Microbiological diagnosis of tuberculosis: a comparison of old and new methods

Diagnostic value of nucleic acid amplification tests for tuberculous pleural effusion

Diagnosing tuberculous pleural effusion (TPE) is challenging for pulmonologists and laboratory scientists. The gold standards for TPE diagnosis are pleural fluid Ziehl-Neelsen staining, Mycobacterium tuberculosis (Mtb) culture and pleural biopsy. These tools have limitations, including low sensitivity, long turnaround time and invasiveness. The nucleic acid amplification test (NAAT) is a rapid and minimally invasive tool for diagnosing TPE. This review summarizes the diagnostic accuracy of available NAATs for TPE, with a focus on the evidence from systematic reviews and meta-analyses. The NAATs summarized in this review include in-house NAATs, GeneXpert-MTB/RIF, GeneXpert-MTB/RIF Ultra, simultaneous amplification and testing-tuberculosis, FluoroType MTB and loop-mediated isothermal amplification.

Utility of GeneXpert in the diagnosis, reliance on urine microscopy and clinical characteristics of genitourinary tuberculosis at a tertiary care hospital

Background

One-third of the world's population is infected with tuberculosis (TB) with new infection occurring every second. In humans, TB is primarily caused by Mycobacterium tuberculosis(MTB). Genitourinary TB (GUTB) is still a major health problem in many developing countries including India and had been declared by the World Health Organisation as 'public health emergency' in 1993.

Materials and Methods

This is a prospective study conducted at a tertiary care hospital involving 46 patients who presented with clinical feature suggestive of GUTB - urine specimens of these 46 patients were analysed for acid-fast bacilli (AFB), AFB culture, GeneXpert, and other relevant investigations were done to reach the diagnosis. Majority of patients were female (65.25%). This is especially relevant to rural and low socioeconomic areas in developing countries where women's health is worse than men's (in terms of nutrition); women's risk of disease may be increased. Most of our patients were above 30 years of age and exhibited nonspecific symptoms such as dysuria, haematuria and frequency. All patients were put on antitubercular drugs and followed as per the guidelines.

Conclusion

The sample size in the present study is small to arrive at a brisk inference, but it may safely be postulated that yield of detection for GeneXpert may be improved using multiple sampling, especially the early morning ones. It is also pertinent to mention here that GeneXpert may not be able to pick up mutant genomes.

Blood culture bottles are superior to conventional media for vitreous culture

BACKGROUND

To compare blood culture bottles and conventional media for the vitreous culture in patients with clinically suspected infectious endophthalmitis.

DESIGN

Retrospective comparative study at KKU Eye Center, Khon Kaen University.

PARTICIPANTS

There were 342 patients with clinically suspected infectious endophthalmitis participated in the study.

METHODS

The vitreous specimens were inoculated in both blood culture bottles and on conventional culture media (blood agar, MacConkey agar, chocolate agar, Sabouraud dextrose agar and thioglycolate broth).

MAIN OUTCOME MEASURES

The number of positive culture yields in both blood culture bottles and conventional media.

RESULTS

Positive culture yields in both methods were found in 151 eyes (49.5%). There were 136 of 151 eyes (90.1%) with positive culture in blood culture bottles, whereas 99 of 151 eyes (65.6%) yielded positive cultures in conventional media. These findings were different with a statistical significance (P < 0.00001) and an odds ratio of 3.47 (95% confidence interval 1.92, 6.63). A combination of blood culture bottles and conventional media improved the yield.

CONCLUSIONS

Blood culture bottles are superior to conventional media for vitreous culture in clinically suspected infectious endophthalmitis. Vitreous culture using blood culture bottles should be recommended as the primary method for microbiological diagnosis. A combination of both methods further improves the positive culture yield.

Clinical presentation and diagnostic approach in cases of genitourinary tuberculosis

Objective:

We herein describe the various modes of presentation in genitourinary tuberculosis (GUTB) and a simple diagnostic approach to it.

Materials and Methods:

We made a literature search through Medline database and various other peer-reviewed online journals to study the various modes of presentation in GUTB. We reviewed over 100 articles published in the last 10 years (1998 -- 2007), which were tracked through the key words like GUTB and extrapulmonary tuberculosis.

Results:

GUTB has varied presentation and the most common way of presentation is in the form of irritative voiding symptoms, which are found in more than 50% of the patients. The usual frequency of organ involvement is: kidney, bladder, fallopian tube, and scrotum. The usual tests used to diagnose GUTB are the demonstration of mycobacterium in urine or body fluid and radiographic examination. Intravenous urography (IVU) has been considered to be one of the most useful tests for the anatomical as well as the functional details of kidneys and ureters. In cases of renal failure, MRI can be used. Newer examinations such as radiometric liquid culture systems (i.e., BACTEC^®, Becton Dickinson, USA) and polymerase chain reaction (PCR) give rapid results and are highly sensitive in the identification of mycobacterium.

Conclusion:

GUTB can involve any part of the genitourinary system and presentation may vary from vague urinary symptoms to chronic kidney disease. Newer tests like radiometric liquid culture systems and polymerase chain reaction give rapid results and carry high diagnostic value.

Familial tuberculosis mimicking advanced ovarian cancer

Genital TB may present as on abdominopelvic mass mimicking ovarian malignancy because clinical and laboratory findings are similar. Family history is very important and should be considered for differential diagnosis. Three cases of genital TB with presentation of abdominopelvic masses and with no signs and symptoms of TB were presented. Two of them had positive family history of pulmonary TB. Tissue diagnosis was the best method for diagnosis of genital TB, but it should be reminded that if positive family history of TB was present, mini laparotomy should be done to take biopsy and to make rapid diagnosis before treatment.

Performance of QuantiFERON-TB testing in a tuberculosis outbreak at a primary school

This study compared the effectiveness of the QuantiFERON-TB Gold (QFT) assay with the Mantoux tuberculin skin test to detect Mycobacterium tuberculosis infection in 29 children during a school outbreak of tuberculosis. Of the 21 children with M. tuberculosis infection, 11 had a radiograph suggestive of the infection. The QFT assay was positive in all 21 of the children, and the Mantoux test was negative at first testing in 2 children (1 of whom was the sentinel case). The findings demonstrate that the QFT test is extremely useful in accurately identifying infected and uninfected children, permitting rapid intervention.

Peritoneal tuberculosis simulating advanced ovarian carcinoma: is clinical impression sufficient to administer neoadjuvant chemotherapy for advanced ovarian cancer?

Peritoneal tuberculosis mimics advanced ovarian cancer because of the similarities in clinical signs and symptoms such as ascites, pelvic and abdominal pain and mass, and elevation of serum CA125 level. We have presented four cases of peritoneal tuberculosis that underwent exploratory laparotomy for suspected advanced ovarian cancer during a 3-year period. Definitive diagnosis of tuberculosis was performed at laparotomy in all the cases. The frozen-section analysis seems to be the gold standard in the differential diagnosis. In view of these data, clinical diagnosis of advanced ovarian cancer is not sufficient for administering neoadjuvant chemotherapy. Cytologic or pathologic findings must be consistent with ovarian cancer for candidates who are being considered for neoadjuvant chemotherapy.

Rapid detection of Mycobacterium tuberculosis in respiratory samples by transcription-reverse transcription concerted reaction with an automated system

The aim of this study was to evaluate the performance of the transcription-reverse transcription concerted (TRC) method for the detection of Mycobacterium tuberculosis complex (MTC) 16S rRNA in clinical respiratory samples for the diagnosis of pulmonary tuberculosis. TRC is a novel method that enables the rapid and the completely homogeneous real-time monitoring of isothermal sequence RNA amplification without any postamplification procedure. The detection limit of the TRC method for MTC was one organism per 100 mul of sputum. The specificity of the method was confirmed by the absence of positive signals for sputum containing 10(6) M. avium or M. kansasii organisms per 100 microl. A total of 201 respiratory samples from patients diagnosed with or suspected of having tuberculosis were tested. Of the 72 MTC culture-positive samples, the TRC method was positive for 52 (sensitivity, 72.2%), whereas the Roche COBAS AMPLICOR PCR was positive for 58 (sensitivity, 80.6%). Both the TRC method and the COBAS AMPLICOR PCR showed no positive identification for any of the 129 culture-negative samples. The percent agreement between the two methods was 95% (191 of 201 samples). The high sensitivity and specificity together with shorter detection time (within 1 h) of the TRC method allow it to be proposed as a useful method for the rapid detection of MTC in respiratory samples.

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.

Diagnostic methods. Current best practices and guidelines for identification of difficult-to-culture pathogens in infective endocarditis

IE is a serious, life-threatening disease. Because treatment must often be adapted to the pathogen involved, rapid identification of the etiologic agent is critical to successful management of each patient. When difficult-to-culture pathogens are involved, routine microbiologic tests, including blood culture, may remain negative. Because such cases may account for up to 31% of all IE cases, alternative diagnostic approaches are necessary. Among the etiologic agents of culture-negative endocarditis, C burnetii and Bartonella spp play a major role; each is responsible for up to 3% of episodes of IE. The authors therefore recommend the systematic use of specific serologies in all cases of clinically suspected endocarditis. The cross-reactivity between C burnetii, Bartonella spp, and Chlamydia spp is of diagnostic importance because all are potential etiologic agents of endocarditis. However, given that the levels of specific antibodies observed in Bartonella endocarditis are extremely high, low-level cross-reactions with other antigens should not lead to misdiagnosis, provided serology for all suspected agents is performed. When serologic test results are negative for both Bartonella spp and C burnetii, special staining by the Gram, Giemsa, Gimenez, PAS, Warthin-Starry, and Grocott methods may guide the use of new diagnostic tools such as PCR and tissue culture for isolation and identification of the causative agent. Such novel approaches may lead to more comprehensive patient evaluations and the discovery of new etiologic agents of IE.

Diagnostic methods current best practices and guidelines for identification of difficult-to-culture pathogens in infective endocarditis

Culture-negative endocarditis currently represents a diagnostic challenge for physicians. Traditional methods such as histology, serology, and culture have been improved and new molecular techniques have been developed to improve the detection of difficult-to-culture agents. Serologic tests for the two most frequent etiologic agents, Coxiella burnetii and Bartonella spp, should be performed first because they can usually be identified easily in this way. The sensitivity of culture for intracellular bacteria has been improved by inoculation of samples in shell vials and by the use of novel tissue cell lines. Recently, universal and species-specific primers have been designated to amplify bacterial DNA directly from resected valves, allowing positive identification.

Diagnostic methods current best practices and guidelines for histologic evaluation in infective endocarditis

Infective endocarditis (IE) often presents diagnostic and therapeutic challenges and continues to cause high morbidity and mortality. Confirmation of the diagnosis of IE is important for the purposes of epidemiologic and clinical studies and is crucial for patient management. Despite recent advances in diagnostic techniques, about 10% of IE cases remain culture-negative. Because pathological examination of cardiac valves to demonstrate vegetations and valvular inflammation remains the gold standard for the diagnosis of IE, the role of the pathologist is often decisive, especially when bacteriologists fail to isolate a microorganism or when a microorganism that has been isolated may be a contaminant. Furthermore, the pathologist may play an important role in identification of previously unknown infectious agents.

Peritoneal tuberculosis with pelvic abdominal mass, ascites and elevated CA 125 mimicking advanced ovarian carcinoma: a series of 10 cases

Ten patients with peritoneal tuberculosis who were operated on for suspected advanced ovarian cancer during a 5-year period were analyzed. These 10 cases constituted 1.4% of the 728 new gynecologic cancer cases diagnosed and treated at our department during the same time period. Data were obtained from patients' files and pathology reports. The mean age of cases was 40.6 +/- 6.1 (median 37; range 18-72). Ascites was present together with ill-defined nodularities or thickening in the Douglas pouch and/or in the adnexal areas on pelvic examination in all patients but three, who presented with well-demarcated adnexal masses of about 5 cm in diameter. All patients had elevated serum CA 125 levels with a median of 331 U/ml, (40-560 U/ml). Ultrasound and abdominopelvic CT examinations revealed omental and mesenteric thickening in addition to ascites in all patients, cystic ovarian masses or ovarian enlargement in five, and peritoneal implants in two. Abdominal paracentesis performed in the six cases in whom the findings were felt to be most inconclusive for the diagnosis of ovarian cancer revealed clear exudative fluid with benign cells. Mycobacteria could not be demonstrated on direct preparations. Tuberculosis was diagnosed at laparotomy in all. Patients received antituberculous therapy and serum CA 125 levels returned to normal within 2 months after the beginning of treatment. This case series demonstrates a high rate of misdiagnosis between advanced ovarian cancer and peritoneal tuberculosis. Whereas abdominal paracentesis is useless in ruling out peritoneal tuberculosis, and serum CA 125 levels are not helpful in the differential diagnosis, the latter marker may be useful in the follow-up of patients.

The ligase chain reaction as a primary screening tool for the detection of culture positive tuberculosis

BACKGROUND

The ligase chain reaction Mycobacterium tuberculosis assay uses ligase chain reaction technology to detect tuberculous DNA sequences in clinical specimens. A study was undertaken to determine its sensitivity and specificity as a primary screening tool for the detection of culture positive tuberculosis.

METHODS

The study was conducted on 2420 clinical specimens (sputum, bronchoalveolar lavage fluid, pleural fluid, urine) submitted for primary screening for Mycobacterium tuberculosis to a regional medical microbiology laboratory. Specimens were tested in parallel with smear, ligase chain reaction, and culture.

RESULTS

Thirty nine patients had specimens testing positive by the ligase chain reaction assay. Thirty two patients had newly diagnosed tuberculosis, one had a tuberculosis relapse, three had tuberculosis (on antituberculous therapy when tested), and three had healed tuberculosis. In the newly diagnosed group specimens were smear positive in 21 cases (66%), ligase chain reaction positive in 30 cases (94%), and culture positive in 32 cases (100%). Using a positive culture to diagnose active tuberculosis, the ligase chain reaction assay had a sensitivity of 93.9%, a specificity of 99.8%, a positive predictive value of 83.8%, and a negative predictive value of 99.9%.

CONCLUSIONS

This study is the largest clinical trial to date to report the efficacy of the ligase chain reaction as a primary screening tool to detect Mycobacterium tuberculosis infection. The authors conclude that ligase chain reaction is a useful primary screening test for tuberculosis, offering speed and discrimination in the early stages of diagnosis and complementing traditional smear and culture techniques.

Improved recovery of Mycobacterium tuberculosis from pleural aspirates: bedside inoculation, heparinized containers and liquid culture media

The effects of bedside inoculation, heparinized containers and liquid culture media on the recovery of Mycobacterium tuberculosis from pleural aspirates were evaluated in this study. Of 155 patients, 63 were diagnosed to have pleural effusion tuberculous in origin. The overall recovery of M. tuberculosis was 57.1%. Bedside inoculation of the specimens produced a significantly higher yield than laboratory inoculation using non-heparinized specimens. When the pleural aspirates were transported in heparinized containers, the recovery rate was comparable to that from bedside inoculation, but lower when non-heparinized containers were used. No significant difference was found in recovery rate between the two liquid media, but the rate was significantly higher with the use of liquid media than conventional solid media. Thus, bedside inoculation of pleural aspirates, use of heparinized containers for transport for delayed inoculation in the laboratory and use of liquid culture media are recommended.

Nonculture Laboratory Methods for the Diagnosis of Infectious Endocarditis

Over the past few years new techniques have been developed to improve the diagnosis of infectious diseases. However, despite the various available culture systems, culture-negative endocarditis currently represents a challenge for physicians. In our laboratory, in an effort to reduce the rate of endocarditis of unknown etiology, we have used several recent histologic, serologic, and molecular tests. We review the latest technical developments for the diagnosis of infectious endocarditis, including those that we are currently using.