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https://www.readbyqxmd.com/read/28531552/the-role-of-next-generation-sequencing-in-infection-prevention-in-human-parainfluenza-virus-3-infections-in-immunocompromised-patients
#1
Atul Kothari, Mary J Burgess, Juan Carlos Rico Crescencio, Joshua L Kennedy, Jesse L Denson, Kurt C Schwalm, Ashley N Stoner, John C Kincaid, Faith E Davies, Darrell L Dinwiddie
BACKGROUND: Respiratory viral infections are a significant problem in patients with hematologic malignancies. We report a cluster of HPIV 3 infections in our myeloma patients, and describe the utility of next generation sequencing (NGS) to identify transmission linkages which can assist in infection prevention. OBJECTIVES: To evaluate the utility of NGS to track respiratory viral infection outbreaks and delineate between community acquired and nosocomial infections in our cancer units...
May 12, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28529837/fifteen-microsatellite-markers-for-herbertia-zebrina-iridaceae-an-endangered-species-from-south-american-grasslands
#2
Cristiane Forgiarini, Manuel Curto, Eudes Maria Stiehl-Alves, Christian Bräuchler, Johannes Kollmann, Harald Meimberg, Tatiana Teixeira de Souza-Chies
PREMISE OF THE STUDY: Polymorphic microsatellite loci were developed and used to genotype individuals of Herbertia zebrina (Iridaceae) as a first step for assessment of intraspecific genetic diversity. METHODS AND RESULTS: Primer pairs for 47 markers were developed: 20 from a microsatellite-enriched library and 27 from a next-generation sequencing run using the Illumina MiSeq platform. Of those, 15 loci were considered successful, of which 12 were polymorphic and three were monomorphic...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28529833/development-and-evaluation-of-microsatellite-markers-for-the-critically-endangered-birch-betula-chichibuensis-betulaceae
#3
Yuji Igarashi, Hiroki Aihara, Yoshihiro Handa, Hiroshi Katsumata, Masanori Fujii, Koichiro Nakano, Toshihide Hirao
PREMISE OF THE STUDY: Microsatellite markers were developed and characterized for the critically endangered birch Betula chichibuensis (Betulaceae) to investigate the genetic structure of this species for conservation purposes. METHODS AND RESULTS: Sixteen microsatellite markers with di-, tri-, and tetranucleotide repeat motifs were developed and optimized using MiSeq paired-end sequencing. Of these, 14 were polymorphic, with two to five alleles per locus, in 47 individuals from two newly discovered populations of B...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28527899/egfr-mutation-analysis-for-prospective-patient-selection-in-two-phase-ii-registration-studies-of-osimertinib
#4
Suzanne Jenkins, James Chih-Hsin Yang, Pasi A Jänne, Kenneth S Thress, Karen Yu, Rachel Hodge, Susie Weston, Simon Dearden, Sabina Patel, Mireille Cantarini, Frances A Shepherd
INTRODUCTION: Osimertinib is an oral, CNS active, epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) for the treatment of EGFR T790M-positive advanced non-small cell lung cancer (NSCLC). Here we evaluate EGFR mutation frequencies in two Phase II studies of osimertinib (AURA extension and AURA2). METHODS: Patients with EGFR mutation-positive advanced NSCLC provided tumor samples following progression on their latest line of therapy for mandatory central T790M testing for study selection criteria...
May 17, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28506684/study-of-preanalytic-and-analytic-variables-for-clinical-next-generation-sequencing-of-circulating-cell-free-nucleic-acid
#5
Meenakshi Mehrotra, Rajesh R Singh, Wei Chen, Richard S P Huang, Alaa A Almohammedsalim, Bedia A Barkoh, Crystal M Simien, Marcos Hernandez, Carmen Behrens, Keyur P Patel, Mark J Routbort, Russell R Broaddus, L Jeffrey Medeiros, Ignacio I Wistuba, Scott Kopetz, Rajyalakshmi Luthra
Detection of mutations in plasma circulating cell-free DNA (cfDNA) by next-generation sequencing (NGS) has opened up new possibilities for monitoring treatment response and disease progression in patients with solid tumors. However, implementation of cfDNA genotyping in diagnostic laboratories requires systematic assessment of preanalytical parameters and analytical performance of NGS platforms. We assessed the effects of peripheral blood collection tube and plasma separation time on cfDNA yield and integrity and performance of the Ion PGM, Proton, and MiSeq NGS platforms...
May 12, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28503178/transcriptomic-response-of-chinese-yew-taxus-chinensis-to-cold-stress
#6
Delong Meng, Xianghua Yu, Liyuan Ma, Jin Hu, Yili Liang, Xueduan Liu, Huaqun Yin, Hongwei Liu, Xiaojia He, Diqiang Li
Taxus chinensis is a rare and endangered shrub, highly sensitive to temperature changes and widely known for its potential in cancer treatment. How gene expression of T. chinensis responds to low temperature is still unknown. To investigate cold response of the genus Taxus, we obtained the transcriptome profiles of T. chinensis grown under normal and low temperature (cold stress, 0°C) conditions using Illumina Miseq sequencing. A transcriptome including 83,963 transcripts and 62,654 genes were assembled from 4...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28502729/improving-mutation-screening-in-patients-with-colorectal-cancer-predisposition-using-next-generation-sequencing
#7
Jean-Marc Rey, Vincent Ducros, Pascal Pujol, Qing Wang, Marie-Pierre Buisine, Hanaa Aissaoui, Thierry Maudelonde, Sylviane Olschwang
Identification of genetic alterations is important for family risk assessment in colorectal cancers. Next-generation sequencing (NGS) technologies provide useful tools for single-nucleotide and copy number variation (CNV) identification in many genes and samples simultaneously. Herein, we present the validation of current Multiplicom MASTR designs of mismatch repair combined to familial adenomatous polyposis genes in a single PCR reamplification test for eight DNA samples simultaneously on a MiSeq apparatus...
May 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28501786/qac-modified-pvdf-membranes-antibiofouling-performance-mechanisms-and-effects-on-microbial-communities-in-an-mbr-treating-municipal-wastewater
#8
Mei Chen, Xingran Zhang, Zhiwei Wang, Liang Wang, Zhichao Wu
Biofouling remains as a critical issue limiting the widespread applications of membrane bioreactors (MBRs). The use of antibiofouling membranes is an emerging method to tackle this issue. In this study, a polyvinylidene fluoride (PVDF) membrane was modified using a quaternary ammonium compound (QAC) to create an antibiofouling membrane. The membrane was used in an MBR and the performance, mechanisms, and effects on microbial communities of this membrane were compared to a control operated in parallel. Results showed that the membrane exhibited a significantly reduced transmembrane pressure increase rate of 0...
May 8, 2017: Water Research
https://www.readbyqxmd.com/read/28495244/rumen-prokaryotic-communities-of-ruminants-under-different-feeding-paradigms-on-the-qinghai-tibetan-plateau
#9
Dan Xue, Huai Chen, Xinquan Zhao, Shixiao Xu, Linyong Hu, Tianwei Xu, Lin Jiang, Wei Zhan
Yak and Tibetan sheep are the major indigenous ruminants on the Qinghai-Tibetan Plateau in China. The aim of this work was to study the differences in ruminal fermentation parameters and rumen prokaryotic community composition between hosts and feeding paradigms. The 16S rRNA genes targeting bacteria and archaea were sequenced using the MiSeq platform. The results showed that the prokaryotic community structure between yak and Tibetan sheep was significantly different (P<0.01). A significant difference in structure was also found between groups of yaks barn fed with a total mixed ration (TMR) and those naturally grazing (NG) (P=0...
April 18, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28495072/reprint-of-application-of-next-generation-sequencing-in-clinical-microbiology-and-infection-prevention
#10
Ruud H Deurenberg, Erik Bathoorn, Monika A Chlebowicz, Natacha Couto, Mithila Ferdous, Silvia García-Cobos, Anna M D Kooistra-Smid, Erwin C Raangs, Sigrid Rosema, Alida C M Veloo, Kai Zhou, Alexander W Friedrich, John W A Rossen
Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test...
May 8, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28490492/molecular-diagnosis-of-orthopaedic-device-infection-direct-from-sonication-fluid-by-metagenomic-sequencing
#11
Teresa L Street, Nicholas D Sanderson, Bridget L Atkins, Andrew J Brent, Kevin Cole, Dona Foster, Martin A McNally, Sarah Oakley, Leon Peto, Adrian Taylor, Tim E A Peto, Derrick W Crook, David W Eyre
Culture of multiple periprosthetic tissue samples is the current gold-standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through sonication fluid culture of explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of total DNA extracts obtained direct from sonication fluid can provide an alternative rapid and sensitive tool for diagnosis of PJI...
May 10, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28489978/sodium-bisulfate-and-a-sodium-bisulfate-tannin-mixture-decreases-ph-when-added-to-an-in-vitro-incubated-poultry-cecal-or-fecal-contents-while-reducing-salmonella-typhimurium-marker-strain-survival-and-altering-the-microbiome
#12
Peter M Rubinelli, Sun Ae Kim, Si Hong Park, Stephanie M Roto, Steven C Ricke
The objective of the present study was to investigate the ability of animal feed-grade sodium bisulfate (SBS) and a mixture of sodium bisulfate/tannin to inhibit the growth of Salmonella using an anerobic in vitro mixed cecal culture to mimic the conditions within the chicken cecum. An initial inoculum of Salmonella Typhimurium was introduced to an anerobic dilution solution containing 1/3000 diluted cecal bacteria and solids consisting of ground chicken feed and different percentages of solid SBS or SBS/tannin, and surviving organisms were enumerated...
May 10, 2017: Journal of Environmental Science and Health. Part. B, Pesticides, Food Contaminants, and Agricultural Wastes
https://www.readbyqxmd.com/read/28489587/ngs-based-identification-of-mutational-hotspots-for-targeted-therapy-in-anaplastic-thyroid-carcinoma
#13
Vera Tiedje, Saskia Ting, Thomas Herold, Sarah Synoracki, Soeren Latteyer, Lars C Moeller, Denise Zwanziger, Martin Stuschke, Dagmar Fuehrer, Kurt Werner Schmid
CONTEXT: Anaplastic thyroid carcinoma (ATC) represents one of the most aggressive carcinomas with no consistent survival benefit when treated with conventional radiochemotherapy. Approaches targeting "oncogene addiction" of ATC are increasingly explored and first promising results have been reported in single case studies. OBJECTIVE: To determine the prevalence of mutations in known thyroid oncogenes and signalling pathways amendable to targeted therapy in a large cohort of ATC...
April 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28484604/cutting-through-the-smoke-the-diversity-of-microorganisms-in-deep-sea-hydrothermal-plumes
#14
Anni Djurhuus, Svein-Ole Mikalsen, Helge-Ansgar Giebel, Alex D Rogers
There are still notable gaps regarding the detailed distribution of microorganisms between and within insular habitats such as deep-sea hydrothermal vents. This study investigates the community composition of black smoker vent microorganisms in the Southern Hemisphere, and changes thereof along a spatial and chemical gradient ranging from the vent plume to surrounding waters. We sampled two hydrothermal vent fields, one at the South West Indian Ridge (SWIR), the other at the East Scotia Ridge (ESR). Samples were collected across vent fields at varying vertical distances from the origin of the plumes...
April 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28484435/role-of-eps-dispersant-and-nutrients-on-the-microbial-response-and-mos-formation-in-the-subarctic-northeast-atlantic
#15
Laura Duran Suja, Stephen Summers, Tony Gutierrez
In this study we report the formation of marine oil snow (MOS), its associated microbial community, the factors influencing its formation, and the microbial response to crude oil in surface waters of the Faroe-Shetland Channel (FSC). The FSC is a subarctic region that is hydrodynamically complex located in the northeast Atlantic where oil extraction is currently occurring and where exploration is likely to expand into its deeper waters (>500 m). A major oil spill in this region may mirror the aftermath that ensued following the Deepwater Horizon (DWH) blowout in the Gulf of Mexico, where the massive influx of Macondo crude oil triggered the formation of copious quantities of rapidly sinking MOS and successional blooms of opportunistic oil-degrading bacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28484429/protective-effect-of-carvacrol-against-gut-dysbiosis-and-clostridium-difficile-associated-disease-in-a-mouse-model
#16
Shankumar Mooyottu, Genevieve Flock, Abhinav Upadhyay, Indu Upadhyaya, Kendra Maas, Kumar Venkitanarayanan
This study investigated the effect of carvacrol (CR), a phytophenolic compound on antibiotic-associated gut dysbiosis and C. difficile infection in a mouse model. Five to six-week-old C57BL/6 mice were randomly divided into seven treatment groups (challenge and control) of eight mice each. Mice were fed with irradiated feed supplemented with CR (0, 0.05, and 0.1%); the challenge groups were made susceptible to C. difficile by orally administering an antibiotic cocktail in water and an intra-peritoneal injection of clindamycin...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28481935/genotypic-and-phenotypic-characterization-of-multidrug-resistant-salmonella-typhimurium-and-salmonella-kentucky-strains-recovered-from-chicken-carcasses
#17
Rizwana Tasmin, Nur A Hasan, Christopher J Grim, Ar'Quette Grant, Seon Young Choi, M Samiul Alam, Rebecca Bell, Christopher Cavanaugh, Kannan V Balan, Uma S Babu, Salina Parveen
Salmonella Typhimurium is the leading cause of human non-typhoidal gastroenteritis in the US. S. Kentucky is one the most commonly recovered serovars from commercially processed poultry carcasses. This study compared the genotypic and phenotypic properties of two Salmonella enterica strains Typhimurium (ST221_31B) and Kentucky (SK222_32B) recovered from commercially processed chicken carcasses using whole genome sequencing, phenotype characterizations and an intracellular killing assay. Illumina MiSeq platform was used for sequencing of two Salmonella genomes...
2017: PloS One
https://www.readbyqxmd.com/read/28481884/new-advances-in-dpyd-genotype-and-risk-of-severe-toxicity-under-capecitabine
#18
Marie-Christine Etienne-Grimaldi, Jean-Christophe Boyer, Christophe Beroud, Litaty Mbatchi, André van Kuilenburg, Christine Bobin-Dubigeon, Fabienne Thomas, Etienne Chatelut, Jean-Louis Merlin, Frédéric Pinguet, Christophe Ferrand, Judith Meijer, Alexandre Evrard, Laurence Llorca, Gilles Romieu, Philippe Follana, Thomas Bachelot, Loic Chaigneau, Xavier Pivot, Véronique Dieras, Rémy Largillier, Mireille Mousseau, Anthony Goncalves, Henri Roché, Jacques Bonneterre, Véronique Servent, Nadine Dohollou, Yann Château, Emmanuel Chamorey, Jean-Pierre Desvignes, David Salgado, Jean-Marc Ferrero, Gérard Milano
BACKGROUND: Deficiency in dihydropyrimidine dehydrogenase (DPD) enzyme is the main cause of severe and lethal fluoropyrimidine-related toxicity. Various approaches have been developed for DPD-deficiency screening, including DPYD genotyping and phenotyping. The goal of this prospective observational study was to perform exhaustive exome DPYD sequencing and to examine relationships between DPYD variants and toxicity in advanced breast cancer patients receiving capecitabine. METHODS: Two-hundred forty-three patients were analysed (88...
2017: PloS One
https://www.readbyqxmd.com/read/28479173/microbial-compositional-changes-in-broiler-chicken-cecal-contents-from-birds-challenged-with-different-salmonella-vaccine-candidate-strains
#19
Si Hong Park, Sun Ae Kim, Peter M Rubinelli, Stephanie M Roto, Steven C Ricke
Previously, we constructed and characterized the vaccine efficacy of Salmonella Typhimurium mutant strains in poultry with either inducible mviN expression (PBAD-mviN) or methionine auxotrophy (ΔΔmetRmetD). The aim of the present study was to assess potential impact of these Salmonella vaccine strains on the cecal microbiota using a next generation sequencing (NGS). The cecal microbial community obtained from unvaccinated (group 1) and vaccinated chickens (group 2, vaccinated with PBAD-mviN; group 3, vaccinated with wild type; group 4, vaccinated with ΔΔmetRmetD) were subjected to microbiome sequencing analysis with an Illumina MiSeq platform...
May 31, 2017: Vaccine
https://www.readbyqxmd.com/read/28476580/comparative-profiling-of-microbial-community-of-three-economically-important-fishes-reared-in-sea-cages-under-tropical-offshore-environment
#20
M K Rasheeda, Vijaya Raghavan Rangamaran, Senthilkumar Srinivasan, Sendhil Kumar Ramaiah, Rajaprabhu Gunasekaran, Santhanakumar Jaypal, Dharani Gopal, Kirubagaran Ramalingam
The present study was undertaken to evaluate the microbial composition of farmed cobia pompano and milkfish, reared in sea-cages by culture-independent methods. This study would serve as a basis for assessing the general health of fish, identifying the dominant bacterial species present in the gut for future probiotic work and in early detection of potential pathogens. High-throughput sequencing of V3-V4 hyper variable regions of 16S rDNA on Illumina MiSeq platform facilitated unravelling of composite bacterial population...
May 2, 2017: Marine Genomics
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