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https://www.readbyqxmd.com/read/29346643/genetic-characterization-of-a-vang-type-vancomycin-resistant-enterococcus-faecium-clinical-isolate
#1
Mohamed Sassi, François Guérin, Léonie Lesec, Christophe Isnard, Marguerite Fines-Guyon, Vincent Cattoir, Jean-Christophe Giard
Objectives: To characterize, phenotypically and genotypically, the first Enterococcus faecium clinical isolate harbouring a vanG operon. Methods: The antibiotic resistance profile of E. faecium 16-346 was determined and its whole genome sequenced using PacBio technology. Attempts to transfer vancomycin resistance by filter mating were performed and the inducibility of expression of the vanG operon was studied by reverse-transcription quantitative PCR (RT-qPCR) in the presence or absence of subinhibitory concentrations of vancomycin...
January 16, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29346622/a-nosocomial-foodborne-outbreak-of-a-vim-carbapenemase-expressing-citrobacter-freundii
#2
Mathias W Pletz, Antje Wollny, Ute-Heike Dobermann, Jürgen Rödel, Svetlana Neubauer, Claudia Stein, Christian Brandt, Anita Hartung, Alexander Mellmann, Sabine Trommer, Birgit Edel, Vladimir Patchev, Oliwia Makarewicz, Jens Maschmann
Background: A foodborne outbreak of VIM carbapenemase-expressing Citrobacter freundii (CPC) occurred between February and June 2016 at a major university hospital in Germany. Methods: An explosive increase of CPC isolated from rectal swabs of patients during weekly routine screening led to the declaration of an outbreak. A hospital-wide prevalence screening was initiated as well as screening of all patients on admission and before transfer to another ward, and canteen staff, patient rooms, medical and kitchen inventory and food...
January 15, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29346588/genome-sequencing-of-museum-specimens-reveals-rapid-changes-in-the-genetic-composition-of-honey-bees-in-california
#3
Julie M Cridland, Santiago R Ramirez, Cheryl A Dean, Amber Sciligo, Neil D Tsutsui
The western honey bee, Apis mellifera, is an enormously influential pollinator in both natural and managed ecosystems. In North America, this species has been introduced numerous times from a variety of different source populations in Europe and Africa. Since then, feral populations have expanded into many different environments across their broad introduced range. Here, we used whole genome sequencing of historical museum specimens and newly collected modern populations from California (USA) to analyze the impact of demography and selection on introduced populations during the past 105 years...
January 15, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29346510/viper-a-web-application-for-rapid-expert-review-of-variant-calls
#4
Marius Wöste, Martin Dugas
Summary: With the rapid development in next-generation sequencing, cost and time requirements for genomic sequencing are decreasing, enabling applications in many areas such as cancer research. Many tools have been developed to analyze genomic variation ranging from single nucleotide variants to whole chromosomal aberrations. As sequencing throughput increases, the number of variants called by such tools also grows. Often employed manual inspection of such calls is thus becoming a time-consuming procedure...
January 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29346504/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus-approach
#5
Anqi Wang, Zhanyu Wang, Zheng Li, Lei M Li
Motivation: It is highly desirable to assemble genomes of high continuity and consistency at low cost. The current bottleneck of draft genome continuity using the Second Generation Sequencing (SGS) reads is primarily caused by uncertainty among repetitive sequences. Even though the Single-Molecule Real-Time sequencing technology is very promising to overcome the uncertainty issue, its relatively high cost and error rate add burden on budget or computation. Many long-read assemblers take the overlap-layout-consensus (OLC) paradigm, which is less sensitive to sequencing errors, heterozygosity and variability of coverage...
January 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29345757/whole-genome-sequencing-analysis-for-cancer-genomics-and-precision-medicine
#6
REVIEW
Hidewaki Nakagawa, Masashi Fujita
Explosive advances of next-generation sequencer (NGS) and computational analyses have been exploring somatic protein-altered mutations in most cancer types and these coding mutation data are intensively accumulated. However, there is limited information on somatic mutations in non-coding regions including introns, regulatory elements, and non-coding RNAs, structural variants and pathogen in cancer genomes remain widely unexplored. Whole genome sequencing (WGS) approaches can comprehensively explore all types of genomic alterations in cancer and help us to better understand the whole landscape of driver mutations and mutational signature in cancer genomes and elucidate functional or clinical implications of these unexplored genomic regions and mutational signature...
January 18, 2018: Cancer Science
https://www.readbyqxmd.com/read/29345635/genetic-risk-dysbiosis-and-treatment-stratification-using-host-genome-and-gut-microbiome-in-inflammatory-bowel-disease
#7
Ahmed Moustafa, Weizhong Li, Ericka L Anderson, Emily H M Wong, Parambir S Dulai, William J Sandborn, William Biggs, Shibu Yooseph, Marcus B Jones, J Craig Venter, Karen E Nelson, John T Chang, Amalio Telenti, Brigid S Boland
OBJECTIVES: Inflammatory bowel diseases (IBD), comprised of Crohn's disease (CD) and ulcerative colitis (UC), are characterized by a complex pathophysiology that is thought to result from an aberrant immune response to a dysbiotic luminal microbiota in genetically susceptible individuals. New technologies support the joint assessment of host-microbiome interaction. METHODS: Using whole genome sequencing and shotgun metagenomics, we studied the clinical features, host genome, and stool microbial metagenome of 85 IBD patients, and compared the results to 146 control individuals...
January 18, 2018: Clinical and Translational Gastroenterology
https://www.readbyqxmd.com/read/29345102/the-mycobiota-of-the-sand-fly-phlebotomus-perniciosus-involvement-of-yeast-symbionts-in-uric-acid-metabolism
#8
Elena Martin, Ilaria Varotto Boccazzi, Leone De Marco, Gioia Bongiorno, Matteo Montagna, Luciano Sacchi, Priscilla Mensah, Irene Ricci, Luigi Gradoni, Claudio Bandi, Sara Epis
The knowledge of the fungal mycobiota of arthropods, including the vectors of human and animal diseases, is still limited. Here, we investigated the mycobiota associated with the sand fly Phlebotomus perniciosus, the main vector of leishmaniasis in the western Mediterranean area, by a culture-dependent approach (microbiological analyses and sequencing of the 26S rRNA gene), internal transcribed spacer (ITS) rRNA amplicon-based next-generation sequencing, fluorescence in situ hybridisation (FISH), and genome sequencing of the dominant yeast species...
January 18, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29345080/environmental-adaptation-and-vertical-dissemination-of-esbl-pampc-producing-escherichia-coli-in-an-integrated-broiler-production-chain-in-the-absence-of-an-antibiotic-treatment
#9
Michaela Projahn, Katrin Daehre, Torsten Semmler, Sebastian Guenther, Uwe Roesler, Anika Friese
High prevalence numbers of extended-spectrum beta-lactamase- (ESBL-)/plasmid-mediated AmpC beta-lactamase- (pAmpC-) producing Escherichia coli in broiler chicken and their distribution along the broiler production chain is an ongoing problem in food production. We, therefore, investigated resistant isolates along the broiler production chain to determine whether there is a constantly occurring direct vertical transmission of the ESBL-/pAmpC-producing E. coli from the parent flocks to their offspring or not...
January 17, 2018: Microbial Biotechnology
https://www.readbyqxmd.com/read/29344954/mixed-ductal-lobular-carcinomas-evidence-for-progression-from-ductal-to-lobular-morphology
#10
Amy E McCart Reed, Jamie R Kutasovic, Katia Nones, Jodi M Saunus, Leonard Da Silva, Felicity Newell, Stephen Kazakoff, Lewis Melville, Janani Jayanthan, Ana Cristina Vargas, Lynne E Reid, Jonathan Beesley, Xiao Qing Chen, Anne Marie Patch, D David Clouston, Alan Porter, Elizabeth Evans, John V Pearson, Georgia Chenevix-Trench, Margaret C Cummings, Nic Waddell, Sunil R Lakhani, Peter T Simpson
Mixed ductal-lobular carcinomas (MDL) display both ductal and lobular morphology, and are an archetypal example of intra-tumour morphological heterogeneity. The mechanisms underlying coexistence of these different morphologic entities are poorly understood, although theories include that these components either represent 'collision' of independent tumours or evolve from a common ancestor. We performed comprehensive clinico-pathological analysis of a cohort of 82 MDLs and found: i) MDLs more frequently co-exist with ductal carcinoma in situ (DCIS) than lobular carcinoma in situ (LCIS); ii) the E-cadherin-catenin complex was normal in the ductal component in 77...
January 18, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29344884/analyzing-dna-methylation-patterns-during-tumor-evolution
#11
Heng Pan, Olivier Elemento
Epigenetic modifications play a key role in cellular development and tumorigenesis. Recent large-scale genomic studies have shown that mutations in players of the epigenetic machinery and concomitant perturbation of epigenomic patterning are frequent events in tumors. Among epigenetic marks, DNA methylation is one of the best studied. Hyper- and hypo-methylation events of specific regulatory elements (such as promoters and enhancers) are sometimes thought to be correlated with expression of nearby genes. High-throughput bisulfite converted sequencing is currently the technology of choice for studying DNA methylation in base-pair resolution and on whole-genome scale...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344848/current-status-and-future-possibilities-of-molecular-genetics-techniques-in-brassica-napus
#12
REVIEW
Muhammad Afzal, Salem Safer Alghamdi, Muhammad Habib Ur Rahman, Awais Ahmad, Tahir Farooq, Mukhtar Alam, Imtiaz Ali Khan, Hidayat Ullah, Wajid Nasim, Shah Fahad
As PCR methods have improved over the last 15 years, there has been an upsurge in the number of new DNA marker tools, which has allowed the generation of high-density molecular maps for all the key Brassica crop types. Biotechnology and molecular plant breeding have emerged as a significant tool for molecular understanding that led to a significant crop improvement in the Brassica napus species. Brassica napus possess a very complicated polyploidy-based genomics. The quantitative trait locus (QTL) is not sufficient to develop effective markers for trait introgression...
January 17, 2018: Biotechnology Letters
https://www.readbyqxmd.com/read/29342444/scarlet-fever-epidemic-in-china-caused-by-streptococcus-pyogenes-serotype-m12-epidemiologic-and-molecular-analysis
#13
Yuanhai You, Mark R Davies, Melinda Protani, Liam McIntyre, Mark J Walker, Jianzhong Zhang
From 2011, Hong Kong and mainland China have witnessed a sharp increase in reported cases, with subsequent reports of epidemic scarlet fever in North Asia and the United Kingdom. Here we examine epidemiological data and investigate the genomic context of the predominantly serotype M12 Streptococcus pyogenes scarlet fever isolates from mainland China. Incident case data was obtained from the Chinese Nationwide Notifiable Infectious Diseases Reporting Information System. The relative risk of scarlet fever in recent outbreak years 2011-2016 was calculated using the median age-standardised incidence rate, compared to years 2003-2010 prior this outbreak...
January 11, 2018: EBioMedicine
https://www.readbyqxmd.com/read/29342270/whole-genome-analysis-reveals-the-evolution-and-transmission-of-an-mdr-dh-nap11-106-clostridium-difficile-clone-in-a-paediatric-hospital
#14
Larry K Kociolek, Egon A Ozer, Dale N Gerding, David W Hecht, Sameer J Patel, Alan R Hauser
Background: Clostridium difficile strain DH/NAP11/106, a relatively antibiotic-susceptible strain, is now the most common cause of C. difficile infection (CDI) among adults in the USA. Objectives: To identify mechanisms underlying the evolution and transmission of an MDR DH/NAP11/106 clone. Methods: WGS (Illumina MiSeq), restriction endonuclease analysis (REA) and antibiotic susceptibility testing were performed on 134 C. difficile isolates collected from paediatric patients with CDI over a 2 year period...
January 12, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29342233/quantumclone-clonal-assessment-of-functional-mutations-in-cancer-based-on-a-genotype-aware-method-for-clonal-reconstruction
#15
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John Maris, Gudrun Schleiermacher, Valentina Boeva
Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering (reducing dispersion in variant allele frequency estimates, VAFs) and using all biologically relevant variants...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29341146/defining-the-molecular-pathology-of-pancreatic-body-and-tail-adenocarcinoma
#16
S B Dreyer, N B Jamieson, R Upstill-Goddard, P J Bailey, C J McKay, A V Biankin, D K Chang
BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) remains a dismal disease, with very little improvement in survival over the past 50 years. Recent large-scale genomic studies have improved understanding of the genomic and transcriptomic landscape of the disease, yet very little is known about molecular heterogeneity according to tumour location in the pancreas; body and tail PDACs especially tend to have a significantly worse prognosis. The aim was to investigate the molecular differences between PDAC of the head and those of the body and tail of the pancreas...
January 2018: British Journal of Surgery
https://www.readbyqxmd.com/read/29340898/epidemiological-aspects-of-healthcare-associated-infections-and-microbial-genomics
#17
C Mirande, I Bizine, A Giannetti, N Picot, A van Belkum
Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determinants. This renders correct and rapid species identification and antibiotic susceptibility testing (AST) important and underscores the relevance of bacterial epidemiological typing. The latter is needed for the sensitive detection and exact tracing of nosocomial spread of these potentially multidrug-resistant microorganisms (MDRO)...
January 17, 2018: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29340588/antimicrobial-resistant-klebsiella-pneumoniae-carriage-and-infection-in-specialized-geriatric-care-wards-linked-to-acquisition-in-the-referring-hospital
#18
Claire L Gorrie, Mirjana Mirceta, Ryan R Wick, Louise M Judd, Kelly L Wyres, Nicholas R Thomson, Richard A Strugnell, Nigel F Pratt, Jill S Garlick, Kerrie M Watson, Peter C Hunter, Steve A McGloughlin, Denis W Spelman, Adam W J Jenney, Kathryn E Holt
Background: Klebsiella pneumoniae is a leading cause of extended-spectrum beta-lactamase (ESBL) producing hospital-associated infections, for which elderly patients are at increased risk. Methods: We conducted a 1-year prospective cohort study, in which a third of patients admitted to two geriatric wards in a specialized hospital were recruited and screened for carriage of K. pneumoniae by microbiological culture. Clinical isolates were monitored via the hospital laboratory...
January 11, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29340235/evidence-based-design-and-evaluation-of-a-whole-genome-sequencing-clinical-report-for-the-reference-microbiology-laboratory
#19
Anamaria Crisan, Geoffrey McKee, Tamara Munzner, Jennifer L Gardy
Background: Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics-including clinicians, laboratorians, epidemiologists, and researchers-is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain...
2018: PeerJ
https://www.readbyqxmd.com/read/29339831/detection-of-antimicrobial-resistance-genes-associated-with-the-international-space-station-environmental-surfaces
#20
C Urbaniak, A Checinska Sielaff, K G Frey, J E Allen, N Singh, C Jaing, K Wheeler, K Venkateswaran
Antimicrobial resistance (AMR) is a global health issue. In an effort to minimize this threat to astronauts, who may be immunocompromised and thus at a greater risk of infection from antimicrobial resistant pathogens, a comprehensive study of the ISS "resistome' was conducted. Using whole genome sequencing (WGS) and disc diffusion antibiotic resistance assays, 9 biosafety level 2 organisms isolated from the ISS were assessed for their antibiotic resistance. Molecular analysis of AMR genes from 24 surface samples collected from the ISS during 3 different sampling events over a span of a year were analyzed with Ion AmpliSeq™ and metagenomics...
January 16, 2018: Scientific Reports
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