixed Paraffin-Embedded Tissues

BACKGROUND

DNA analysis has potential for screening for and diagnosing a variety of conditions as well as the characterization of various pathogens for many purposes including to identify genetic disorders and mutations, study genetic diversity, and establish evolutional trends.

METHODS

Our study compared the performance of 2 DNA extraction kits: Qiagen and prepIT•MAX. The study tested 160 formalin-fixed paraffin-embedded (FFPE) human tissue samples that had been collected at Muhimbili National Hospital (MNH) between 2010 and 2016. For each sample, DNA extraction was performed using both the Qiagen and prepIT•MAX kits followed by polymerase chain reaction (PCR) tests to target the RNA polymerase gene and gel electrophoresis.

RESULTS

The findings showed that the Qiagen was 3 times superior to the prepIT•MAX kit in successfully extracting mycobacterial DNA from presumptive tuberculosis (TB) FFPE tissues. Of the 160 previously Ziehl-Neelsen stain-negative Mycobacterium tuberculosis suspicious tissue samples, 12 (7.5%) tested positive with the PCR. Of the 12 PCR-detected positive samples, 8 (66.7%) yielded positive results with the Qiagen kit only and 4 (33.3%) yielded positive results with both Qiagen and prepIT•MAX kits. Additionally, 10 (83.3%) came from well-formed granuloma, 1 (8%) from caseous necrosis, and 1 (8.3%) Langhans-type giant cells endorsing their potential for housing infection such as TB adenitis.

CONCLUSIONS

A combination of molecular techniques, microscopy, and pathological features increases detection of M. tuberculosis from FFPE tissues. Both the Qiagen and the prepIT•MAX DNA extraction kits have shown a remarkable capability for extracting DNA from M. tuberculosis, although examination of FFPE tissues is not an intended use for the prepIT MAX, according to the manufacturer. In resource-limited countries, however, these kits may complement each other. We recommend further studies for validation and optimization, which includes the cost effectiveness of prepIT•MAX extraction kit to advocate for its use in extraction of mycobacterial DNA from FFPE tissues.

Performance of the BD ProbeTec ET direct detection assay for the analysis of Mycobacterium tuberculosis in respiratory and non-respiratory clinical specimens

Objectives

Early detection of Mycobacterial tuberculosis infection (MTB) is pivotal for the treatment of tuberculosis (TB).

Background

This study was performed to evaluate the performance of BD ProbeTec ET direct detection assay (DTB) against the gold standard culture technique for confirmation of MTB infection.

Methods

A total of 266 consecutive and non-duplicate clinical specimens for detection of MTB were included in this study. There were 118 respiratory and 148 non-respiratory samples. All samples were tested by microscopy for acid-fast bacillus (AFB), MTB culture and biochemical identification with simultaneous testing by DTB.

Results

A total of 88 samples (33%) were culture-positive for MTB including 39/118 respiratory, 29/99 fluid and 20/49 tissue samples. DTB sensitivity for respiratory samples was 97% and specificity was 96% with a positive predictive value (PPV) of 93% and negative predictive value (NPV) of 99%. Sensitivity of DTB in fluid samples was 80%, specificity 88%, PPV 69% and NPV 93% whereas sensitivity of DTB for tissue samples was 25%, specificity 90%, PPV 63% and NPV 63%. Of the 50 (56.8%) smear-positive samples, DTB sensitivity was 100% for respiratory, 85% for fluid and 100% for tissue samples.

Conclusion

DTB performed within acceptable limits for the rapid detection of MTB in respiratory samples compared to fluid and tissue specimens.

Necrotizing granulomatous inflammation of the liver

A 73-year-old patient with necrotizing granulomatous inflammation of the liver is presented. The computed tomography demonstrated 2 hypodense tumors with progressive enhancement in the liver. They became nearly isodense to the normal hepatic parenchyma on the delayed phase.

Detection of Mycobacterium bovis in bovine and bubaline tissues using nested-PCR for TbD1

In the present study, a nested-PCR system, targeting the TbD1 region, involving the performance of conventional PCR followed by real-time PCR, was developed to detect Mycobacterium bovis in bovine/bubaline tissue homogenates. The sensitivity and specificity of the reactions were assessed with DNA samples extracted from tuberculous and non-tuberculous mycobacteria, as well as other actinomycetales species and DNA samples extracted directly from bovine and bubaline tissue homogenates. In terms of analytical sensitivity, the DNA of M. bovis AN5 was detected up to 1.56 ng with conventional PCR, 97.6 pg with real-time PCR, and 1.53 pg with nested-PCR in the reaction mixture. The nested-PCR exhibited 100% analytical specificity for M. bovis when tested with the DNA of reference strains of environmental mycobacteria and closely-related Actinomycetales. A clinical sensitivity value of 76.0% was detected with tissue samples from animals that exhibited positive results in the comparative intradermal tuberculin test (CITT), as well as from those with lesions compatible with tuberculosis (LCT) that rendered positive cultures. A clinical specificity value of 100% was detected with tissue samples from animals with CITT- results, with no visible lesions (NVL) and negative cultures. No significant differences were found between the nested-PCR and culture in terms of detecting CITT+ animals with LCT or with NVL. No significant differences were recorded in the detection of CITT- animals with NVL. However, nested-PCR detected a significantly higher number of positive animals than the culture in the group of animals exhibiting LCT with no previous records of CITT. The use of the nested-PCR assay to detect M. bovis in tissue homogenates provided a rapid diagnosis of bovine and bubaline tuberculosis.

The continuing search for Mycobacterium tuberculosis involvement in sarcoidosis: a study on archival biopsy specimens

INTRODUCTION

Increasing evidence indicates that mycobacteria may be involved in the aetiology and pathophysiology of sarcoidosis.

OBJECTIVES

To investigate the association between Mycobacterium tuberculosis complex infection and sarcoidosis.

METHODS

Mediastinal lymph node biopsy specimens (formalin-fixed, paraffin-embedded) from 52 Danish patients with sarcoidosis, 50 patients with mediastinal lymphadenopathy of other non-mycobacterial causes (negative controls) and 12 patients with histologically and/or culture-verified mycobacteriosis (positive controls) were included in the study. Biopsy samples were analysed for the presence of Mycobacterium tuberculosis complex by strand displacement assay and a subset of specimens were examined for bacterial rRNA by fluorescent in situ hybridisation using an eubacterial probe with general bacterial specificity (EUB338).

RESULTS

One patient with sarcoidosis displayed a positive M. tuberculosis complex test. All negative controls were negative in the test and 5/12 patients with mycobacteriosis were positive in the test. We detected M. tuberculosis complex DNA in 10-year-old biopsy samples. Thirty-six samples were tested with the eubacterial probe; of these, 67% were positive with no difference between patients and controls.

CONCLUSION

Our results do not support the hypothesis that M. tuberculosis complex infection is involved in the pathogenesis of sarcoidosis. However, we stress the importance of excluding mycobacteriosis in the diagnostic workup of sarcoidosis patients.

Comparative analysis of four methods to extract DNA from paraffin-embedded tissues: effect on downstream molecular applications

Background

A large portion of tissues stored worldwide for diagnostic purposes is formalin-fixed and paraffin-embedded (FFPE). These FFPE-archived tissues are an extremely valuable source for retrospective (genetic) studies. These include mutation screening in cancer-critical genes as well as pathogen detection. In this study we evaluated the impact of several widely used DNA extraction methods on the quality of molecular diagnostics on FFPE tissues.

Findings

We compared 4 DNA extraction methods from 4 identically processed FFPE mammary-, prostate-, colon- and lung tissues with regard to PCR inhibition, real time SNP detection and amplifiable fragment size. The extraction methods, with and without proteinase K pre-treatment, tested were: 1) heat-treatment, 2) QIAamp DNA-blood-mini-kit, 3) EasyMAG NucliSens and 4) Gentra Capture-Column-kit.

Amplifiable DNA fragment size was assessed by multiplexed 200-400-600 bp PCR and appeared highly influenced by the extraction method used. Proteinase K pre-treatment was a prerequisite for proper purification of DNA from FFPE. Extractions with QIAamp, EasyMAG and heat-treatment were found suitable for amplification of fragments up to 400 bp from all tissues, 600 bp amplification was marginally successful (best was QIAamp). QIAamp and EasyMAG extracts were found suitable for downstream real time SNP detection. Gentra extraction was unsuitable. Hands-on time was lowest for heat-treatment, followed by EasyMAG.

Conclusions

We conclude that the extraction method plays an important role with regard to performance in downstream molecular applications.

Intestinal tuberculosis

PURPOSE OF REVIEW

Intestinal tuberculosis (TB) is increasing due partly to the HIV pandemic. Its clinical presentation mimics inflammatory conditions such as Crohn's disease and malignancies, which are becoming more prevalent, so the diagnosis is problematic.

RECENT FINDINGS

Greater awareness of intestinal TB is needed, both in countries where TB is endemic and developed countries with immigrant populations. Some strains of Mycobacterium tuberculosis are associated with more extrapulmonary disease and greater dissemination, thereby exacerbating the rise in HIV-associated extrathoracic TB. Recent retrospective and prospective studies are leading to the development of diagnostic algorithms. A wide range of imaging techniques is available for sampling and diagnosis. New biochemical, immunological and molecular diagnostic methods are being developed but must be standardized and validated. Developments in drug delivery will facilitate oral therapy even in patients suffering from malabsorption.

SUMMARY

There is an increasing consensus on the risk factors and clinical presentations of intestinal TB. Imaging techniques, coupled with fine needle biopsies, are useful aids to diagnosis, but most important is a greater awareness of the condition by clinicians.

Genetic diversity of feline cowpox virus, Germany 2000-2008

Recent cowpox virus (CPXV) infections of humans in Europe transmitted from cats and pet rats have risen public awareness of this rare zoonosis. Based on serosurveys wild rodents are regarded as primary reservoir hosts. Cats can become infected while hunting and could therefore serve as a sentinel for CPXV strains circulating in wild rodents. In a retrospective study we analysed 73 formalin-fixed paraffin-embedded skin samples from cats with a histologically proven CPXV infection. Specimens had been collected in different parts of Germany during 2000-2008. Following DNA extraction part of the hemagglutinin gene was amplified and sequenced from 72 samples. A phylogenetic analysis was inferred resulting in a total of 21 different CPXV genetic variants. The geographic distribution was imposed on a map.

Detection and identification of aquatic mycobacteria in formalin-fixed, paraffin-embedded fish tissues

The isolation of mycobacteria from field samples is problematic, and isolation of the bacterium is sometimes not even attempted. The detection of mycobacteria through traditional histology using formalin-fixed, paraffin-embedded (FFPE) tissues is neither sensitive nor specific. However, detection of mycobacterial DNA from FFPE specimens, suspected of being infected with mammalian mycobacteriosis, is a routine clinical procedure. In the present study, a polymerase chain reaction (PCR)-based method was used to detect and identify mycobacteria in FFPE specimens sampled from fish suspected of being infected with fish mycobacteriosis. A total of 45 fish tissue samples, comprising of 12 tissue samples obtained from experimentally infected fish and the remainder from fish naturally infected with mycobacteria, were analysed using a PCR protocol which amplifies a fragment of the mycobacterial 65 kDa heat-shock protein (hsp65) gene. PCR-restriction enzyme analysis and/or sequencing were employed to further analyse the PCR amplicons. The PCR results were compared with those obtained by histology and culture. Mycobacterial DNA was detected in 34 of the 45 samples examined, of which 16 samples (47%) showed granulomatous reactions on histological examination. Using histology as the gold standard, no false-negative PCR results were obtained. Also, considering the presence or absence of granulomas as a diagnostic criterion, the sensitivity and specificity of PCR in 42 of the FFPE tissues were 16/16 (100%) and 8/26 (approximately 30.8%), respectively. Corresponding microbiological cultures were available for 15 cases, of which 13 were pure Mycobacterium cultures. Of these, 13 were PCR positive (100% sensitivity and 50% specificity). The PCR-based methods used here proved sensitive, specific and rapid for the detection of mycobacteria in routinely processed paraffin wax-embedded and formalin-fixed histological samples, and the results of the study suggest that this method has potential use in retrospective epidemiological studies.

Effects of tissue handling and processing steps on PCR for detection of Mycobacterium tuberculosis in formalin-fixed paraffin-embedded samples

Development and standardization of reliable methods for detection of Mycobacterium tuberculosis in clinical samples is an important goal in laboratories throughout the world. In this work, lung and spleen fragments from a patient who died with the diagnosis of miliary tuberculosis were used to evaluate the influence of the type of fixative as well as the fixation and paraffin inclusion protocols on PCR performance in paraffin embedded specimens. Tissue fragments were fixed for four h to 48 h, using either 10% non-buffered or 10% buffered formalin, and embedded in pure paraffin or paraffin mixed with bee wax. Specimens were submitted to PCR for amplification of the human beta-actin gene and separately for amplification of the insertion sequence IS6110, specific from the M. tuberculosis complex. Amplification of the beta-actin gene was positive in all samples. No amplicons were generated by PCR-IS6110 when lung tissue fragments were fixed using 10% non-buffered formalin and were embedded in paraffin containing bee wax. In conclusion, combined inhibitory factors interfere in the detection of M. tuberculosis in stored material. It is important to control these inhibitory factors in order to implement molecular diagnosis in pathology laboratories.

Detection of Haemophilus influenzae type B DNA in a murine pneumonia model by in situ PCR

This study estimated the value of in situ PCR (ISPCR) in the detection of Haemophilus influenzae type b (Hib) DNA in paraffin-embedded lung tissues of a murine pneumonia model. ICR mice were infected with Hib solution intranasally. In study group A (n=20), physiological changes and the number of deaths were recorded for 7 consecutive days after infection. In study group B (n=10), blood samples and lung tissues were obtained from the infected mice on the brink of death. In both groups, portions of the lung tissue were cultured for Hib, while other portions were submitted for histopathological studies. Conventional PCR, PCR followed by Southern blotting and ISPCR were performed to detect Hib in paraffin-embedded lung tissues. In control group A, six mice were inoculated intranasally with the same concentration of heat-inactivated Hib solution. In control group B, six healthy mice served as a blank control. Both control groups were managed using the same methods as those used in the study groups. The white blood cell count of the mice in the study group increased (F=3.295, P<0.01), with a high neutrophil count (F=0.127, P<0.05). In the histopathological study, various stages of pneumonia were found in the lung tissues of the infected mice examined by microscope; 80% of the mice had moderate or severe pneumonia. Cultures of lung tissues in the study groups were all positive for Hib, while no bacteria were found in the control groups. Hib was detected in only 4 of 30 samples (13.3%) of the study groups using conventional PCR, but in all 30 samples (100%) using both Southern blotting and ISPCR. All three methods did not detect Hib in the control groups. Because of its sensitivity and specificity and its ability to locate the micro-organism, ISPCR can be considered suitable for the detection of Hib in paraffin-embedded lung tissues.

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.