Polymerase chain reaction in the diagnosis of urinary tract tuberculosis

PCR inhibitors and facilitators - Their role in forensic DNA analysis

Since its inception, DNA typing technology has been practiced as a robust tool in criminal investigations. Experts usually utilize STR profiles to identify and individualize the suspect. However, mtDNA and Y STR analyses are also considered in some sample-limiting conditions. Based on DNA profiles thus generated, forensic scientists often opine the results as Inclusion, exclusion, and inconclusive. Inclusion and exclusion were defined as concordant results; the inconclusive opinions create problems in conferring justice in a trial- since nothing concrete can be interpreted from the profile generated. The presence of inhibitor molecules in the sample is the primary factor behind these indefinite results. Recently, researchers have been emphasizing studying the sources of PCR inhibitors and their mechanism of inhibition. Furthermore, several mitigation strategies- to facilitate the DNA amplification reaction -have now found their place in the routine DNA typing assays with compromised biological samples. The present review paper attempts to provide a comprehensive review of PCR inhibitors, their source, mechanism of inhibition, and ways to mitigate their effect using PCR facilitators.

Multicentre evaluation of Xpert MTB/RIF assay in detecting urinary tract tuberculosis with urine samples

Genitourinary tuberculosis (GUTB) accounts for up to 40% of extrapulmonary tuberculosis cases. Rapid tests for GUTB are urgently needed because it is often associated with delayed health-care seeking, leading to serious consequences. This study evaluated the performance of the Xpert MTB/RIF assay in the rapid diagnosis of urinary tract tuberculosis (UTB) and rifampicin-resistant tuberculosis with urine specimens. In all, 302 patients were included from four hospitals in China. Suspected UTB patients were tested with Xpert, smear, and MGIT 960 culture. Drug susceptibility testing (DST) was conducted for culture-positive cases. The performance of the assays was evaluated against MGIT 960 culture and a composite reference standard (CRS). Among all participants, 150 (49.7%) had CRS-positive UTB, of whom 36 (24.0%) were culture-confirmed. Against culture, Xpert and smear achieved a sensitivity of 94.4% (95% CI: 81.3-99.3%) and 22.2% (95% CI: 10.1-39.2%), respectively. Against CRS, the sensitivity of Xpert, smear and culture was 41.3% (95% CI: 33.4-49.7%), 7.3% (95% CI: 3.7-12.7%), and 24.0% (95% CI: 17.4-31.6%). Xpert had better performance than smear and culture in detecting UTB from urine samples and could be considered for the diagnosis of UTB. Moreover, Xpert showed better performance than MGIT 960-based DST using urine culture.

Diagnostic accuracy of nucleic acid amplification tests (NAATs) in urine for genitourinary tuberculosis: a systematic review and meta-analysis

Background

Genitourinary tuberculosis is the third most common form of extrapulmonary tuberculosis. Diagnosis is difficult because of unspecific clinical manifestations and low accuracy of conventional tests. Unfortunately, the delayed diagnosis impacts the urinary tract severely. Nucleic acid amplification tests yield fast results, and among these, new technologies can also detect drug resistance. There is lack of consensus regarding the use of these tests in genitourinary tuberculosis; we therefore aimed to assess the accuracy of nucleic acid amplification tests in the diagnosis of genitourinary tuberculosis and to evaluate the heterogeneity between studies.

Methods

We did a systematic review and meta-analysis of research articles comparing the accuracy of a reference standard and a nucleic acid amplification test for diagnosis of urinary tract tuberculosis. We searched Medline, EMBASE, Web of Science, LILACS, Cochrane Library, and Scopus for articles published between Jan 1, 1990, and Apr 14, 2016. Two investigators identified eligible articles and extracted data for individual study sites. We analyzed data in groups with the same index test. Then, we generated pooled summary estimates (95% CIs) for sensitivity and specificity by use of random-effects meta-analysis when studies were not heterogeneous.

Results

We identified eleven relevant studies from ten articles, giving information on PCR, LCR and Xpert MTB/RIF tests. All PCR studies were “in-house” tests, with different gene targets and had several quality concerns therefore we did not proceed with a pooled analysis. Only one study used LCR. Xpert studies were of good quality and not heterogeneous, pooled sensitivity was 0·87 (0·66–0·96) and specificity was 0·91 (0·84–0·95).

Conclusion

PCR studies were highly heterogeneous. Among Xpert MTB/RIF studies, specificity was favorable with an acceptable confidence interval, however new studies can update meta-analysis and get more precise estimates. Further high-quality studies are urgently needed to improve diagnosis of genitourinary tuberculosis.

Protocol registration

PROSPERO CRD42016039020.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-017-2476-8) contains supplementary material, which is available to authorized users.

Early morning urine collection to improve urinary lateral flow LAM assay sensitivity in hospitalised patients with HIV-TB co-infection

Background

Urine LAM testing has been approved by the WHO for use in hospitalised patients with advanced immunosuppression. However, sensitivity remains suboptimal. We therefore examined the incremental diagnostic sensitivity of early morning urine (EMU) versus random urine sampling using the Determine® lateral flow lipoarabinomannan assay (LF-LAM) in HIV-TB co-infected patients.

Methods

Consenting HIV-infected inpatients, screened as part of a larger prospective randomized controlled trial, that were treated for TB, and could donate matched random and EMU samples were included. Thus paired sample were collected from the same patient, LF-LAM was graded using the pre-January 2014, with grade 1 and 2 manufacturer-designated cut-points (the latter designated grade 1 after January 2014). Single sputum Xpert-MTB/RIF and/or TB culture positivity served as the reference standard (definite TB). Those treated for TB but not meeting this standard were designated probable TB.

Results

123 HIV-infected patients commenced anti-TB treatment and provided matched random and EMU samples. 33% (41/123) and 67% (82/123) had definite and probable TB, respectively. Amongst those with definite TB LF-LAM sensitivity (95%CI), using the grade 2 cut-point, increased from 12% (5–24; 5/43) to 39% (26–54; 16/41) with random versus EMU, respectively (p = 0.005). Similarly, amongst probable TB, LF-LAM sensitivity increased from 10% (5–17; 8/83) to 24% (16–34; 20/82) (p = 0.001). LF-LAM specificity was not determined.

Conclusion

This proof of concept study indicates that EMU could improve the sensitivity of LF-LAM in hospitalised TB-HIV co-infected patients. These data have implications for clinical practice.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-017-2313-0) contains supplementary material, which is available to authorized users.

Should men with idiopathic obstructive azoospermia be screened for genitourinary tuberculosis?

OBJECTIVE

Infertility may be the sole manifestation of genitourinary tuberculosis (TB) and men with idiopathic obstructive azoospermia are often screened for TB using semen polymerase chain reaction (PCR) test. We assessed the benefits of such screening.

DESIGN

Totally, 100 infertile men with idiopathic obstructive azoospermia were screened with a kit-based PCR for semen TB. Confirmatory tests for TB were performed in PCR positive men before administering anti-tubercular therapy (ATT) for 6 months. Semen analysis was repeated to assess benefits of treatment.

RESULTS

Seven subjects (7%) had positive semen PCR for TB. Four of them had other clinical evidence of TB (history and physical signs) and were administered ATT. None had any improvement in semen parameters. No subject had any other laboratory evidence of TB and no other subject (96%) was administered ATT.

CONCLUSIONS

Screening for TB using semen PCR did not identify any men who would have been missed on clinical evaluation and is thus not indicated in men with idiopathic obstructive azoospermia.

Concomitant urothelial cancer and renal tuberculosis

We report a case of coexisting urothelial cancer and renal tuberculosis in the same kidney. The patient is a 72-year-old female with a remote history of treated pulmonary tuberculosis who presented with haematuria, initial investigation of which elucidated no definitive cause. Almost 1 year later, a diagnosis of metastatic urinary tract cancer was made. The patient received chemotherapy for advanced collecting duct type renal cell carcinoma, based on histological features of renal biopsy. Subsequent confirmatory immunostains however led to a revised diagnosis of urothelial cancer, necessitating a change in chemotherapy regimen. A diagnosis of ipsilateral renal tuberculosis was made based on TB-PCR testing of renal biopsy tissue and anti-TB therapy was coadministered with chemotherapy. The patient died 9 months after diagnosis of metastatic urothelial cancer.

Assessment of diagnostic techniques of urinary tuberculosis

Early diagnosis of active tuberculosis remains an elusive challenge. In addition, one third of the world's population is latently infected with Mycobacterium tuberculosis (Mtb) and up to 10% of infected individuals develop tuberculosis (TB) in their lifetime. In this investigation, the incidence of urinary tuberculosis among renal patients was studied. Three hundreds urine samples were processed for detection of Mtb by Ziehl-Neelsen (ZN) smear examination, Lowenstein Jensen (LJ) medium, radiometric BACTEC460 system as well as polymerase chain reaction (PCR) followed by DNA Enzyme Immunoassay (DEIA) test. Out of 300 urine samples, 2 were positive by both ZN smears and LJ medium with incidence rate of 0.66 %, 3 positive samples by BACTEC460 culture system with incidence of 1%. PCR assay gave more positive results than smear and culture examination (i.e. 8 positive samples with incidence rate of 2.6%). The specificities were 25% for both ZN smears and LJ medium, 37.5% for BACTEC460 culture system, and 100% for PCR test, while sensitivities of all assays were 100%. Thus PCR is a rapid and sensitive method for the early diagnosis of urinary tuberculosis.

Renal tuberculosis in the modern era

Tuberculosis (TB) is a disease caused by Mycobacterium tuberculosis. The disease remains as an important public health problem in developing countries. Extrapulmonary TB became more common with the advent of infection with human immunodeficiency virus and by the increase in the number of organ transplantation, which also leads to immunosuppression of thousand of persons. Urogenital TB represents 27% of extrapulmonary cases. Renal involvement in TB can be part of a disseminated infection or a localized genitourinary disease. Renal involvement by TB infection is underdiagnosed in most health care centers. Most patients with renal TB have sterile pyuria, which can be accompanied by microscopic hematuria. The diagnosis of urinary tract TB is based on the finding of pyuria in the absence of common bacterial infection. The first choice drugs include isoniazide, rifampicin, pirazinamide, ethambutol, and streptomycin. Awareness of renal TB is urgently needed by physicians for suspecting this disease in patients with unexplained urinary tract abnormalities, mainly in those with any immunosuppression and those coming from TB-endemic areas.

Direct molecular detection of Mycobacterium tuberculosis complex from clinical samples - An adjunct to cultural method of laboratory diagnosis of tuberculosis

Background:

Tuberculosis, a communicable disease with significant morbidity and mortality, is the leading cause of death in the world from bacterial infectious disease. Because of its public health importance, there is need for rapid and definitive method of detecting the causative organism. Several approaches have been attempted, but the molecular methods, especially Polymerase Chain Reaction assays are the most promising for rapid detection of Mycobacterium tuberculosis complex from clinical samples.

Aim:

This study was aimed at using Polymerase Chain Reaction for detection of Mycobacterium tuberculosis complex from clinical samples using universal sample processing methodology.

Subjects and Methods:

Two hundred clinical samples sent to Tuberculosis laboratories in Ibadan and Osogbo, Nigeria, were enrolled in this study. The samples were processed by universal sample processing methodology for PCR; smear microscopy was carried out on sputum samples by Ziehl Nelseen staining technique; and cultured on Middlebrook agar medium containing oleic acid albumin dextrose complex supplement after decontamination of samples.

Results:

Ninety six (48%) samples were detected positive for M. tuberculosis complex by polymerase chain reaction using the combination of boiling and vortexing and microscopy detected 72 (36%) samples positive for acid fast bacilli. Using culture method as gold standard, it was found that polymerase chain reaction assay was more sensitive (75.5%) and specific (94.8%) than microscopy (sensitivity of 48.5% and specificity of 85.7%) in detecting M. tuberculosis complex from clinical samples. There was significant difference in detecting M. tuberculosis from clinical samples when compared to microscopy (p<0.05).

Conclusion:

The study recommends that direct molecular detection of M. tuberculosis complex is sensitive and specific and polymerase chain reaction method should be used as an adjunct to other methods of laboratory diagnosis of tuberculosis.

Growth of mycobacteria in urine determined by isothermal microcalorimetry: implications for urogenital tuberculosis and other mycobacterial infections

OBJECTIVE

To overcome the limitations of current urine-based diagnostic assays of urogenital tuberculosis, we used isothermal microcalorimetry to detect the metabolic activity of Mycobacterium tuberculosis and other commonly neglected pathogenic mycobacteria in urine and accurately determine their growth parameters.

METHODS

A microcalorimeter equipped with 48 channels was used. Detection was accomplished, and growth was monitored for 4 different Mycobacterium species in sterilized and modified urine at 37 °C by measuring metabolic heat flow (μW = μJ/s) as a function of time. These strains were M. smegmatis, M. phlei, M. kansasii, and M. tuberculosis. The data were integrated to perform curve fitting and extract the growth parameter from the raw data.

RESULTS

In sterilized urine, M. smegmatis showed the fastest growth rate (0.089 ± 0.017 [h(-1)]), followed by M. phlei (0.072 ± 0.016 [h(-1)]) and M. kansasii (0.007 ± 0.001 [h(-1)]). No growth of M. tuberculosis was detected in sterilized urine. However, in serum-supplemented urine, growth of M. tuberculosis was observed within 3 weeks at a growth rate of 0.008 ± 0.001 [h(-1)]. Biofilm formation was enhanced in the serum supplemented urine.

CONCLUSION

Isothermal microcalorimetry allows rapid and accurate detection of mycobacterial growth in urine. Given the absence of data on the mycobacterial growth in urine, isothermal microcalorimetry could be used to unravel key aspects of Mycobacterium physiology in the urinary tract and potentially contribute to improvement in the diagnosis and treatment of urogenital tuberculosis.

Proinflammatory Cytokine Profile in Active Kidney Tuberculosis Patients

INTRODUCTION

Mycobacterium tuberculosis is a facultative intracellular pathogen that developes specific T cell response expressed by the production of IL-12, IFN-gamma, and TNF-alpha. The response has been quite well investigated in the experimental models, however, there is little information about certain cytokine levels in patients with extrapulmonary tuberculosis. The shortage of data pertains also to its most common form-kidney tuberculosis, especially when bacilli dissemination into the blood circulation has occurred.

OBJECTIVES

The aim of our study was to examine simultaneously the frequency of Mycobacterium tuberculosis presence in the blood circulation and the serum cytokine concentration during kidney tuberculosis to approach their relationship in the clinical infection process. It is considered that cytokine levels do not correlate with localisation of tuberculosis (pulmonary vs. extrapulmonary), however, there is little information about the cytokine levels in patients with kidney tuberculosis.

MATERIALS AND METHODS

30 patients attending the urology clinic with suspicion of kidney tuberculosis were evaluated. Serum concentrations of selected cytokines in patients with urine, urine and blood Mycobacterium tuberculosis presence were quantified by ELISA and compared to PCR negative patient and group of healthy people.

RESULTS

Our study demonstrates the increase of TNF-alpha and IL-12 level in comparison to control group. TNF-alpha concentration was about 2-fold higher in the positive patients than it was in control group; IL-12 concentration was about 4-fold higher and the differences between IL-12 levels were statistically important (p < 0.05). However, no significant differences were found in IFN-gamma level among all groups. Using Spearman correlation rank test, a significant correlation was found between TNF-alpha and IL-12 in the positive patient group. The correlation factor was more significant for the group of patients with Mycobacterium tuberculosis present in blood and urine than it was in urine positive PCR group (r = -0.66 vs. r = -0.51).

Clinical features of confirmed versus suspected urogenital tuberculosis in region with extremely high prevalence of pulmonary tuberculosis

OBJECTIVES

To compare the characteristics of confirmed vs suspected cases of urogenital tuberculosis (UGTB) in a geographic region with an extremely high prevalence of pulmonary tuberculosis. UGTB is notoriously difficult to diagnose.

METHODS

A retrospective clinical record review was performed of 68 patients treated from March 1998 to July 2007. Group 1 (n = 45) had UGTB confirmed by microbiologic or histologic examination. Group 2 (n = 23) had a high suspicion of UGTB because of the clinical features, but no microbiologic or histologic confirmation. The data were collected and statistically analyzed using Student's t test for parametric data and Fisher's exact test for contingency tables (P < .05 was accepted as statistically significant).

RESULTS

The clinical characteristics were not significantly different statistically, except for flank pain (14% vs 43%), renal cavitation (14% vs 44%), urolithiasis (0% vs 25%), and ureteral stricture formation (7% vs 39%) in groups 1 and 2, respectively. Anti-TB medication was given to 7 patients (30%) in group 2 despite the lack of a confirmed diagnosis. The outcome in terms of complications and renal function loss was not significantly different between the 2 groups.

CONCLUSIONS

Flank pain, renal cavitation, urolithiasis, and ureteral stricture formation were significantly more common in the group with suspected UGTB than in those with confirmed UGTB. However, other clinical characteristics did not differ significantly between the 2 groups. In patients with clinical features highly suspicious of UGTB, it appears reasonable to institute anti-TB treatment, despite the lack of a confirmed diagnosis.

Current survey of urinary tuberculosis in Hokkaido, Japan

Urinary tuberculosis has been rare in recent years and its diagnosis is difficult because there are no disease-specific symptoms. We tried to clarify the occurrence of urinary tuberculosis in recent years in our area. During the past 5 years, there were 12 patients with urinary tuberculosis in the clinics that participated in this study. Their chief complaints were frequent voiding in 7 patients and gross hematuria in 3 patients. They were diagnosed by nucleic acid amplification tests and imaging modalities such as excretory urography, computed tomography, and/or cystoscopy. Most of the patients received multidrug treatment and had relatively favorable treatment outcomes. There has been a small but neglected number of patients with urinary tuberculosis in recent years. We should keep this rare and difficult-to-diagnose disease in mind and suspect it when patients complain of longstanding urinary symptoms with no obvious cause.

Clinical relevance of nucleic acid amplification test for patients with urinary tuberculosis during antituberculosis treatment

The nucleic acid amplification test (NAAT) has been valuable in the diagnosis of urinary tuberculosis; however, no studies have attempted to determine the significance of NAAT post treatment. We encountered three patients with urinary tuberculosis who underwent sequential NAAT during antituberculosis chemotherapy and post treatment. All patients were diagnosed as having urinary tuberculosis by positive NAAT and specific renal deformity revealed by imaging. In two of the three patients, positive culture results were obtained and one was negative in standard culture. During antituberculosis chemotherapy, a negative NAAT was obtained from 3 to 5 months after the start of treatment and no positive culture results were obtained during the same period. At the end of chemotherapy, 6 months or more after the start of medication, all patients had negative NAAT results. These results suggest that NAAT for Mycobacterium tuberculosis provides an effective and rapid detection method for urinary tuberculosis both pre- and post-treatment.

Removal of PCR inhibitors by silica membranes: evaluating the Amplicor Mycobacterium tuberculosis kit

The effectiveness of PCR inhibitor removal by silica membranes in combination with the Amplicor Mycobacterium tuberculosis kit was analyzed for 655 respiratory and nonrespiratory specimens. The overall inhibition rate was reduced from 12.5%, when applying the Amplicor kit alone, to 1.1% with the addition of silica membrane DNA purification.

Polymerase chain reaction in clinically suspected genitourinary tuberculosis: comparison with intravenous urography, bladder biopsy, and urine acid fast bacilli culture

OBJECTIVES

To evaluate the role of urinary polymerase chain reaction (PCR) in the detection of Mycobacterium tuberculosis (MTb) in patients with a clinical suspicion of genitourinary tuberculosis (GUTB) and to compare its sensitivity with intravenous urography (IVU), bladder biopsy, and urine culture for acid fast bacilli (AFB).

METHODS

The study was carried out between September 1997 and December 1998 in 42 patients with a clinical suspicion of GUTB. Their clinical features, organ involvement, and investigation results were studied. The diagnostic yield of urinary PCR for MTb and its sensitivity in comparison with routine urine AFB culture, bladder biopsy, and IVU were assessed.

RESULTS

There were 25 male and 17 female patients, with a mean age of 31.04 years. Patients suspected of having GUTB most often presented with irritative voiding symptoms. Two patients had abnormal renal parameters. Of the 42 patients clinically suspected of having GUTB, radiologic abnormalities suggestive of GUTB were found in 37 (88.09%); MTb was isolated in the urine AFB culture in 13 (30.95%); bladder biopsy was positive in 11 (45.83%); and urinary PCR for MTb was positive in 34 cases (80.95%). Of 35 cases of proven GUTB, IVU was suggestive of the diagnosis in 32 (91.42%) and MTb was isolated in the urine AFB culture in 13 cases (37.14%). Bladder biopsy was positive in 11 (45. 83%) of 24 patients in whom biopsy was taken, and urinary PCR for MTb was positive in 33 (94.29%).

CONCLUSIONS

A high index of suspicion is necessary for a diagnosis of GUTB. In clinically suspected cases, IVU may be suggestive of GUTB, but it is not specific. In the present study, IVU was suggestive in 88.09% of patients. MTb was isolated in the urine AFB culture in only 37.14% of patients, and bladder biopsy was positive in 45.83%. Urinary PCR for MTb was the most sensitive indicator and was positive in 94.29% of patients. It is evident from this series that PCR provides a much faster diagnosis of urinary MTb. It is a rapid, sensitive, and specific diagnostic method and avoids a delay in starting treatment.

Rapid identification of Mycobacterium tuberculosis complex on urine samples by Gen-Probe amplification test

The aim of the study was to evaluate the applicability to urine samples of the Amplified Mycobacterium tuberculosis Direct Detection Test (AMTD), which is currently used to identify this organism in respiratory specimens within a few hours. The study was performed on 95 patients, comprising 35 subjects with a high index of suspicion for active tuberculosis of the urinary tract and 60 subjects with evidence of non-mycobacterial disease. One urine specimen from each subject was examined by microscopy, culture and AMTD. AMTD was positive in 38 specimens and negative in 57. Assuming culture as the reference standard, the sensitivity, specificity, positive predictive value and negative predictive value of AMTD were 100%, 91.93%, 86.84% and 100%, respectively. Reassessing the discrepancies between AMTD and culture by review of patients' charts, the sensitivity, specificity, positive predictive value and negative predictive value of AMTD were 100%, 93.44%, 89.47% and 100%. The results of the study as well as the characteristics of AMTD encourage its use for the rapid recognition of urinary tract tuberculosis, although its findings should be interpreted cautiously when the clinical picture is not consistent with an active tuberculosis.

False-negative results of a ligase chain reaction assay to detect Chlamydia trachomatis due to inhibitors in urine

The aim of this study was to assess the presence of inhibitors in urine specimens causing false-negative results in a commercial Chlamydia trachomatis gap-filling ligase chain reaction (Gap-LCR) assay. On testing of urine samples by the Gap-LCR assay and urethral swab specimens by cell culture, 73 (19%) Chlamydia trachomatis positive subjects were detected among 382 men attending a clinic for sexually transmitted diseases. In 56 subjects, the agent was detected in both the urine and the urethral samples, while 309 subjects were negative in both tests. In seven subjects urine samples were Gap-LCR positive (confirmed by a different Gap-LCR assay), but the corresponding urethral swab samples were cell culture-negative. In another ten subjects the urethral swab samples were cell culture positive, but their urine samples were Gap-LCR negative. Subsequent re-analysis of the urine samples including the addition of external Chlamydia trachomatis DNA indicated full or partial inhibition in nine of the cell culture-positive Gap-LCR negative subjects. When urine preparations were freeze-thawed and diluted prior to testing, Chlamydia trachomatis was detected in six of the ten initially Gap-LCR-negative samples. Gap-LCR inhibitors were present in at least nine (12%) of the 73 urine preparations from the Chlamydia trachomatis positive individuals. Identification of samples containing Gap-LCR inhibitors and subsequent processing to reduce the inhibition increased the sensitivity of the test from 86% to 95%.