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Digital data of quality control strains under general deposit at Microbial Culture Collection (MCC), NCCS, Pune, India: A bioinformatics approach.

ABSTRACT: A total of 13 short DNA sequences of quality control strains (MCC 2052, MCC 2077, MCC 2078, MCC 2080, MCC 2309, MCC 2322, MCC 2408, MCC 2409, MCC 2412, MCC 2413, MCC 2415, MCC 2483 and MCC 2515) were retrieved from NCBI BioSample database and generated quick response (QR) codes for sequences. 16S rRNA was used for creation of Chaose Game representation (CGR), Chaose Game Representation of Frequencies (FCGR) and measurement of GC percentage. Digital data in the form of QR codes, CGR, FCGR and GC plot would be useful for identification, visual comparison and evaluation of newly isolated strains with quality control strains. The digital data of QR codes, CGR, FCGR and GC content all the quality control strains are made available to users through this paper. This generated digital data helps to evaluate and compare newly isolated strains, less laborious and avoid misinterpretation of newly isolated species.

SUBMITTER: Rekadwad BN

PROVIDER: S-EPMC4865665 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Digital data of quality control strains under general deposit at Microbial Culture Collection (MCC), NCCS, Pune, India: A bioinformatics approach.

Rekadwad Bhagwan N BN Khobragade Chandrahasya N CN

Data in brief 20160426

A total of 13 short DNA sequences of quality control strains (MCC 2052, MCC 2077, MCC 2078, MCC 2080, MCC 2309, MCC 2322, MCC 2408, MCC 2409, MCC 2412, MCC 2413, MCC 2415, MCC 2483 and MCC 2515) were retrieved from NCBI BioSample database and generated quick response (QR) codes for sequences. 16S rRNA was used for creation of Chaose Game representation (CGR), Chaose Game Representation of Frequencies (FCGR) and measurement of GC percentage. Digital data in the form of QR codes, CGR, FCGR and GC ...[more]

PMID: 27222847

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Project description:Background and aimThe main purpose of a national bioresource center is to standardize, centralize, preserve, and ensure accessibility of microbial bioresources that accumulate there because of state research programs. The establishment of national bioresource centers for antibiotic-resistant microorganisms allows to solve practical problems in the field of veterinary service, as well as to develop effective chemotherapeutic and disinfectant drugs to overcome the mechanisms of resistance. This study aimed to outline the process of forming a national culture collection of antibiotic-resistant strains of zoonotic bacteria in the Russian Federation using two microbial strains.Materials and methodsThe object of research was isolates of Salmonella spp., Escherichia coli, Enterococcus spp., Campylobacter spp., Listeria monocytogenes, and Staphylococcus spp., all of which were obtained from biomaterials of farm animals, feed samples, bedding, water from livestock buildings, washouts from environmental objects, and food products. The resistance of bacterial isolates was determined using microbiological and molecular-genetic research methods.ResultsDuring monitoring studies, 1489 bacterial isolates were isolated. In total, 408 bacterial isolates were tested for sensitivity to antimicrobial agents, including E. coli (47.6%), Salmonella spp. (30.4%), Enterococcus spp. (11.3%), and Campylobacter spp. (10.8%). For genetic characterization, 95 isolates of Salmonella enterica, E. coli, Campylobacter spp., L. monocytogenes, Staphylococcus spp., Enterococcus spp. were chosen from the research collection, which was formed as part of the monitoring program for antibiotic resistance.ConclusionDeposited isolates that underwent whole-genome analysis can be used as positive control samples both in the development and use of methods or test systems for the detection of various resistance genes in zoonotic bacteria. In addition, such isolates can also be used for microbiological studies related to determining the sensitivity of microorganisms to antibacterial drugs, for phenotypic studies in the diagnosis of various bacterial infections in animals and birds, and retrospective analysis of strains from numerous collections.

Project description:BackgroundIndia has among the highest rates of infant malnutrition. Few studies investigating the growth patterns of HIV-exposed infants in India or the impact of timing of HIV infection on growth in settings such as India exist.MethodsWe used data from the Six Week Extended Nevirapine (SWEN) trial to compare the growth patterns of HIV-infected and HIV-exposed but uninfected infants accounting for timing of HIV infection, and to identify risk factors for stunting, underweight and wasting. Growth and timing of HIV infection were assessed at weeks 1, 2, 4, 6, 10, 14 weeks and 6, 9, 12 months of life. Random effects multivariable logistic regression method was used to assess factors associated with stunting, underweight and wasting.ResultsAmong 737 HIV-exposed infants, 93 (13%) were HIV-infected by 12 months of age. Among HIV-infected and uninfected infants, baseline prevalence of stunting (48% vs. 46%), underweight (27% vs. 26%) and wasting (7% vs. 11%) was similar (p>0.29), but by 12 months stunting and underweight, but not wasting, were significantly higher in HIV-infected infants (80% vs. 56%, 52% vs. 29%, p< 0.0001; 5% vs. 6%, p=0.65, respectively). These differences rapidly manifested within 4-6 weeks of birth. Infants infected in utero had the worst growth outcomes during the follow-up period. SWEN was associated with non-significant reductions in stunting and underweight among HIV-infected infants and significantly less wasting in HIV-uninfected infants. In multivariate analysis, maternal CD4 < 250, infant HIV status, less breastfeeding, low birth weight, non-vaginal delivery, and infant gestational age were significant risk factors for underweight and stunting.ConclusionBaseline stunting and underweight was high in both HIV-infected and uninfected infants; growth indices diverged early and were impacted by timing of infection and SWEN prophylaxis. Early growth monitoring of all HIV-exposed infants is an important low-cost strategy for improving health and survival outcomes of these infants.Trial registrationNCT00061321.

Dataset Information

Digital data of quality control strains under general deposit at Microbial Culture Collection (MCC), NCCS, Pune, India: A bioinformatics approach.

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Digital data of quality control strains under general deposit at Microbial Culture Collection (MCC), NCCS, Pune, India: A bioinformatics approach.

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