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.
Ventilator associated pneumonia; aetiology; drug resistance
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.
Candida co-infection; C. glabrata; prevalence; tuberculosis
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 (http://crdd.osdd.net/raghava/genomesrs/burkholderia/).
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.
VAP; incidence; risk factors
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.
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.
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.
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.
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.
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.
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 http://crdd.osdd.net/raghava/cancerdr/
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.
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.
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.
PRESENTATION OF CASE
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.
Strangulation; Traumatic diaphragmatic hernia
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.
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.
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.
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.
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.
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.
We report the 8.231-Mb genome sequence of Rhodococcus imtechensis RKJ300, isolated from pesticide-contaminated soil in Punjab, India. The genome sequence of the strain RKJ300 will be helpful in exploring the molecular pathways involved in the degradation of nitrophenols.
Urinary tract infections are the most commonly acquired bacterial infections and they account for an estimated 25-40% of the nosocomial infections. The microbial biofilms pose a public health problem for the persons who require indwelling medical devices, as the microorganisms in the biofilms are difficult to treat with antimicrobial agents.
The present study included the isolation and the biofilm formation of the uropathogens in patients with catheter associated urinary tract infections.
Methods and Materials
This prospective analysis which was carried out over a period of two months, included 50 urine samples from catheterized patients with symptoms of UTI. Following their isolation and identification, all the isolates were subjected to the biofilm detection by the tube adherence method and the Congo Red agar method.
E.coli was found to be the most frequently isolated uropathogen 35(70%), followed by Klebsiella pneumoniae 8(16%), Pseudomona aeruginosa 2(4%), Acinetobacter spp 1(2%), coagulase negative Staphylococci 3(6%) and Enterococci spp 1(2%). In the current study, 30 (60%) strains were positive in vitro for the biofilm production.
To conclude, there was significant bacteriuria in all the symptomatic catheterized patients and E.coli was the most frequent isolate. Diabetes (44%) was the most common factor which was associated with the UTIs in the catheterized patients.
Biofilm; Uropathogens; The tube adherence method; The Congo Red agar method
We report the 7.85-Mb genome sequence of Burkholderia sp. strain SJ98, isolated from agricultural fields of Assam, India. The draft genome of this strain will be helpful in studying the genetic pathways involved in the degradation of aromatic compounds.
Microbial biofilms pose a public health problem for persons requiring indwelling medical devices, as micro-organisms in biofilms are difficult to treat with antimicrobial agents. Thus the present study includes biofilm formation and antibiotic resistance pattern of uropathogens in hospitalised patients with catheter associated urinary tract infections (UTI).
This prospective analysis included 100 urine samples from catheterised patients with symptoms of UTI over a period of six months. Following identification, all isolates were subjected to antibiotic sensitivity using modified Kirby- Bauer disc diffusion method. Detection of biofilms was done by tube adherence method and Congo red agar method.
E.coli was found to be the most frequently isolated uropathogen 70%, followed by Klebsiella pneumoniae 16%, Pseudomonas aeruginosa 4%, Acinetobacter spp 2%, coagulase negative Staphylococci 6% and Enterococci Spp 2%. In the current study 60% of strains were in vitro positive for biofilm production. Biofilm positive isolates showed 93.3%, 83.3%, 73.3% and 80% resistance to nalidixic acid, ampicillin, cephotaxime and cotrimoxazole, respectively, compared to 70%, 60%, 35%, 60% resistance showed by biofilm non-producers for the respective antibiotics. Approximately 80% of the biofilm producing strains showed multidrug resistant phenotype
To conclude E.coli was the most frequent isolate, of which 63% were biofilm producers. The antibiotic susceptibility pattern in the present study showed quinolones were the least active drug against uropathogens. The uropathogens showed the highest sensitivity to carbapenems. The next best alternatives were aminoglycosides. Significant correlation between biofilm production and multi-drug resistance was observed in our study.
Biofilm; Uropathogens; Tube adherence method; Congo red agar method
We studied the prevalence of ceftazidime resistance in Pseudomonas aeruginosa and the rates of extended-spectrum β-lactamase (ESBL), AmpC β-lactamase (AmpC) and metallo-β-lactamase (MBL) production among the ceftazidime resistant Pseudomonas aeruginosa. A very high rate of MBL production was observed, which suggested it to be an important contributing factor for ceftazidime resistance among Pseudomonas aeruginosa.
Extended-spectrum β-lactamases; AmpC; metallo-β-lactamases; ceftazidime resistance; Pseudomonas aeruginosa