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https://www.readbyqxmd.com/read/28103259/characterization-and-genetic-variation-of-vibrio-cholerae-isolated-from-clinical-and-environmental-sources-in-thailand
#1
Achiraya Siriphap, Pimlapas Leekitcharoenphon, Rolf S Kaas, Chonchanok Theethakaew, Frank M Aarestrup, Orasa Sutheinkul, Rene S Hendriksen
Cholera is still an important public health problem in several countries, including Thailand. In this study, a collection of clinical and environmental V. cholerae serogroup O1, O139, and non-O1/non-O139 strains originating from Thailand (1983 to 2013) was characterized to determine phenotypic and genotypic traits and to investigate the genetic relatedness. Using a combination of conventional methods and whole genome sequencing (WGS), 78 V. cholerae strains were identified. WGS was used to determine the serogroup, biotype, virulence, mobile genetic elements, and antimicrobial resistance genes using online bioinformatics tools...
2017: PloS One
https://www.readbyqxmd.com/read/28100602/find-tuberculosis-strain-bank-a-resource-for-researchers-and-developers-working-on-tests-to-detect-mycobacterium-tuberculosis-and-related-drug-resistance
#2
Belay Tessema, Pamela Nabeta, Eloise Valli, Audrey Albertini, Jimena Collantes, Nguyen Huu Lan, Elena Romancenco, Nestani Tukavdze, Claudia M Denkinger, David L Dolinger
BACKGROUND: The spread of multidrug-resistant tuberculosis and extensively drug-resistant TB hampers the global efforts in the fight against tuberculosis. To enhance the development and evaluation of diagnostic tests quickly and efficiently, well characterized strains and samples from drug resistant tuberculosis patients are necessary. In this project, FIND has focused on the collection, characterization and storage of such well-characterized reference materials and to make them available to researchers and developers...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28098136/exome-and-genome-sequencing-of-nasopharynx-cancer-identifies-nf-%C3%AE%C2%BAb-pathway-activating-mutations
#3
Yvonne Y Li, Grace T Y Chung, Vivian W Y Lui, Ka-Fai To, Brigette B Y Ma, Chit Chow, John K S Woo, Kevin Y Yip, Jeongsun Seo, Edwin P Hui, Michael K F Mak, Maria Rusan, Nicole G Chau, Yvonne Y Y Or, Marcus H N Law, Peggy P Y Law, Zoey W Y Liu, Hoi-Lam Ngan, Pok-Man Hau, Krista R Verhoeft, Peony H Y Poon, Seong-Keun Yoo, Jong-Yeon Shin, Sau-Dan Lee, Samantha W M Lun, Lin Jia, Anthony W H Chan, Jason Y K Chan, Paul B S Lai, Choi-Yi Fung, Suet-Ting Hung, Lin Wang, Ann Margaret V Chang, Simion I Chiosea, Matthew L Hedberg, Sai-Wah Tsao, Andrew C van Hasselt, Anthony T C Chan, Jennifer R Grandis, Peter S Hammerman, Kwok-Wai Lo
Nasopharyngeal carcinoma (NPC) is an aggressive head and neck cancer characterized by Epstein-Barr virus (EBV) infection and dense lymphocyte infiltration. The scarcity of NPC genomic data hinders the understanding of NPC biology, disease progression and rational therapy design. Here we performed whole-exome sequencing (WES) on 111 micro-dissected EBV-positive NPCs, with 15 cases subjected to further whole-genome sequencing (WGS), to determine its mutational landscape. We identified enrichment for genomic aberrations of multiple negative regulators of the NF-κB pathway, including CYLD, TRAF3, NFKBIA and NLRC5, in a total of 41% of cases...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28096484/evolutionary-dynamics-of-pandemic-methicillin-sensitive-staphylococcus-aureus-st398-and-its-international-spread-via-routes-of-human-migration
#4
Anne-Catrin Uhlemann, Paul R McAdam, Sean B Sullivan, Justin R Knox, Hossein Khiabanian, Raul Rabadan, Peter R Davies, J Ross Fitzgerald, Franklin D Lowy
: Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for the majority of S. aureus infections globally, and yet surprisingly little is known about its clonal evolution. We applied comparative whole-genome sequencing (WGS) analyses to epidemiologically and geographically diverse ST398-MSSA, a pandemic lineage affecting both humans and livestock. Bayesian phylogenetic analysis predicted divergence of human-associated ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and veterinarians differed substantially from those in New York City (NYC)...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28095770/the-unique-genomic-landscape-surrounding-the-epsps-gene-in-glyphosate-resistant-amaranthus-palmeri-a-repetitive-path-to-resistance
#5
William T Molin, Alice A Wright, Amy Lawton-Rauh, Christopher A Saski
BACKGROUND: The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment...
January 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28093482/dissemination-of-blaoxa-58-in-proteus-mirabilis-isolates-from-germany
#6
Felix Lange, Niels Pfennigwerth, Sonja Gerigk, Frank Gohlke, Klaus Oberdorfer, Ingvill Purr, Nikolaus Wohanka, Andreas Roggenkamp, Sören G Gatermann, Martin Kaase
OBJECTIVES: Characterization of Proteus mirabilis isolates harbouring blaOXA-58 with emphasis on the genetic environment of this resistance determinant. METHODS: Strains of P. mirabilis (n = 37) isolated from different patients were tested for the presence of blaOXA-58 The genetic context of blaOXA-58 was determined by WGS of two strains and Sanger sequencing. Clonality of the strains was assessed by PFGE. Susceptibility testing was performed by microdilution according to EUCAST...
January 15, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28093063/whole-genome-sequence-based-genomic-prediction-in-laying-chickens-with-different-genomic-relationship-matrices-to-account-for-genetic-architecture
#7
Guiyan Ni, David Cavero, Anna Fangmann, Malena Erbe, Henner Simianer
BACKGROUND: With the availability of next-generation sequencing technologies, genomic prediction based on whole-genome sequencing (WGS) data is now feasible in animal breeding schemes and was expected to lead to higher predictive ability, since such data may contain all genomic variants including causal mutations. Our objective was to compare prediction ability with high-density (HD) array data and WGS data in a commercial brown layer line with genomic best linear unbiased prediction (GBLUP) models using various approaches to weight single nucleotide polymorphisms (SNPs)...
January 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28090077/clinical-and-biological-insights-from-viral-genome-sequencing
#8
Charlotte J Houldcroft, Mathew A Beale, Judith Breuer
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages...
January 16, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28089252/practical-approaches-for-whole-genome-sequence-analysis-of-heart-and-blood-related-traits
#9
Alanna C Morrison, Zhuoyi Huang, Bing Yu, Ginger Metcalf, Xiaoming Liu, Christie Ballantyne, Josef Coresh, Fuli Yu, Donna Muzny, Elena Feofanova, Navin Rustagi, Richard Gibbs, Eric Boerwinkle
Whole-genome sequencing (WGS) allows for a comprehensive view of the sequence of the human genome. We present and apply integrated methodologic steps for interrogating WGS data to characterize the genetic architecture of 10 heart- and blood-related traits in a sample of 1,860 African Americans. In order to evaluate the contribution of regulatory and non-protein coding regions of the genome, we conducted aggregate tests of rare variation across the entire genomic landscape using a sliding window, complemented by an annotation-based assessment of the genome using predefined regulatory elements and within the first intron of all genes...
January 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28088766/staphylococcus-aureus-cc395-harbours-a-novel-composite-staphylococcal-cassette-chromosome-mec-element
#10
Jesper Larsen, Paal S Andersen, Volker Winstel, Andreas Peschel
BACKGROUND: CoNS species are likely reservoirs of the staphylococcal cassette chromosome mec (SCCmec) in Staphylococcus aureus S aureus CC395 is unique as it is capable of exchanging DNA with CoNS via bacteriophages, which are also known to mediate transfer of SCCmec OBJECTIVES: To analyse the structure and putative origin of the SCCmec element in S aureus CC395. METHODS: The only MRSA CC395 strain described in the literature, JS395, was subjected to WGS, and its SCCmec element was compared with those found in CoNS species and other S...
January 14, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28087584/emergence-of-klebsiella-variicola-positive-for-ndm-9-a-variant-of-new-delhi-metallo-%C3%AE-lactamase-in-an-urban-river-in-south-korea
#11
Doris Y W Di, Jeonghwan Jang, Tatsuya Unno, Hor-Gil Hur
OBJECTIVES: To examine the presence of pathogenic bacteria carrying New Delhi metallo-β-lactamase in the environment and to characterize the genome structures of these strains. METHODS: Phenotypic screening of antimicrobial susceptibility and WGS were conducted on three Klebsiella variicola strains possessing NDM-9 isolated from an urban river. RESULTS: Three carbapenem-resistant K. variicola isolated from Gwangju tributary were found to possess blaNDM-9 genes...
January 12, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28073969/characterization-of-carbapenemase-producing-enterobacteriaceae-in-the-west-midlands-region-of-england-2007-14
#12
Jacqueline Findlay, Katie L Hopkins, Adela Alvarez-Buylla, Daniéle Meunier, Nazim Mustafa, Robert Hill, Rachel Pike, Li-Xu McCrae, Peter M Hawkey, Neil Woodford
OBJECTIVES: Carbapenemase-producing Enterobacteriaceae (CPE) have been increasingly reported in the UK since 2003. We analysed patient and isolate data for CPE confirmed by the national reference laboratory from laboratories in the West Midlands region from November 2007 to December 2014. METHODS: MICs were determined by BSAC agar dilution methodology and isolates exhibiting resistance to one or more carbapenems were screened for carbapenemase genes by PCR. Plasmid analyses were performed after electro-transformation of carbapenemase-encoding plasmids...
January 10, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28073082/vibrio-parahaemolyticus-o4-k8-forms-a-potential-predominant-clone-in-southern-china-as-detected-by-whole-genome-sequence-analysis
#13
Baisheng Li, Xingfen Yang, Hailing Tan, Bixia Ke, Dongmei He, Changwen Ke, Yonghui Zhang
Vibrio parahaemolyticus has been the most common food-borne pathogen in southern China, especially the O3:K6 pandemic clone and its serovariants. Recently, the serotype O4:K8 became more and more prevalent in southern China, which was different from the O3:K6 pandemic clone. Thus, the aim of the present work was to elucidate the molecular characteristics of the O4:K8. Some O3:K6 pandemic clone and its serovariants isolated in the same period were selected for comparative analysis, which were still dominant clone locally...
January 4, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28066711/metagenomic-analysis-of-microbial-community-of-a-parasitoid-wasp-megaphragma-amalphitanum
#14
A V Nedoluzhko, F S Sharko, S V Tsygankova, E S Boulygina, A S Sokolov, S M Rastorguev, V V Kadnikov, A V Mardanov, N V Ravin, A M Mazur, A A Polilov, N M Gruzdeva, E B Prokhortchouk, K G Skryabin
The vast majority of multicellular organisms coexist with bacterial symbionts that may play various roles during their life cycle. Parasitoid wasp Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae) belongs to the smallest known insects whose size is comparable with some bacteria. Using 16S rRNA gene sequencing and Whole Genome Sequencing (WGS), we described microbiota diversity for this arthropod and its potential impact on their lifecycle. Metagenomic sequences were deposited to SRA database which is available at NCBI with accession number SRX2363723 and SRX2363724...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28065891/genetic-and-biochemical-characterization-of-hmb-1-a-novel-subclass-b1-metallo-%C3%AE-lactamase-found-in-a-pseudomonas-aeruginosa-clinical-isolate
#15
Niels Pfennigwerth, Felix Lange, Cristina Belmar Campos, Moritz Hentschke, Sören G Gatermann, Martin Kaase
OBJECTIVES: To characterize a novel subclass B1 metallo-β-lactamase (MBL) found in an MDR Pseudomonas aeruginosa clinical isolate. METHODS: The isolate P. aeruginosa NRZ-03096 was recovered in 2012 from an anal swab from a patient hospitalized in Northern Germany and showed high MICs of carbapenems. MBL production was analysed by several phenotypic tests. Genetic characterization of the novel bla gene and MLST was performed by WGS. The novel bla gene was expressed in Escherichia coli TOP10 and the enzyme was subjected to biochemical characterization to determine the kinetic parameters Km and kcat RESULTS: P...
January 8, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28065470/the-rare-variant-generalized-disequilibrium-test-for-association-analysis-of-nuclear-and-extended-pedigrees-with-application-to-alzheimer-disease-wgs-data
#16
Zongxiao He, Di Zhang, Alan E Renton, Biao Li, Linhai Zhao, Gao T Wang, Alison M Goate, Richard Mayeux, Suzanne M Leal
Whole-genome and exome sequence data can be cost-effectively generated for the detection of rare-variant (RV) associations in families. Causal variants that aggregate in families usually have larger effect sizes than those found in sporadic cases, so family-based designs can be a more powerful approach than population-based designs. Moreover, some family-based designs are robust to confounding due to population admixture or substructure. We developed a RV extension of the generalized disequilibrium test (GDT) to analyze sequence data obtained from nuclear and extended families...
January 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28060810/whole-genome-sequence-analysis-of-salmonella-typhi-isolated-in-thailand-before-and-after-the-introduction-of-a-national-immunization-program
#17
Zoe A Dyson, Duy Pham Thanh, Ladaporn Bodhidatta, Carl Jeffries Mason, Apichai Srijan, Maia A Rabaa, Phat Voong Vinh, Tuyen Ha Thanh, Guy E Thwaites, Stephen Baker, Kathryn E Holt
Vaccines against Salmonella Typhi, the causative agent of typhoid fever, are commonly used by travellers, however, there are few examples of national immunization programs in endemic areas. There is therefore a paucity of data on the impact of typhoid immunization programs on localised populations of S. Typhi. Here we have used whole genome sequencing (WGS) to characterise 44 historical bacterial isolates collected before and after a national typhoid immunization program that was implemented in Thailand in 1977 in response to a large outbreak; the program was highly effective in reducing typhoid case numbers...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28057588/global-gene-expression-patterns-and-somatic-mutations-in-sporadic-intracranial-aneurysms
#18
Zhili Li, Haibin Tan, Yi Shi, Guangfu Huang, Zhenyu Wang, Ling Liu, Cheng Yin, Qi Wang
BACKGROUND: High-throughput sequencing technologies can expand our understanding of the pathological basis of intracranial aneurysms (IAs). Our study was aimed to decipher the gene expression signature and genetic factors associated with IAs. METHODS: We determined the gene expression levels of three cases of IAs by RNA sequencing. Bioinformatics analysis was conducted to identify the differentially expressed genes (DEGs) and uncover their biological function. Moreover, whole genome sequencing (WGS) on additional six cases of IAs was performed to detect the potential somatic alterations in DEGs...
January 2, 2017: World Neurosurgery
https://www.readbyqxmd.com/read/28056767/bacterial-whole-genome-based-phylogeny-construction-of-a-new-benchmarking-dataset-and-assessment-of-some-existing-methods
#19
Johanne Ahrenfeldt, Carina Skaarup, Henrik Hasman, Anders Gorm Pedersen, Frank Møller Aarestrup, Ole Lund
BACKGROUND: Whole genome sequencing (WGS) is increasingly used in diagnostics and surveillance of infectious diseases. A major application for WGS is to use the data for identifying outbreak clusters, and there is therefore a need for methods that can accurately and efficiently infer phylogenies from sequencing reads. In the present study we describe a new dataset that we have created for the purpose of benchmarking such WGS-based methods for epidemiological data, and also present an analysis where we use the data to compare the performance of some current methods...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28053218/singleton-st382-an-emerging-clonal-group-of-listeria-monocytogenes-associated-with-three-multistate-outbreaks-linked-to-contaminated-stone-fruit-caramel-apples-and-leafy-green-salad
#20
Yi Chen, Yan Luo, James Pettengill, Ruth Timme, David Melka, Matthew Doyle, Alikeh Jackson, Mickey Parish, Thomas S Hammack, Marc Allard, Eric W Brown, Errol A Strain
Three multistate outbreaks between 2014 and 2016, involving case patients in and outside the United States, were linked to stone fruit, caramel apples and packaged leafy green salad contaminated with Listeria monocytogenes singleton ST382. Isolates from these outbreaks and other ST382 isolates not associated with these outbreaks were analyzed by whole genome sequencing (WGS) analysis. The primary difference among these three ST382 outbreak strains were single nucleotide polymorphisms (SNPs). WGS analysis using these SNPs differentiated ST382 from a clonal complex 1 outbreak strain co-contaminating the caramel apples...
January 4, 2017: Journal of Clinical Microbiology
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