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Whole-genome sequencing

Charlene M C Rodrigues, Jay Lucidarme, Ray Borrow, Andrew Smith, J Claire Cameron, E Richard Moxon, Martin C J Maiden
In September 2015, 4CMenB meningococcal vaccine was introduced into the United Kingdom infant immunization program without phase 3 trial information. Understanding the effect of this program requires enhanced surveillance of invasive meningococcal disease (IMD) Neisseria meningitidis isolates and comparison with prevaccination isolates. Bexsero Antigen Sequence Types (BASTs) were used to analyze whole-genome sequences of 3,073 prevaccine IMD N. meningitidis isolates obtained during 2010-2016. Isolates exhibited 803 BASTs among 31 clonal complexes...
April 2018: Emerging Infectious Diseases
Maria Dolores Fernandez-Garcia, Romain Volle, Marie-Line Joffret, Serge Alain Sadeuh-Mba, Ionela Gouandjika-Vasilache, Ousmane Kebe, Michael R Wiley, Manasi Majumdar, Etienne Simon-Loriere, Anavaj Sakuntabhai, Gustavo Palacios, Javier Martin, Francis Delpeyroux, Kader Ndiaye, Maël Bessaud
We analyzed whole-genome sequences of 8 enterovirus A71 isolates (EV-A71). We confirm the circulation of genogroup C and the new genogroup E in West Africa. Our analysis demonstrates wide geographic circulation and describes genetic exchanges between EV-A71 and autochthonous EV-A that might contribute to the emergence of pathogenic lineages.
April 2018: Emerging Infectious Diseases
Joseph D Lutgring, Wenming Zhu, Tom J B de Man, Johannetsy J Avillan, Karen F Anderson, David R Lonsway, Lori A Rowe, Dhwani Batra, J Kamile Rasheed, Brandi M Limbago
Oxacillinase (OXA)-48-like carbapenemases remain relatively uncommon in the United States. We performed phenotypic and genotypic characterization of 30 Enterobacteriaceae producing OXA-48-like carbapenemases that were recovered from patients during 2010-2014. Isolates were collected from 12 states and not associated with outbreaks, although we could not exclude limited local transmission. The alleles β-lactamase OXA-181 (blaOXA-181 ) (43%), blaOXA-232 (33%), and blaOXA-48 (23%) were found. All isolates were resistant to ertapenem and showed positive results for the ertapenem and meropenem modified Hodge test and the modified carbapenem inactivation method; 73% showed a positive result for the Carba Nordmann-Poirel test...
April 2018: Emerging Infectious Diseases
Michael Marks, Maria Fookes, Josef Wagner, Rosanna Ghinai, Oliver Sokana, Yaw-Adu Sarkodie, Anthony W Solomon, David C W Mabey, Nicholas R Thomson
Haemophilus ducreyi, which causes chancroid, has emerged as a cause of pediatric skin disease. Isolation of H. ducreyi in low-income settings is challenging, limiting phylogenetic investigation. Next-generation sequencing demonstrates that cutaneous strains arise from class I and II H. ducreyi clades and that class II may represent a distinct subspecies.
April 2018: Emerging Infectious Diseases
Chang Xu
Detection of somatic mutations holds great potential in cancer treatment and has been a very active research field in the past few years, especially since the breakthrough of the next-generation sequencing technology. A collection of variant calling pipelines have been developed with different underlying models, filters, input data requirements, and targeted applications. This review aims to enumerate these unique features of the state-of-the-art variant callers, in the hope to provide a practical guide for selecting the appropriate pipeline for specific applications...
2018: Computational and Structural Biotechnology Journal
Andrew S Fister, Lena Landherr, Siela N Maximova, Mark J Guiltinan
Theobroma cacao , the source of cocoa, suffers significant losses to a variety of pathogens resulting in reduced incomes for millions of farmers in developing countries. Development of disease resistant cacao varieties is an essential strategy to combat this threat, but is limited by sources of genetic resistance and the slow generation time of this tropical tree crop. In this study, we present the first application of genome editing technology in cacao, using Agrobacterium-mediated transient transformation to introduce CRISPR/Cas9 components into cacao leaves and cotyledon cells...
2018: Frontiers in Plant Science
Magdalena Nüesch-Inderbinen, Katrin Zurfluh, Marc J A Stevens, Roger Stephan
OBJECTIVES: Carbapenem-resistant Klebsiella pneumoniae (CRKP) have emerged worldwide and represent a major threat to human health. Here, we report the genome sequence of K. pneumoniae 002SK2, an NDM-9 and CTX-M-15 producing strain isolated from wastewater in Switzerland and belonging to the international high-risk clone ST147. METHODS: Whole genome sequencing of K. pneumoniae 002SK2 was performed using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology RS2 reads (C4/P6 chemistry)...
March 15, 2018: Journal of Global Antimicrobial Resistance
Liang-Qing Dong, Yang Shi, Li-Jie Ma, Liu-Xiao Yang, Xiao-Ying Wang, Shu Zhang, Zhi-Chao Wang, Meng Duan, Zhao Zhang, Long-Zi Liu, Bo-Hao Zheng, Zhen-Bin Ding, Ai-Wu Ke, Da-Ming Gao, Ke Yuan, Jian Zhou, Jia Fan, Ruibin Xi, Qiang Gao
BACKGROUND & AIMS: Intrahepatic cholangiocarcinoma (ICC) is the second-most lethal primary liver cancer. Little is known about intratumoral heterogeneity (ITH) and its impact on ICC progression. We aim to investigate its ITH in hope of helping develop new therapeutic strategies. METHODS: We obtained 69 spatially distinct regions from 6 operable ICCs. Patient-derived primary cancer cells (PDPCs) were established for each region, followed by whole-exome sequencing(WES) and multi-level validation...
March 15, 2018: Journal of Hepatology
Ye Jianwen, Hu Dingkai, Che Xuemei, Jiang Xiaoran, Li Teng, Chen Jinchun, Zhang Haoqian, Chen Guo-Qiang
Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] is one of the most promising biomaterials expected to be used in a wide range of scenarios. However, its large-scale production is still hindered by the high cost. Here we report the engineering of Halomonas bluephagenesis as a low-cost platform for non-sterile and continuous fermentative production of P(3HB-co-4HB) from glucose. Two interrelated 4-hydroxybutyrate (4HB) biosynthesis pathways were constructed to guarantee 4HB monomer supply for P(3HB-co-4HB) synthesis by working in concert with 3-hydroxybutyrate (3HB) pathway...
March 15, 2018: Metabolic Engineering
Trevor J Pemberton, Zachary A Szpiech
Genomic regions of autozygosity (ROAs) represent segments of individual genomes that are homozygous for haplotypes inherited identical-by-descent (IBD) from a common ancestor. ROAs are nonuniformly distributed across the genome, and increased ROA levels are a reported risk factor for numerous complex diseases. Previously, we hypothesized that long ROAs are enriched for deleterious homozygotes as a result of young haplotypes with recent deleterious mutations-relatively untouched by purifying selection-being paired IBD as a consequence of recent parental relatedness, a pattern supported by ROA and whole-exome sequence data on 27 individuals...
March 10, 2018: American Journal of Human Genetics
Sharon R Browning, Brian L Browning, Ying Zhou, Serena Tucci, Joshua M Akey
Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania...
March 15, 2018: Cell
Jana Amlerova, Ibrahim Bitar, Jaroslav Hrabak
Tuberculosis (TB) is considered one of the most serious infectious diseases worldwide. Effective control of tuberculosis infection involves multiple steps, such as reliable detection, treatment, an epidemiological control as a part of case management, and further surveillance and monitoring of TB spread in the human population. Due to the accelerating advances in molecular biology, especially in DNA sequencing, in the past decade, the application of these methods has become crucial for TB evolution studies, differentiation of Mycobacterium tuberculosis genotypes, and their distribution...
March 17, 2018: Folia Microbiologica
Asher Haug-Baltzell, Tushar R Bhangale, Diana Chang, Amy Dressen, Brian L Yaspan, Ward Ortmann, Matthew J Brauer, Julie Hunkapiller, Jens Reeder, Kiran Mukhyala, Karen T Cuenco, Jennifer A Tom, Amy Cowgill, Jan Vogel, William F Forrest, Timothy W Behrens, Robert R Graham, Arthur Wuster
In clinical trials, a placebo response refers to improvement in disease symptoms arising from the psychological effect of receiving a treatment rather than the actual treatment under investigation. Previous research has reported genomic variation associated with the likelihood of observing a placebo response, but these studies have been limited in scope and have not been validated. Here, we analyzed whole-genome sequencing data from 784 patients undergoing placebo treatment in Phase III Asthma or Rheumatoid Arthritis trials to assess the impact of previously reported variation on patient outcomes in the placebo arms and to identify novel variants associated with the placebo response...
March 18, 2018: Genes and Immunity
Chiara Nicoletti, Mattia Forcato, Silvio Bicciato
In all organisms, chromatin is packed to fulfil structural constraints and functional requirements. The hierarchical model of chromatin organization in the 3D nuclear space encompasses different topologies at diverse scale lengths, with chromosomes occupying distinct volumes, further organized in compartments, inside which the chromatin fibers fold into large domains and short-range loops. In the recent years, the combination of chromosome conformation capture (3C) techniques and high-throughput sequencing allowed probing chromatin spatial organization at the whole genome-scale...
March 15, 2018: Current Opinion in Biotechnology
J Richard Pilsner, Alex Shershebnev, Yulia Medvedeva, Alexander Suvorov, Haotian Wu, Andrey Goltsov, Evgeny Loukianov, Tatiana Andreeva, Fedor Gusev, Andrey Manakhov, Luidmila Smigulina, Maria Logacheva, Victoria Shtratnikova, Irina Kuznetsova, Peter Speranskiy-Podobed, Jane S Burns, Paige L Williams, Susan Korrick, Mary M Lee, Evgeny Rogaev, Russ Hauser, Oleg Sergeyev
BACKGROUND: The association of exposure to endocrine disrupting chemicals in the peripubertal period with subsequent sperm DNA methylation is unknown. OBJECTIVE: We examined the association of peripubertal serum 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) concentrations with whole-genome bisulfite sequencing (WGBS) of sperm collected in young adulthood. METHODS: The Russian Children's Study is a prospective cohort of 516 boys who were enrolled at 8-9 years of age and provided semen samples at 18-19 years of age...
March 14, 2018: Reproductive Toxicology
Stephan J Sanders, Benjamin M Neale, Hailiang Huang, Donna M Werling, Joon-Yong An, Shan Dong, Goncalo Abecasis, P Alexander Arguello, John Blangero, Michael Boehnke, Mark J Daly, Kevin Eggan, Daniel H Geschwind, David C Glahn, David B Goldstein, Raquel E Gur, Robert E Handsaker, Steven A McCarroll, Roel A Ophoff, Aarno Palotie, Carlos N Pato, Chiara Sabatti, Matthew W State, A Jeremy Willsey, Steven E Hyman, Anjene M Addington, Thomas Lehner, Nelson B Freimer
In the version of this article initially published, the consortium authorship and corresponding authors were not presented correctly. In the PDF and print versions, the Whole Genome Sequencing for Psychiatric Disorders (WGSPD) consortium was missing from the author list at the beginning of the paper, where it should have appeared as the seventh author; it was present in the author list at the end of the paper, but the footnote directing readers to the Supplementary Note for a list of members was missing. In the HTML version, the consortium was listed as the last author instead of as the seventh, and the line directing readers to the Supplementary Note for a list of members appeared at the end of the paper under Author Information but not in association with the consortium name itself...
March 16, 2018: Nature Neuroscience
Nathaly M Sweeney, Shareef A Nahas, Shimul Chowdhury, Miguel Del Campo, Marilyn C Jones, David P Dimmock, Stephen F Kingsmore, Rcigm Investigators
Congenital diaphragmatic hernia (CDH) results from incomplete formation of the diaphragm leading to herniation of abdominal organs into the thoracic cavity. CDH is associated with pulmonary hypoplasia, congenital heart disease and pulmonary hypertension. Genetically, it is associated with aneuploidies, chromosomal copy number variants, and single gene mutations. CDH is the most expensive non-cardiac congenital defect: Management frequently requires implementation of Extracorporeal Membrane Oxygenation (ECMO), which increases management expenditures 2...
March 16, 2018: Cold Spring Harbor Molecular Case Studies
Sophia David, Massimo Mentasti, Julian Parkhill, Victoria J Chalker
OBJECTIVES: Legionella pneumophila is the leading cause of Legionnaires' disease, a severe form of pneumonia acquired from environmental sources. Investigations of both sporadic cases and outbreaks mostly rely on analysis of a single to a few colony pick(s) isolated from each patient. However, due to the lack of data describing diversity within single patients, the optimal number of picks is unknown. Here, we investigated diversity within individual patients using sequence based typing (SBT) and whole genome sequencing (WGS)...
March 13, 2018: Clinical Microbiology and Infection
Jacob B Hall, Zhaoyuan Cong, Yuka Imamura-Kawasawa, Brian A Kidd, Joel T Dudley, Diane M Thiboutot, Amanda M Nelson
Our understanding of the microbiome and the role of P. acnes in skin homeostasis and acne pathogenesis is evolving. Multiple methods for sampling and identifying the skin's microbiome exist and understanding the differences between the abilities of various methods to characterize the microbial landscape is warranted. This study compared the microbial diversity of samples obtained from the cheeks of twenty volunteers, collected by surface swab, pore strips, and cyanoacrylate glue follicular biopsy, all sequenced with 16S rRNA sequencing (V1-V3) and whole-genome metagenomic sequencing (WGS)...
March 13, 2018: Journal of Investigative Dermatology
Marco van Zwetselaar, Balthazar Nyombi, Tolbert Sonda, Happiness Kumburu, Nyasatu Chamba, Marieke C J Dekker, Kajiru G Kilonzo, Sarah J Urasa, Blandina T Mmbaga
BACKGROUND: Aeromonas species have been documented to yield false positive results in microbiological tests for Vibrio cholerae. They share many biochemical properties with Vibrio species, with which they were jointly classified in the family Vibrionaceae until genotypic information provided new insights. Aeromonas species are increasingly associated with gastrointestinal infections, albeit with great apparent variation in pathogenicity and virulence both between and within species of the genus...
March 17, 2018: Journal of Medical Case Reports
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