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https://www.readbyqxmd.com/read/28729954/clinical-streptococcal-isolates-distinct-from-streptococcus-pneumoniae-but-containing-the-%C3%AE-glucosyltransferase-tts-gene-and-expressing-serotype-37-capsular-polysaccharide
#1
Carmen L Sheppard, Georgia Kapatai, Karen Broughton, Ulf Schaefer, Matthew Hannah, David J Litt, Norman K Fry
The major virulence factor of the pneumococcus, and target for conjugate vaccines, is the polysaccharide capsule, which is usually encoded by the highly variable cps locus. Serotype 37 is an unusual pneumococcal type in which the single β-glucosyltransferase gene responsible for serotype capsule production (tts) is located outside of the capsular operon region. Using a previously described automated whole genome sequence (WGS)-based serotyping bioinformatics tool, PneumoCaT, we identified and investigated seven clinical isolates (three from blood cultures) of non-pneumococcal streptococci containing a highly homologous tts and included them in a study panel of 20 isolates which included a 11 further clinical isolates of S...
2017: PeerJ
https://www.readbyqxmd.com/read/28729679/a-population-specific-reference-panel-empowers-genetic-studies-of-anabaptist-populations
#2
Liping Hou, Rachel L Kember, Jared C Roach, Jeffrey R O'Connell, David W Craig, Maja Bucan, William K Scott, Margaret Pericak-Vance, Jonathan L Haines, Michael H Crawford, Alan R Shuldiner, Francis J McMahon
Genotype imputation is a powerful strategy for achieving the large sample sizes required for identification of variants underlying complex phenotypes, but imputation of rare variants remains problematic. Genetically isolated populations offer one solution, however population-specific reference panels are needed to assure optimal imputation accuracy and allele frequency estimation. Here we report the Anabaptist Genome Reference Panel (AGRP), the first whole-genome catalogue of variants and phased haplotypes in people of Amish and Mennonite ancestry...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717172/evolution-of-the-pseudomonas-aeruginosa-mutational-resistome-in-an-international-cystic-fibrosis-clone
#3
Carla López-Causapé, Lea Mette Sommer, Gabriel Cabot, Rosa Rubio, Alain A Ocampo-Sosa, Helle Krogh Johansen, Joan Figuerola, Rafael Cantón, Timothy J Kidd, Soeren Molin, Antonio Oliver
Emergence of epidemic clones and antibiotic resistance development compromises the management of Pseudomonas aeruginosa cystic fibrosis (CF) chronic respiratory infections. Whole genome sequencing (WGS) was used to decipher the phylogeny, interpatient dissemination, WGS mutator genotypes (mutome) and resistome of a widespread clone (CC274), in isolates from two highly-distant countries, Australia and Spain, covering an 18-year period. The coexistence of two divergent CC274 clonal lineages was revealed, but without evident geographical barrier; phylogenetic reconstructions and mutational resistome demonstrated the interpatient transmission of mutators...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716462/rapid-identification-of-a-mycobacterium-tuberculosis-full-genetic-drug-resistance-profile-through-whole-genome-sequencing-directly-from-sputum
#4
Camus Nimmo, Ronan Doyle, Carrie Burgess, Rachel Williams, Rebecca Gorton, Timothy D McHugh, Mike Brown, Stephen Morris-Jones, Helen Booth, Judith Breuer
INTRODUCTION: Resistance to second line tuberculosis drugs is common, but slow to diagnose with phenotypic drug sensitivity testing. Rapid molecular tests speed up diagnosis, but can only detect limited mutations. Whole genome sequencing (WGS) of culture isolates can generate a complete genetic drug resistance profile, but is delayed by the initial culture step. We previously successfully achieved WGS directly from sputum using targeted enrichment. CASE REPORT: A 29-year-old Nigerian lady was diagnosed with tuberculosis...
July 14, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28712319/primary-liver-cancer-genome-sequencing-translational-implications-and-challenges
#5
Demosthenes E Ziogas, Ioannis D Kyrochristos, Georgios K Glantzounis, Dimitrios Christodoulou, Evangelos Felekouras, Dimitrios H Roukos
The prognosis of primary liver cancer (PLC) remains poor and is explained by the slow progress in understanding the molecular pathways driving tumorigenesis, therapeutic resistance and relapse. For early PLCs, complete surgical resection is the only effective treatment, with sorafenib and, more recently, regorafenib prolonging overall survival by a few months. Areas covered: Application of next-generation sequencing (NGS), including targeted NGS (tNGS), whole-exome sequencing (WES), whole-genome sequencing (WGS) and RNA sequencing (RNAseq), on clinical samples from patients with hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) could aid in comprehending tumorigenesis, genetic and genomic heterogeneity, as well as developing molecular classifications for specialized targeted therapy...
July 17, 2017: Expert Review of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28711315/characterization-of-mobile-genetic-elements-carrying-vim-1-and-kpc-2-carbapenemases-in-citrobacter-freundii-isolates-in-madrid
#6
Jennifer Villa, David M Arana, Esther Viedma, Dafne Perez-Montarelo, Fernando Chaves
Carbapenemase producing Citrobacter freundii (CPCF) infections are still uncommon in European countries. Here we report a molecular study conducted in a tertiary care facility in southern Madrid, Spain, from 2009 to 2014 to investigate the epidemiology of CPCF. The blaIMP-1,blaIMP-2,blaKPC,blaNDM,blaOXA-48,blaVIM-1 and blaVIM-2 genes were screened by PCR. Molecular typing was carried out by Pulsed-field gel electrophoresis analysis (PFGE) and multilocus sequence typing (MLST). Whole genome sequencing (WGS) was performed to characterize the resistome and the mobile genetic elements associated with the carbapenems resistance of CPCF...
July 8, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/28710117/genetic-and-epigenetic-drivers-of-neuroendocrine-tumors-net
#7
Annunziata Di Domenico, Tabea Wiedmer, Ilaria Marinoni, Aurel Perren
Neuroendocrine tumors (NET) of the gastrointestinal tract and the lung are a rare and heterogeneous group of tumors. The molecular characterization and the clinical classification of these tumors have been evolving slowly and show differences according to organs of origin. Novel technologies such as next-generation sequencing revealed new molecular aspects of NET over the last years. Notably, whole exome/genome sequencing (WES/WGS) approaches underlined the very low mutation rate of well differentiated NET of all organs compared to other malignancies, while the engagement of epigenetic changes in driving NET evolution is emerging...
July 14, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28706569/supercritical-antisolvent-precipitation-of-amorphous-copper-zinc-georgeite-and-acetate-precursors-for-the-preparation-of-ambient-pressure-water-gas-shift-copper-zinc-oxide-catalysts
#8
Paul J Smith, Simon A Kondrat, James H Carter, Philip A Chater, Jonathan K Bartley, Stuart H Taylor, Michael S Spencer, Graham J Hutchings
A series of copper-zinc acetate and zincian georgeite precursors have been produced by supercritical CO2 antisolvent (SAS) precipitation as precursors to Cu/ZnO catalysts for the water gas shift (WGS) reaction. The amorphous materials were prepared by varying the water/ethanol volumetric ratio in the initial metal acetate solutions. Water addition promoted georgeite formation at the expense of mixed metal acetates, which are formed in the absence of the water co-solvent. Optimum SAS precipitation occurs without water to give high surface areas, whereas high water content gives inferior surface areas and copper-zinc segregation...
May 10, 2017: ChemCatChem
https://www.readbyqxmd.com/read/28697278/when-more-really-means-more-wgs-standards-and-quality-control
#9
George P Patrinos
No abstract text is available yet for this article.
August 2017: Human Mutation
https://www.readbyqxmd.com/read/28696555/copy-number-variants-detection-by-low-pass-whole-genome-sequencing
#10
Zirui Dong, Weiwei Xie, Haixiao Chen, Jinjin Xu, Huilin Wang, Yun Li, Jun Wang, Fang Chen, Kwong Wai Choy, Hui Jiang
Emerging studies have demonstrated that whole-genome sequencing (WGS) is an efficient tool for copy-number variants (CNV) detection, particularly in probe-poor regions, as compared to chromosomal microarray analysis (CMA). However, the cost of testing is beyond economical for routine usage and the lengthy turn-around time is not ideal for clinical implementation. In addition, the demand for computational resources also reduces the probability of clinical integration into each laboratory. Herein, a protocol providing CNV detection from low-pass, whole-genome sequencing (0...
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28694793/comparative-genomic-characterization-of-the-highly-persistent-and-potentially-virulent-cronobacter-sakazakii-st83-cc65-strain-h322-and-other-st83-strains
#11
Hannah R Chase, Gopal R Gopinath, Athmanya K Eshwar, Andrea Stoller, Claudia Fricker-Feer, Jayanthi Gangiredla, Isha R Patel, Hediye N Cinar, HyeJin Jeong, ChaeYoon Lee, Flavia Negrete, Samantha Finkelstein, Roger Stephan, Ben D Tall, Angelika Lehner
Cronobacter (C.) sakazakii is an opportunistic pathogen and has been associated with serious infections with high mortality rates predominantly in pre-term, low-birth weight and/or immune compromised neonates and infants. Infections have been epidemiologically linked to consumption of intrinsically and extrinsically contaminated lots of reconstituted powdered infant formula (PIF), thus contamination of such products is a challenging task for the PIF producing industry. We present the draft genome of C. sakazakii H322, a highly persistent sequence type (ST) 83, clonal complex (CC) 65, serotype O:7 strain obtained from a batch of non-released contaminated PIF product...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28694792/context-is-everything-harmonization-of-critical-food-microbiology-descriptors-and-metadata-for-improved-food-safety-and-surveillance
#12
Emma Griffiths, Damion Dooley, Morag Graham, Gary Van Domselaar, Fiona S L Brinkman, William W L Hsiao
Globalization of food networks increases opportunities for the spread of foodborne pathogens beyond borders and jurisdictions. High resolution whole-genome sequencing (WGS) subtyping of pathogens promises to vastly improve our ability to track and control foodborne disease, but to do so it must be combined with epidemiological, clinical, laboratory and other health care data (called "contextual data") to be meaningfully interpreted for regulatory and health interventions, outbreak investigation, and risk assessment...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28691770/influence-of-the-water-phase-state-on-the-thermodynamics-of-aqueous-phase-reforming-for-hydrogen-production
#13
Séverine Le Gac, Renée M Ripken, Jan Meuldijk, Johannes G E Gardeniers
Hydrogen is a promising renewable energy source that can be produced from biomass using Aqueous Phase Reforming (APR). Here, using data obtained from AspenPlus and the literature, we evaluated the phase state, temperature-dependent enthalpy, and Gibbs free energy for the APR of small biomass model substrates. Phase equilibrium studies reveal that, under typical APR reaction conditions, the reaction mixture is in the liquid phase. Therefore, we show for the first time that the water-gas-shift (WGS), which is the second main reaction of APR, must be modeled in the liquid phase, resulting in an endothermic instead of an exothermic enthalpy of reaction...
July 10, 2017: ChemSusChem
https://www.readbyqxmd.com/read/28686503/characterization-of-carbapenem-resistant-escherichia-coli-isolates-through-the-whole-genome-sequencing-analysis
#14
Yanping Luo, Rong Luo, Hong Ding, Xiu Ren, Haipeng Luo, Ying Zhang, Liyan Ye, Shenghui Cui
Limited studies have characterized multiple carbapenem-resistant Escherichia coli isolates and compared their genetic characteristics through whole-genome sequencing (WGS) because of the scarcity of these isolates. In this study, we determined the prevalence of carbapenem resistance in 2,993 E. coli isolates collected from three Chinese hospitals. The carbapenem-resistant isolates were further characterized by WGS, and the molecular epidemiological characters and resistance mechanisms were explored through the publicly available platforms from the Center for Genomic Epidemiology...
July 7, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28681718/co-circulation-of-multiple-subtypes-of-enterovirus-a71-ev-a71-genotype-c-including-novel-recombinants-characterised-by-use-of-whole-genome-sequencing-wgs-denmark-2016
#15
Sofie E Midgley, Astrid G Nielsen, Ramona Trebbien, Mille W Poulsen, Peter H Andersen, Thea K Fischer
In Europe, enterovirus A71 (EV-A71) has primarily been associated with sporadic cases of neurological disease. The recent emergence of new genotypes and larger outbreaks with severely ill patients demonstrates a potential for the spread of new, highly pathogenic EV-A71 strains. Detection and characterisation of these new emerging EV variants is challenging as standard EV assays may not be adequate, necessitating the use of whole genome analysis.
June 29, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28671645/qtl-mapping-and-crispr-cas9-editing-to-identify-a-drug-resistance-gene-in-toxoplasma-gondii
#16
Bang Shen, Robin H Powell, Michael S Behnke
Scientific knowledge is intrinsically linked to available technologies and methods. This article will present two methods that allowed for the identification and verification of a drug resistance gene in the Apicomplexan parasite Toxoplasma gondii, the method of Quantitative Trait Locus (QTL) mapping using a Whole Genome Sequence (WGS) -based genetic map and the method of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 -based gene editing. The approach of QTL mapping allows one to test if there is a correlation between a genomic region(s) and a phenotype...
June 22, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28671497/use-of-whole-genome-sequencing-and-evaluation-of-the-apparent-sensitivity-and-specificity-of-antemortem-tuberculosis-tests-in-the-investigation-of-an-unusual-outbreak-of-mycobacterium-bovis-infection-in-a-michigan-dairy-herd
#17
Colleen S Bruning-Fann, Suelee Robbe-Austerman, John B Kaneene, Bruce V Thomsen, John D Tilden, Jean S Ray, Richard W Smith, Scott D Fitzgerald, Steven R Bolin, Daniel J O'Brien, Thomas P Mullaney, Tod P Stuber, James J Averill, David Marks
OBJECTIVE To describe use of whole-genome sequencing (WGS) and evaluate the apparent sensitivity and specificity of antemortem tuberculosis tests during investigation of an unusual outbreak of Mycobacterium bovis infection in a Michigan dairy herd. DESIGN Bovine tuberculosis (bTB) outbreak investigation. ANIMALS Cattle, cats, dog, and wildlife. PROCEDURES All cattle in the index dairy herd were screened for bTB with the caudal fold test (CFT), and cattle ≥ 6 months old were also screened with a γ-interferon (γIFN) assay...
July 15, 2017: Journal of the American Veterinary Medical Association
https://www.readbyqxmd.com/read/28670449/no-nosocomial-transmission-under-standard-hygiene-precautions-in-short-term-contact-patients-in-case-of-an-unexpected-esbl-or-q-a-e-coli-positive-patient-a-one-year-prospective-cohort-study-within-three-regional-hospitals
#18
Dennis Souverein, Sjoerd M Euser, Bjorn L Herpers, Corry Hattink, Patricia Houtman, Amerens Popma, Jan Kluytmans, John W A Rossen, Jeroen W Den Boer
BACKGROUND: Many Highly Resistant Gram Negative Rod (HR-GNR) positive patients are found unexpectedly in clinical cultures, besides patients who are screened and isolated based on risk factors. As unexpected HR-GNR positive patients are isolated after detection, transmission to contact patients possibly occurred. The added value of routine contact tracing in such situations within hospitals with standard hygiene precautions is unknown. METHODS: In 2014, this study was performed as a prospective cohort study...
2017: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/28666130/tracking-of-listeria-monocytogenes-in-meat-establishment-using-whole-genome-sequencing-as-a-food-safety-management-tool-a-proof-of-concept
#19
Ivan Nastasijevic, Dubravka Milanov, Branko Velebit, Vesna Djordjevic, Craig Swift, Anais Painset, Brankica Lakicevic
Repeated Listeria outbreaks particularly associated with Ready-To-Eat (RTE) delicatessen meat products have been reported annually at global level. The most frequent scenario that led to foodborne outbreaks was the post-thermal treatment cross-contamination of deli meat products during slicing and modified atmosphere packaging (MAP). The precondition for such cross contamination is the previous introduction of Listeria into meat processing facilities and subsequent colonization of the production environment, associated with formation of biofilms resilient to common sanitation procedures regularly applied in meat establishments...
June 20, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28662764/pulsenet-international-vision-for-the-implementation-of-whole-genome-sequencing-wgs-for-global-food-borne-disease-surveillance
#20
Celine Nadon, Ivo Van Walle, Peter Gerner-Smidt, Josefina Campos, Isabel Chinen, Jeniffer Concepcion-Acevedo, Brent Gilpin, Anthony M Smith, Kai Man Kam, Enrique Perez, Eija Trees, Kristy Kubota, Johanna Takkinen, Eva Møller Nielsen, Heather Carleton
PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives...
June 8, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
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