Intestinal mucormycosis in a patient with COVID-19: A case report

The novel coronavirus disease (COVID-19) has spread to all the continents posing a serious threat to global health. It can present with myriad symptoms and complications including susceptibility to fungal co-infections. We hereby describe a case of mucormycosis in a 17 year old COVID-19 positive female with no known comorbidities presenting with abdominal pain and distention and ultimately developing intestinal perforation. Early identication of the symptoms is essential to make a correct and early diagnosis to prevent complications.

Extracranial Schwannomas of the Head and Neck: A Literature Review and Audit of Diagnosed Cases Over a Period of Eight Years

Schwannoma is a benign, slow growing, usually solitary and encapsulated tumor derived from Schwann cells of the nerve sheath. Schwannomas can be divided into central, or intraosseous, and peripheral lesions. The etiology is unknown, but it is postulated that lesions arise by the proliferation of Schwann cells at one point inside the perineurium. Schwannomas may mimic other diseases of the head and neck, such as infection, tumor or metastasis. Extracranial schwannomas are rare; in this study we review a series of 22 cases of schwannomas originating in the head and neck region over a period of eight years. All tumors were benign and well-encapsulated. Tumor size ranged from 0.5 to 9 cm. The age range of patients studied was 15-74 years with a mean age of 35 years and a male predilection (M:F, 2.6:1)was noted. Four cases of schwannomas occurred in the tongue (18.18%) and lower lip (18.18%), three in the nasal cavity (13.64%), two each (9.09%) in the buccal mucosa, parapharyngeal space (9.09%), and eyebrow (9.09%), and one each in the upper lip (4.55%), lateral canthus of the eye (4.55%), intraorbital region (4.55%), submandibular gland (4.55%), and ear (4.55%). Schwannomas can present in a wide variety of sites within the head and neck. The tumor is benign and tend to be asymptomatic for long periods of time. Histopathology is the gold standard for diagnosis. Our study describes the clinicopathologic features of extracranial head and neck schwannomas, highlights the histopathologic features, and discusses pertinent findings with correlation to the present literature. It is important that both clinicians and pathologists be familiar with the uncommon sites of occurrence and the potential pitfalls associated with the diagnosis and management of these tumors.

Omental desmoplastic small round cell tumor with metastasis

Desmoplastic small round cell tumor (DSRCT) is a very rare diagnosis with about 200 cases reported in literature. DSRCT is a recently described histopathological entity by Gerald and Rosai in 1989. Abdominopelvic cavity especially peritoneum is the most common site. We report a case of a huge omental DSRCT with lymph node metastasis which was initially misdiagnosed as gastrointestinal stromal tumor on radiology. A 26-year-old male presented with complaints of upper abdominal swelling associated with constant dull pain. On examination there was a large 15 × 12 cm intraabdominal mass in the epigastric and umbilical region. Imaging studies were suggestive of neoplastic mesenchymal etiology. Image-guided fine-needle aspiration cytology (FNAC) was suggestive of mesenchymal neoplastic etiology. On laparotomy, there was a huge 20 × 15 cm mass arising from omentum with multiple omental and mesenteric seedlings and mesenteric, peripancreatic and perigastric lymphadenopathy. The patient underwent debulking surgery with uneventful post-operative recovery. Histopathological examination with immunohistochemistry revealed a diagnosis of DSRCT of omentum and small bowel mesentery with lymph node metastasis. Patient then received adjuvant chemotherapy with multiple chemotherapeutic drugs as per P6 protocol and has stable disease at 1 year follow up.

Extraction of Rhododendron arboreum Smith flowers from the forest for the livelihood and rural income in Garhwal Himalaya, India

Rhododendron arboreum locally known as ‘Burans', that bears magnificent flowers is one of the valuable non timber forest produces (NTFPs) in Garhwal Himalaya. These flowers are good source of income for local populace and help them to their subsistence up to some extent. R. arboreum flower can help local population to improve their livelihoods if potential harvesting is carried out sustainably. An attempt has been made to estimate the flower yield, examine extraction techniques, marketing trends and various uses of flowers. Stratified random sampling method was carried out in eight sites varying in altitudes and geographic locations. Flower yield kg/ha for each site was calculated as standard process. Questionnaire based survey was carried out in selected villages for flower extraction and marketing trends. Projections of potential (probable/-could generate) income were made and cost–benefit analysis was also estimated. Tree density of R. arboreum ranked first and Q. leucotrichophora had second rank while 16–25 cm cbh class tree density for R. arboreum was found highest across the sites. Flower yield was significantly (p < 0.001) higher at Khirsu site with 26–35 and 46–55 cm cbh class. There was positively significant correlation (n = 446, p < 0.001, r = 0.53) between flower yield and actual cbh. Flower yield has a direct relation with size of tree whereas yield has been less impacted by the sites. Average yield of flowers across the sites was about 25.3 ton/ha. On average 30% households are engaged in the extraction and trade activities with the extraction rate of 25–350 kg/household/year. A net household income of Rs. 6000–37,000 (89–545 USD) per year was computed from Rhododendron flower extraction and marketing business. The total monetary benefit was significantly higher than the inputs for all value added items on a per day basis. R. arboreum plays important role in ecological and economic sustainability of poor rural people and unemployed youths in Himalayan region. This can reduce unemployment through development of small cottage industry and entrepreneurship at village level by making different food products i.e. juice, squash, sauce and pickle etc.

Coronary arteritis as a cause of sudden cardiac death in a young girl

A case of probable coronary arteritis in a young girl who died suddenly and unexpectedly is presented. The histologic presentation of the disorder is discussed, especially the differential diagnosis of arteritis of the coronary arteries with an emphasis on tuberculosis (TB). TB myocarditis with or without concomitant lung involvement is rare, and tubercular coronary arteritis without underlying pulmonary Koch’s disease is all the rarer. We herein describe a case where the cause of death was ascertained on post-mortem examination.

Epithelioid inflammatory myofibroblastic sarcoma: the youngest case reported

Epithelioid inflammatory myofibroblastic sarcoma (EIMS) is a rare variant of the inflammatory myofibroblastic tumor. It has an aggressive clinical course and a high rate of recurrence. EIMS primarily affects children and young adults. Hereby, we report this entity in a 4-month-old infant who presented with an abdominal mass. Imaging studies revealed a large hypodense mesentery-based lesion involving the right half and mid-region of the abdomen. The mass with an attached segment of the small bowel was excised in toto. Grossly, a large encapsulated tumor was identified arising from the mesentery of the small bowel. The histological examination showed a tumor consisting of epithelioid to spindle cells loosely arranged in a myxoid background with numerous blood vessels and lymphoplasmacytic inflammatory infiltrate. On immunohistochemistry, the tumor cells showed positivity for ALK1 (nuclear), desmin, SMA, CD68, and focal positivity for CD30. A final diagnosis of EIMS of the small intestine was rendered. To the best of our knowledge, this case is the youngest reported case in literature.

A clinicopathological study of peripheral schwannomas

Aim and objective

Schwannomas are benign neoplasms of neural origin with sporadic or syndromic occurence. They are commonly seen in cranial nerves. Peripheral schwannomas occur rarely and may have unique presentations. The aim of this study is to evaluate the clinico-pathological characteristics of peripheral schwannomas.

Methods

A retrospective cross sectional study of peripheral schwannomas excluding head neck region was conducted. The study group consisted of 18 cases which were recorded over a period of seven years. The corresponding data were collected from the archives of the Department of Pathology.

Results

Male to female ratio was 1:1. The average age of the cases was 47 years. The most common site was the upper limbs (55.55%) followed by lower limbs, chest and penis. The lesions mostly presented as painless swellings (62%). Histopathological examination revealed classic features of schwannoma. Secondary changes included cystic degeneration, foam cells, epitheloid cells, hyalinization, microcystic change and collection of plasma cells. All cases were confirmed by positive S100 staining.

Conclusion

Peripheral schwannomas may be missed due to its rarity and atypical presentations. Both clinicians and pathologists should be aware of this common entity at unusual sites for the proper management of the patients. Surgery is usually the treatment of choice.

Multicentric validation of indigenous molecular test Truenat™ MTB for detection of Mycobacterium tuberculosis in sputum samples from presumptive pulmonary tuberculosis patients in comparison with reference standards

Background & objectives:

Early case detection is essential to interrupt transmission and to prevent further spread of tuberculosis (TB) in high endemic settings. Nucleic acid amplification tests (NAATs) with visual read-outs are ideal as point-of-care tests. Truenat™ MTB is an indigenous chip-based NAAT for detection of Mycobacterium tuberculosis, which involves extraction of DNA and real-time polymerase chain reaction (PCR) using portable, automated, battery-operated instruments. The current multicentric study was aimed to evaluate Truenat for detection of MTB in sputum samples obtained from patients with presumptive pulmonary TB with reference to culture as gold standard and Xpert as a comparator.

Methods:

The study was conducted at four sites, namely ICMR-National Institute for Research in Tuberculosis, Chennai; All India Institute of Medical Sciences, New Delhi; ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra; and National Institute of TB and Respiratory Diseases, New Delhi. Patients suspected to have TB were screened for eligibility. Two sputum samples were collected from each patient. Tests included smear, Xpert and Truenat directly from the sputum sample and culture by Lowenstein-Jensen (L-J) medium and MGIT960 from decontaminated pellets. Sample used for Truenat assay was coded. Resolution of Truenat false positives was done using an in-house PCR with TRC₄ primers.

Results:

The study enrolled 2419 presumptive TB patients after screening 2465 patients, and 3541 sputum samples were collected from the enrolled patients. Results of 2623 samples were available for analysis. Truenat showed a positivity rate of 48.5 per cent as compared to 37.0 per cent by Xpert. The sensitivities of Truenat and Xpert were was 88.3 and 79.7 per cent, respectively in comparison with culture.

Interpretation & conclusions:

Truenat MTB identified more positives among culture-confirmed samples than Xpert and had higher sensitivity. In addition, other advantageous operational features of Truenat MTB were identified which would be useful in field settings.

Validation of an indigenous assay for rapid molecular detection of rifampicin resistance in presumptive multidrug-resistant pulmonary tuberculosis patients

Background & objectives:

There is a need for an affordable, easy, high-sensitivity test usable at the peripheral health facility for diagnosis of drug-resistant (DR) tuberculosis (TB) to interrupt disease transmission. Nucleic acid amplification tests (NAATs) for early detection of DR-TB are ideal to bring testing near to the patient. Truenat™ MTB (Mycobacterium tuberculosis) and Truenat™ MTB-RIF (rifampicin) is an indigenous chip-based real-time polymerase chain reaction (PCR) based test for detection of multidrug-resistant (MDR) TB. The test involves extraction of DNA using automated, battery operated Trueprep instrument and real-time PCR performed on the Truelab analyzer. We report here multicentric validation of Truenat MTB-RIF for detection of DR-TB in suspected DR-TB patients.

Methods:

Consecutive patients aged 18-65 yr, with symptoms suggestive of TB and with a history of previous treatment, reporting to the National TB Elimination Programme (NTEP) clinics under four national institutes, namely AIIMS (All India Institute of Medical Sciences, New Delhi), NITRD (National Institute of Tuberculosis and Respiratory Diseases, New Delhi), NIRT (National Institute for Research in Tuberculosis, Chennai) and ICMR-National JALMA Institute for Leprosy and other Mycobacterial Diseases, Agra, were included in the study. Two sputum samples (one spot and one morning) were collected from each patient, after obtaining informed written consent. The samples were subjected to smear, GeneXpert and MGIT 960 culture (and drug susceptibility testing to RIF) (surrogate for MDR-TB) to serve as reference tests. The samples were coded to ensure blinding and subjected to Truenat MTB-RIF. Truenat MTB-RIF Version 1.5 was used for testing 1084 samples for RIF resistance, while Version 2.0 was used to test another 1201 samples.

Results:

Truenat MTB-RIF Version 1.5 in comparison with comprehensive laboratory reference standards yielded sensitivity and specificity of 76.2 and 94.7 per cent, respectively for the detection of RIF resistance in 1084 samples, collected across four sites. Based on the analysis of discordant samples, Version 2.0 of Truenat was developed by the manufacturer and this was further tested on additional 1201 samples, yielding a sensitivity of 87.5 per cent and specificity of 99.5 per cent.

Interpretation & conclusions:

Multicentric trial of Truenat™ MTB-RIF demonstrated a great potential of this point of care NAAT for detection of MDR-TB. The test would be useful in limited resource settings and inaccessible areas without need for any additional infrastructure.

Adrenocortical Carcinoma in a 6-Month-Old Infant

Adrenocortical carcinoma (ACC) is a rare malignant tumor arising from the adrenal cortex and it is even rarer in infancy. These tumors are usually hormonally active. We report a case of ACC in a 6-month-old infant who was brought by her mother with complaints of hirsutism and abnormally looking genitalia. Serum 17-alpha-hydroxyprogesterone and serum cortisol levels were raised. Subsequently, imaging studies revealed a large well-circumscribed soft-tissue mass in the right suprarenal region. The tumor was excised, and on histopathology in conjunction with immunohistochemistry, a diagnosis of ACC was given. Only four other cases of ACC have been reported till date in the literature, with an age of 6 months or younger. Hereby, we present a case of ACC in a young infant.

Primitive neuroectodermal tumor of the kidney: A rare case report

Renal primitive neuroectodermal tumor (PNET) is a rare primary renal neoplasm. Morphologically, it may mimic small blue round-cell tumor. Hence, histopathology in conjunction with immunohistochemistry plays a significant role in correctly diagnosing this malignancy. We report a case of PNET of kidney in a 30-year-old female with an extension to inferior vena cava, who succumbed following an aggressive course of illness.

Unusual presentation of renal cell carcinoma: A rare case report

Cutaneous and intraoral metastasis from any malignancy is not common. Cutaneous spread is usually noted in 5%-10% of high-grade malignancies, as in carcinoma breast, lung, colon, ovary, and malignant melanoma. Only 4.6% cases of cutaneous spread are from renal cell carcinoma (RCC). Intraoral spread from RCC is much rarer with an incidence of approximately 1% of all malignant oral tumors, noted sometimes in tongue, palate, buccal mucosa, gingiva, and lips. RCC is a highly aggressive tumor which requires early diagnosis for increasing the chance of cure. In our case, a 54-year-old male presented with swelling over upper lip, scalp, and retromolar area, which on histopathology and immunohistochemistry revealed clear cell carcinoma compatible with metastatic RCC.

Strain diversity and relative transmission of Mycobacterium tuberculosis in south coastal Karnataka, India

BACKGROUND

There are no published reports on the strain diversity and relative transmission of Mycobacterium tuberculosis isolates circulating in Karnataka State, India.

OBJECTIVE

To explore the strain diversity of M. tuberculosis isolates and their relative transmission in south coastal Karnataka using spoligotyping and mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) typing.

DESIGN

A total of 108 clinical isolates of M. tuberculosis were processed for spoligotyping, and 12-locus MIRU-VNTR typing and cluster analysis was performed.

RESULTS

Spoligotyping data of 108 isolates revealed 63 spoligotype patterns: 36 (80 isolates, 74.1%) patterns corresponded to spoligotype international types (SITs), whereas 27 (28 isolates, 25.9%) patterns were orphans. A further 57 (52.8%) isolates were clustered into 12 clusters; 51 (47.2%) isolates were unique. The largest spoligotype cluster comprised SIT 48 (L1.2.2), followed by SIT 1942 (L3) and SIT 11 (L1.1.2). Combined MIRU-VNTR typing and spoligotyping analysis further differentiated these 108 isolates into five clusters of two isolates each and 98 individual patterns.

CONCLUSIONS

Combined use of spoligotyping and MIRU-VNTR typing is best suited for genotyping studies in this region. Very high genetic diversity was observed among the clinical isolates. Further elaborate studies are required for a better understanding of the genetic diversity and transmission dynamics of the strains circulating in this region.

Rapid detection of ethambutol-resistant Mycobacterium tuberculosis in clinical specimens by real-time polymerase chain reaction hybridisation probe method

Background

Early diagnosis of drug resistance (DR) to ethambutol (EMB) in tuberculosis (TB) remains a challenge. Simple and reliable method (s) are needed for rapid detection of DR Mycobacterium tuberculosis (MTB) in clinical specimens.

Objectives

The aim of this study was to design fluorescence resonance energy transfer hybridisation probe-based real-time polymerase chain reaction (PCR) method for the early detection of EMB-resistant MTB direct from clinical sputa.

Materials and Methods

Primers and probes were designed against 306 codon of embB gene which is commonly associated with EMB resistance. A comparative study was done between Lowenstein-Jenson (L-J) proportion and hybridisation probe-based real-time PCR method for susceptibility testing. DNA sequencing was used in nine representative isolates to validate the efficiency of real-time PCR method to detect emb306 mutation of MTB.

Results

A total of 52 clinical sputum samples and corresponding culture isolates (from category II pulmonary TB cases) were included in this study. Out of 52 MTB isolates, 32 and 20 were resistant and susceptible to EMB, respectively, as determined by L-J proportion method. Real-time PCR showed 95% specificity, 75% sensitivity and 82.69% accuracy when compared with L-J proportion method. A 100% of concordance was observed by validating the real-time PCR results with DNA sequencing.

Conclusions

Our real-time PCR hybridisation probe method promises for rapid detection of EMB-resistant MTB directly from clinical specimens. However, future studies and modifications of method by incorporating other potential loci along with targeted mutation (emb306) are still required to increase the sensitivity of method.

Expression profile of CXCL12 chemokine during M. tuberculosis infection with different therapeutic interventions in guinea pig

Mycobacterium indicus pranii (MIP) already established as an immune-modulator in mycobacterial infections generates immune response by acting on CXC chemokines. In the present study, the immunomodulatory effect of MIP in conjunction with chemotherapy against M.tb infection was evaluated by colony forming units (CFUs) following aerosol infection to guinea pig and by measuring CXCL12 chemokine expression using q-PCR and in situ RT-PCR. Different experimental groups included, infection (Rv), immunoprophylaxis (RvMw), chemotherapy (RvCh) and combination of immunoprophylaxis+chemotherapy (RvChMw) group and normal healthy (NH) group. In the combination of immunoprophylaxis+chemotherapy (RvChMw) group, the CFU counts reduced significantly (p<0.001) at 4th week of infection as compared to other treated groups (RvMw and RvCh group). The expression of CXCL12 was recorded in all the treated groups of animals. The study demonstrated suppressed expression of CXCL 12 in both immunoprophylaxis as well as chemotherapy groups (6th and 8th week) that become elevated in immunoprophylaxis plus chemotherapy group (10th week), at which time point no CFUs were detected in RvCh and RvChMw group. The findings indicate that the expression of CXCL12 is associated with good response to anti - tubercular treatment. Thus, prior immunization with MIP appears to show good immunomodulatory effect to release CXCL12 chemokine during infection and also correlates with enhanced effect to chemotherapy.

Effect of Cholesterol-loaded Cyclodextrin on Membrane and Acrosome Status of Hariana Bull Sperm during Cryopreservation

BACKGROUND

The membrane and acrosomal integrity of sperm play a vital role in fertilization process; however they are compromised upon cryopreservation.

OBJECTIVE

To study the effect of cholesterol-loaded cyclodextrin (CLC) on membrane and acrosome status of Hariana bull sperm during cryopreservation.

MATERIALS AND METHODS

Semen samples collected from Hariana bulls with mass motility ≥ 3+ and individual progressive motility ≥ 70% were utilized in the study. Each ejaculate was split into two parts, one part being evaluated freshly for various seminal attributes and the other part being diluted in Tris diluent (without egg yolk and glycerol) to obtain a final concentration of 120×10⁶ sperm/mL. The diluted semen was divided into four treatments: Group I, without CLC (control); Group II, with CLC at 0.5 mg per 120 million sperm; Group III, at 1.0 mg per 120 million sperm; Group IV, at 2.0 mg per 120 million sperm. All aliquots were incubated for 15 min at 37°C and each sample was diluted with Egg yolk-Tris-Glycerol (EYTG) extender up to 80×10⁶ sperm/mL. The diluted semen samples were packed in French mini straws (0.25 mL), sealed and equilibrated at 4°C for 4 h followed by cryopreservation. The samples at pre-freeze and post-thaw stage were evaluated for membrane and acrosomal integrity, as well as primary, secondary and tertiary acrosomal damages.

RESULTS

The membrane and acrosomal integrity was significantly higher in group II as compared to groups I, III, and IV, at pre-freeze and post-thaw stage (P<0.05). The primary and secondary acrosomal damage were significantly reduced in group II compared to other groups (P<0.05). No significant difference in tertiary acrosomal damage was found among different groups.

CONCLUSION

CLC improves the membrane and acrosomal integrity, and reduces primary and secondary acrosomal damages during cryopreservation of Hariana bull sperm.

Efficacy and Safety of Mycobacterium indicus pranii as an adjunct therapy in Category II pulmonary tuberculosis in a randomized trial

Prolonged treatment of tuberculosis (TB) often leads to poor compliance, default and relapse, converting primary TB patients into category II TB (Cat IITB) cases, many of whom may convert to multi-drug resistant TB (MDR-TB). We have evaluated the immunotherapeutic potential of Mycobacterium indicus pranii (MIP) as an adjunct to Anti-Tubercular Treatment (ATT) in Cat II pulmonary TB (PTB) patients in a prospective, randomized, double blind, placebo controlled, multicentric clinical trial. 890 sputum smear positive Cat II PTB patients were randomized to receive either six intra-dermal injections (2 + 4) of heat-killed MIP at a dose of 5 × 10⁸ bacilli or placebo once in 2 weeks for 2 months. Sputum smear and culture examinations were performed at different time points. MIP was safe with no adverse effects. While sputum smear conversion did not show any statistically significant difference, significantly higher number of patients (67.1%) in the MIP group achieved sputum culture conversion at fourth week compared to the placebo (57%) group (p = 0.0002), suggesting a role of MIP in clearance of the bacilli. Since live bacteria are the major contributors for sustained incidence of TB, the potential of MIP in clearance of the bacilli has far reaching implications in controlling the spread of the disease.

Genetic diversity & drug sensitivity profiles of Mycobacterium tuberculosis isolates from two slums of Jaipur city, Rajasthan, India

Background & objectives:

Slums are considered as hotspots of tuberculosis (TB). The study of genetic diversity and drug susceptibility profile of Mycobacterium tuberculosis (MTB) will help understand the transmission dynamics and can be used for better prevention and control of the disease. The aim of this study was to determine the drug susceptibility profiles and genetic diversity using the random amplified polymorphic DNA (RAPD) and mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU VNTR) of MTB isolates from sputum samples of pulmonary TB patients residing in the two slums of Jaipur city in Rajasthan, India.

Methods:

Sputum samples collected from pulmonary TB patients, their contacts and suspects during 2010-2012 were processed for microscopy and mycobacterial culture. Drug susceptibility testing was done by one per cent indirect proportion method on Lowenstein–Jensen medium for first-line anti-TB drugs rifampicin, isoniazid, ethambutol and streptomycin. MTB DNA was extracted by physicochemical method, and DNA fingerprinting was done by RAPD and MIRU VNTR analysis.

Results:

Among 175 sputum samples collected, 75 were positive (43.8%) for acid-fast bacilli, 83 for MTB culture and four were contaminated. Fifty two isolates (62.7%) were fully sensitive to four drugs, and five (6%) were multidrug resistant (MDR). RAPD analysis of 81 isolates revealed six clusters containing 23 (28.4%) isolates, and 58 (71.6%) were unique. MIRU VNTR analysis clustered 20 (24.7%) isolates, and 61 (75.3%) were unique.

Interpretation & conclusions:

About 62.7 per cent isolates from the sputum samples from slum areas were sensitive to four drugs; six per cent of isolates were MDR. Poly-resistance other than MDR was high (16%). About one-fourth isolates were clustered by either method. RAPD was rapid, less expensive but had low reproducibility. MIRU VNTR analysis could identify to greater extent the epidemiological link in the population studied.

Genetic diversity of Mycobacterium tuberculosis isolates from central India

Background & objectives:

There is a paucity of data available on genetic biodiversity of Mycobacterium tuberculosis isolates from central India. The present study was carried out on isolates of M. tuberculosis cultured from diagnostic clinical samples of patients from Bhopal, central India, using spoligotyping as a method of molecular typing.

Methods:

DNA was extracted from 340 isolates of M. tuberculosis from culture, confirmed as M. tuberculosis by molecular and biochemical methods and subjected to spoligotyping. The results were compared with the international SITVIT2 database.

Results:

Sixty five different spoligo international type (SIT) patterns were observed. A total of 239 (70.3%) isolates could be clustered into 25 SITs. The Central Asian (CAS) and East African Indian (EAI) families were found to be the two major circulating families in this region. SIT26/CAS1_DEL was identified as the most predominant type, followed by SIT11/EAI3_IND and SIT288/CAS2. Forty (11.8%) unique (non-clustered) and 61 (17.9%) orphan isolates were identified in the study. There was no significant association of clustering with clinical and demographic characteristics of patients.

Interpretation & conclusions:

Well established SITs were found to be predominant in our study. SIT26/CAS1_DEL was the most predominant type. However, the occurrence of a substantial number of orphan isolates may indicate the presence of active spatial and temporal evolutionary dynamics within the isolates of M. tuberculosis.

Clonal diversity and drug resistance in Mycobacterium tuberculosis isolated from extra-pulmonary samples in central India--a pilot study

In India, extrapulmonary tuberculosis (EPTB) accounts for 10 - 15% of all types of tuberculosis. To identify and compare predominant spoligotypes and drug-resistance patterns in strains of Mycobacterium tuberculosis isolated from extrapulmonary and pulmonary specimens in central India, drug susceptibility testing and spoligotyping were carried out. Spoligotyping data was analyzed using SITVIT2 database. ST11/EAI3_Ind with 33% isolates among extrapulmonary specimens and ST26/CAS1_DEL with 28% isolates among pulmonary specimens were the most predominant lineages. Multidrug resistance was found in 5.5% of the strains isolated from extrapulmonary specimens in contrast to 17% isolated from pulmonary specimens.

A pilot study to determine genetic polymorphism in Mycobacterium tuberculosis isolates in Central India

This study was carried out to identify predominant spoligotypes responsible for transmission and prevalence of tuberculosis in central India since there is no data available about the genetic biodiversity of Mycobacterium tuberculosis isolates from patients with tuberculosis in this region. 35 strains of Mycobacterium tuberculosis were subjected to spoligotyping according to the standard protocol. A total of 25 strains out of the 35 (71.42%) could be grouped in to 6 clusters. The largest cluster comprised 8 isolates. Unique (Non-clustered) spoligotypes were seen in 10 isolates, Nine strains did not match the data base (Spol DB-4 data base). The results indicate that there may be a number of orphan strains unique to this geographical area. Further studies on a larger sample size derived from this area would help us delineate the epidemiology of Mycobacterium tuberculosis infection in this area.

Diagnostic value of interferon- gamma release assays (QuantiFERON-TB Gold® In Tube) in childhood tuberculosis

OBJECTIVE

To evaluate the efficacy and diagnostic potential of interferon- gamma release assays QuantiFERON-TB Gold® In Tube (QFT-TB-IT) for the detection of gamma interferon against the antigen ESAT-6, CFP-10, TB 7.7(p4) of Mycobacterium tuberculosis and compare the reactivity with other methods (smear, culture and IS6110 targeting PCR).

METHODS

The study was carried out on children with pulmonary and extra pulmonary tuberculosis along with matching and PPD+ controls (82 cases, 48 matching controls and 20 PPD+ controls).

RESULTS

QFT-TB-IT showed a significantly higher sensitivity (51.2%) as compared with LJ medium culture method (11.0%; p < 0.001), BacT/Alert 3D system (12.1%; p < 0.001), ZN staining (19.5%; p < 0.001) and PCR (45.1%; p < 0.05). Specificity of QFT-TB-IT was 48.0%.

CONCLUSIONS

Less specificity of this assay may be due to high endemicity of tuberculosis. However, further studies are recommended.

Potential of Mycobacterium vanbaalenii as a model organism to study drug transporters of Mycobacterium tuberculosis, Mycobacterium marinum and Mycobacterium ulcerans: homology analysis of M. tuberculosis drug transporters among mycobacterial species

Drug efflux pumps have been one of the important mechanisms of drug resistance in Mycobacterium tuberculosis. There is a prerequisite to study the behavior and mechanisms of these drug efflux pumps in detail for being considered in future anti-TB drug designing. The need of a rapid grower non-pathogenic mycobacterium with significant genomic homology for such type of studies is often being felt. During microarray and Real-Time PCR analysis of drug efflux pump genes of M. tuberculosis, we found 10 genes to be over-expressed during stress induced by common anti-TB drugs. In the present study homology analysis of these genes was done in order to know its phylogenetic relationship among other bacteria/mycobacteria. It was found that amino acid sequences of 7 out of 10 genes were significantly (>40%) identical to a non-pathogenic rapid grower environmental mycobacterium, Mycobacterium vanbaalenii. The protein sequences of M. vanbaalenii share important sequence motifs with M. tuberculosis useful for drug efflux mechanism based study across species. Like Mycobacterium smegmatis, it can be used as a model organism to study drug efflux pumps of M. tuberculosis and also other pathogenic mycobacteria such as Mycobacterium ulcerans and Mycobacterium marinum.

jefA (Rv2459), a drug efflux gene in Mycobacterium tuberculosis confers resistance to isoniazid & ethambutol

BACKGROUND & OBJECTIVES

Drug efflux pumps have been contributing factor(s) in the development of multidrug resistance in various clinically relevant bacteria. During efflux pump gene expression studies on mycobacteria, we have found a previously uncharacterized open reading frame (ORF) Rv2459 to be overexpressed in drug stressed conditions. The objective of the present study was to investigate the role of this ORF as a drug efflux pump, which might add new information in our understanding about the alternative mechanisms of drug resistance in mycobacteria.

METHODS

The open reading frame Rv2459 of Mycobacterium tuberculosis encoding a probable drug efflux protein has been cloned using pSD5 E.coli-Mycobacterium shuttle vector and overexpressed in M. tuberculosis H(37)Rv. This ORF was named as jefA. Overexpression of this gene in clones has been verified by real-time reverse transcription PCR. Minimum inhibitory concentrations (MICs) of recombinant as well as non-recombinant clones were determined by resazurin microtitre assay plate method (REMA) with and without efflux pump inhibitors carbonyl cyanide m-chlorophenylhydrazone (CCCP) and verapamil.

RESULTS

In recombinant strains of M. tuberculosis, the overexpression of this gene led to an increase in MIC of anti-tubercular drugs isoniazid and ethambutol when tested by REMA. In the presence of CCCP and verapamil, the recombinant strains showed decrease in MIC for these drugs. Bioinformatic analysis has shown a close relation of JefA protein with drug efflux pumps of other clinically relevant bacteria. In homology derived structure prepared from nearest available model, it was observed that amino acids forming TMH 1, 8 and 11 participated in ethambutol specificity and those forming TMH 2, 7 and 10 participated in isoniazid specificity in JefA.

INTERPRETATION & CONCLUSION

The increased transcription of jefA leads to increased resistance to ethambutol and isoniazid in M. tuberculosis via efflux pump like mechanism and contributes in the development of resistance to these drugs. JefA amino acid sequence is well conserved among clinically important bacterial genera, which further provides evidence of being a potent drug efflux pump. The involvement in drug resistance and very little homology with any of the human proteins makes JefA important to be included in the list of potential drug targets.

Potential of a metabolic gene (accA3) of M. leprae as a marker for leprosy reactions

Understanding the mechanism(s) of reactions in leprosy remains a challenging task for both clinicians and basic scientists. While there is some understanding of host processes associated with different type of lepra reactions, there is very little information about bacterial factors triggering these inflammatory processes. This study is continuation of our earlier research programme on leprosy genomics in which significant transcription of 11 genes was observed during active disease and these included accA3 gene. In present study, we have investigated the potential of this gene or its gene product as molecular and or immunological marker for studying the reactions. Using quantitative Real-Time RT-PCR significant higher expression (mean log2 ratio=3.39) of accA3 was observed in specimens from leprosy reaction cases compared with cases without reactions. in silico homology model of this protein was analyzed for hydrophilic and B-cell epitope regions. Peptides with maximum antigenecity were selected, cloned, expressed and used to study sero-reactivity across the disease spectrum by indirect ELISA. While sero-reactivity was observed in leprosy cases the antibody levels did not vary significantly between the patient/s of same clinical type with and without reaction thereby indicating the limitation of this approach for this purpose. Measurement of transcription of this gene has, thus, potential as a molecular marker for monitoring the reactions.

Comparative growth pattern of multi drug resistance versus susceptible isolates of Mycobacterium tuberculosis in mice lungs

BACKGROUND & OBJECTIVE

Rise in prevalence of multi-drug resistance (MDR) in tubercle bacilli is a serious cause of concern. As mutations with two house keeping genes rpoB and katG are associated with resistance to two important anti-tubercular drugs rifampicin and isoniazid respectively, there is a need to understand the growth kinetics of organisms with such mutated genes in experimental animals. This study was undertaken to study the growth kinetics of susceptible as well multi-drug resistance Mycobacterium tuberculosis isolates in mice.

METHODS

Two MDR (having mutations in rpoB and catG) and two drug susceptible isolates of M. tuberculosis along with H37Rv were grown in mice after aerogenic infection.

RESULTS

The MDR isolates grew slowly up to 3 wk though the growth was significantly different from sensitive strains. However, after 3 wk, the growth in sensitive as well MDR strains was similar, suggesting that even the mutations in the MDR strains did not have any impact on the growth kinetics.

INTERPRETATION & CONCLUSION

The effect of mutations in other parts of these genes need to be studied. Retention of property of MDR strains to establish infection after aerogenic infection has epidemiological significance in terms of the transmission of MDR tuberculosis.

In vitro effect of fluoroquinolones against Mycobacterium tuberculosis isolates from Agra & Kanpur region of north India

BACKGROUND & OBJECTIVE

Fluoroquinolones (FQs) are important drugs used for treatment of drug resistant tuberculosis and are also now being considered as first line drugs to shorten the duration of treatment of tuberculosis (TB). In order to find out useful FQs for treatment of tuberculosis, the comparative efficacy of five FQs, namely, ofloxacin (OFL), ciprofloxacin (CIP), sparfloxacin (SPX), gatifloxacin (GAT) and levofloxacin (LEVX) was studied against Mycobacterium tuberculosis (MTB) isolates obtained from both treated and untreated patients from Agra and Kanpur regions of north India.

METHODS

A total of 162 MTB isolates [including 110 MTB isolates obtained from untreated patients (Cat-I) and 52 isolates from treated patients (Cat-II)] were tested for their susceptibilities to FQs using standard minimum inhibitory concentration (MIC) method on Löwenstein-Jensen medium.

RESULTS

Keeping in view the therapeutically achievable drug levels, it was found that in Cat-I 97.2 per cent (107/110) isolates were sensitive to GAT, 89 per cent (98/110) to LEVX at 1 microg/ml whereas 92.7 per cent (102/110) isolates were inhibited by OFL at 2 microg/ml and 73.6 per cent (81/110) to SPX at 0.5 microg/ml. Only 63.6 per cent (70/110) isolates were found to be sensitive to CIP at 2 microg/ml which increased to 89 per cent (98/110) at 4 microg/ml (higher than achievable peak serum level). On the other hand, among 52 isolates for Cat-II, 37 (71.2%) were found to be sensitive to GAT and 33 (63.5%) to LEVX at 1 microg/ml concentration, 28 (53.8%) to SPX at 0.5 microg/ml whereas 33 (63.5%) and 24 (46.2%) isolates were found to be sensitive to OFL and CIP at 2 microg/ml, respectively.

INTERPRETATION & CONCLUSION

It appears that GAT has higher activity against MTB isolates followed by OFL, LEVX and SPX whereas CIP showed the lowest activity. GAT was also found to be the most effective FQ against multi-drug resistant (MDR) isolates both from Cat-I and Cat-II patients. Thus, except CIP, other FQs showed potential to be included in the treatment regimens of tuberculosis including MDR-TB.

Identification of environmental mycobacteria isolated from Agra, north India by conventional & molecular approaches

BACKGROUND & OBJECTIVE

Several environmental mycobacteria have been shown to be important human pathogens linked to immunomodulation especially in relation to effect on vaccination. Hence identification of mycobacteria to the species level is not only relevant to patient management but also to understand epidemiology of mycobacterial diseases and effect on vaccination. We undertook this study to assess the usefulness of various conventional and molecular methods in identification of environmental mycobacterial species from Agra, north India.

METHODS

One hundred nineteen isolates of environmental mycobacteria were grown from 291 (116 soil and 175 water) samples. These isolates were identified by standard biochemical tests, and a simple, rapid and cost-effective in-house developed gene amplification restriction analysis targeting 16S-23S rRNA spacer and flanking region and 16S rRNA sequencing.

RESULTS

Biochemical tests could clearly identify only 68.1 per cent (81/119) of isolates to species level. An in-house developed gene amplification--restriction analysis method could confirm the identity of 102 of 119 (85.7%) isolates and the remaining 17 isolates (14.3%) were confirmed by 16S rRNA sequencing also. These 119 environmental mycobacterial isolates, included several potentially pathogenic species such as M. fortuitum, M. chelonae, M. avium, M. marinum, M. manitobense, M. kansasii and others belonged to nonpathogenic species, M. terrae, M. smegmatis and M. flavescens. M. chelonae was isolated from water samples only whereas M. fortuitum was isolated from both water as well as soil samples.

INTERPRETATION & CONCLUSION

The in-house developed gene amplification restriction analysis method though failed to accurately identify 14.3 per cent of isolates, facilitated rapid differentiation of most of environmental mycobacteria including potential pathogens from this area and thus would have diagnostic potential in cases with NTM infections. This combination strategy using PCR-RFLP and 16S rRNA sequencing may be useful for characterization of mycobacteria from similar environmental settings from other parts of world.

Serological diagnosis of tuberculosis

OBJECTIVE

To evaluate the efficacy of ELISA for the detection of IgG antibodies against antigen 85 complex (Ag 85 complex) of Mycobacterium tuberculosis.

METHODS

Children of either sex, 0-18 years of age, attending the outpatient department and admitted in the casualty and wards of the Department of Pediatrics, S.N. Medical College, Agra, were included in present study. The study was carried out on children with pulmonary and CNS tuberculosis along with matching controls (83 cases and 32 controls). Informed consents of their parents or guardians were taken. They were subjected to clinical examination, relevant laboratory investigations, tuberculin test and chest radiograph. Relevant body fluids were subjected to bacteriological tests; ELISA was applied to serum samples for detection of IgG antibodies against antigen 85 complex (Ag85). The result of ELISA was compared with bacteriological tests [Ziehl Neelson (ZN) staining for acid-fast bacilli, culture on Lowenstein Jensen (LJ) medium and culture on BacT/Alert 3D system].

RESULTS

ELISA tests showed a significantly higher sensitivity (59.1%) as compared with LJ medium culture method (19.3%), BacT/Alert 3D system (24.1%) and ZN staining (16.9%) in all patients (p<0.001). Specificity of ELISA test was 71.9%.

CONCLUSION

In view of the convenience, low cost and good sensitivity, ELISA tests have a promising future in the diagnosis of childhood tuberculosis.

Development and evaluation of real-time RT-PCR assay for quantitative estimation of viable Mycobacterium leprae in clinical samples

Detection of live organisms by molecular methods has special significance in leprosy where causative organism can not be cultivated in vitro. Such techniques would be especially important for monitoring the progress of the disease. While real-time RT- PCR technology will be appropriate for this purpose, there is very little experience of use of such tools in leprosy. This study describes the development of a quantitative RT-PCR targeting 16S rRNA based on primers used in a semi quantitative RT-PCR and its application on clinical samples including slit scraping and biopsies. RNA was extracted from biopsies from 3 lepromatous leprosy (LL) cases and standard curve was generated by plotting crossing over point against the dilutions of input RNA quantity (number of bacilli used for RNA extraction). Real-time RT-PCR was performed for quantitative detection of live M. leprae in 28 slit (13/28 smear positive) scrappings and 32 biopsies (22/32 smear positive). Number of viable bacteria as estimated by solid stained bacilli and real-time PCR correlated (no difference p>0.05). The test achieved a theoretical analytical sensitivity limit of up to single live bacillus even considering 11.3% efficiency of RNA preparation which was calculated by spiking of known number of leprosy bacilli in non leprosy skin biopsies (PCR negative). All smear positive cases were positive by this assay. This assay appears to be a promising tool for detection and quantification of viable bacilli in selected clinical situations and should be of use even in smear negative cases also.

Predominance of Mycobacterium fortuitum-chelonae complex in Ghatampur field area, endemic for leprosy

Non-tuberculous mycobacteria (NTM) are commonly found in the environment. As exposure to environmental mycobacteria has been reported to immunomodulatory in this study, the presence of environmental mycobacteria was investigated in soil, drinking water and drainage sample in Ghatampur, India, which is known for high endemicity for leprosy. Soil, drinking water from the hand pumps/wells and also drainage water collected in pools was collected in clean containers and cultured for environmental mycobacteria. Samples were processed according to the protocol established earlier. 69 soil, 62 drinking water and 31 drainage water samples were analysed from soil and water collected from 48 villages of this field area. After decontamination, cultures were set upon Lowenstein Jensen (LJ) medium. Mycobacteria were identified using biochemical tests and molecular techniques such as PCR-RFLP targeting hsp65 kD and rpoB region as well as 16S ribosomal sequencing in case of isolates showing variable biochemical features. NTM (non-tubercular mycobacteria) were isolated from 47.82% of soil samples, 20.69% of drinking water samples and 19.35% of the drainage water samples, overall mycobacteria could be isolated 52/162 of samples (32.09%). Among these mycobacteria, M. fortuitum-chelonae complex was predominant in this area; other species isolated were M. phlei, M. vaccae, M. terrae and M. flavescens. Relevance of exposure to these mycobacteria on endemicity needs to be studied by immunological and epidemiological parameters.

Isolation of Mycobacterium bovis & M. tuberculosis from cattle of some farms in north India--possible relevance in human health

BACKGROUND & OBJECTIVE

Infection due to Mycobacterium bovis typically occurs in cattle and animals transmit infection to each other. The choice of appropriate clinical specimen is very important for isolation of M. bovis and M. tuberculosis from cattle. The present study reports the isolation of M. tuberculosis and M. bovis from different types of specimens from cattle suspected to be suffering from tuberculosis in certain organized cattle farms in north India.

METHODS

A total of 768 specimens (heparinized or EDTA containing blood (162), fine needle aspirates from prescapular lymph gland (PSLG,160), milk (154), pharyngeal swab (PhS, 98), rectal pinch (RP, 97) and faecal sample (97) from 161 cattle of organized cattle farms in north India suspected to be suffering from tuberculosis were analyzed. After decontamination by modified Petroff's method isolation of M.tuberculosis complex was done on Lowenstein-Jensen medium (with and without pyruvate). The culture isolates were identified as M. tuberculosis and M. bovis on the basis of biochemical tests.

RESULTS

A total of 54 M. tuberculosis complex isolates were obtained, of them 40 were identified as M.bovis and 14 as M. tuberculosis. M.bovis were isolated from 12 of 38 animals in group A (Tuberculin +ve with signs of tuberculosis), 7 of 37 animals in group B (Tuberculin +ve and apparently healthy), 9 of 21 group C animals in (Tuberculin -ve with clinical signs of tuberculosis), 4 of 26 animals in group D (Tuberculin -ve and apparently healthy), 4 of 27 group E animals (having non-mycobacterial infection) and 4 of 12 animals in group F (having clinical signs such as debilitated condition, cough, decreasing milk production, etc). Maximum number of M. bovis (19/40, 47.5%) and M. tuberculosis (5/14, 35.7%) isolates were grown from prescapular lymph gland biopsy (PSLG) followed by blood from which 9/40 (22.5%) M. bovis and 4/14 (28.5%) M. tuberculosis were isolated. M. bovis [6/40(15%)] and M. tuberculosis [4/14(28.5%)] were also isolated from milk. Only 3/40 (7.5%) isolates of M.bovis could be isolated from 97 rectal pinch followed by 98 pharyngeal swab 2/40 (5%) and 97 fecal samples 1/40 (2.5%) while 1/14 (7.1%) M.tuberculosis isolates were obtained from pharyngeal swab.

INTERPRETATION & CONCLUSION

Among the samples analyzed, PSLG was found to be most suitable specimen for isolation of M. tuberculosis complex from cattle and is thus of diagnostic importance. M. bovis in milk indicates the need to investigate the transmission to human in such settings. Isolation of M. bovis and/or M. tuberculosis from apparently healthy cattle indicates sub-clinical infection in the herd. Further, isolation of a significant number of M. tuberculosis from cattle suggests possible human-to-cattle transmission which need to be confirmed by prospective studies including tools like DNA fingerprinting.

PCR and in-situ hybridization for diagnosis of leprosy

OBJECTIVE

To assess the diagnostic value of Polymerase Chain Reaction (PCR) and in situ hybridization.

METHODS

This prospective study was carried out in 22 patients

RESULTS

The histopathological examination confirmed the clinical diagnosis in 27.2% cases only. In situ hybridization showed a positivity of 42.8% in early (I/BT) and 46.7% in BB/BL group. In situ hybridization thus enhanced the diagnosis by 18.1%. PCR targeting 36 kDa gene of M. leprae was performed on 15 cases. In these 15 cases, histopathology confirmed the diagnosis in 4 cases (26.6%) and PCR confirmed the diagnosis in 10 cases (66.6%), thus enhancing the diagnosis by 40%.

CONCLUSION

36 kDa PCR and in situ hybridization enhance the diagnosis of leprosy when compared to routine histopathology. They are important diagnostic tools for definitive diagnosis in early and doubtful cases of leprosy.

Determination of ethambutol MICs for Mycobacterium tuberculosis and Mycobacterium avium isolates by resazurin microtitre assay

OBJECTIVES

To test susceptibilities of Mycobacterium tuberculosis (MTB) isolates to ethambutol by the Löwenstein-Jensen (LJ) proportion method and resazurin microtitre assay (REMA) and to evaluate REMA for the determination of ethambutol MICs for MTB and Mycobacterium avium isolates.

METHODS

A total of 50 MTB and 20 M. avium isolates were tested to determine the MICs of ethambutol by REMA and agar dilution method. MTB isolates were also tested by the LJ proportion method.

RESULTS

REMA provided ethambutol susceptibility results for all the isolates within 8-9 days. For MTB isolates, REMA showed 96.7% sensitivity, 100.0% specificity and 98.0% accuracy when LJ proportion results were taken as 'gold standard'. For both MTB and M. avium isolates, the MICs determined by REMA were lower than those determined in agar medium, indicating that MIC values determined by REMA are closer to the actual MICs for the isolates.

CONCLUSIONS

REMA can be used as a rapid and inexpensive method for mycobacterial drug susceptibility testing against ethambutol. In comparison with the agar method, the MICs determined by REMA can more accurately be correlated with achievable plasma concentrations of antimycobacterial agents.

Molecular typing of Mycobacterium tuberculosis isolates from different parts of India based on IS6110 element polymorphism using RFLP analysis

BACKGROUND & OBJECTIVE

IS 6110 based typing remains the internationally accepted standard and continues to provide new insights into the epidemiology of Mycobacterium tuberculosis. The aim of the study was to characterize M. tuberculosis isolates obtained from different parts of India based on IS6110 element polymorphism using restriction fragment length polymorphism (RFLP) analysis.

METHODS

RFLP was analyzed among 308 isolates of M. tuberculosis deposited in the Mycobacterial Repository Centre, Agra, from different parts of India. DNAs isolated from these strains were restricted with Pvu II, transferred on to nylon membrane and hybridized with a PCR amplified DIG-labeled 245 bp IS6110 probe.

RESULTS

Based on the copy number, M. tuberculosis isolates were classified into four groups, (i) lacking IS6110 element; (ii) low copy number (1-2); (iii) intermediate copy number (3-5); and (iv) high copy number (6-19). Copy number higher than 19 however was not observed in any of the isolates studied. At the national level, 56 per cent of the isolates showed high copy number of IS6110, 13 per cent showed intermediate copy number, 20 per cent showed low copy number, whereas 11 per cent isolates lacked IS6110 element. At the regional level, there was not much difference in the RFLP profiles of isolates (IS6110 copy numbers/patterns) from different parts of the country.

INTERPRETATION & CONCLUSION

IS6110 DNA based fingerprinting could be a potentially useful tool for investigating the epidemiology of tuberculosis in India.

Recent advances in molecular biology of leprosy

The last three decades have witnessed rapid progress in understanding the molecular biology of Mycobacterium leprae. Following the availability of complete genome sequence of leprosy bacillus in 2001, things have drastically changed. With the information about genetic structure, several techniques have been developed for diagnosis, molecular epidemiology and also detection of drug resistance. With the decline in the prevalence of leprosy globally, there has been some reduction in interest in the molecular methods for diagnosis, yet molecular techniques for studying the transmission dynamics and detection of drug resistance continue to be relevant. Knowledge about complete genome sequence has made it possible to undertake studies that can improve our understanding of the structure and function of this enigmatic organism. Newer information emerging about biology of M. leprae would provide insight into mechanisms of its survival and persistence in host and is likely to lead to better diagnostics and also therapeutics for mycobacterial infections in general.

Rapid identification of mycobacteria by gene amplification restriction analysis technique targeting 16S-23S ribosomal RNA internal transcribed spacer & flanking region

BACKGROUND & OBJECTIVE

Conventional identification of a clinical isolate of mycobacteria primarily based on culture characteristics and biochemical tests needs several weeks and may remain inconclusive. This study was undertaken to develop a new rapid method to identify the mycobacterial isolates at species level by gene amplification restriction analysis using primers encoding 16S-23S rRNA internal transcribed spacer (ITS) region and flanking parts of the 16S as well as 23S rRNA gene.

METHODS

This system is based on the amplification of approximately 1.8 kb fragment encoding 16S-23S rRNA spacer region and flanking parts of the 16S as well as 23S rRNA gene. This assay was applied on 13 reference strains and 480 clinical isolates of mycobacteria to validate the technique. Restriction was carried out with three restriction endonucleases Hha I, Hinf I and Rsa I.

RESULTS

Distinct gene amplification restriction analysis patterns were obtained by restriction of amplicons with three distinct restriction endonucleases (Hha I, Hinf I and Rsa I) which could differentiate various mycobacterial species.

INTERPRETATION & CONCLUSION

Restriction patterns with the enzymes used in this study could clearly distinguish Mycobacterium tuberculosis complex from other non chromogenic clinically important species M. avium and M. intracellulare. Results indicated this assay to be a simple, rapid and reproducible method to identify clinically relevant mycobacteria.

Comparative evaluation of Löwenstein-Jensen proportion method, BacT/ALERT 3D system, and enzymatic pyrazinamidase assay for pyrazinamide susceptibility testing of Mycobacterium tuberculosis

Pyrazinamide (PZA) is an important first-line antituberculosis drug because of its sterilizing activity against semidormant tubercle bacilli. In spite of its very high in vivo activity, its in vitro activity is not apparent unless an acidic environment is available, which makes PZA susceptibility testing difficult by conventional methods. The present study was, therefore, planned to assess the performance of the colorimetric BacT/ALERT 3D system and compare the results with those from conventional tests, i.e., the Löwenstein-Jensen (LJ) proportion method (pH 4.85) and Wayne's pyrazinamidase (PZase) assay, using 107 clinical isolates. The concordance among all of these tests was 89.71% after the first round of testing and reached 92.52% after resolution of the discordant results by retesting. Prolonged incubation of the PZase tube for up to 10 days was found to increase the specificity of the PZase test. The concordances between LJ proportion and BacT/ALERT 3D, LJ proportion and the PZase assay, and BacT/ALERT 3D and the PZase assay were found to be 99.06%, 93.46%, and 92.52%, respectively. Using the LJ results as the gold standard, the sensitivities of BacT/ALERT 3D and the PZase assay were 100 and 82.85%, respectively, while the specificity was 98.61% for both of the tests. The difference between the sensitivities of BacT/ALERT 3D and the PZase assay was significant (P = 0.025). The mean turnaround times for the detection of resistant and susceptible results by BacT/ALERT 3D were 8.04 and 11.32 days, respectively. While the major limitations associated with the PZase assay and the LJ proportion method are lower sensitivity in previously treated patients and a longer time requirement, respectively, the BacT/ALERT 3D system was found to be rapid, highly sensitive, and specific.

Applications of real-time PCR technology to mycobacterial research

Real-time polymerase chain reaction (PCR) is being used worldwide for various research purposes. In this review we discuss the principles of real-time PCR, different methodologies and chemistries available and their applications in mycobacterial research. This technology allows for the direct detection of PCR product during the exponential phase of the reaction. Being a very powerful, accurate, rapid and sensitive method, this technique holds immense promise for detection of mycobacteria, differentiation of mycobacterial species, quantification of mycobacterial load and detection of drug resistance in mycobacterial infection.

Cytomorphological features of nodular hidradenoma highlighting eccrine differentiation: a case report

We report a case of nodular hidradenoma in a 90 year old male, presenting with an eyelid swelling. The cytomorphological features are described with special emphasis on cytoplasmic granularity and tubule formation as an important feature in diagnosing and differentiating eccrine tumors from other adnexal neoplasms on FNAC.

Characterization of mycobacteria isolated from bovines by PRA-targetting hsp 65 gene region

Bovine tuberculosis caused by the bacterium Mycobacterium bovis is a major infectious disease of animals and has zoonotic importance for humans. Even though the incidence is believed to be very low in India, human tuberculosis caused by M. bovis has been increasingly recognized in many other countries of the world. As differentiation of mycobacterial species take long time, a method for the rapid identification of mycobacteria isolated from bovine samples to the species level was used, which is based on polymerase chain reaction (PCR) of the gene encoding for the 65-kD protein followed by restriction analysis. The method involves restriction enzyme analysis of PCR products obtained with primers common to all mycobacteria and generate M. tuberculosis complex specific pattern. PRA was performed on 33 bovine isolates of which 90.9% (30/33) isolates were identified clearly as M. tuberculosis complex, M. fortuitum, M. phlei and M. smegmatis using restriction enzyme Hae III.

The paradox of pyrazinamide: an update on the molecular mechanisms of pyrazinamide resistance in Mycobacteria

Pyrazinamide (PZA) is an important front line anti-tuberculosis drug because of its sterilizing activity against semi-dormant tubercle bacilli. In spite of its remarkable role in shortening the treatment duration from 9 months to 6 months when used in combination with Rifampicin and Isoniazid, PZA remains a difficult paradox because of its incompletely understood mode of action and mechanism of resistance. PZA is a nicotinamide analog prodrug which is converted into the active bactericidal form pyrazinoic acid by the bacterial enzyme pyrazinamidase (PZase). PZA does not appear to have a specific cellular target and instead, exerts its bactericidal effect by disrupting the membrane energetics and acidification of cytoplasm. Majority (72-97%) of PZA-resistant isolates of M. tuberculosis exhibit mutations in their pncA gene or upstream area leading to loss of PZase activity. A wide diversity of pncA mutations scattered along the entire length of pncA gene is unique to PZA resistance. However, PZA resistant isolates with normal PZase activity and wild type pncA sequences have also been reported in several studies which indicate that alternate mechanisms of PZA resistance exist. Investigations into these mechanisms would be useful in developing alternative diagnostic/therapeutic measures. This review presents the update of various mechanisms of PZA resistance in different mycobacteria with special emphasis on mode of action of PZA and mechanisms of resistance in Mycobacterium tuberculosis.