Mycobacterium tuberculosis polyclonal infections through treatment and recurrence.

BACKGROUND: Mixed/polyclonal infections due to different genotypes are reported in Tuberculosis. The current study was designed to understand the fate of mixed infections during the course of treatment and follow-up and its role in disease pathogenesis. METHODS: Sputum samples were collected on 0,1,2,3,6,12 and 24 months from 157 treatment-naïve patients, cultures subjected to Drug-Susceptibility-testing (MGIT 960), spoligotyping, MIRU-VNTR and SNP genotyping. All isolated colonies on thin layer agar (7H11) were subjected to spoligotyping. FINDINGS: One thirty three baseline cultures were positive (133/157, 84.7%), 43(32.3%) had mixture of genotypes. Twenty-four of these patients (55.8%) showed change in genotype while six showed different drug-susceptibility patterns while on treatment. Twenty-three (53.5%) patients with polyclonal infections showed resistance to at least one drug compared to 10/90 (11.1%) monoclonal infections (P<0.0001). Eight patients had recurrent TB, two with a new genotype and two with altered phenotypic DST. CONCLUSIONS: The coexistence of different genotypes and change of genotypes during the same disease episode, while on treatment, confirms constancy of polyclonal infections. The composition of the mixture of genotypes and the relative predominance may be missed by culture due to its limit of detection. Polyclonal infections in TB could be a rule rather than exception and challenges the age-old dogma of reactivation/reinfection.

Genome-Wide Association Study in Craniosynostosis Condition Using Innovative Systematic Bioinformatic Analysis Tools and Techniques: Future Prospective and Clinical Practice.

BACKGROUND: Craniosynostosis (CS) conditions are included with the premature fusion of one or more multiple cranial sutures. As the second leading and most common craniofacial anomaly and orofacial clefts globally. Syndromic and nonsyndromic CS (NSCS) occur as a part of a genetic syndrome unlike Apert, Crouzon, Pfeiffer, Muenke, and Saethre-Chotzen syndromes. Approximately, 90% of the cases of CS arises from NSCS group and it is now a great challenge for the researcher and neurosurgeon for Indian-origin children, a great burden worldwide. MATERIAL AND METHODS: Study design: Prospective study of analysis sequence pattern on CS and NSCS from January 2007 to 2018 was carried out.Inclusion criteria: Diagnosed cases in syndromic and NSCS patients between 3 months and 14 years of age either preoperative or postoperative were included in the study of both groups (syndromic and NSCS).Exclusion criteria: Patients with primary microcephaly (secondary CS), postural plagiocephaly, incomplete data, no visual perception, and who were lost to follow-up, and who had no interest to participate the study were excluded from the study.Bioinformatic analysis: We have performed systematic bioinformatic analysis for all responsible genes by combining with using through the GeneDecks, Gene Runner, DAVID, and STRING databases.Genes testing: FGF family genes, MSX genes, such as Irf6, TP63, Dlx2, Dlx5, Pax3, Pax9, Bmp4, Tgf-beta2, and Tgf-beta3 were found to be involved in Cleft lip and cleft palate (CL/P), and Fgfr2, Fgfr1, Fgfr3, and TWIST, MSX, MSX1, 2 were found to be involved in both the groups of CS (SCS + NSCS). RESULTS: FGFR, MSX, Irf6, TP63, Dlx2, Dlx5, Pax3, Pax9, Bmp4, Tgf-beta2, and Tgf-beta3 demonstrated and find out that in CL/P, and Fgfr2, Fgfr1, Fgfr3, and Twist1 had accurate sequence data with more than accuracy of 95% reported with proper order with additional anomalies CS through newly developed tools. CONCLUSION: Newly developed techniques of GeneDecks, Gene Runner, DAVID, and STRING databases gave better picture to analyze the larger population, patients (SCS + NSCS) with complex genetic, maternal, parental age, environmental, and stochastic factors contributing to NSCS networking, signaling, and pathways involvement. This bioinformatic tools analyzed better prediction of CS and NSCS sequences guiding us the newer invention modalities of pattern of screening and further development of recent future application.

A Comparative Study of Serum, Urine and Saliva Using rk39 Strip for the Diagnosis of Visceral Leishmaniasis.

BACKGROUND: Immunochromatographic based rk39 antibody detection test became popular for the diagnosis of visceral leishmaiasis (VL) because of high sensitivity, rapidity, easy to interpret, and cost effectiveness. However, false positive result after complete cure of the patients is the major limitation with this test. The aim of the study to access the usefulness of non-invasive samples i.e. urine and saliva by rk39 test for the diagnosis of visceral leishmaniasis in comparison to serum. METHODS: Seventy two clinically suspected VL patients were enrolled in the study among which 61 cases were confirmed as VL and 11 cases were included in the control group. Serum, urine, and saliva samples of all the cases were tested for rk39 dip stick test. RESULTS: Urine and saliva both were equally sensitive as serum for the diagnosis kala-azar. In the control group, rk39 antibody test was negative in 10 cases out 11 (91%) with saliva in comparison to 4 cases with serum (36%), thereby found to be more specific. CONCLUSION: Saliva sample found to be highly reliable for the diagnosis of VL cases by rk39 test. The test with saliva sample showed less false positive result in comparison to serum sample, thereby can be used an adjunct with serum sample for the diagnosis of kala-azar in endemic areas.

Genotypic, Phenotypic and Clinical Validation of GeneXpert in Extra-Pulmonary and Pulmonary Tuberculosis in India.

BACKGROUND: Newer molecular diagnostics have brought paradigm shift in early diagnosis of tuberculosis [TB]. WHO recommended use of GeneXpert MTB/RIF [Xpert] for Extra-pulmonary [EP] TB; critics have since questioned its efficiency. METHODS: The present study was designed to assess the performance of GeneXpert in 761 extra-pulmonary and 384 pulmonary specimens from patients clinically suspected of TB and compare with Phenotypic, Genotypic and Composite reference standards [CRS]. RESULTS: Comparison of GeneXpert results to CRS, demonstrated sensitivity of 100% and 90.68%, specificity of 100% and 99.62% for pulmonary and extra-pulmonary samples. On comparison with culture, sensitivity for Rifampicin [Rif] resistance detection was 87.5% and 81.82% respectively, while specificity was 100% for both pulmonary and extra-pulmonary TB. On comparison to sequencing of rpoB gene [Rif resistance determining region, RRDR], sensitivity was respectively 93.33% and 90% while specificity was 100% in both pulmonary and extra-pulmonary TB. GeneXpert assay missed 533CCG mutation in one sputum and dual mutation [517 & 519] in one pus sample, detected by sequencing. Sequencing picked dual mutation [529, 530] in a sputum sample sensitive to Rif, demonstrating, not all RRDR mutations lead to resistance. CONCLUSIONS: Current study reports observations in a patient care setting in a high burden region, from a large collection of pulmonary and extra-pulmonary samples and puts to rest questions regarding sensitivity, specificity, detection of infrequent mutations and mutations responsible for low-level Rif resistance by GeneXpert. Improvements in the assay could offer further improvement in sensitivity of detection in different patient samples; nevertheless it may be difficult to improve sensitivity of Rif resistance detection if only one gene is targeted. Assay specificity was high both for TB detection and Rif resistance detection. Despite a few misses, the assay offers major boost to early diagnosis of TB and MDR-TB, in difficult to diagnose pauci-bacillary TB.

MALDI-TOF mass spectrometry for rapid identification of clinical fungal isolates based on ribosomal protein biomarkers.

This study aimed to evaluate the identification of clinical fungal isolates (yeast and molds) by protein profiling using Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS). A total of 125 clinical fungal culture isolates (yeast and filamentous fungi) were collected. The test set included 88 yeast isolates (Candida albicans, Candida glabrata, Candida guilliermondii, Candida kefyr, Candida krusei, Candida parapsilosis, Candida rugosa, Candida tropicalis and Cryptococcus neoformans) and 37 isolates of molds (Alternaria spp., Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger, Cunninghamella spp., Histoplasma capsulatum, Microsporum gypseum, Microsporum nanum, Rhizomucor spp. and Trichophyton spp.). The correlation between MALDI TOF MS and conventional identification for all these 125 fungal isolates included in the study was 87.2% at the species level and 90.4% at the genus level. MALDI TOF MS results revealed that the correlation in yeast (n=88) identification was 100% both at the genus and species levels whereas, the correlation in mold (n=37) identification was more heterogeneous i.e. 10.81% isolates had correct identification up to the genus level, 56.7% isolates had correct identification both at the genus and species levels, whereas 32.42% isolates were deemed Not Reliable Identification (NRI). But, with the modification in sample preparation protocol for molds, there was a significant improvement in identification. 86.4% isolates had correct identification till the genus and species levels whereas, only 2.7% isolates had Not Reliable Identification. In conclusion, this study demonstrates that MALDI-TOF MS could be a possible alternative to conventional techniques both for the identification and differentiation of clinical fungal isolates. However, the main limitation of this technique is that MS identification could be more precise only if the reference spectrum of the fungal species is available in the database.

Coupling electrochemical response of a DNA biosensor with PCR for Neisseria gonorrhoeae detection.

Early diagnosis of gonococcal infections is important with regard to a patient's health and stage of infection. In this context, we report the development of an opa-gene-based electrochemical DNA biosensor for detection of Neisseria gonorrhoeae by monitoring redox peak of methylene blue indicator. The fabricated biosensor has been shown to be highly sensitive and specific when evaluated with complementary, non-complementary, and 1-base mismatch DNA sequences and polymerase chain reaction (PCR) amplified products (amplicons) of standard strain of N. gonorrhoeae (ATCC49226). The biosensor has been further evaluated using amplicons of known positive and negative clinical samples, and cut-off for positives has been determined using receiver operating characteristic curve. The sensitivity (SN), specificity (SP), positive predictive value, and negative predictive value of the biosensor have been found to be 96.2%, 88.2%, 92.6%, and 93.8%, respectively. We conclude that the combination of PCR amplification with electrochemical detection shows distinct advantage of high SN and increased SP for gonococcal detection.

MALDI-TOF mass spectrometry proteomic based identification of clinical bacterial isolates.

BACKGROUND & OBJECTIVES: Pathogenic bacteria often cause life threatening infections especially in immunocompromised individuals. Therefore, rapid and reliable species identification is essential for a successful treatment and disease management. We evaluated a rapid, proteomic based technique for identification of clinical bacterial isolates by protein profiling using matrix-assisted laser desorption-ionization time - of - flight mass spectrometry (MALDI-TOF MS). METHODS: Freshly grown bacterial isolates were selected from culture plates. Ethanol/formic acid extraction procedure was carried out, followed by charging of MALDI target plate with the extract and overlaying with α-cyano-4 hydroxy-cinnamic acid matrix solution. Identification was performed using the MALDI BioTyper 1.1, software for microbial identification (Bruker Daltonik GmbH, Bremen, Germany). RESULTS: A comparative analysis of 82 clinical bacterial isolates using MALDI -TOF MS and conventional techniques was carried out. Amongst the clinical isolates, the accuracy at the species level for clinical isolates was 98.78%. One out of 82 isolates was not in accordance with the conventional assays because MALDI-TOF MS established it as Streptococcus pneumoniae and conventional methods as Streptococcus viridans. INTERPRETATION & CONCLUSIONS: MALDI - TOF MS was found to be an accurate, rapid, cost-effective and robust system for identification of clinical bacterial isolates. This innovative approach holds promise for earlier therapeutic intervention leading to better patient care.

Disseminated intravascular coagulation following malaria due to Plasmodium vivax: a thromboelastography-based study.

BACKGROUND: Disseminated intravascular coagulation (DIC) due to Plasmodium vivax is scarcely reported in comparison to Plasmodium falciparum. In complicated malaria, thrombocytopaenia and haemostatic alterations lead to increased activation of coagulation cascade and fibrinolytic system. Thromboelastography (TEG) is a haemostasis system which measures the viscoelastic strength of blood clot in the coagulation pathway. It detects the initial derangement in clotting cascade involving in platelet interaction and fibrinolysis. Hence, it can document the early changes in coagulation in vitro, and thereby guide the management. The current study was aimed at detection of DIC in patients with P. vivax malaria based on TEG. METHODS: Ethylene diamine tetraacetic acid (EDTA) blood samples from acute febrile patients were tested by microscopy and immunochromatographic test for malaria. A total of 31 confirmed cases of vivax malaria were enrolled for this study. All the samples were tested by thromboelastography and conventional tests parameters for detection of any coagulation derangement. RESULTS: Of 31, 17 (55%) were classified as complicated and 14/31 (45%) were uncomplicated. Among 23 cases with thrombocytopaenia, non-overt (early stage) DIC was detected in 18 cases by TEG and 17 cases by the conventional methods. CONCLUSION: It seems that the burden of DIC in vivax malaria is much higher than the world literature reported. TEG can be utilized as an important tool for early detection of DIC and guiding the management in malaria patients.

Two-dimensional difference gel electrophoresis (DIGE) analysis of sera from visceral leishmaniasis patients.

INTRODUCTION: Visceral leishmaniasis is a parasitic infection caused by Lesihmania donovani complex and transmitted by the bite of the phlebotomine sand fly. It is an endemic disease in many developing countries with more than 90% of the cases occurring in Bangladesh, India, Nepal, Sudan, Ethiopia and Brazil. The disease is fatal if untreated. The disease is conventionally diagnosed by demonstrating the intracellular parasite in bone marrow or splenic aspirates. This study was carried out to discover differentially expressed proteins which could be potential biomarkers. METHODS: Sera from six visceral leishmaniasis patients and six healthy controls were depleted of high abundant proteins by immunodepletion. The depleted sera were compared by 2-D Difference in gel electrophoresis (DIGE). Differentially expressed proteins were identified the by tandem mass spectrometry. Three of the identified proteins were further validated by western blotting. RESULTS: This is the first report of serum proteomics study using quantitative Difference in gel electrophoresis (DIGE) in visceral leishmaniasis. We identified alpha-1-acidglycoprotein and C1 inhibitor as up regulated and transthyretin, retinol binding protein and apolipoprotein A-I as down regulated proteins in visceral leishmaniasis sera in comparison with healthy controls. Western blot validation of C1 inhibitor, transthyretin and apolipoprotein A-I in a larger cohort (n = 29) confirmed significant difference in the expression levels (p < 0.05). CONCLUSIONS: In conclusion, DIGE based proteomic analysis showed that several proteins are differentially expressed in the sera of visceral leishmaniasis. The five proteins identified here have potential, either independently or in combination, as prognostic biomarkers.

Automated detection of malaria with haematology analyzer Sysmex XE-2100.

BACKGROUND: Diagnosis of malaria is usually made by microscopy [Giemsa, Acridine Orange (AO), and Quantitative Buffy Coat (QBC) assay], which requires expertise. Currently, automated haematology analyzers are being used for complete blood count (CBC), in all acute febrile and non-febrile illnesses which simultaneously detects malaria. The normal scattergram by the analyzer (Sysmex 2100) comprises of five parameters i.e. lymphocytes (pink), monocytes (green), neutrophils (blue), eosinophils (red) with a space between the neutrophil and eosinophil populations. AIMS: We carried out a prospective study to compare the efficacy of Sysmex XE-2100 (Sysmex Corporation, Kobe) for detection of malaria in comparison to other conventional techniques. MATERIALS AND METHODS: 430 cases were analyzed for malaria by microscopy (QBC, AO, Giemsa), ICT (Immunochromatography) and flowcytometric analyzer (Sysmex XE-2100). The abnormal scattergrams were observed as double neutrophil, double eosinophil, grey zone, extended neutrophil zone with a decrease space between eosinophil and neutrophil, and a combination of above patterns. RESULTS: Out of 70 positive cases [49/70 (70%) P. vivax, 18/70 (25.7%) P. falciparum, and 3/70 (4.2%) both P. vivax and P. falciparum], 52 showed abnormal scattergrams by the analyzer. The sensitivity and specificity of hematology analyzer found to be 74.2% and 88%, respectively. CONCLUSION: Flowcytometric analyzer is a rapid, high throughput device which needs less expertization for the diagnosis of malaria. Hence, it can be used in the diagnostic laboratories as an early modality for diagnosis of malaria in suspected as well as clinically in apparent cases.