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https://www.readbyqxmd.com/read/27907129/meningococcal-carriage-in-military-recruits-and-university-students-during-the-pre-menb-vaccination-era-in-greece-2014-2015
#1
Kyriaki Tryfinopoulou, Konstantinos Kesanopoulos, Athanasia Xirogianni, Nektarios Marmaras, Anastasia Papandreou, Vassiliki Papaevangelou, Maria Tsolia, Aftab Jasir, Georgina Tzanakaki
PURPOSE: The aim of the study was to estimate the meningococcal carriage rate and to identify the genotypic characteristics of the strains isolated from healthy military recruits and university students in order to provide data that might increase our understanding on the epidemiology of meningococcus and obtain information which helps to evaluate the potential effects on control programs such as vaccination. METHODS: A total of 1420 oropharyngeal single swab samples were collected from military recruits and university students on voluntary basis, aged 18-26 years...
2016: PloS One
https://www.readbyqxmd.com/read/27899957/next-generation-sequencing-in-nsclc-and-melanoma-patients-a-cost-and-budget-impact-analysis
#2
Rosa A van Amerongen, Valesca P Retèl, Veerle Mh Coupé, Petra M Nederlof, Maartje J Vogel, Wim H van Harten
Next-generation sequencing (NGS) has reached the molecular diagnostic laboratories. Although the NGS technology aims to improve the effectiveness of therapies by selecting the most promising therapy, concerns are that NGS testing is expensive and that the 'benefits' are not yet in relation to these costs. In this study, we give an estimation of the costs and an institutional and national budget impact of various types of NGS tests in non-small-cell lung cancer (NSCLC) and melanoma patients within The Netherlands...
2016: Ecancermedicalscience
https://www.readbyqxmd.com/read/27899564/genbank
#3
Dennis A Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi, David J Lipman, James Ostell, Eric W Sayers
GenBank(®) (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for 370 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or the NCBI Submission Portal. GenBank staff assign accession numbers upon data receipt...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895637/high-prevalence-of-esbl-producing-klebsiella-pneumoniae-causing-community-onset-infections-in-china
#4
Jing Zhang, Kai Zhou, Beiwen Zheng, Lina Zhao, Ping Shen, Jinru Ji, Zeqing Wei, Lanjuan Li, Jianying Zhou, Yonghong Xiao
The aim of this work was to investigate the epidemiological and genetic characteristics of ESBL-producing Klebsiella pneumoniae (ESBL-Kp) causing community-onset infections. K. pneumoniae isolates were collected from 31 Chinese secondary hospitals between August 2010 and 2011. Genes encoding ESBL and AmpC beta-lactamases were detected by PCR. The isolates were assigned to sequence types (STs) using multi-locus sequence typing (MLST). Eleven ESBL-Kp strains were selected for whole-genome sequencing (WGS) for investigating the genetic environment and plasmids encoding ESBL genes...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27890457/the-role-of-whole-genome-sequencing-wgs-in-antimicrobial-susceptibility-testing-of-bacteria-report-from-the-eucast-subcommittee
#5
REVIEW
Matthew J Ellington, Oskar Ekelund, Frank M Aarestrup, Rafael Canton, Michel Doumith, Christian Giske, Hajo Grundman, Henrik Hasman, Matthew Holden, Katie L Hopkins, Jon Iredell, Gunnar Kahlmeter, Claudio U Köser, Alasdair MacGowan, Dik Mevius, Mike Mulvey, Thierry Naas, Tim Peto, Jean-Marc Rolain, Ørjan Samuelsen, Neil Woodford
Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion...
November 23, 2016: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/27889877/maldi-tof-ms-meets-wgs-in-a-vre-outbreak-investigation
#6
S Schlebusch, G R Price, R L Gallagher, V Horton-Szar, L D H Elbourne, P Griffin, D J Venter, S O Jensen, S J Van Hal
The use of MALDI-TOF MS (matrix-assisted laser desorption/ ionization-time of flight mass spectrometry) and WGS (whole genome sequencing) has been described for identification and strain relatedness determination. We describe the complementary use of MALDI-TOF MS and WGS in a VRE (vancomycin-resistant enterococci) outbreak investigation, and discuss some of the challenges with defining strain similarity across these two platforms. Although both assays indicated multiple clusters involved in the outbreak of vancomycin resistant Enterococcus faecium isolates from positive blood cultures of four haematology-oncology patients, the small cohort and discrepancies between findings indicate the limitations of MALDI-TOF MS and the cautious interpretation of MALDI-TOF MS dendrograms during outbreaks...
November 26, 2016: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/27888547/towards-a-whole-genome-sequence-for-rye-secale-cereale-l
#7
Eva Bauer, Thomas Schmutzer, Ivan Barilar, Martin Mascher, Heidrun Gundlach, Mihaela M Martis, Sven O Twardziok, Bernd Hackauf, Andres Gordillo, Peer Wilde, Malthe Schmidt, Viktor Korzun, Klaus F X Mayer, Karl Schmid, Chris-Carolin Schön, Uwe Scholz
We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun (WGS) sequencing of the 7.9 Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27,784 rye gene models based on homology to sequenced grass genomes...
November 26, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27888232/parents-perspectives-on-whole-genome-sequencing-for-their-children-qualified-enthusiasm
#8
J A Anderson, M S Meyn, C Shuman, R Zlotnik Shaul, L E Mantella, M J Szego, S Bowdin, N Monfared, R Z Hayeems
OBJECTIVE: To better understand the consequences of returning whole genome sequencing (WGS) results in paediatrics and facilitate its evidence-based clinical implementation, we studied parents' experiences with WGS and their preferences for the return of adult-onset secondary variants (SVs)-medically actionable genomic variants unrelated to their child's current medical condition that predict adult-onset disease. METHODS: We conducted qualitative interviews with parents whose children were undergoing WGS as part of the SickKids Genome Clinic, a research project that studies the impact of clinical WGS on patients, families, and the healthcare system...
November 25, 2016: Journal of Medical Ethics
https://www.readbyqxmd.com/read/27881973/livestock-associated-methicillin-resistant-staphylococcus-aureus-la-mrsa-clonal-complex-cc-398-isolated-from-uk-animals-belong-to-european-lineages
#9
Meenaxi Sharma, Javier Nunez-Garcia, Angela M Kearns, Michel Doumith, Patrick R Butaye, M Angeles Argudín, Angela Lahuerta-Marin, Bruno Pichon, Manal AbuOun, Jon Rogers, Richard J Ellis, Christopher Teale, Muna F Anjum
In recent years, there has been an increase in the number of livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 recovered from S. aureus isolated animals in the UK. To determine possible origins of 12 LA-MRSA CC398 isolates collected after screening more than a thousand S. aureus animal isolates from the UK between 2013 and 2015, whole genome sequences (WGS) of CC398 European, including UK, and non-European isolates from diverse animal hosts were compared. Phylogenetic reconstruction applied to WGS data to assess genetic relatedness of all 89 isolates, clustered the 12 UK CC398 LA-MRSA within the European sub-lineages, although on different nodes; implicating multiple independent incursions into the UK, as opposed to a single introduction followed by clonal expansion...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27875980/comparative-genomics-of-european-avian-pathogenic-e-coli-apec
#10
Guido Cordoni, Martin J Woodward, Huihai Wu, Mishaal Alanazi, Tim Wallis, Roberto M La Ragione
BACKGROUND: Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. However, the diversity between isolates remains poorly understood. Here, a total of 272 APEC isolates collected from the United Kingdom (UK), Italy and Germany were characterised using multiplex polymerase chain reactions (PCRs) targeting 22 equally weighted factors covering virulence genes, R-type and phylogroup. Following these analysis, 95 of the selected strains were further analysed using Whole Genome Sequencing (WGS)...
November 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27874836/whole-genome-sequence-snp-chips-and-pedigree-structure-building-demographic-profiles-in-domestic-dog-breeds-to-optimize-genetic-trait-mapping
#11
Dayna L Dreger, Maud Rimbault, Brian W Davis, Adrienne Bhatnagar, Heidi G Parker, Elaine A Ostrander
In the decade following publication of the draft genome sequence of the domestic dog, extraordinary advances with application to several fields have been credited to the canine genetic system. Taking advantage of closed breeding populations and the subsequent selection for aesthetic and behavioral characteristics, researchers have leveraged the dog as an effective natural model for the study of complex traits, such as disease susceptibility, behavior, and morphology, generating unique contributions to human health and biology...
November 17, 2016: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/27871225/genomic-epidemiology-of-lineage-4-mycobacterium-tuberculosis-subpopulations-in-new-york-city-and-new-jersey-1999-2009
#12
Tyler S Brown, Apurva Narechania, John R Walker, Paul J Planet, Pablo J Bifani, Sergios-Orestis Kolokotronis, Barry N Kreiswirth, Barun Mathema
BACKGROUND: Whole genome sequencing (WGS) has rapidly become an important research tool in tuberculosis epidemiology and is likely to replace many existing methods in public health microbiology in the near future. WGS-based methods may be particularly useful in areas with less diverse Mycobacterium tuberculosis populations, such as New York City, where conventional genotyping is often uninformative and field epidemiology often difficult. This study applies four candidate strategies for WGS-based identification of emerging M...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27865400/new-mycobacterium-tuberculosis-lam-sublineage-with-geographical-specificity-for-the-old-world-revealed-by-phylogenetical-and-bayesian-analyses
#13
Yann Reynaud, Nalin Rastogi
We recently showed that the Mycobacterium tuberculosis sublineage LAM9 could be subdivided as two distinct subpopulations - each reflecting its unique biogeographical structure and evolutionary history. We subsequently attempted to verify if this genetic structuration could be traced in an enlarged global sample. For this purpose, we analyzed global evolutionary relationships of LAM strains in a large dataset (n = 1923 isolates from 35 countries worldwide) with concomitant spoligotyping and MIRU-VNTR data, followed by a deeper analysis of LAM9 sublineage (n = 851 isolates)...
December 2016: Tuberculosis
https://www.readbyqxmd.com/read/27865394/recent-developments-in-genomics-bioinformatics-and-drug-discovery-to-combat-emerging-drug-resistant-tuberculosis
#14
REVIEW
Soumya Swaminathan, Jagadish Chandrabose Sundaramurthi, Alangudi Natarajan Palaniappan, Sujatha Narayanan
Emergence of drug-resistant tuberculosis (DR-TB) is a big challenge in TB control. The delay in diagnosis of DR-TB leads to its increased transmission, and therefore prevalence. Recent developments in genomics have enabled whole genome sequencing (WGS) of Mycobacterium tuberculosis (M. tuberculosis) from 3-day-old liquid culture and directly from uncultured sputa, while new bioinformatics tools facilitate to determine DR mutations rapidly from the resulting sequences. The present drug discovery and development pipeline is filled with candidate drugs which have shown efficacy against DR-TB...
December 2016: Tuberculosis
https://www.readbyqxmd.com/read/27863452/mutation-in-non-coding-rna-rnu12-causes-early-onset-cerebellar-ataxia
#15
Mahmoud Fawzi Elsaid, Nader Chalhoub, Tawfeg Ben-Omran, Pankaj Kumar, Hussein Kamel, Khalid Ibrahim, Yasmin Mohamoud, Eman Al-Dous, Iman Al-Azwani, Joel A Malek, Karsten Suhre, M Elizabeth Ross, Alice Abdel Aleem
OBJECTIVE: Exome sequences account for only 2% of the genome and may overlook mutations causing disease. To obtain a more complete view, whole genome sequencing (WGS) was analyzed in a large consanguineous family in which members displayed autosomal recessively inherited cerebellar ataxia manifesting before two years of age. METHODS: WGS from blood derived gDNA was used for homozygosity mapping and a rare variant search. RNA from isolated blood leukocytes was used for quantitative PCR, RNA sequencing and comparison of the transcriptomes of affected and unaffected family members...
November 18, 2016: Annals of Neurology
https://www.readbyqxmd.com/read/27852675/serotype-distribution-population-structure-and-antimicrobial-resistance-of-group-b-streptococcus-strains-recovered-from-colonized-pregnant-women
#16
Sarah Teatero, Patricia Ferrieri, Irene Martin, Walter Demczuk, Allison McGeer, Nahuel Fittipaldi
Using serotyping, multilocus sequence typing and whole-genome sequencing (WGS) of selected strains, we studied the population structure of 102 group B Streptococcus isolates prospectively sampled in 2014 from vaginal/rectal swabs of healthy pregnant women in metropolitan Toronto, Canada. We also determined the susceptibilities of all colonizing isolates to penicillin, erythromycin, clindamycin, tetracycline and other antimicrobial agents. Overall, we observed a high rate of tetracycline resistance (89%) among colonizing GBS...
November 16, 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27846907/copy-number-analysis-by-low-coverage-whole-genome-sequencing-using-ultra-low-input-dna-from-formalin-fixed-paraffin-embedded-tumor-tissue
#17
Tanjina Kader, David L Goode, Stephen Q Wong, Jacquie Connaughton, Simone M Rowley, Lisa Devereux, David Byrne, Stephen B Fox, Gisela Mir Arnau, Richard W Tothill, Ian G Campbell, Kylie L Gorringe
Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays...
November 15, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27830191/comparative-genome-analysis-of-extended-spectrum-%C3%AE-lactamase-producing-escherichia-coli-sequence-type-131-strains-from-nepal-and-japan
#18
Tohru Miyoshi-Akiyama, Jatan Bahadur Sherchan, Yohei Doi, Maki Nagamatsu, Jeevan B Sherchand, Sarmila Tandukar, Norio Ohmagari, Teruo Kirikae, Hiroshi Ohara, Kayoko Hayakawa
The global spread of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) has largely been driven by the pandemic sequence type 131 (ST131). This study aimed to determine the molecular epidemiology of their spread in two Asian countries with contrasting prevalence. We conducted whole-genome sequencing (WGS) of ESBL-E. coli ST131 strains collected prospectively from Nepal and Japan, two countries in Asia with a high and low prevalence of ESBL-E. coli, respectively. We also systematically compared these genomes with those reported from other regions using publicly available WGS data for E...
September 2016: MSphere
https://www.readbyqxmd.com/read/27828398/mode-tailoring-in-subwavelength-dimensional-semiconductor-micro-nanowaveguides-by-coupling-optical-microfibers
#19
Fuxing Gu, Hongbin Cui, Feng Liao, Xing Lin, Haifeng Wang, Heping Zeng
Benefitted from large fraction of evanescent wave and high endface reflectivity, we have realized mode tailoring in subwavelength-dimensional semiconductor micro/nanowaveguides (MN-WGs) by coupling optical silica microfibers. By investigating the reflection spectra, it was found that the microfiber tips could offer effective reflection and can been used to continuously and reversibly tune the interference wavelengths by changing the contact points with the MN-WGs. The measured extinction ratio in the interference patterns was as high as ~10 dB...
October 3, 2016: Optics Express
https://www.readbyqxmd.com/read/27824078/pgadb-builder-a-web-service-tool-for-creating-pan-genome-allele-database-for-molecular-fine-typing
#20
Yen-Yi Liu, Chien-Shun Chiou, Chih-Chieh Chen
With the advance of next generation sequencing techniques, whole genome sequencing (WGS) is expected to become the optimal method for molecular subtyping of bacterial isolates. To use WGS as a general subtyping method for disease outbreak investigation and surveillance, the layout of WGS-based typing must be comparable among laboratories. Whole genome multilocus sequence typing (wgMLST) is an approach that achieves this requirement. To apply wgMLST as a standard subtyping approach, a pan-genome allele database (PGAdb) for the population of a bacterial organism must first be established...
November 8, 2016: Scientific Reports
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