Search tips
Search criteria

Results 1-25 (37)

Clipboard (0)

Select a Filter Below

Year of Publication
author:("Kumar, shales")
1.  PCMdb: Pancreatic Cancer Methylation Database 
Scientific Reports  2014;4:4197.
Pancreatic cancer is the fifth most aggressive malignancy and urgently requires new biomarkers to facilitate early detection. For providing impetus to the biomarker discovery, we have developed Pancreatic Cancer Methylation Database (PCMDB,, a comprehensive resource dedicated to methylation of genes in pancreatic cancer. Data was collected and compiled manually from published literature. PCMdb has 65907 entries for methylation status of 4342 unique genes. In PCMdb, data was compiled for both cancer cell lines (53565 entries for 88 cell lines) and cancer tissues (12342 entries for 3078 tissue samples). Among these entries, 47.22% entries reported a high level of methylation for the corresponding genes while 10.87% entries reported low level of methylation. PCMdb covers five major subtypes of pancreatic cancer; however, most of the entries were compiled for adenocarcinomas (88.38%) and mucinous neoplasms (5.76%). A user-friendly interface has been developed for data browsing, searching and analysis. We anticipate that PCMdb will be helpful for pancreatic cancer biomarker discovery.
PMCID: PMC3935225  PMID: 24569397
2.  Detection of metallo-beta-lactamase producing Pseudomonas aeruginosa in intensive care units 
The Australasian Medical Journal  2013;6(12):686-693.
Metallo-beta-lactamase (MBL) producing Pseudomonas aeruginosa has emerged as a threat to hospital infection control, due to its multi-drug resistance, especially in intensive care units (ICUs).
This study was carried out to detect MBL producing P. aeruginosa isolates from medical and surgical ICUs, to compare and evaluate different phenotypic methods currently in use and to determine antibiograms.
A prospective study was undertaken to detect MBLs in P. aeruginosa isolates obtained from various clinical samples. A total of 49 strains were recovered from patients admitted in inpatient wards and ICUs, and screened for imipenem resistance by Kirby Bauer disk diffusion method. Detection of MBLs was further done by imipenem-EDTA disk synergy test and combined disk test.
Out of 49 isolates, 11 isolates (22.4 per cent) were imipenem resistant. All 11 imipenem resistant P. aeruginosa strains, when further tested, were positive for MBL production by combined disk test, but, only eight showed positive results by imipenem-EDTA disk synergy test.
MBL production was the main resistance mechanism in the 11 carbapenem resistant P. aeruginosa isolates collected, with multidrug resistance associating significantly with MBL production in P. aeruginosa from our institution.
PMCID: PMC3877850  PMID: 24391679
Metallo-beta-lactamases; infection control; Pseudomonas aeruginosa; Multidrug resistance
3.  Genes Involved in Degradation of para-Nitrophenol Are Differentially Arranged in Form of Non-Contiguous Gene Clusters in Burkholderia sp. strain SJ98 
PLoS ONE  2013;8(12):e84766.
Biodegradation of para-Nitrophenol (PNP) proceeds via two distinct pathways, having 1,2,3-benzenetriol (BT) and hydroquinone (HQ) as their respective terminal aromatic intermediates. Genes involved in these pathways have already been studied in different PNP degrading bacteria. Burkholderia sp. strain SJ98 degrades PNP via both the pathways. Earlier, we have sequenced and analyzed a ~41 kb fragment from the genomic library of strain SJ98. This DNA fragment was found to harbor all the lower pathway genes; however, genes responsible for the initial transformation of PNP could not be identified within this fragment. Now, we have sequenced and annotated the whole genome of strain SJ98 and found two ORFs (viz., pnpA and pnpB) showing maximum identity at amino acid level with p-nitrophenol 4-monooxygenase (PnpM) and p-benzoquinone reductase (BqR). Unlike the other PNP gene clusters reported earlier in different bacteria, these two ORFs in SJ98 genome are physically separated from the other genes of PNP degradation pathway. In order to ascertain the identity of ORFs pnpA and pnpB, we have performed in-vitro assays using recombinant proteins heterologously expressed and purified to homogeneity. Purified PnpA was found to be a functional PnpM and transformed PNP into benzoquinone (BQ), while PnpB was found to be a functional BqR which catalyzed the transformation of BQ into hydroquinone (HQ). Noticeably, PnpM from strain SJ98 could also transform a number of PNP analogues. Based on the above observations, we propose that the genes for PNP degradation in strain SJ98 are arranged differentially in form of non-contiguous gene clusters. This is the first report for such arrangement for gene clusters involved in PNP degradation. Therefore, we propose that PNP degradation in strain SJ98 could be an important model system for further studies on differential evolution of PNP degradation functions.
PMCID: PMC3871574  PMID: 24376843
4.  Changing Trends in Resistance Pattern of Methicillin Resistant Staphylococcus aureus 
Background: Methicillin resistance in Staphylococcus aureus is associated with multidrug resistance, an aggressive course, increased mortality and morbidity in both community and health care facilities. Monitoring of newly emerging and prevalent Methicillin Resistant Staphylococcus aureus (MRSA) strains for their resistance patterns to conventional as well as novel drugs, are essential for infection control.
Aims: To study the changing trends in resistance patterns of MRSA at our hospital.
Settings and Design: This cross sectional study was carried out in a 750 bed tertiary care hospital in south India.
Material and Methods: One hundred and two clinical isolates of MRSA which were obtained in 2004-2011 were identified by using oxacillin, cefoxitin disc diffusion test and oxacillin screening agar test. Antibiotic susceptibility test was done for commonly used non beta lactam anti-Staphylococcal drugs, as well as for anti-MRSA drugs like vancomycin, linezolid, mupirocin and rifampicin. Minimum inhibitory concentration (MIC) of vancomycin was determined by using Vancomycin HiComb strip (Himedia, Mumbai, India).
Statistical Analysis which was done: Chi-square test and proportions were used to compare the two groups.
Results: MRSA isolates showed high resistance to co-trimoxazole (82.3%), ciprofloxacin (76.4%), gentamicin (64.7%) and tetracycline (49%) as compared to other drugs. High prevalence of ciprofloxacin resistance was detected, particularly among outpatients. Multi resistant MRSA with a ≥ 3 non-beta lactam agent resistance was 79%. All MRSA isolates were sensitive to vancomycin, linezolid, mupirocin and rifampicin. MRSA had displayed increase in resistance to most antibiotics except tetracycline in recent years.
Conclusions: Taking into consideration the prevalence of multidrug resistance in MRSA, resistance patterns should be evaluated periodically and antibiotic therapy should be guided by susceptibility testing.
PMCID: PMC3809653  PMID: 24179914
Methicillin resistant Staphylococcus aureus; Vancomycin; Multidrug resistance
5.  Bacteriophage types of methicillin-resistant Staphylococcus aureus in a tertiary care hospital 
The Australasian Medical Journal  2013;6(10):496-503.
Phage typing had been utilised extensively to characterise methicillin-resistant Staphylococcus aureus (MRSA) outbreak strains in the past. It is an invaluable tool even today to monitor emergence and dissemination of MRSA strains.
The aim of this study was to determine the prevalent phage types of MRSA in south India and the association between phage types, antibiotic resistance pattern and risk factors.
A total of 48 non-duplicate MRSA strains recovered from various clinical samples during January to December, 2010 were tested against a panel of anti-staphylococcal antibiotics. Phage typing was carried out at the National Staphylococcal Phage Typing Centre, New Delhi. Out of 48, 32 hospitalised patients were followed up for risk factors and response to empirical and post sensitivity antibiotic therapy. The risk factors were compared with a control group of 30 patients with methicillin sensitive Staphylococcus aureus (MSSA) infection.
Amongst the five prevalent phage types, 42E was most common (52%), followed by a non-typable variant (22.9%), 42E/47/54/75 (16.6%), 42E/47 (6.2%) and 47 (2%). Phage type 42E was the predominant strain in all wards and OPDs except in the ICU where 42E/47/54/75 was most common. Although not statistically significant, strain 42E/47/54/75 (n=8) showed higher resistance to all drugs, except ciprofloxacin and amikacin, and were mostly D-test positive (87.5%) compared to the 42E strain (32%). Duration of hospital stay, intravenous catheterisation and breach in skin were the most significant risk factors for MRSA infection.
We found MRSA strain diversity in hospital wards with differences in their antibiotic susceptibility pattern. The findings may impact infection control and antibiotic policy significantly.
PMCID: PMC3821046  PMID: 24223065
MRSA; phage types; stairs; risk factors
6.  Aetiological agents of ventilator-associated pneumonia and its resistance pattern – a threat for treatment 
The Australasian Medical Journal  2013;6(9):430-434.
Ventilator-associated pneumonia (VAP) is a common type of nosocomial pneumonia encountered in intensive care units. There are several aetiological agents which make treatment challenging. Improper antibiotic treatment of ventilated patients may lead to the emergence of multidrug resistant (MDR) pathogens.
A prospective study was performed over a period of 20 months. Our study had two arms: the first, ‘Incidence and risk factors of VAP in a tertiary care hospital’ was the subject of an earlier publication; we therefore present the second investigative arm in this work. The aetiological agents of patients on mechanical ventilation (MV) were identified by standard bacteriological method. The susceptibility pattern was evaluated by Kirby-Bauer disc diffusion method. Extended spectrum beta lactamase (ESBL) testing was performed by combination disc method, and metallo-beta lactamase (MBL) testing was performed by EDTA disk synergy test (EDS).
Late-onset VAP was associated with Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli, while early-onset VAP was commonly caused by members of Enterobacteriaceae, Candida albicans and Staphylococcus aureus. 72.2 per cent of VAP patients had monomicrobial and 27.8 per cent had polymicrobial infection. Out of the 24 isolates obtained from patients with VAP, seven (29.2 per cent) were MDR pathogens. ESBL and MBL production was detected in 40 per cent and 20 per cent of Klebsiella pneumoniae isolated in our study. Around 50 per cent of isolates associated with late-onset VAP were MDR, while 22.2 per cent isolates obtained from patients with earlyonset VAP were MDR.
VAP is a nosocomial pneumonia that is common among ventilated patients. The aetiological agents vary from common organisms to MDR pathogens that are difficult to treat. A proper knowledge of MDR pathogens and early isolation followed by prevention of prolonged antibiotic therapy can reduce the mortality of late onset VAP.
PMCID: PMC3794413  PMID: 24133535
Ventilator associated pneumonia; aetiology; drug resistance
7.  Prevalence of Candida co-infection in patients with pulmonary tuberculosis 
The Australasian Medical Journal  2013;6(8):387-391.
Candida species are emerging as a potentially pathogenic fungus in patients with broncho-pulmonary diseases. The synergistic growth promoting association of Candida and Mycobacterium tuberculosis has raised increased concern for studying the various Candida spp . and its significance in pulmonary tuberculosis patients during current years.
This study was undertaken with the objective of discovering the prevalence of co-infection caused by different Candida species in patients with pulmonary tuberculosis.
A total of 75 patients with pulmonary tuberculosis diagnosed by sputum Ziehl-Neelsen staining were included in the study. Candida co-infection was confirmed using the Kahanpaa et al. criteria. Candida species were identified using gram stain morphology, germ tube formation, morphology on cornmeal agar with Tween-80, sugar fermentation tests and HiCrome Candida Agar.
Candida co-infection was observed in 30 (40%) of patients with pulmonary tuberculosis. Candida albicans was the most common isolate observed in 50% of the patients with co-infection, followed by C. tropicalis (20%) and C. glabrata (20%). Candida co-infection was found in 62.5% of female patients, while it was observed in only 29.4% of the male patients (P value 0.0133). Mean ± SD age of the patients with C. glabrata infection was 65.83 ± 3.19, while the mean ± SD age of the patients with other Candida infections was 43.25 ± 20.44 (P value 0.0138).
Many patients with pulmonary tuberculosis have co-infection with Candida spp. The prevalence of non-albicans Candida species is increasing and may be associated with inadequate response to anti-tubercular drugs. C. glabrata infection has a strong association with old age.
PMCID: PMC3767025  PMID: 24039631
Candida co-infection; C. glabrata; prevalence; tuberculosis
8.  Genome Annotation of Burkholderia sp. SJ98 with Special Focus on Chemotaxis Genes 
PLoS ONE  2013;8(8):e70624.
Burkholderia sp. strain SJ98 has the chemotactic activity towards nitroaromatic and chloronitroaromatic compounds. Recently our group published draft genome of strain SJ98. In this study, we further sequence and annotate the genome of stain SJ98 to exploit the potential of this bacterium. We specifically annotate its chemotaxis genes and methyl accepting chemotaxis proteins. Genome of Burkholderia sp. SJ98 was annotated using PGAAP pipeline that predicts 7,268 CDSs, 52 tRNAs and 3 rRNAs. Our analysis based on phylogenetic and comparative genomics suggest that Burkholderia sp. YI23 is closest neighbor of the strain SJ98. The genes involved in the chemotaxis of strain SJ98 were compared with genes of closely related Burkholderia strains (i.e. YI23, CCGE 1001, CCGE 1002, CCGE 1003) and with well characterized bacterium E. coli K12. It was found that strain SJ98 has 37 che genes including 19 methyl accepting chemotaxis proteins that involved in sensing of different attractants. Chemotaxis genes have been found in a cluster along with the flagellar motor proteins. We also developed a web resource that provides comprehensive information on strain SJ98 that includes all analysis data (
PMCID: PMC3734258  PMID: 23940608
9.  Incidence and risk factors of ventilator associated pneumonia in a tertiary care hospital 
The Australasian Medical Journal  2013;6(4):178-182.
Ventilator associated pneumonia (VAP) is a type of nosocomial pneumonia associated with increased morbidity and mortality. Knowledge about the incidence and risk factors is necessary to implement preventive measures to reduce mortality in these patients.
A prospective study was conducted at a tertiary care teaching hospital for a period of 20 months from November 2009 to July 2011. Patients who were on mechanical ventilation (MV) for more than 48 hours were monitored at frequent intervals for development of VAP using clinical and microbiological criteria until discharge or death.
Of the 76 patients, 18 (23.7%) developed VAP during their ICU stay. The incidence of VAP was 53.25 per 1,000 ventilator days. About 94% of VAP cases occurred within the first week of MV. Early-onset and late-onset VAP was observed in 72.2% and 27.8%, respectively. Univariate analysis showed chronic lung failure, H2 blockers usage, and supine head position were significant risk factors for VAP. Logistic regression revealed supine head position as an independent risk factor for VAP.
VAP occurred in a sizeable number of patients on MV. Chronic lung failure, H2 blockers usage, and supine head position were the risk factors associated with VAP. Awareness about these risk factors can be used to inform simple and effective preventive measures.
PMCID: PMC3650308  PMID: 23671462
VAP; incidence; risk factors
10.  Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15 
Genome Announcements  2013;1(2):e00150-13.
We report the 7.3-Mbp genome sequence of Streptomyces gancidicus strain BKS 13-15, isolated from mangrove sediment samples collected from the Bhitar Kanika Mangrove Reserve Forest, Odissha, India. The draft genome of strain Streptomyces gancidicus strain BKS 13-15 consists of 7,300,479 bp with 72.6% G+C content, 6,631 protein-coding genes, and 71 RNAs.
PMCID: PMC3630403  PMID: 23599292
11.  Draft Genome Sequence of Rhodococcus ruber Strain BKS 20-38 
Genome Announcements  2013;1(2):e00139-13.
We report the 6.1-Mb genome sequence of Rhodococcus ruber strain BKS 20-38, isolated from the palm tree rhizosphere soil of Bhitarkanika National Park, Odhisha, India. The draft genome sequence of strain BKS 20-38 consists of 6,126,900 bp, with a G+C content of 69.72%, 5,716 protein-coding genes, and 49 RNAs.
PMCID: PMC3623001  PMID: 23558535
12.  Draft Genome Sequence of Amycolatopsis decaplanina Strain DSM 44594T 
Genome Announcements  2013;1(2):e00138-13.
We report the 8.5-Mb genome sequence of Amycolatopsis decaplanina strain DSM 44594T, isolated from a soil sample from India. The draft genome of strain DSM 44594T consists of 8,533,276 bp with a 68.6% G+C content, 7,899 protein-coding genes, and 57 RNAs.
PMCID: PMC3623004  PMID: 23558534
13.  Draft Genome Sequence of Acinetobacter baumannii Strain MSP4-16 
Genome Announcements  2013;1(2):e00137-13.
We report the 4.0-Mb draft genome sequence of Acinetobacter baumannii strain MSP4-16, isolated from a mangrove soil sample from Parangipettai (11°30′N, 79°47′E), Tamil Nadu, India. The draft genome sequence of strain MSP4-16 consists of 3,944,542 bp, with a G+C content of 39%, 5,387 protein coding genes, and 69 RNAs.
PMCID: PMC3622989  PMID: 23558533
14.  Draft Genome Sequence of Rhodococcus qingshengii Strain BKS 20-40 
Genome Announcements  2013;1(2):e00128-13.
We report the 5.8-Mb genome sequence of Rhodococcus qingshengii strain BKS 20-40, isolated from a palm tree rhizosphere soil sample from Bhitarkanika National Park, Odisha, India. The strain is capable of degrading cholesterol moiety. The draft genome of strain BKS 20-40 consists of 6,601,618 bp, with 62.4% G+C content.
PMCID: PMC3622981  PMID: 23538906
15.  Draft Genome Sequence of Rhodococcus triatomae Strain BKS 15-14 
Genome Announcements  2013;1(2):e00129-13.
We report the 5.8-Mb genome sequence of Rhodococcus triatomae BKS 15-14, isolated from an ant hill soil sample, collected from Bhitarkanika Mangrove Reserve Forest, Odisha, India. The draft genome of strain BKS 15-14 consists of 5,824,349 bp, with a G+C content of 69%, 5,387 protein-coding genes, and 57 RNAs.
PMCID: PMC3622983  PMID: 23538907
16.  CancerDR: Cancer Drug Resistance Database 
Scientific Reports  2013;3:1445.
Cancer therapies are limited by the development of drug resistance, and mutations in drug targets is one of the main reasons for developing acquired resistance. The adequate knowledge of these mutations in drug targets would help to design effective personalized therapies. Keeping this in mind, we have developed a database “CancerDR”, which provides information of 148 anti-cancer drugs, and their pharmacological profiling across 952 cancer cell lines. CancerDR provides comprehensive information about each drug target that includes; (i) sequence of natural variants, (ii) mutations, (iii) tertiary structure, and (iv) alignment profile of mutants/variants. A number of web-based tools have been integrated in CancerDR. This database will be very useful for identification of genetic alterations in genes encoding drug targets, and in turn the residues responsible for drug resistance. CancerDR allows user to identify promiscuous drug molecules that can kill wide range of cancer cells. CancerDR is freely accessible at
PMCID: PMC3595698  PMID: 23486013
17.  Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon 
Genome Announcements  2013;1(2):e00058-13.
We report the 4.39-Mb draft genome sequence of the 2-chloro-4-nitrophenol-degrading bacterium Arthrobacter sp. strain SJCon, isolated from a pesticide-contaminated site. The draft genome sequence of strain SJCon will be helpful in studying the genetic pathways involved in the degradation of several aromatic compounds.
PMCID: PMC3593328  PMID: 23516196
18.  Genome Sequence of the “Indian Bison Type” Biotype of Mycobacterium avium subsp. paratuberculosis Strain S5 
Genome Announcements  2013;1(1):e00005-13.
We report the 4.79-Mb genome sequence of the “Indian Bison Type” biotype of Mycobacterium avium subsp. paratuberculosis strain S5, isolated from a terminally sick Jamunapari goat at the CIRG (Central Institute for Research on Goats) farm in India. This draft genome will help in studying novelties of this biotype, which is widely distributed in animals and human beings in India.
PMCID: PMC3587920  PMID: 23469332
19.  An undiagnosed left sided traumatic diaphragmatic hernia presenting as small intestinal strangulation: A case report 
Post traumatic diaphragmatic hernia is very often missed particularly in polytrauma patients. We present case of an isolated post traumatic diaphragmatic hernia with strangulation, a very rare finding.
A 35 year old man presented with features of intestinal obstruction with past history of a seemingly trivial blunt thoracic injury 15 years back. Findings of X-ray abdomen and chest with high leukocyte count raised suspicion of obstructed diaphragmatic hernia which on exploration revealed obstructed diaphragmatic hernia with gangrenous bowel segment.
Blunt injury of diaphragm is relatively common and is considered as a marker of severe trauma and it can clinically be occult as other violent injuries may mask and disguise its initial clinical presentation1 resulting in late presentation with obstruction and/or rarely strangulation. An early diagnosis of the condition is prudent to avoid morbidity and mortality associated with late presentations.
In a patient of intestinal obstruction with history of even trivial throraco- abdominal injury, diagnosis of diaphragmatic hernia should be kept in mind.
PMCID: PMC3731691  PMID: 23548705
Strangulation; Traumatic diaphragmatic hernia
20.  Energy efficiency in nanoscale synthesis using nanosecond plasmas 
Scientific Reports  2013;3:1221.
We report a nanoscale synthesis technique using nanosecond-duration plasma discharges. Voltage pulses 12.5 kV in amplitude and 40 ns in duration were applied repetitively at 30 kHz across molybdenum electrodes in open ambient air, generating a nanosecond spark discharge that synthesized well-defined MoO3 nanoscale architectures (i.e. flakes, dots, walls, porous networks) upon polyamide and copper substrates. No nitrides were formed. The energy cost was as low as 75 eV per atom incorporated into a nanostructure, suggesting a dramatic reduction compared to other techniques using atmospheric pressure plasmas. These findings show that highly efficient synthesis at atmospheric pressure without catalysts or external substrate heating can be achieved in a simple fashion using nanosecond discharges.
PMCID: PMC3564032  PMID: 23386976
21.  Genome Sequence of the Oleaginous Red Yeast Rhodosporidium toruloides MTCC 457 
Eukaryotic Cell  2012;11(8):1083-1084.
We report the de novo assembled 20.05-Mb draft genome of the red yeast Rhodosporidium toruloides MTCC 457, predicted to encode 5,993 proteins, 4 rRNAs, and 125 tRNAs. Proteins known to be unique to oleaginous fungi are present among the predicted proteins. The genome sequence will be valuable for molecular genetic analysis and manipulation of lipid accumulation in this yeast and for developing it as a potential host for biofuel production.
PMCID: PMC3416060  PMID: 22858828
22.  Draft Genome Sequence of the Type Species of the Genus Citrobacter, Citrobacter freundii MTCC 1658 
Genome Announcements  2013;1(1):e00120-12.
We report the 5.0-Mb genome sequence of the type species of the genus Citrobacter, Citrobacter freundii strain MTCC 1658, isolated from canal water. This draft genome sequence of C. freundii strain MTCC 1658T consists of 5,001,265 bp with a G+C content of 51.61%, 4,691 protein-coding genes, 70 tRNAs, and 10 rRNAs.
PMCID: PMC3569269  PMID: 23405287
23.  Genome Sequence of the Halotolerant Bacterium Imtechella halotolerans K1T 
Journal of Bacteriology  2012;194(14):3731.
We report the 3.087-Mb genome sequence of Imtechella halotolerans K1T, isolated from an estuarine water sample collected from Kochi, Kerala, India. Strain K1 was recently reported as a novel genus of the family Flavobacteriaceae.
PMCID: PMC3393483  PMID: 22740661
24.  Genome Sequence of the Marine Bacterium Marinilabilia salmonicolor JCM 21150T 
Journal of Bacteriology  2012;194(14):3746.
We report the 4.98-Mb genome sequence of Marinilabilia salmonicolor JCM 21150T, which was isolated from marine mud in the year 1961. The draft genome of strain Marinilabilia salmonicolor JCM 21150T contains 4,982,627 bp with a G+C content of 41.92% and 4,227 protein coding genes, 52 tRNAs, and 3 rRNAs.
PMCID: PMC3393510  PMID: 22740671
25.  Draft Genome Sequence of Salt-Tolerant Yeast Debaryomyces hansenii var. hansenii MTCC 234 
Eukaryotic Cell  2012;11(7):961-962.
Debaryomyces hansenii is one of the most halotolerant species of yeast, and the genome sequence of D. hansenii strain CBS767 is already available. Here we report the 11.46-Mb draft genome of D. hansenii strain MTCC 234, which is even more halotolerant than strain CBS767. Comparative analysis of these sequences would definitely provide further insight into the halotolerance of this yeast.
PMCID: PMC3416502  PMID: 22744717

Results 1-25 (37)