Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 11 de 11
Filter
Add more filters











Publication year range
1.
J Lab Physicians ; 14(1): 6-10, 2022 Mar.
Article in English | MEDLINE | ID: mdl-36186260

ABSTRACT

Background Evaluating the expression pattern of oxacillinases (OXA) carbapenemases is essential to understand the prevalence and spread of carbapenem resistance Acinetobacter baumannii . Objectives The aim of the study is to evaluate the presence of OXA carbapenemase genes and IS Aba1 upstream to these genes in carbapenem-resistant A. baumannii clinical isolates. Materials and Methods A. baumannii isolated from clinical samples were phenotypically identified and antibiotics sensitivity was performed. Multiplex polymerase chain reaction (PCR) was used to detect OXA51-like gene, OXA carbapenemases genes (OXA-23-like, OXA-24-like, and OXA-58-like), and IS Aba1 in carbapenem-resistant isolates. Results Out of 55 Acinetobacter isolates, 54 were confirmed as A. baumannii by PCR. Bla OXA-23 -like gene was observed in 51 isolates of A. baumannii and none of the isolates showed the presence of bla OXA-24 -like and bla OXA-58 -like genes. Presence of IS Aba1 upstream to OXA-23-like gene, OXA-51-like gene, and both OXA-51-like/OXA-23-like genes was observed in 51, 7, and 4 A. baumannii isolates, respectively. Conclusion The genetic pattern of carbapenem-resistant A. baumannii isolated in this study was unique, which should be factored for clinical protocols to manage infections caused by emerging resistant strains of A. baumannii .

2.
Med J Armed Forces India ; 78(3): 271-276, 2022 Jul.
Article in English | MEDLINE | ID: mdl-35855708

ABSTRACT

Background: Since the last two decades, substantial increase in fungal infections has been observed in immunocompromised hosts. Virulence factors of Candida albicans play a role in adherence, haemolytic activity, phenotypic switching and production of hydrolytic enzymes. The secreted aspartyl proteinases (SAP family) contribute to adhesion, tissue damage and invasion, while phospholipase (PLB) supports the hydrolysis of phospholipids. Very few studies showed the correlation of phenotypic activity and detection of genes contributing to the similar enzyme activity. Therefore, our study aimed at demonstrating correlation between in vitro phenotypic production of phospholipase and proteinase enzymes with genetic level detection of SAP and PLB genes. Methods: The present study was carried out on a total of 799 samples over a period of one year. Culturing was carried out on Sabouraud's dextrose agar. Confirmation and speciation of Candida spp. was carried out using cornmeal agar and CHROMagar and by the germ tube test, urease test and automated identification system Vitek-2, and antifungal susceptibility testing was performed on Candida isolates. Phenotypic phospholipase and proteinase activity was analysed, and molecular detection of SAP4 and PLB genes was carried out. Results: In our study, we have screened 799 samples for mycological protocol; of which, 269 (33.6%) were Candida species, 44% (119) of which were C. albicans. Proteinase activity was exhibited by 77 (64.7%) and phospholipase activity was exhibited by 73 (61.34%) isolates, while 46.2% exhibited both activities among the C. albicans species. The PLB gene was detected in 97.3% isolates, while SAP4 was detected in 94.7% of C. albicans isolates. Conclusion: The study of in vitro expression of virulence factors and gene detection of C. albicans will help to improve the prognosis despite the nature of the sample.

3.
Genome Announc ; 6(25)2018 Jun 21.
Article in English | MEDLINE | ID: mdl-29930036

ABSTRACT

Whole-genome sequencing has emerged as a powerful tool to map genetic diversity among Mycobacterium tuberculosis isolates and identify the genomic signatures associated with drug resistance, pathogenesis, and disease transmission. Isolate LJ319 of the Mycobacterium tuberculosis complex (MTC)-Beijing genotype circulating in Maharashtra, India, which was obtained from the cerebrospinal fluid (CSF) of an immunocompetent patient, was subjected to whole-genome sequencing.

4.
Afr Health Sci ; 17(3): 762-772, 2017 Sep.
Article in English | MEDLINE | ID: mdl-29085404

ABSTRACT

BACKGROUND: Hepatitis B Virus (HBV) infection is one of the major causes of liver cirrhosis, hepatocellular carcinoma and deaths due to the acute or chronic consequences worldwide. HBV is distributed into various genotypes based on nucleic acid sequence variation. OBJECTIVES: To develop a method of HBV genotyping and drug resistance interpretation using partial sequencing of polymerase gene. METHODS: This study was performed on 98 HBV infected patients' serum samples from Western India. A nested PCR protocol was designed for amplification of pol gene from HBV genome and Sanger's sequencing of the gene fragment. Sequences were aligned with HBV reference sequences for phylogenetic analysis and for characterization of genetic diversity. Drug resistance mutations were screened using HBVSeq program from Stanford University. RESULTS: Distribution of HBV genotypes showed predominance of genotype D, circulating in 76 (77.55%) patients (p < 0.05). Genotypes A and C were less prevalent and were identified in 4 (4.08%) and 18 (18.37%) patients, respectively. Anti-retroviral drug resistance mutations were not detected in any patient. CONCLUSION: A method for determination of HBV genotypes using pol gene sequencing which simultaneously detects major drug resistance mutations has been established. HBV genetic diversity may play an important role in treatment decision.


Subject(s)
DNA, Viral/genetics , Hepatitis B virus/classification , Hepatitis B virus/genetics , Hepatitis B, Chronic/virology , Mutation , Polymerase Chain Reaction/methods , Polymorphism, Genetic/genetics , Adult , DNA, Viral/blood , DNA-Directed DNA Polymerase , Genetic Variation , Genotype , Hepatitis B virus/isolation & purification , Hepatitis B, Chronic/blood , Hepatitis B, Chronic/epidemiology , Humans , India/epidemiology , Male , Molecular Epidemiology , Phylogeny
5.
BMJ Case Rep ; 20142014 Sep 19.
Article in English | MEDLINE | ID: mdl-25239983

ABSTRACT

A 67-year-old man with type 2 diabetes mellitus and hypertension since 7 years presented with a 3-month history of low-grade fever and malaise. Cardiac auscultation revealed the presence of an ejection systolic murmur in the primary aortic area. Most of the investigations for febrile illness were reported normal. His two-dimensional (2D) echocardiogram revealed a calcified aortic valve with mild aortic stenosis. In view of the prolonged fever and calcified aortic valve with mild aortic stenosis, a transoesophageal echocardiogram was performed, which showed small vegetation noted on right coronary cusp about 2.2 mm with free independent mobility. Blood culture was positive for Brucella spp from all the three venepuncture sites. Medical therapy for brucellosis was given with ciprofloxacin, doxycycline, co-trimoxazole and streptomycin, resulting in complete recovery. Brucella endocarditis is a rare, mostly ignored and missed clinical infection. It requires a high index of clinical suspicion for prompt diagnosis and treatment.


Subject(s)
Bacteremia/microbiology , Brucella , Brucellosis/diagnosis , Endocarditis, Bacterial/diagnosis , Endocardium , Fever/diagnosis , Aged , Anti-Bacterial Agents/therapeutic use , Aortic Valve/pathology , Brucellosis/complications , Brucellosis/drug therapy , Brucellosis/microbiology , Endocarditis, Bacterial/complications , Endocarditis, Bacterial/drug therapy , Endocarditis, Bacterial/microbiology , Endocardium/microbiology , Endocardium/pathology , Fever/etiology , Humans , Male , Myocardium/pathology
6.
J Clin Diagn Res ; 8(7): DD01-2, 2014 Jul.
Article in English | MEDLINE | ID: mdl-25177564

ABSTRACT

The incidence of fungal keratitis is less common than bacterial and viral keratitis. However, it remains a diagnostic and therapeutic challenge. Delayed clinical diagnosis is common mainly because of lack of suspicion. Further slow growth of fungus increases the time for confirmed laboratory diagnosis. After accurate diagnosis, patient's management remains inadequate due to lack of availability of antifungal agents and its poor corneal penetration. Multitude of genera of molds and yeast have been identified in fungal keratitis. Due to their ubiquitous nature and easy isolation from the environment, their role in true pathogenesis is difficult to ascertain. Worldwide, incidence of fungal keratitis is rising at present. The predisposing factors comprises trauma, use of contact lenses and topical steroids. Filamentous fungi and dematiaceous fungi are the frequently encountered etiological agents of fungal keratitis. Dimorphic fungi are reported less frequently. Fungal keratitis tends to occur more frequently in young males and usually in winter and monsoon. Penicillium genera includes several species. By far Penicillium marneffei (P. marneffei) infection is most common, mainly associated with AIDS. A number of infections caused by species other than P. marneffei have been reported as well. Here we report a case of Penicillium keratitis in a young, HIV negative male farmer.

7.
PLoS One ; 9(8): e105790, 2014.
Article in English | MEDLINE | ID: mdl-25157501

ABSTRACT

Human Immunodeficiency Virus-1 (HIV-1) drug resistance genotyping assay is a part of clinical management of HIV-1 positive individuals under treatment with highly active antiretroviral therapy (HAART). Routine monitoring of drug resistance mutations in resource limited settings like India is not possible due to high cost of commercial drug resistance assays. In this study we developed an in-house, cost effective HIV-1 drug resistance genotyping assay for Indian patients and validated it against the US-FDA-approved ViroSeq HIV-1 drug resistance testing system. A reference panel of 20 clinical samples was used to develop and validate the assay against ViroSeq HIV-1 drug resistance testing system which was subsequently used to genotype a clinical panel of 225 samples. The Stanford HIV database was used to identify drug resistant mutations. The analytical sensitivity of the assay was 1000 HIV-1 RNA copies/ml of plasma sample while precision and reproducibility was 99.68 ± 0.16% and 99.76 ± 0.18% respectively. One hundred and one drug resistant mutations were detected by the in-house assay compared to 104 by ViroSeq system in the reference panel. The assay had 91.55% success rate in genotyping the clinical panel samples and was able to detect drug resistant mutations related to nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse-transcriptase inhibitor (NNRTI) as well as protease inhibitor (PI) classes of antiretroviral drugs. It was found to be around 71.9% more cost effective compared to ViroSeq genotyping system. This evaluation of the assay on the clinical panel demonstrates its potential for monitoring clinical HIV-1 drug resistance mutations and population-based surveillance in resource limited settings like India.


Subject(s)
Drug Resistance, Viral/genetics , Genotyping Techniques/economics , HIV Infections/virology , HIV-1/genetics , Adult , Anti-HIV Agents/pharmacology , Cost-Benefit Analysis , DNA Mutational Analysis , Female , HIV Infections/drug therapy , HIV-1/drug effects , Humans , India , Male , Phylogeny , RNA, Viral/genetics , RNA, Viral/isolation & purification , Reproducibility of Results , Sensitivity and Specificity
8.
Biol Res ; 47: 22, 2014 May 30.
Article in English | MEDLINE | ID: mdl-25028193

ABSTRACT

BACKGROUND: Human Immunodeficiency Virus Type 1 (HIV-1) viral load testing at regular intervals is an integral component of disease management in Acquired Immunodeficiency Syndrome (AIDS) patients. The need in countries like India is therefore an assay that is not only economical but efficient and highly specific for HIV-1 sub type C virus. This study reports a SYBR Green-based HIV-1 real time PCR assay for viral load testing and is designed for enhanced specificity towards HIV-1 sub type C viruses prevalent in India. RESULTS: Linear regression of the observed and reference concentration of standards used in this study generated a correlation coefficient of 0.998 (p<0.001). Lower limit of detection of the test protocol was 50 copies/ml of plasma. The assay demonstrated 100% specificity when tested with negative control sera. The Spearman coefficient of the reported assay with an US-FDA approved, Taqman probe-based commercial kit was found to be 0.997. No significant difference in viral load was detected when the SYBR Green based assay was used to test infected plasma stored at -20°C and room temperature for 7 days respectively (Wilcoxon signed rank test, p=0.105). In a comparative study on 90 pretested HIV-1 positive samples with viral loads ranging from 5,000-25,000 HIV-1 RNA copies/ml and between two commercial assays it was found that the later failed to amplify in 13.33% and 10% samples respectively while in 7.77% and 4.44% samples the copy number values were reduced by >0.5 log value, a figure that is considered clinically significant by physicians. CONCLUSION: The HIV-1 viral load assay reported in this study was found to be robust, reliable, economical and effective in resource limited settings such as those existing in India. PCR probes specially designed from HIV-1 Subtype C-specific nucleotide sequences originating from India imparted specificity towards such isolates and demonstrated superior results when compared to two similar commercial assays widely used in India.


Subject(s)
HIV Infections/diagnosis , HIV-1/isolation & purification , RNA, Viral/blood , Viral Load/methods , Base Sequence/genetics , Disease Management , Genes, gag/genetics , HIV-1/classification , Humans , India , Inventions , Limit of Detection , Linear Models , Organic Chemicals , Reagent Kits, Diagnostic/economics , Real-Time Polymerase Chain Reaction , Sensitivity and Specificity , Statistics, Nonparametric
9.
Biol. Res ; 47: 1-8, 2014. graf, tab
Article in English | LILACS | ID: biblio-950718

ABSTRACT

BACKGROUND: Human Immunodeficiency Virus Type 1 (HIV-1) viral load testing at regular intervals is an integral component of disease management in Acquired Immunodeficiency Syndrome (AIDS) patients. The need in countries like India is therefore an assay that is not only economical but efficient and highly specific for HIV-1 sub type C virus. This study reports a SYBR Green-based HIV-1 real time PCR assay for viral load testing and is designed for enhanced specificity towards HIV-1 sub type C viruses prevalent in India. RESULTS: Linear regression of the observed and reference concentration of standards used in this study generated a correlation coefficient of 0.998 (p<0.001). Lower limit of detection of the test protocol was 50 copies/ml of plasma. The assay demonstrated 100% specificity when tested with negative control sera. The Spearman coefficient of the reported assay with an US-FDA approved, Taqman probe-based commercial kit was found to be 0.997. No significant difference in viral load was detected when the SYBR Green based assay was used to test infected plasma stored at -20°C and room temperature for 7 days respectively (Wilcoxon signed rank test, p=0.105). In a comparative study on 90 pretested HIV-1 positive samples with viral loads ranging from 5,000 - 25,000 HIV-1 RNA copies/ml and between two commercial assays it was found that the later failed to amplify in 13.33% and 10% samples respectively while in 7.77% and 4.44% samples the copy number values were reduced by >0.5 log value, a figure that is considered clinically significant by physicians. CONCLUSION: The HIV-1 viral load assay reported in this study was found to be robust, reliable, economical and effective in resource limited settings such as those existing in India. PCR probes specially designed from HIV-1 Subtype C-specific nucleotide sequences originating from India imparted specificity towards such isolates and demonstrated superior results when compared to two similar commercial assays widely used in India.


Subject(s)
Humans , RNA, Viral/blood , HIV Infections/diagnosis , HIV-1/isolation & purification , Viral Load/methods , Organic Chemicals , Reagent Kits, Diagnostic/economics , Base Sequence/genetics , Genes, gag/genetics , Linear Models , Sensitivity and Specificity , HIV-1/classification , Statistics, Nonparametric , Disease Management , Limit of Detection , Real-Time Polymerase Chain Reaction , Inventions , India
10.
Curr HIV Res ; 11(4): 295-303, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23862569

ABSTRACT

A portion of the gag gene cDNA for p24 protein from 30 Indian HIV-1 proviral DNA was amplified by PCR and sequenced. Phylogenetic analysis with reference samples of A1, A2, B, C, D, F1, F2, G, H, J, K, N and O subtypes revealed that 29 test samples aligned with subtype C reference strain while 1 matched with HIV-1 subtype A. Multiple alignment of predicted amino acid sequence of the Indian test samples and reference C subtype of HIV-1 samples from other countries indicated a molecular signature by way of rigid conservation of the amino acid 'S' at position 41 of the gag p24 protein in all Indian HIV-1 samples analyzed in this study as opposed to 'T' in the same position in C subtype sequences from other parts of the world. A phylogenetic analysis and visualization of the resulting tree in radial position showed distinct clubbing of all Indian C subtypes and formation of a cluster when compared to C subtype sequences from other countries with a single Chinese sample as an exception which was found in the Indian cluster. The use of a portion of p24 gene sequence as tool for subtyping as well as phylogenetic grouping with special reference to its geographical location is discussed.


Subject(s)
HIV Core Protein p24/genetics , HIV Infections/virology , HIV-1/genetics , Adult , Amino Acid Sequence , Cluster Analysis , Female , Gene Products, gag , HIV Infections/epidemiology , HIV-1/isolation & purification , Humans , India/epidemiology , Male , Middle Aged , Molecular Sequence Data , Phylogeny , Pilot Projects , Prospective Studies , Protein Precursors , Sequence Analysis, DNA , Sequence Analysis, Protein/methods , Young Adult
11.
Roum Arch Microbiol Immunol ; 71(1): 29-38, 2012.
Article in English | MEDLINE | ID: mdl-22838217

ABSTRACT

Human MECP2 gene located at q28 arm of X chromosome was identified as target for thermal co-amplification with HIV-1 proviral DNA of infected individuals. The selected MECP2 gene-specific primers functioned at a wide range of annealing temperature, extension time and exhibited no significant interaction with pathogen specific primers. A 466 bp PCR amplicon originating from human MECP2 gene was found to be diagnostic for inhibition-free PCR reaction when co-amplified with the HIV-1 target gene in a multiplexed, nested PCR reaction. The 5' end of the MECP2 primers were engineered to position an EcoRI restriction endonuclease site to facilitate rapid cloning in various DNA vector molecules at the corresponding EcoRI sites. Cell mass of Escherichia coli (XL1Blue) harboring the recombinant plasmid when added to pleural fluid of HIV-1 infected individuals co-infected with Mycobacterium tuberculosis, generated the diagnostic 466 bp MECP2 PCR amplicon as well as the 194 bp PCR amplicon of target gene from M. tuberculosis. The experiment underlined potential of the region spanning nucleotide position 4118099 to 4118552 of human MECP2 gene (NCBI accession number NT_011726.13) as a reliable target for multiplex PCR to accommodate a wide range of thermal cycling and multiplex reaction conditions. In both cases of this study, electrophoresis-based separation of the 466 bp MECP2 fragment and the 232 bp and 194 bp HIV-1 and M. tuberculosis fragments respectively was distinct and unambiguous. The potential of this human MECP2 gene available from human genome or recombinant plasmid as a potent target to monitor PCR inhibition for a range of different PCR reactions is discussed.


Subject(s)
Chromosomes, Human, X , DNA, Viral/analysis , HIV-1/isolation & purification , Methyl-CpG-Binding Protein 2/genetics , Multiplex Polymerase Chain Reaction/methods , Humans
SELECTION OF CITATIONS
SEARCH DETAIL