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https://www.readbyqxmd.com/read/29453418/periodic-reanalysis-of-whole-genome-sequencing-data-enhances-the-diagnostic-advantage-over-standard-clinical-genetic-testing
#1
Gregory Costain, Rebekah Jobling, Susan Walker, Miriam S Reuter, Meaghan Snell, Sarah Bowdin, Ronald D Cohn, Lucie Dupuis, Stacy Hewson, Saadet Mercimek-Andrews, Cheryl Shuman, Neal Sondheimer, Rosanna Weksberg, Grace Yoon, M Stephen Meyn, Dimitri J Stavropoulos, Stephen W Scherer, Roberto Mendoza-Londono, Christian R Marshall
Whole-genome sequencing (WGS) as a first-tier diagnostic test could transform medical genetic assessments, but there are limited data regarding its clinical use. We previously showed that WGS could feasibly be deployed as a single molecular test capable of a higher diagnostic rate than current practices, in a prospectively recruited cohort of 100 children meeting criteria for chromosomal microarray analysis. In this study, we report on the added diagnostic yield with re-annotation and reanalysis of these WGS data ~2 years later...
February 16, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29449781/whole-genome-sequencing-of-multidrug-resistant-salmonella-enterica-serovar-typhimurium-isolated-from-humans-and-poultry-in-burkina-faso
#2
Assèta Kagambèga, Taru Lienemann, Jonathan G Frye, Nicolas Barro, Kaisa Haukka
Background: Multidrug-resistant Salmonella is an important cause of morbidity and mortality in developing countries. The aim of this study was to characterize and compare multidrug-resistant Salmonella enterica serovar Typhimurium isolates from patients and poultry feces. Methods: Salmonella strains were isolated from poultry and patients using standard bacteriological methods described in previous studies. The strains were serotype according to Kaufmann-White scheme and tested for antibiotic susceptibility to 12 different antimicrobial agents using the disk diffusion method...
2018: Tropical Medicine and Health
https://www.readbyqxmd.com/read/29448938/comparative-genomic-analysis-of-ten-clinical-streptococcus-pneumoniae-collected-from-a-malaysian-hospital-reveal-31-new-unique-drug-resistant-snps-using-whole-genome-sequencing
#3
Hassan Mahmood Jindal, Babu Ramanathan, Cheng Foh Le, Ranganath Gudimella, Rozaimi Razali, Rishya Manikam, Shamala Devi Sekaran
BACKGROUND: Streptococcus pneumoniae or pneumococcus is a leading cause of morbidity and mortality worldwide, specifically in relation to community-acquired pneumonia. Due to the overuse of antibiotics, S. pneumoniae has developed a high degree of resistance to a wide range of antibacterial drugs. METHODS: In this study, whole genome sequencing (WGS) was performed for 10 clinical strains of S. pneumoniae with different levels of sensitivity to standard antibiotics...
February 15, 2018: Journal of Biomedical Science
https://www.readbyqxmd.com/read/29447223/virome-and-bacteriome-characterization-of-children-with-pneumonia-and-asthma-in-mexico-city-during-winter-seasons-2014-and-2015
#4
Jose A Romero-Espinoza, Yazmin Moreno-Valencia, Rodrigo H Coronel-Tellez, Manuel Castillejos-Lopez, Andres Hernandez, Aaron Dominguez, Angel Miliar-Garcia, Arturo Barbachano-Guerrero, Rogelio Perez-Padilla, Alejandro Alejandre-Garcia, Joel A Vazquez-Perez
BACKGROUND: Acute asthma exacerbations and pneumonia are important causes of morbidity and mortality in children and may coexist in the same children, although symptom overlap may lead to difficulties in diagnosis. Microbial and viral diversity and differential abundance of either may play an important role in infection susceptibility and the development of acute and chronic respiratory diseases. OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively...
2018: PloS One
https://www.readbyqxmd.com/read/29446766/are-whole-exome-and-whole-genome-sequencing-approaches-cost-effective-a-systematic-review-of-the-literature
#5
Katharina Schwarze, James Buchanan, Jenny C Taylor, Sarah Wordsworth
PurposeWe conducted a systematic literature review to summarize the current health economic evidence for whole-exome sequencing (WES) and whole-genome sequencing (WGS).MethodsRelevant studies were identified in the EMBASE, MEDLINE, Cochrane Library, EconLit and University of York Centre for Reviews and Dissemination databases from January 2005 to July 2016. Publications were included in the review if they were economic evaluations, cost studies, or outcome studies.ResultsThirty-six studies met our inclusion criteria...
February 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29439654/prospective-study-on-human-fecal-carriage-of-enterobacteriaceae-possessing-mcr-1-and-mcr-2-genes-in-a-regional-hospital-in-hong-kong
#6
Wai-Sing Chan, Chun-Hang Au, Dona N Ho, Tsun-Leung Chan, Edmond Shiu-Kwan Ma, Bone Siu-Fai Tang
BACKGROUND: Human fecal carriage of Enterobacteriaceae possessing mobilized colistin resistance genes (mcr-1 and mcr-2) remains obscure in Hong Kong. As part of routine surveillance on emerging antibiotic resistance, we conducted a prospective study on this topic in a regional hospital in Hong Kong. METHODS: From October 31 to November 25, 2016, all fecal specimens submitted for routine analysis were included in this surveillance study. These comprised 672 consecutive routine fecal specimens collected from 616 individuals...
February 13, 2018: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29438544/emergence-and-control-of-linezolid-resistant-staphylococcus-epidermidis-in-an-icu-of-a-german-hospital
#7
Christina Weßels, Birgit Strommenger, Ingo Klare, Jennifer Bender, Sabine Messler, Frauke Mattner, Michael Krakau, Guido Werner, Franziska Layer
Objectives: To investigate an outbreak of linezolid-resistant Staphylococcus epidermidis (LRSE) in an interdisciplinary ICU, linezolid consumption and infection control measures taken. Methods: Routine surveillance of nosocomial infections revealed colonization and infection with LRSE affecting 14 patients during a 15 month period. LRSE isolates were analysed with respect to their clonal relatedness, antimicrobial susceptibility, the presence of cfr and/or mutations in the 23S rRNA, rplC, rplD and rplV genes...
February 9, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29438479/novel-tn916-like-elements-confer-aminoglycoside-macrolide-co-resistance-in-clinical-isolates-of-streptococcus-gallolyticus-ssp-gallolyticus
#8
Stanimir Kambarev, Frédéric Pecorari, Stéphane Corvec
Background: Streptococcus gallolyticus ssp. gallolyticus (Sgg) is a commensal bacterium and an opportunistic pathogen. In humans it has been clinically associated with the incidence of colorectal cancer (CRC) and epidemiologically recognized as an emerging cause of infective endocarditis (IE). The standard therapy of Sgg includes the administration of a penicillin in combination with an aminoglycoside. Even though penicillin-resistant isolates have still not been reported, epidemiological studies have shown that this microbe is a reservoir of multiple acquired genes, conferring resistance to tetracyclines, aminoglycosides, macrolides and glycopeptides...
February 9, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29436358/ethical-implications-of-rapid-whole-genome-sequencing-in-neonates
#9
Susan Givens Bell
Using rapid whole-genome sequencing (WGS), an infant's genome can now be sequenced in as little as 26 hours allowing for rapid diagnosis and precise, individualized management of monogenetic causes of disease. The potential for decreasing cost and valuable time to diagnosis along with pain and suffering is becoming a reality in the NICU. Coupled with rapidly developing technology is a need to explore the associated ethical implication.
January 1, 2018: Neonatal Network: NN
https://www.readbyqxmd.com/read/29426279/genomic-analyses-of-the-chlamydia-trachomatis-core-genome-show-an-association-between-chromosomal-genome-plasmid-type-and-disease
#10
Bart Versteeg, Sylvia M Bruisten, Yvonne Pannekoek, Keith A Jolley, Martin C J Maiden, Arie van der Ende, Odile B Harrison
BACKGROUND: Chlamydia trachomatis (Ct) plasmid has been shown to encode genes essential for infection. We evaluated the population structure of Ct using whole-genome sequence data (WGS). In particular, the relationship between the Ct genome, plasmid and disease was investigated. RESULTS: WGS data from 157 Ct isolates deposited in the Chlamydiales pubMLST database ( http://pubMLST.org/chlamydiales/ ) were annotated with 902 genes including the core and accessory genome...
February 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29425282/presence-and-molecular-characteristics-of-oxazolidinone-resistance-in-staphylococci-from-household-animals-in-rural-china
#11
Chengtao Sun, Peng Zhang, Xing Ji, Run Fan, Baoli Chen, Yang Wang, Stefan Schwarz, Congming Wu
Objectives: To investigate the presence and molecular characteristics of oxazolidinone resistance genes cfr and optrA in staphylococci from household animals in rural China. Methods: Various samples were collected from household animals in 12 rural villages. Staphylococcal isolates showing florfenicol MICs ≥10 mg/L were identified and screened for the presence of cfr and/or optrA. PCR-positive isolates were characterized by antimicrobial susceptibility testing, S1 nuclease PFGE and Southern blotting...
February 7, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29423797/whole-genome-library-construction-for-next-generation-sequencing
#12
Jonathan J Keats, Lori Cuyugan, Jonathan Adkins, Winnie S Liang
With the rapid evolution of genomics technologies over the past decade, whole genome sequencing (WGS) has become an increasingly accessible tool in biomedical research. WGS applications include analysis of genomic DNA from single individuals, multiple related family members, and tumor/normal samples from the same patient in the context of oncology. A number of different modalities are available for performing WGS; this chapter focuses on wet lab library construction procedures for complex short insert WGS libraries using the KAPA Hyper Prep Kit (Kapa Biosystems), and includes a discussion of appropriate quality control measures for sequencing on the Illumina HiSeq2000 platform...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29413790/effectiveness-of-prowling-with-proprioceptive-training-on-knee-hyperextension-among-stroke-subjects-using-videographic-observation-a-randomised-controlled-trial
#13
Khushboo K Dalal, Abraham M Joshua, Akshatha Nayak, Prasanna Mithra, Zulkifli Misri, Bhaskaran Unnikrishnan
INTRODUCTION: Knee hyperextension is seen in 40-68% of ambulating hemiparetics. If left untreated it may lead to laxity of posterior structures of knee resulting in early degeneration of knee leading to pain, reduced independence in activities of daily living (ADL), deformities and instability. In this study we hypothesize walking with bent knee attitude (prowling) along with proprioceptive training may help to reduce knee hyperextension during the stance phase of gait cycle. OBJECTIVE: To test the efficacy of prowling along with proprioceptive training on knee hyperextension range, dorsiflexion range and spatio temporal parameters of gait using Wisconsin gait scale (WGS) as compared to routine physiotherapy...
January 26, 2018: Gait & Posture
https://www.readbyqxmd.com/read/29408896/comparison-of-snp-based-subtyping-workflows-for-bacterial-isolates-using-wgs-data-applied-to-salmonella-enterica-serotype-typhimurium-and-serotype-1-4-5-12-i
#14
Assia Saltykova, Véronique Wuyts, Wesley Mattheus, Sophie Bertrand, Nancy H C Roosens, Kathleen Marchal, Sigrid C J De Keersmaecker
Whole genome sequencing represents a promising new technology for subtyping of bacterial pathogens. Besides the technological advances which have pushed the approach forward, the last years have been marked by considerable evolution of the whole genome sequencing data analysis methods. Prior to application of the technology as a routine epidemiological typing tool, however, reliable and efficient data analysis strategies need to be identified among the wide variety of the emerged methodologies. In this work, we have compared three existing SNP-based subtyping workflows using a benchmark dataset of 32 Salmonella enterica subsp...
2018: PloS One
https://www.readbyqxmd.com/read/29408647/whole-exome-mutational-and-transcriptional-landscapes-of-combined-hepatocellular-cholangiocarcinoma-and-intrahepatic-cholangiocarcinoma-reveal-molecular-diversity
#15
Zhen-Hao Liu, Bao-Feng Lian, Qiong-Zhu Dong, Han Sun, Jin-Wang Wei, Yuan-Yuan Sheng, Wei Li, Yixue Li, Lu Xie, Lei Liu, Lun-Xiu Qin
BACKGROUND: Primary liver cancer (PLC) is the third largest contributor to cancer mortality in the world. PLC is a heterogeneous disease that encompasses several biologically distinct subtypes including hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC). CHC is a distinct, albeit rare, subtype of PLC and is comprised of cells with histopathological features of both HCC and ICC. Several studies have focused on the mutation and expression landscapes of HCC and ICC...
January 31, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29404424/signatures-of-selection-at-drug-resistance-loci-in-mycobacterium-tuberculosis
#16
Tatum D Mortimer, Alexandra M Weber, Caitlin S Pepperell
Tuberculosis (TB) is the leading cause of death by an infectious disease, and global TB control efforts are increasingly threatened by drug resistance in Mycobacterium tuberculosis . Unlike most bacteria, where lateral gene transfer is an important mechanism of resistance acquisition, resistant M. tuberculosis arises solely by de novo chromosomal mutation. Using whole-genome sequencing data from two natural populations of M. tuberculosis , we characterized the population genetics of known drug resistance loci using measures of diversity, population differentiation, and convergent evolution...
January 2018: MSystems
https://www.readbyqxmd.com/read/29403466/the-novel-phages-phicd5763-and-phicd2955-represent-two-groups-of-big-plasmidial-siphoviridae-phages-of-clostridium-difficile
#17
Gabriel Ramírez-Vargas, Shan Goh, César Rodríguez
Until recently, Clostridium difficile phages were limited to Myoviruses and Siphoviruses of medium genome length (32-57 kb). Here we report the finding of phiCD5763, a Siphovirus with a large extrachromosomal circular genome (132.5 kb, 172 ORFs) and a large capsid (205.6 ± 25.6 nm in diameter) infecting MLST Clade 1 strains of C. difficile. Two subgroups of big phage genomes similar to phiCD5763 were identified in 32 NAPCR1/RT012/ST-54 C. difficile isolates from Costa Rica and in whole genome sequences (WGS) of 41 C...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29402227/covacs-a-consensus-variant-calling-system
#18
Matteo Chiara, Silvia Gioiosa, Giovanni Chillemi, Mattia D'Antonio, Tiziano Flati, Ernesto Picardi, Federico Zambelli, David Stephen Horner, Graziano Pesole, Tiziana Castrignanò
BACKGROUND: The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and precision medicine. The body of genome resequencing data is progressively increasing underlining the need for accurate and time-effective bioinformatics systems for genotyping - a crucial prerequisite for identification of candidate causal mutations in diagnostic screens...
February 5, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29399559/molecular-diagnosis-of-tuberculosis
#19
REVIEW
Fariz Nurwidya, Diah Handayani, Erlina Burhan, Faisal Yunus
Tuberculosis (TB) is one of the leading causes of adult death in the Asia-Pacific Region, including Indonesia. As an infectious disease caused by Mycobacterium tuberculosis (MTB), TB remains a major public health issue especially in developing nations due to the lack of adequate diagnostic testing facilities. Diagnosis of TB has entered an era of molecular detection that provides faster and more cost-effective methods to diagnose and confirm drug resistance in TB cases, meanwhile, diagnosis by conventional culture systems requires several weeks...
January 2018: Chonnam Medical Journal
https://www.readbyqxmd.com/read/29397858/-application-of-next-generation-sequencing-in-genetic-diagnosis-of-hereditary-platelet-disorders-review
#20
Hui-Ping Shi, Zhao-Yue Wang
Hereditary platelet disorders are a heterogeneous group of disorders characterized by abnormal number or function of platelets, sometimes even involving other systems apart from blood abnormalities. The great clinical and genetic heterogeneity makes the diagnosis and treatment of hereditary platelet disorders as a huge challenge for clinicians. At present, only a small number of patients have received a clear molecular diagnosis of hereditary platelet diseases, and a lot of pathogenic genetic variations still remain unknown...
February 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
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