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https://www.readbyqxmd.com/read/28819148/analysis-and-comparative-genomics-of-r997-the-first-sxt-r391-integrative-and-conjugative-element-ice-of-the-indian-sub-continent
#1
Michael P Ryan, Patricia Armshaw, John A O'Halloran, J Tony Pembroke
The aim of this study was to analyse R997, the first integrative and conjugative element (ICE) isolated from the Indian Sub-Continent, and to determine its relationship to the SXT/R391 family of ICEs. WGS of Escherichia coli isolate AB1157 (which contains R997) was performed using Illumina sequencing technology. R997 context was assessed by de novo assembly, gene prediction and annotation tools, and compared to other SXT/R391 ICEs. R997 has a size of 85 Kb and harbours 85 ORFs. Within one of the variable regions a HMS-1 β-lactamase resistance gene is located...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819111/community-outbreaks-of-group-a-streptococcus-revealed-by-genome-sequencing
#2
Claire E Turner, Luke Bedford, Nicholas M Brown, Kim Judge, M Estée Török, Julian Parkhill, Sharon J Peacock
The frequent occurrence of disease outbreaks in humans caused by group A Streptococcus (GAS) is an on-going public health threat. Conventional bacterial typing methods lack the discriminatory power to confidently confirm or refute outbreaks in hospital and community settings. Microbial whole genome sequencing (WGS) provides a potential solution to this, but, there has been limited population-based surveillance with accompanying sequence data. We performed retrospective genomic surveillance of 93 clinical GAS isolates from individuals in a defined geographic region...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818651/genomic-characterization-of-a-paediatric-mrsa-outbreak-by-next-generation-sequencing
#3
Elisabetta Ugolotti, Eddi Di Marco, Roberto Bandettini, Roberto Biassoni
INTRODUCTION: Twelve strains of meticillin-resistant Staphylococcus aureus (MRSA) isolated during a suspected outbreak in a Paediatric Intensive Care Unit were analyzed by Whole Genome Sequence (WGS). AIM: To define the clonality of MRSA strains to a high discriminative power and to evaluate the presence of genetic determinants responsible for antibiotic resistance and for virulence. RESULTS: Ten out of 12 strains belonged to the MLST ST2625, while the other two were ST8...
August 14, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28813472/an-intronic-line-1-insertion-in-mertk-is-strongly-associated-with-retinopathy-in-swedish-vallhund-dogs
#4
Richard Everson, Louise Pettitt, Oliver P Forman, Olivia Dower-Tylee, Bryan McLaughlin, Saija Ahonen, Maria Kaukonen, András M Komáromy, Hannes Lohi, Cathryn S Mellersh, Jane Sansom, Sally L Ricketts
The domestic dog segregates a significant number of inherited progressive retinal diseases, several of which mirror human retinal diseases and which are collectively termed progressive retinal atrophy (PRA). In 2014, a novel form of PRA was reported in the Swedish Vallhund breed, and the disease was mapped to canine chromosome 17. The causal mutation was not identified, but expression analyses of the retinas of affected Vallhunds demonstrated a 6-fold increased expression of the MERTK gene compared to unaffected dogs...
2017: PloS One
https://www.readbyqxmd.com/read/28811336/catastrophic-unbalanced-genome-rearrangements-cause-somatic-loss-of-berry-color-in-grapevine
#5
Pablo Carbonell-Bejerano, Carolina Royo, Rafael Torres-Pérez, Jérôme Grimplet, Lucie Fernandez, Jose M Franco-Zorrilla, Diego Lijavetzky, Elisa Baroja, Juana Martínez, Enrique García-Escudero, Javier Ibáñez, José M Martínez-Zapater
Grape color somatic variants that can be used to develop new grapevine cultivars occasionally appear associated to deletion events of uncertain origin. To understand the mutational mechanisms generating somatic structural variation in grapevine, we compared the Tempranillo Blanco (TB) white berry somatic variant to its black berry ancestor, Tempranillo Tinto. Whole-genome sequencing (WGS) uncovered a catastrophic genome rearrangement in TB that caused the hemizygous deletion of 313 genes, including the loss of the functional copy for the MYB transcription factors required for anthocyanin pigmentation in the berry skin...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28811315/quantitative-whole-genome-sequencing-of-circulating-tumor-cells-enables-personalized-combination-therapy-of-metastatic-cancer
#6
Natali Gulbahce, Mark Jesus M Magbanua, Robert Chin, Misha R Agarwal, Xuhao Luo, Jia Liu, Daniel M Hayden, Qing Mao, Serban Ciotlos, Zhenyu Li, Yanxiang Chen, Xingpeng Chen, Yuxiang Li, Rebecca Yu Zhang, Katharine Lee, Rick Tearle, Emily Park, Snezana Drmanac, Hope S Rugo, John W Park, Radoje Drmanac, Brock A Peters
Much effort has been dedicated to developing circulating tumor cells (CTC) as a noninvasive cancer biopsy, but with limited success as yet. In this study, we combine a method for isolation of highly pure CTCs using immunomagnetic enrichment/fluorescence-activated cell sorting with advanced whole genome sequencing (WGS), based on long fragment read technology, to illustrate the utility of an accurate, comprehensive, phased, and quantitative genomic analysis platform for CTCs. Whole genomes of 34 CTCs from a patient with metastatic breast cancer were analyzed as 3,072 barcoded subgenomic compartments of long DNA...
August 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28801276/transferability-of-antimicrobial-resistance-from-multidrug-resistant-escherichia-coli-isolated-from-cattle-in-the-united-states-to-escherichia-coli-and-salmonella-newport-recipients
#7
T L Poole, T R Callaway, K N Norman, H M Scott, G H Loneragan, S A Ison, R C Beier, D M Harhay, B Norby, D J Nisbet
OBJECTIVE: To evaluate conjugative transfer of cephalosporin resistance among (n=100) strains of multi-drug resistant Escherichia coli (MDRE) to Salmonella Newport and E. coli DH5α recipients. METHODS: Phenotypic and genotypic profiles were determined for MDRE, Salmonella Newport (trSN) and E. coli DH5α (trDH) transconjugants. RESULTS: Twenty-seven percent (n=26) and 28% (n=27) of (n=95) MDR E. coli donor isolates transferred resistance to trSN and trDH recipient isolates, respectively...
August 8, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28794425/transmission-is-a-noticeable-cause-of-resistance-among-treated-tuberculosis-patients-in-shanghai-china
#8
Chijioke A Nsofor, Qi Jiang, Jie Wu, Mingyu Gan, Qingyun Liu, Tianyu Zuo, Guofeng Zhu, Qian Gao
It is generally believed that drug resistance among treated tuberculosis (TB) patients is as a result of acquired drug resistance due to inappropriate treatment. Previous studies have shown that primary drug resistance caused by transmission also plays a role among treated cases. Differentiating the two types of drug resistance will help in developing appropriate strategies for control of drug resistant tuberculosis. In this study, we tested the hypothesis that drug resistance among treated TB patients is mainly caused by primary resistance rather than acquired resistance...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28794063/the-glyphosate-based-herbicide-roundup%C3%A2-does-not-elevate-genome-wide-mutagenesis-of-escherichia-coli
#9
Clayton Tincher, Hongan Long, Megan G Behringer, Noah Walker, Michael Lynch
Mutations induced by pollutants may promote pathogen evolution for example by accelerating mutations conferring antibiotic resistance. Generally, evaluating the genome-wide mutagenic effects of long-term sublethal pollutant exposure at single-nucleotide resolution is extremely difficult. To overcome this technical barrier, we use the mutation accumulation/whole genome sequencing (MA/WGS) method as a mutagenicity test, to quantitatively evaluate genome-wide mutagenesis of Escherichia coli after long-term exposure to a wide gradient of the glyphosate-based herbicide (GBH) Roundup® Concentrate Plus...
August 9, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28782651/emergence-of-dalbavancin-non-susceptible-vancomycin-intermediate-staphylococcus-aureus-visa-after-treatment-of-mrsa-central-line-associated-bloodstream-infection-with-a-dalbavancin-and-vancomycin-containing-regimen
#10
Brian J Werth, Rupali Jain, Andrew Hahn, Lisa Cummings, Tatiana Weaver, Adam Waalkes, Dhruba Sengupta, Stephen J Salipante, Robert M Rakita, Susan M Butler-Wu
OBJECTIVES: Dalbavancin is a long-acting lipoglycopeptide with activity against Gram-positives, including methicillin-resistant Staphylococcus aureus(MRSA). The potential for lipoglycopeptides, with half-lives greater than one-week, to select for resistance is unknown. Here we explore a case of MRSA central line-associated blood stream infection in which dalbavancin and vancomycin non-susceptibility emerged in a urine isolate collected after the patient was treated with vancomycin and dalbavancin sequentially...
August 3, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28782648/whole-genome-sequencing-of-campylobacter-jejuni-isolated-from-danish-routine-human-stool-samples-reveals-surprising-degree-of-clustering
#11
K G Joensen, K G Kuhn, L Müller, J T Björkman, M Torpdahl, J Engberg, H M Holt, H L Nielsen, A M Petersen, S Ethelberg, E M Nielsen
OBJECTIVES: Outbreaks of Campylobacter are traditionally considered to be rare, however rather than being the true nature of the disease, this may reflect our present inability to detect them. The aim of this study was to determine the genetic and epidemiological degree of clustering among Campylobacter jejuni isolates from Danish patients. METHODS: Whole-genome sequencing (WGS) was applied to 245 C. jejuni isolates from patients with domestically acquired infection over a 9-month period in 2015 and 2016...
August 3, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28781756/tiddit-an-efficient-and-comprehensive-structural-variant-caller-for-massive-parallel-sequencing-data
#12
Jesper Eisfeldt, Francesco Vezzi, Pall Olason, Daniel Nilsson, Anna Lindstrand
Reliable detection of large structural variation ( > 1000 bp) is important in both rare and common genetic disorders. Whole genome sequencing (WGS) is a technology that may be used to identify a large proportion of the genomic structural variants (SVs) in an individual in a single experiment. Even though SV callers have been extensively used in research to detect mutations, the potential usage of SV callers within routine clinical diagnostics is hindered by high computational costs, usage of non-standard output format, and limited support for the various sequencing platforms and libraries...
2017: F1000Research
https://www.readbyqxmd.com/read/28780272/current-challenges-in-the-accurate-identification-of-streptococcus-pneumoniae-and-its-serogroups-serotypes-in-the-vaccine-era
#13
REVIEW
Rosemol Varghese, Ranjith Jayaraman, Balaji Veeraraghavan
Streptococcus pneumoniae is a major cause of pneumonia, meningitis and other invasive diseases resulting in high mortality and morbidity among children under the age of five. Inaccurate identification of S. pneumoniae masks the exact estimation of disease burden and could delay treatment options. This is the common problem most frequently faced in developing countries due to several reasons that include poor infrastructure, insensitive operational procedures and lack of expertise. Inconsistent methods for phenotypic detection often delay the early identification and confirmation of S...
August 2, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28771251/improved-diagnostic-yield-compared-with-targeted-gene-sequencing-panels-suggests-a-role-for-whole-genome-sequencing-as-a-first-tier-genetic-test
#14
Anath C Lionel, Gregory Costain, Nasim Monfared, Susan Walker, Miriam S Reuter, S Mohsen Hosseini, Bhooma Thiruvahindrapuram, Daniele Merico, Rebekah Jobling, Thomas Nalpathamkalam, Giovanna Pellecchia, Wilson W L Sung, Zhuozhi Wang, Peter Bikangaga, Cyrus Boelman, Melissa T Carter, Dawn Cordeiro, Cheryl Cytrynbaum, Sharon D Dell, Priya Dhir, James J Dowling, Elise Heon, Stacy Hewson, Linda Hiraki, Michal Inbar-Feigenberg, Regan Klatt, Jonathan Kronick, Ronald M Laxer, Christoph Licht, Heather MacDonald, Saadet Mercimek-Andrews, Roberto Mendoza-Londono, Tino Piscione, Rayfel Schneider, Andreas Schulze, Earl Silverman, Komudi Siriwardena, O Carter Snead, Neal Sondheimer, Joanne Sutherland, Ajoy Vincent, Jonathan D Wasserman, Rosanna Weksberg, Cheryl Shuman, Chris Carew, Michael J Szego, Robin Z Hayeems, Raveen Basran, Dimitri J Stavropoulos, Peter N Ray, Sarah Bowdin, M Stephen Meyn, Ronald D Cohn, Stephen W Scherer, Christian R Marshall
PurposeGenetic testing is an integral diagnostic component of pediatric medicine. Standard of care is often a time-consuming stepwise approach involving chromosomal microarray analysis and targeted gene sequencing panels, which can be costly and inconclusive. Whole-genome sequencing (WGS) provides a comprehensive testing platform that has the potential to streamline genetic assessments, but there are limited comparative data to guide its clinical use.MethodsWe prospectively recruited 103 patients from pediatric non-genetic subspecialty clinics, each with a clinical phenotype suggestive of an underlying genetic disorder, and compared the diagnostic yield and coverage of WGS with those of conventional genetic testing...
August 3, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28770012/discovery-of-rare-diagnostic-aluyb8-9-elements-in-diverse-human-populations
#15
Julie Feusier, David J Witherspoon, W Scott Watkins, Clément Goubert, Thomas A Sasani, Lynn B Jorde
BACKGROUND: Polymorphic human Alu elements are excellent tools for assessing population structure, and new retrotransposition events can contribute to disease. Next-generation sequencing has greatly increased the potential to discover Alu elements in human populations, and various sequencing and bioinformatics methods have been designed to tackle the problem of detecting these highly repetitive elements. However, current techniques for Alu discovery may miss rare, polymorphic Alu elements...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28761782/targeted-ngs-for-species-level-phylogenomics-made-to-measure-or-one-size-fits-all
#16
Malvina Kadlec, Dirk U Bellstedt, Nicholas C Le Maitre, Michael D Pirie
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae)...
2017: PeerJ
https://www.readbyqxmd.com/read/28757348/draft-genome-sequence-of-an-aminoglycoside-resistant-rmtd-2-producing-enterobacter-cloacae-subsp-cloacae-st-395-in-brazil
#17
Evelin Rodrigues Martins, Maria Fernanda Campagnari Bueno, Gabriela Rodrigues Francisco, Fernanda Modesto Tolentino, Louise Cerdeira, Tiago Casella, Monalisa Nogueira Costa, Carla Cevada, Nilton Lincopan, Doroti de Oliveira Garcia, Mara Corrêa Lelles Nogueira
OBJECTIVES: Enterobacter cloacae has recently emerged as an important agent of nosocomial infections, due to the diffusion of extended spectrum β-lactamases and carbapenemases in this species. In this context, a raise in the use of aminoglycosides for therapy was noticed, being followed by the accelerated development of resistance mechanisms. In this study, we report the draft genome sequence of a multidrug-resistant Enterobacter cloacae subsp. cloacae strain (Ec2), isolated from active surveillance culture of a patient with Chagas disease...
July 27, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28751886/salmonella-enterica-serovar-infantis-from-food-and-human-infections-switzerland-2010-2015-poultry-related-multidrug-resistant-clones-and-an-emerging-esbl-producing-clonal-lineage
#18
Denise Hindermann, Gopal Gopinath, Hannah Chase, Flavia Negrete, Denise Althaus, Katrin Zurfluh, Ben D Tall, Roger Stephan, Magdalena Nüesch-Inderbinen
Objectives: The aim of this study was to characterize a collection of 520 Salmonella enterica serovar Infantis strains isolated from food (poultry meat), human infections and environmental sources from the years 2010, 2013 and 2015 in Switzerland. Methods: We performed antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE) analysis on all 520 S. Infantis isolates, and whole genome sequencing (WGS) on 32 selected isolates. Results: The majority (74.8%) of the isolates was multidrug resistant (MDR)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28750619/the-practical-use-of-genome-sequencing-data-in-the-management-of-a-feline-colony-pedigree
#19
Fabiana H G Farias, Chad Tomlinson, Jeffrey Labuda, Gerardo Perez-Camargo, Rondo Middleton, Wesley C Warren
BACKGROUND: A higher prevalence of inherited disorders among companion animals are often rooted in their historical restricted artificial selection for a variety of observed phenotypes that eventually decreased genetic diversity. Cats have been afflicted with many inherited diseases due to domestication and intense breed selection. Advances in sequencing technology have generated a more comprehensive way to access genetic information from an individual, allowing identification of putative disease-causing variants and in practice a means to avoid their spread and thus better pedigree management...
July 27, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28747373/investigation-of-respiratory-syncytial-virus-outbreak-on-an-adult-stem-cell-transplant-unit-using-whole-genome-sequencing
#20
Yijun Zhu, Teresa R Zembower, Kristen E Metzger, Zhengdeng Lei, Stefan J Green, Chao Qi
A viral whole genome sequencing strategy, based on PCR amplification followed by Next-generation Sequencing, was used to investigate a nosocomial RSV-B outbreak in a hematology-oncology and stem cell transplant unit. RSV-B genomes from 16 patients and healthcare workers (HCWs) suspected to be involved in the outbreak were compared to RSV-B genomes acquired from outpatients during the same time period but epidemiologically unrelated to the outbreak. Phylogenetic analysis of the whole genome identified a cluster of 11 patients and HCWs with an identical RSV-B strain which were clearly distinct from strains recovered from individuals unrelated to the outbreak...
July 26, 2017: Journal of Clinical Microbiology
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