keyword
MENU ▼
Read by QxMD icon Read
search

genomic epidemiology

keyword
https://www.readbyqxmd.com/read/28430818/comparative-genomics-of-burkholderia-multivorans-a-ubiquitous-pathogen-with-a-highly-conserved-genomic-structure
#1
Charlotte Peeters, Vaughn S Cooper, Philip J Hatcher, Bart Verheyde, Aurélien Carlier, Peter Vandamme
The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B...
2017: PloS One
https://www.readbyqxmd.com/read/28428977/19th-workshop-of-the-international-stroke-genetics-consortium-april-28-29-2016-boston-massachusetts-usa-2016-001-mri-defined-cerebrovascular-genomics-the-charge-consortium
#2
S Debette, Y Saba, D Vojinovic, X Jian, H Adams, G Chauhan, M Sargurupremraj, S Kaffashian, J Ding, J C Bis, P Nyquist, K Mather, C Van Duijn, L J Launer, M A Ikram, H Schmidt, W T Longstreth, M Fornage, S Seshadri
The CHARGE consortium is an investigator-initiated collaboration to facilitate meta-analyses of genome-wide association studies (GWAS) and genomic analyses based on next generation sequencing (NGS), among multiple large and well-phenotyped population-based cohort studies around the world (http://www.chargeconsortium.com). Within the neuro-CHARGE working group, we are presenting an update of ongoing genomic studies on MRI-markers of cerebrovascular disease. Large population-based studies have shown that the burden of cerebrovascular disease extends far beyond that of clinical stroke...
March 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28428775/genomics-reveals-a-unique-clone-of-burkholderia-cenocepacia-harboring-an-actively-excising-novel-genomic-island
#3
Prashant P Patil, Swapna Mali, Samriti Midha, Vikas Gautam, Lona Dash, Sunil Kumar, Jayanthi Shastri, Lipika Singhal, Prabhu B Patil
Burkholderia cenocepacia is a clinically dominant form among the other virulent species of Burkholderia cepacia complex (Bcc). In the present study, we sequenced and analyzed the genomes of seven nosocomial Bcc isolates, five of which were isolated from the bloodstream infections and two isolates were recovered from the hospital setting during the surveillance. Genome-based species identification of the Bcc isolates using a type strain explicitly identified the species as B. cenocepacia. Moreover, single nucleotide polymorphism analysis revealed that the six isolates were clonal and phylogenetically distinct from the other B...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28428772/molecular-characterization-of-staphylococcus-aureus-isolated-from-bovine-mastitis-and-close-human-contacts-in-south-african-dairy-herds-genetic-diversity-and-inter-species-host-transmission
#4
Tracy Schmidt, Marleen M Kock, Marthie M Ehlers
Staphylococcus aureus is one of the most common etiological agents of contagious bovine mastitis worldwide. The purpose of this study was to genetically characterize a collection of S. aureus isolates (bovine = 146, human = 12) recovered from cases of bovine mastitis and nasal swabs of close human contacts in the dairy environment. Isolates were screened for a combination of clinically significant antimicrobial and virulence gene markers whilst the molecular epidemiology of these isolates and possible inter-species host transmission was investigated using a combination of genotyping techniques...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28424184/demographic-lifestyle-and-genetic-determinants-of-circulating-concentrations-of-25-hydroxyvitamin-d-and-vitamin-d-binding-protein-in-african-american-and-european-american-women
#5
Song Yao, Chi-Chen Hong, Elisa V Bandera, Qianqian Zhu, Song Liu, Ting-Yuan David Cheng, Gary Zirpoli, Stephen A Haddad, Kathryn L Lunetta, Edward A Ruiz-Narvaez, Susan E McCann, Melissa A Troester, Lynn Rosenberg, Julie R Palmer, Andrew F Olshan, Christine B Ambrosone
Background: Vitamin D may have anticancer activities. The high prevalence of vitamin D deficiency in African Americans (AAs) may be a contributing factor to the cancer health disparities between AAs and European Americans (EAs).Objectives: We compared concentrations of 25(OH)D and vitamin D-binding protein (VDBP) in AA and EA women and investigated determinants of the vitamin D-biomarker concentrations in both populations.Design: We used data and biospecimens from 909 AA and 847 EA healthy control subjects from the Carolina Breast Cancer Study (CBCS) and the Women's Circle of Health Study (WCHS) in the African American Breast Cancer Epidemiology and Risk Consortium...
April 19, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28419202/genomic-characterization-of-usa300-mrsa-to-evaluate-intraclass-transmission-and-recurrence-of-ssti-among-high-risk-military-trainees
#6
Eugene V Millar, Gregory K Rice, Emad M Elassal, Carey D Schlett, Jason W Bennett, Cassie L Redden, Deepika Mor, Natasha N Law, David R Tribble, Theron Hamilton, Michael W Ellis, Kimberly A Bishop-Lilly
Background.: Military trainees are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infection (SSTI). Whole genome sequencing (WGS) can refine our understanding of MRSA transmission and microevolution in congregate settings. Methods.: We conducted a prospective case-control study of SSTI among US Army Infantry trainees at Fort Benning, GA from July 2012-December 2014. We identified clusters of USA300 MRSA SSTI within select training classes and performed WGS on clinical isolates...
April 17, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28417249/virus-vector-relationship-in-the-citrus-leprosis-pathosystem
#7
Aline Daniele Tassi, Laura Cristina Garita-Salazar, Lilian Amorim, Valdenice Moreira Novelli, Juliana Freitas-Astúa, Carl C Childers, Elliot W Kitajima
Citrus leprosis has been one of the most destructive diseases of citrus in the Americas. In the last decade important progress has been achieved such as the complete genome sequencing of its main causal agent, Citrus leprosis virus C (CiLV-C), belonging to a new genus Cilevirus. It is transmitted by Brevipalpus yothersi Baker (Acari: Tenuipalpidae), and is characterized by the localized symptoms it induces on the leaves, fruits and stems. It occurs in the American continents from Mexico to Argentina. The virus was until recently considered restricted to Citrus spp...
April 17, 2017: Experimental & Applied Acarology
https://www.readbyqxmd.com/read/28412860/modeling-vascular-inflammation-and-atherogenicity-after-inhalation-of-ambient-levels-of-ozone-exploratory-lessons-from-transcriptomics
#8
Andrea Tham, Dominic Lullo, Sarah Dalton, Siyang Zeng, Ian van Koeverden, Mehrdad Arjomandi
BACKGROUND: Epidemiologic studies have linked inhalation of air pollutants such as ozone to cardiovascular mortality. Human exposure studies have shown that inhalation of ambient levels of ozone causes airway and systemic inflammation and an imbalance in sympathetic/parasympathetic tone. METHODS: To explore molecular mechanisms through which ozone inhalation contributes to cardiovascular mortality, we compared transcriptomics data previously obtained from bronchoalveolar lavage (BAL) cells obtained from healthy subjects after inhalational exposure to ozone (200 ppb for 4 h) to those of various cell samples from 11 published studies of patients with atherosclerotic disease using the Nextbio genomic data platform...
April 16, 2017: Inhalation Toxicology
https://www.readbyqxmd.com/read/28411164/high-levels-of-local-inter-and-intra-host-genetic-variation-of-west-nile-virus-and-evidence-of-fine-scale-evolutionary-pressures
#9
Dylan J Ehrbar, Kiet A Ngo, Scott R Campbell, Laura D Kramer, Alexander T Ciota
West Nile virus (WNV; Flaviviridae, Flavivirus) has been endemic in New York State (NYS) since its 1999 introduction, yet prevalence in Culex mosquitoes varies substantially over small spatial and temporal scales. It is unclear if viral genetics plays a role in this variability, as genetic and phenotypic characterization on local scales has generally been lacking. In addition, intrahost diversity of circulating strains have not been fully characterized despite the documented role of minority variants in viral fitness and virulence...
April 11, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28408664/complete-genome-sequence-of-a-novel-porcine-circovirus-type-3-strain-pcv3-cn-hubei-618-2016-isolated-from-china
#10
Shengxian Fan, Xugang Ku, Fangzhou Chen, Ying Wang, Xuexiang Yu, Qigai He
In October 2016, porcine circovirus type 3 (PCV3) was identified as a pathogen agent for pigs in the United States. Here, we report the genome sequence of a Chinese PCV3 strain, PCV3/CN/Hubei-618/2016. This will help us better understand the epidemiology and genetic characteristics of PCV3.
April 13, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28405360/towards-an-integrated-food-safety-surveillance-system-a-simulation-study-to-explore-the-potential-of-combining-genomic-and-epidemiological-metadata
#11
A A Hill, M Crotta, B Wall, L Good, S J O'Brien, J Guitian
Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. Next-generation sequencing technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks...
March 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28404677/comparison-of-two-whole-genome-sequencing-methods-for-analysis-of-three-methicillin-resistant-staphylococcus-aureus-outbreaks
#12
Scott A Cunningham, Nicholas Chia, Patricio R Jeraldo, Daniel J Quest, Julie A Johnson, Dave J Boxrud, Angela J Taylor, Jun Chen, Gregory D Jenkins, Travis M Drucker, Heidi Nelson, Robin Patel
Whole genome sequencing (WGS) can provide excellent resolution in global and local epidemiological investigations of Staphylococcus aureus outbreaks. A variety of sequencing approaches and analytical tools have been used; it is not clear which is ideal. We compared two WGS strategies and two analytical approaches to the standard method of SmaI restriction digestion pulsed-field gel electrophoresis (PFGE) for typing S. aureus Forty-two S. aureus isolates from three outbreaks and 12 reference isolates were studied...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404483/anaconda-paramyxovirus-infection-in-an-adult-green-anaconda-after-prolonged-incubation-pathological-characterization-and-whole-genome-sequence-analysis
#13
Patrick C Y Woo, Paolo Martelli, Suk-Wai Hui, Candy C Y Lau, Joseph M Groff, Rachel Y Y Fan, Susanna K P Lau, Kwok-Yung Yuen
From July 2011 to June 2012, 31 out of 33 green anaconda juveniles from an oceanarium in Hong Kong died over a 12-month period. These anacondas were progeny of a female anaconda purchased from Japan and added to the collection in May 2011. The juvenile anacondas were born in July 2011. A novel paramyxovirus, named anaconda paramyxovirus (AnaPV), was isolated from these affected juvenile anacondas. In July 2015, one of the remaining two anacondas, that survived the cluster of fatal infections, died at the age of four...
April 9, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28404232/pcr-based-molecular-characterization-of-blastocystis-hominis-subtypes-in-southwest-of-iran
#14
Shahram Khademvatan, Rahim Masjedizadeh, Ehsan Yousefi-Razin, Hamidreza Mahbodfar, Fakher Rahim, Elham Yousefi, Masoud Foroutan
Blastocystis hominis is the most common intestinal parasite found in humans and many other hosts. Pathogenicity of Blastocystis sp. remains controversial and it has been suggested that it may be associated with certain subtypes of organism. The aim of this study was to evaluate the molecular epidemiology of B. hominis and its subtype distribution in Ahvaz, southwest of Iran. During 2012-2014, a total of 481 samples were collected from patients referred to the medical laboratory centers in Ahvaz for stool examination...
April 9, 2017: Journal of Infection and Public Health
https://www.readbyqxmd.com/read/28401650/caenorhabditis-elegans-orthologs-of-human-genes-differentially-expressed-with-age-are-enriched-for-determinants-of-longevity
#15
George L Sutphin, Grant Backer, Susan Sheehan, Shannon Bean, Caroline Corban, Teresa Liu, Marjolein J Peters, Joyce B J van Meurs, Joanne M Murabito, Andrew D Johnson, Ron Korstanje
We report a systematic RNAi longevity screen of 82 Caenorhabditis elegans genes selected based on orthology to human genes differentially expressed with age. We find substantial enrichment in genes for which knockdown increased lifespan. This enrichment is markedly higher than published genomewide longevity screens in C. elegans and similar to screens that preselected candidates based on longevity-correlated metrics (e.g., stress resistance). Of the 50 genes that affected lifespan, 46 were previously unreported...
April 12, 2017: Aging Cell
https://www.readbyqxmd.com/read/28398847/traceback-a-proposed-framework-to-increase-identification-and-genetic-counseling-of-brca1-and-brca2-mutation-carriers-through-family-based-outreach
#16
Goli Samimi, Marcus Q Bernardini, Lawrence C Brody, Charlisse F Caga-Anan, Ian G Campbell, Georgia Chenevix-Trench, Fergus J Couch, Michael Dean, Joanne A de Hullu, Susan M Domchek, Ronny Drapkin, Heather Spencer Feigelson, Michael Friedlander, Mia M Gaudet, Marline G Harmsen, Karen Hurley, Paul A James, Janice S Kwon, Felicitas Lacbawan, Stephanie Lheureux, Phuong L Mai, Leah E Mechanic, Lori M Minasian, Evan R Myers, Mark E Robson, Susan J Ramus, Lisa F Rezende, Patricia A Shaw, Thomas P Slavin, Elizabeth M Swisher, Masataka Takenaka, David D Bowtell, Mark E Sherman
In May 2016, the Division of Cancer Prevention and the Division of Cancer Control and Population Sciences, National Cancer Institute, convened a workshop to discuss a conceptual framework for identifying and genetically testing previously diagnosed but unreferred patients with ovarian cancer and other unrecognized BRCA1 or BRCA2 mutation carriers to improve the detection of families at risk for breast or ovarian cancer. The concept, designated Traceback, was prompted by the recognition that although BRCA1 and BRCA2 mutations are frequent in women with ovarian cancer, many such women have not been tested, especially if their diagnosis predated changes in testing guidelines...
April 11, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28398773/genetic-characterization-of-a-unique-recombinant-strain-identified-in-yunnan-with-genome-comprised-of-b-and-c
#17
Xiaolin Wang, Min Zhang, Jianjian Li, Tianyi Li, Changrong Sun, Hanping Li, Yongjian Liu, Siyang Liu, Daomin Zhuang, Zuoyi Bao, Jingwan Han, Jingyun Li, Lin Li
Since the first identification of HIV-1 outbreak in Dehong, Yunnan province has been the epidemic center of HIV in China. Due to the special geographic location and the frequent population mobility, Yunnan province contained complex HIV subtype distribution. Many new CRFs and URFs have been found in recently years. In this study, a unique HIV-1 recombinant strain (URF) genome (YN10134) was characterized from an HIV-positive female in Yunnan, China. This virus genome had a complex intersubtype recombinant structure with 8 breakpoints, composed of subtype B and subtype C...
February 10, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28395986/a-decade-of-progress-on-the-genetic-basis-of-coronary-artery-disease-practical-insights-for-the-internist
#18
REVIEW
Domenico Girelli, Chiara Piubelli, Nicola Martinelli, Roberto Corrocher, Oliviero Olivieri
Clinicians are well aware of the importance of a positive family history for coronary artery disease (CAD). Nonetheless, elucidation of the genetic basis of CAD has long proven difficult. The scenario changed in the last decade through the application of modern genomic technologies, like genome-wide association studies (GWAS) and next generation sequencing (NGS). GWAS have discovered over 60 common variants highly associated with CAD. For predictive purposes, such variants have been used to build up Genetic Risk Scores (GRSs), but their incorporation into classical prediction models does not appear substantially outperform the simple addition of family history...
April 7, 2017: European Journal of Internal Medicine
https://www.readbyqxmd.com/read/28394942/evidence-for-the-evolutionary-steps-leading-to-meca-mediated-%C3%AE-lactam-resistance-in-staphylococci
#19
Joana Rolo, Peder Worning, Jesper Boye Nielsen, Rita Sobral, Rory Bowden, Ons Bouchami, Peter Damborg, Luca Guardabassi, Vincent Perreten, Henrik Westh, Alexander Tomasz, Hermínia de Lencastre, Maria Miragaia
The epidemiologically most important mechanism of antibiotic resistance in Staphylococcus aureus is associated with mecA-an acquired gene encoding an extra penicillin-binding protein (PBP2a) with low affinity to virtually all β-lactams. The introduction of mecA into the S. aureus chromosome has led to the emergence of methicillin-resistant S. aureus (MRSA) pandemics, responsible for high rates of mortality worldwide. Nonetheless, little is known regarding the origin and evolution of mecA. Different mecA homologues have been identified in species belonging to the Staphylococcus sciuri group representing the most primitive staphylococci...
April 10, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28394350/population-and-individual-specific-regulatory-variation-in-sardinia
#20
Mauro Pala, Zachary Zappala, Mara Marongiu, Xin Li, Joe R Davis, Roberto Cusano, Francesca Crobu, Kimberly R Kukurba, Michael J Gloudemans, Frederic Reinier, Riccardo Berutti, Maria G Piras, Antonella Mulas, Magdalena Zoledziewska, Michele Marongiu, Elena P Sorokin, Gaelen T Hess, Kevin S Smith, Fabio Busonero, Andrea Maschio, Maristella Steri, Carlo Sidore, Serena Sanna, Edoardo Fiorillo, Michael C Bassik, Stephen J Sawcer, Alexis Battle, John Novembre, Chris Jones, Andrea Angius, Gonçalo R Abecasis, David Schlessinger, Francesco Cucca, Stephen B Montgomery
Genetic studies of complex traits have mainly identified associations with noncoding variants. To further determine the contribution of regulatory variation, we combined whole-genome and transcriptome data for 624 individuals from Sardinia to identify common and rare variants that influence gene expression and splicing. We identified 21,183 expression quantitative trait loci (eQTLs) and 6,768 splicing quantitative trait loci (sQTLs), including 619 new QTLs. We identified high-frequency QTLs and found evidence of selection near genes involved in malarial resistance and increased multiple sclerosis risk, reflecting the epidemiological history of Sardinia...
April 10, 2017: Nature Genetics
keyword
keyword
65785
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"