Kandarpa Kumar Saikia

New Delhi metallo-β-lactamase and extended spectrum β-lactamases co-producing isolates are high in community-acquired urinary infections in Assam as detected by a novel multiplex polymerase chain reaction assay.

Background: The ability of microorganisms to evade antibiotic pressure is challenging in healthcare as patients have little or no drug treatment options. Detection of the prevalence of antibacterial resistance pattern helps towards improved antibiotic policy and empirical treatment. Objectives: We carried out antibiogram profiling and documented the prevalence and co-prevalence of New Delhi metallo-β-lactamase (NDM) and extended spectrum β-lactamases (ESBL) encoding genes in urinary Escherichia coli and Klebsiella pneumonia isolates. Materials and Methods: Antibiotic susceptibilities were tested for 241 isolates of E. coli and K. pneumoniae from urine samples collected from out- and hospitalised patients. Polymerase chain reaction (PCR) was carried out on isolates tested positive for phenotypic production of metallo-β-lactamase and ESBL. A multiplex PCR assay was designed to detect the genes. Results: Multiplex PCR assay designed had a limit of detection of 10 3 CFU/mL in vitro. NDM detected was significantly higher among K. pneumoniae compared to E. coli (69.2% vs. 18.2%; P = 0.001). Of 17, 14 NDM positive isolates also harboured ESBL genes. The co-production of CTX-M + TEM + NDM (3/9; 33.3% and 5/8; 62.5%) was most common in K. pneumoniae and E. coli, respectively while CTX-M + TEM + SHV + NDM was found in one isolate. Of the 156 phenotypically ESBL producing isolates, CTX-M, TEM and SHV was detected by PCR in 85, 53 and 24 isolates, respectively. Conclusion: NDM and ESBL co-producing isolates were both community (64.7%) and hospital (35.29%) acquired among E. coli. Antibiotic resistance can be effectively evaluated by a cost and time effective molecular method, such as the multiplex PCR used in this study, which complement culture and sensitivity tests.

Outcome of HER2 Testing by FISH applying ASCO/CAP 2007 and 2013 guideline in IHC equivocal group of breast cancer: Experience at tertiary cancer care centre

Background and Objectives: HER2 testing guideline of ASCO/CAP for interpretation and reporting has recently been revised. The study is aimed to measure the impact of 2013 CAP guideline on equivocal HER2 test outcome (immunohistochemistry [IHC] 2+) when tested by fluorescent in situ hybridization (FISH). The study also aims at finding the frequency of polysomy and monosomy of chromosome 17. Materials and Methods: Specimens were collected in Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India. IHC was performed in every case, and FISH was performed in IHC2+ cases. Results: In final analysis includes 557 subjects on the basis of CAP guideline 2007 and CAP guideline 2013. One hundred ninety-two subjects (34.4%) were HER2 amplified according to CAP scoring 2007, and 246 subjects (44%) according to 2013 CAP scoring. Conclusions: FISH results were evaluated (IHC2 + interpreted according to CAP 2007 guideline) with both 2007 and 2013 ASCO/CAP scoring criteria, we identified significantly more HER2 positive cases as compared to cases evaluated using the 2007 criteria (P < 0.05). We also found that in breast carcinoma, HER2 status in the presence of polysomy 17 may vary with the scoring criteria used. Evaluation of FISH result using 2013 ASCO/CAP criteria means that more patients with breast cancer may be appropriate for targeted treatment with trastuzumab, potentially improving their outcome.

Quantification of DNA Extracted from Formalin Fixed Paraffin-Embeded Tissue Comparison of Three Techniques: Effect on PCR Efficiency

INTRODUCTION Mutation detection from Formalin Fixed Paraffin-Embedding (FFPE) tissue in molecular lab became a necessary tool for defining potential targeted drug. Accurate quantification of DNA extracted from FFPE tissue is necessary for downstream applications like Polymerase Chain Reaction (PCR), sequencing etc. AIM To check and define which method for FFPE DNA quantification is suitable for downstream processes. MATERIALS AND METHODS In this experimental experience study Biorad Smartspec Plus spectrophotomery, Qubit Fluorometer, and Qiagen Rotorgene qPCR was used to compare 20 FFPE DNA quantification in Rajiv Gandhi Cancer Institute and Research Centre, in 2015 and quantified amount of DNA used for PCR reaction. RESULTS The average concentration of DNA extracted from FFPE tissue measured using the spectrophotometer was much higher than the concentration measured using the Qubit Fluorometer and qPCR. CONCLUSION Results varied depending upon the technique used. A fluorometric analysis may be more suitable for quantification of DNA samples extracted from FFPE tissue compared with spectrophotometric analysis. But qPCR is the best technique because it details DNA quantity along with quality of amplifiable DNA from FFPE tissue.

First report on the detection of OXA-48 β-lactamase gene in Escherichia coli and Pseudomonas aeruginosa co-infection isolated from a patient in a Tertiary Care Hospital in Assam.

of extended-spectrum beta-lactamase production by Enterobacteriaceae. J Clin Microbiol 2011;49:1048-57. 6. Espinar MJ, Rocha R, Ribeiro M, Gonçalves Rodrigues A, Pina-Vaz C. Extended-spectrum ß-lactamases of Escherichia coli and Klebsiella pneumoniae screened by the VITEK 2 system. J Med Microbiol 2011;60 (Pt 6):756-60. 7. ß‐Lactamase Classification and Amino Acid Sequences for TEM, SHV and OXA Extended-Spectrum and Inhibitor Resistant Enzymes. Available from: http://www.lahey.org/ studies/. [Last accessed on 2015 Apr 11]. 8. BushK. The ABCD’s of ß-lactamase nomenclature. J Infect Chemother 2013;19:549-59.

Prevalence pattern of key polymorphisms in the Vitamin D receptor gene among patients of Type 2 diabetes mellitus in Northeast India

Aims: To investigate the association between Vitamin D receptor gene polymorphisms (BsmI, TaqI and FokI) and type 2 diabetes mellitus in patients in north eastern India. Settings and Design: This was a case control study with 40 cases of type 2 diabetes and 20 controls. Materials and Methods: Genomic DNA was extracted from blood and genotyped for the single nucleotide polymorphism (SNPs) of BsmI [rs1544410], TaqI [rs731236] and FokI [rs2228570] by polymerase chain reaction and gene sequencing. Genotype distribution and allelic frequencies were compared between patients and controls. Data was expressed as mean ±standard deviation. Chi square test and t test were used to compare groups. Statistical analysis was done using SAS version 9.3 software. P value of <0.05 was considered significant. Results: Body weight and BMI were significantly associated with VDR polymorphisms BsmI and TaqI while BsmI was significantly associated with HbA1C. Vitamin D deficiency was significantly greater in cases than controls. The frequency of the heterozygous genotype of the BsmI polymorphism was significantly greater in type 2 diabetics than in controls. Conclusions: Vitamin D receptor polymorphisms are associated with type 2 diabetes in our population and require larger scale studies to be considered as possible risk factors or type 2 diabetes mellitus.

NPM1 mutation analysis in Acute Myeloid Leukemia: Comparison of three techniques Sanger Sequencing, Pyrosequencing, and Real Time PCR

Objective: Nucleophosmin-1 (NPM1) mutations have prognostic importance in acute myeloid leukemia (AML) patients with intermediate-risk karyotype at diagnosis. Approximately 30% of newly diagnosed cytogenetically normal AML (CN-AML) patients harbor the NPM1 mutation in India. In this study we compared the efficiency of three molecular techniques in detecting NPM1 mutation in peripheral blood and bone marrow samples. Materials and Methods: In a single-center cohort we analyzed 165 CN-AML bone marrow/peripheral blood samples for NPM1 mutation analysis. About 30% of the CN-AML samples revealed NPM1 mutations. For the detection, three methods were compared: Sanger sequencing, pyrosequencing, and real-time polymerase chain reaction (PCR). Results: NPM1 exon 12 mutations were observed in 52 (31.51%) of all CN-AML cases. The sensitivity of Sanger sequencing, pyrosequencing, and real-time PCR was 80%, 90%, and 95%, whereas specificity was 95%, 100%, and 100%, respectively. The minimum limit of mutation detection was 20%-30% for Sanger sequencing, 1%-5% for pyrosequencing, and 0.1%-1% for real-time PCR. Conclusion: The sequencing method, which is the reference method, has the lowest sensitivity and is sometimes difficult to interpret. Real-time PCR is a highly sensitive method for mutation detection but is limited for specific mutation types. In our study, pyrosequencing emerged as the most suitable technique for the detection of NPM1 mutations on the basis of its easy interpretation and less time-consuming processes than Sanger sequencing.

Molecular analysis of childhood B-acute lymphoblastic leukemia: Identification and prognosis of rare breakpoints

Acute lymphoblastic leukaemia (ALL) is the most common subtype of childhood cancer. Detection of a specific gene rearrangement allows the identification of prognostically relevant subgroups in childhood B-ALL. There are four common gene rearrangements which are widely studied to see prognostical values (TEL-AML1, BCR-ABL, E2A-PBX1, MLL-AF4) in childhood B-ALL. In this study we show the prevalence of these common gene rearrangements and also explain the way to identify some rare breakpoints which also occur in these gene rearrangements. 97 samples received for diagnosis from paediatric B-ALL patients were included in this study. Qualitative reverse transcriptase PCR was used for detection of the TEL-AML1-t(12;21), E2A-PBX1-t(1;19), BCR-ABL1-t(9;22) and MLL-AF4 t(4;11) fusion transcripts. Unusually sized amplicons were confirmed by FISH and DNA sequencing to confirm atypical breakpoints. Amongst the paediatric B-ALL samples t(12;21), was detected in (∼20%), t(9;22), was detected in (∼8%), t(1;19) was detected in (∼9%) and t(4;11) was detected in 2 cases. t(12;21) with intron 1of the AML1 gene was detected as the most common gene rearrangement in paediatric ALL, whereas one rare form of the TEL-AML1 breakpoint in which TEL is fused with intron 2 of AML1 was also observed. In the t(9;22) breakpoints e13a2, e14a2 and e1a2 were detected as the common breakpoints. Two atypical and rare breakpoint of t(9;22) were detected namely e6a2 and e13a3 in paediatric ALL. TEL-AML1 was found to be the most common translocation in Paediatric B-ALL. Identification of the rare breakpoints through RT-PCR technique requires designing of PCR in such a way that it can detect these rare breakpoints also.