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https://www.readbyqxmd.com/read/28538739/multiplex-pcr-method-for-minion-and-illumina-sequencing-of-zika-and-other-virus-genomes-directly-from-clinical-samples
#1
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler, Dennis R Burton, Lia Laura Lewis-Ximenez, Jaqueline Goes de Jesus, Marta Giovanetti, Sarah C Hill, Allison Black, Trevor Bedford, Miles W Carroll, Marcio Nunes, Luiz Carlos Alcantara, Ester C Sabino, Sally A Baylis, Nuno R Faria, Matthew Loose, Jared T Simpson, Oliver G Pybus, Kristian G Andersen, Nicholas J Loman
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28538734/zika-virus-evolution-and-spread-in-the-americas
#2
Hayden C Metsky, Christian B Matranga, Shirlee Wohl, Stephen F Schaffner, Catherine A Freije, Sarah M Winnicki, Kendra West, James Qu, Mary Lynn Baniecki, Adrianne Gladden-Young, Aaron E Lin, Christopher H Tomkins-Tinch, Simon H Ye, Daniel J Park, Cynthia Y Luo, Kayla G Barnes, Rickey R Shah, Bridget Chak, Giselle Barbosa-Lima, Edson Delatorre, Yasmine R Vieira, Lauren M Paul, Amanda L Tan, Carolyn M Barcellona, Mario C Porcelli, Chalmers Vasquez, Andrew C Cannons, Marshall R Cone, Kelly N Hogan, Edgar W Kopp, Joshua J Anzinger, Kimberly F Garcia, Leda A Parham, Rosa M Gélvez Ramírez, Maria C Miranda Montoya, Diana P Rojas, Catherine M Brown, Scott Hennigan, Brandon Sabina, Sarah Scotland, Karthik Gangavarapu, Nathan D Grubaugh, Glenn Oliveira, Refugio Robles-Sikisaka, Andrew Rambaut, Lee Gehrke, Sandra Smole, M Elizabeth Halloran, Luis Villar, Salim Mattar, Ivette Lorenzana, Jose Cerbino-Neto, Clarissa Valim, Wim Degrave, Patricia T Bozza, Andreas Gnirke, Kristian G Andersen, Sharon Isern, Scott F Michael, Fernando A Bozza, Thiago M L Souza, Irene Bosch, Nathan L Yozwiak, Bronwyn L MacInnis, Pardis C Sabeti
Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28538723/genomic-epidemiology-reveals-multiple-introductions-of-zika-virus-into-the-united-states
#3
Nathan D Grubaugh, Jason T Ladner, Moritz U G Kraemer, Gytis Dudas, Amanda L Tan, Karthik Gangavarapu, Michael R Wiley, Stephen White, Julien Thézé, Diogo M Magnani, Karla Prieto, Daniel Reyes, Andrea M Bingham, Lauren M Paul, Refugio Robles-Sikisaka, Glenn Oliveira, Darryl Pronty, Carolyn M Barcellona, Hayden C Metsky, Mary Lynn Baniecki, Kayla G Barnes, Bridget Chak, Catherine A Freije, Adrianne Gladden-Young, Andreas Gnirke, Cynthia Luo, Bronwyn MacInnis, Christian B Matranga, Daniel J Park, James Qu, Stephen F Schaffner, Christopher Tomkins-Tinch, Kendra L West, Sarah M Winnicki, Shirlee Wohl, Nathan L Yozwiak, Joshua Quick, Joseph R Fauver, Kamran Khan, Shannon E Brent, Robert C Reiner, Paola N Lichtenberger, Michael J Ricciardi, Varian K Bailey, David I Watkins, Marshall R Cone, Edgar W Kopp, Kelly N Hogan, Andrew C Cannons, Reynald Jean, Andrew J Monaghan, Robert F Garry, Nicholas J Loman, Nuno R Faria, Mario C Porcelli, Chalmers Vasquez, Elyse R Nagle, Derek A T Cummings, Danielle Stanek, Andrew Rambaut, Mariano Sanchez-Lockhart, Pardis C Sabeti, Leah D Gillis, Scott F Michael, Trevor Bedford, Oliver G Pybus, Sharon Isern, Gustavo Palacios, Kristian G Andersen
Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016-several months before its initial detection...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28538249/norovirus-and-clostridium-difficile-outbreaks-squelching-the-wildfire
#4
Ann Fisher, Louise M Dembry
PURPOSE OF REVIEW: Gastrointestinal outbreaks in the healthcare setting cause increased morbidity and mortality in an already vulnerable population. Optimization of infection prevention measures can be a challenge in healthcare settings. This review describes new literature that may change the traditional infection prevention approach to such outbreaks. RECENT FINDINGS: Asymptomatic carriers of both norovirus and Clostridium difficile can pose risk of transmission to others and the environment...
May 22, 2017: Current Opinion in Infectious Diseases
https://www.readbyqxmd.com/read/28538110/the-effect-of-individual-movements-and-interventions-on-the-spread-of-influenza-in-long-term-care-facilities
#5
Mehdi Najafi, Marek Laskowski, Pieter T de Boer, Evelyn Williams, Ayman Chit, Seyed M Moghadas
BACKGROUND: Nosocomial influenza poses a serious risk among residents of long-term care facilities (LTCFs). OBJECTIVE: We sought to evaluate the effect of resident and staff movements and contact patterns on the outcomes of various intervention strategies for influenza control in an LTCF. METHODS: We collected contact frequency data in Canada's largest veterans' LTCF by enroling residents and staff into a study that tracked their movements through wireless tags and signal receivers...
May 1, 2017: Medical Decision Making: An International Journal of the Society for Medical Decision Making
https://www.readbyqxmd.com/read/28538044/mycobacterium-chimaera-infections-associated-with-heater-cooler-units-in-cardiac-surgery
#6
Peter W Schreiber, Hugo Sax
PURPOSE OF REVIEW: Mycobacterium chimaera infections following cardiac surgery have been reported from an increasing number of countries. These infections are characterized by a poor prognosis with a case fatality rate around 50% despite treatment. Since the first description in 2013, our understanding has grown steadily. Several outbreak investigations, case series, and experiments with heater-cooler units (HCUs) have been published. This review summarizes the current knowledge. RECENT FINDINGS: M...
May 19, 2017: Current Opinion in Infectious Diseases
https://www.readbyqxmd.com/read/28535299/analysis-of-bacterial-metagenomes-from-the-southwestern-gulf-of-mexico-for-pathogens-detection
#7
Wendy Escobedo-Hinojosa, Liliana Pardo-López
Little is known about the diversity of bacteria in the Southwestern Gulf of Mexico. The aim of the study illustrated in this perspective was to search for the presence of bacterial pathogens in this ecosystem, using metagenomic data recently generated by the Mexican research group known as the Gulf of Mexico Research Consortium. Several genera of bacteria annotated as pathogens were detected in water and sediment marine samples. As expected, native and ubiquitous pathogenic bacteria genera such as Burkolderia, Halomonas, Pseudomonas, Shewanella, and Vibrio were highly represented...
May 23, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28534929/teratogens-a-public-health-issue-a-brazilian-overview
#8
Thiago Mazzu-Nascimento, Débora Gusmão Melo, Giorgio Gianini Morbioli, Emanuel Carrilho, Fernanda Sales Luiz Vianna, André Anjos da Silva, Lavinia Schuler-Faccini
Congenital anomalies are already the second cause of infant mortality in Brazil, as in many other middle-income countries in Latin America. Birth defects are a result of both genetic and environmental factors, but a multifactorial etiology has been more frequently observed. Here, we address the environmental causes of birth defects - or teratogens - as a public health issue and present their mechanisms of action, categories and their respective maternal-fetal deleterious effects. We also present a survey from 2008 to 2013 of Brazilian cases involving congenital anomalies (annual average of 20,205), fetal deaths (annual average of 1,530), infant hospitalizations (annual average of 82,452), number of deaths of hospitalized infants (annual average of 2,175), and the average cost of hospitalizations (annual cost of $7,758)...
May 22, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28534888/hepatitis-a-outbreaks-in-european-homosexual-men
#9
Pablo Barreiro, Vicente Soriano
Hepatitis A virus (HAV) is a small RNA, non-enveloped agent predominantly transmitted via the fecal/oral route through person-to-person contact or contaminated food and water. The mean incubation period is 28 days (range: 15-50). Acute hepatitis A is always self-limited and very rarely fatal. Moreover, it never progresses to chronicity. Acutely infected persons are most likely to transmit HAV before the onset of jaundice, when viral particle concentration in stool is highest.
May 23, 2017: AIDS Reviews
https://www.readbyqxmd.com/read/28533530/the-impact-of-hand-foot-and-mouth-disease-control-policies-in-singapore-a-qualitative-analysis-of-public-perceptions
#10
Karen Siegel, Alex R Cook, Hanh La
Hand foot and mouth disease (HFMD) is a widespread pediatric disease in Asia. Most cases are relatively mild and caused by Coxsackie viruses, but in epidemics caused by Enterovirus 71, severe complications can occur. In response to the deaths of dozens of children in a 1997 outbreak (Podin in BMC Public Health 6:180,1 Abubakar in Virus Res 61(1):1-9,2 WHO in3), Singapore practices childcare centre surveillance, case-isolation, and short-term closure of centres. We conducted 44 in-depth interviews with teachers, principals, and parents at four childcare centres in Singapore to better understand experiences with current control policies...
May 2017: Journal of Public Health Policy
https://www.readbyqxmd.com/read/28533207/who-ready-to-deploy-ebola-vaccine-in-disease-outbreak
#11
Anne Gulland
No abstract text is available yet for this article.
May 22, 2017: BMJ: British Medical Journal
https://www.readbyqxmd.com/read/28533186/delayed-identification-of-acinetobacter-baumannii-during-an-outbreak-owing-to-disrupted-blaoxa-51-like-by-isaba19
#12
Amjad Ahmadi, Himen Salimizand
Early detection of Acinetobacter baumannii, an emerging pathogen in hospital settings, is of interest. The blaOXA-51-like family had been used as a marker to detect A. baumannii. During an infection outbreak, 14 isolates produced a 1.7-kb PCR band instead of 353 bp for this marker. This work sought the reasons behind the increased marker size. Characterisation of isolates was done by API-20NE, gyrB multiplex PCR and 16S-23S rRNA ITS sequencing. The 1.7-kb band generated and the complete blaOXA-51-like variant were sequenced to find the probable integrated element...
May 19, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/28533172/new-drug-strategies-to-tackle-viral-host-interactions-for-the-treatment-of-influenza-virus-infections
#13
REVIEW
Simonides I van de Wakker, Marcel J E Fischer, Ronald S Oosting
The influenza virus (IV) is a highly contagious virus causing seasonal global outbreaks affecting annually up to 20% of the world's population and leading to 250,000-500,000 deaths worldwide. Current vaccines have variable effectiveness, and, in particular during a pandemic outbreak, they are probably not available in the amounts needed to protect the world population. Therefore we need effective small molecule drugs to combat an IV infection and that can be produced, in case of pandemic, rapidly and in large quantities...
May 19, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/28532991/estimating-population-density-for-disease-risk-assessment-the-importance-of-understanding-the-area-of-influence-of-traps-using-wild-pigs-as-an-example
#14
Amy J Davis, Bruce Leland, Michael Bodenchuk, Kurt C VerCauteren, Kim M Pepin
Population density is a key driver of disease dynamics in wildlife populations. Accurate disease risk assessment and determination of management impacts on wildlife populations requires an ability to estimate population density alongside management actions. A common management technique for controlling wildlife populations to monitor and mitigate disease transmission risk is trapping (e.g., box traps, corral traps, drop nets). Although abundance can be estimated from trapping actions using a variety of analytical approaches, inference is limited by the spatial extent to which a trap attracts animals on the landscape...
June 1, 2017: Preventive Veterinary Medicine
https://www.readbyqxmd.com/read/28532988/molecular-and-serological-detection-of-trypanosoma-cruzi-in-dogs-canis-lupus-familiaris-suggests-potential-transmission-risk-in-areas-of-recent-acute-chagas-disease-outbreaks-in-colombia
#15
Jeiczon Jaimes-Dueñez, Omar Triana-Chávez, Omar Cantillo-Barraza, Carolina Hernández, Juan David Ramírez, Agustín Góngora-Orjuela
Chagas disease is a zoonotic infection widely distributed in tropical and subtropical regions of America, including more than 50% of the Colombian territory. In the last years, an increase of outbreaks of acute Chagas disease has been observed in the east of the country due to environmental changes and mammal movements toward human settlements. Given the importance of dogs (Canis lupus familiaris) as reservoir hosts and sentinels of Trypanosoma cruzi infection across different regions of America, in this study we reported a serological and molecular detection of T...
June 1, 2017: Preventive Veterinary Medicine
https://www.readbyqxmd.com/read/28532976/microbiological-problems-and-biofilms-associated-with-mycobacterium-chimaera-in-heater-cooler-units-used-for-cardiopulmonary-bypass
#16
REVIEW
J Walker, G Moore, S Collins, S Parks, M I Garvey, T Lamagni, G Smith, L Dawkin, S Goldenberg, M Chand
The role of heater-cooler units (HCUs) in the transmission of Mycobacterium chimaera during open heart surgery has been recognized since 2013. Subsequent investigations uncovered a remarkable global outbreak reflecting the wide distribution of implicated devices. HCUs are an essential component of cardiopulmonary bypass operations and their withdrawal would severely affect capacity for life-saving cardiac surgery. However, studies have demonstrated that many HCUs are contaminated with a wide range of micro-organisms, including M...
April 26, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28532975/emission-of-extensively-drug-resistant-acinetobacter-baumannii-from-hospital-settings-to-the-natural-environment
#17
M Seruga Music, J Hrenovic, I Goic-Barisic, B Hunjak, D Skoric, T Ivankovic
BACKGROUND: Acinetobacter baumannii is a leading emerging pathogen that is frequently recovered from patients during hospital outbreaks. The role of environmental A. baumannii reservoirs is therefore of great concern worldwide. AIM: To investigate the connection between A. baumannii causing hospital outbreaks and environmental isolates from hospital wastewater, urban sewage and river water as the final natural recipient of wastewaters. METHODS: Clinical isolates from patients with hospital-acquired pneumonia and environmental isolates from water were collected during a two-month monitoring period...
April 11, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28532811/bovine-vaccinia-inactivated-vaccinia-virus-vaccine-induces-protection-in-murine-model
#18
Ana Carolina Diniz Matos, Maria Isabel Maldonado Coelho Guedes, Izabelle Silva Rehfeld, Erica Azevedo Costa, Aristoteles Gomes Costa, Natalia Lopes da Silva, Andrey Pereira Lage, Zélia Inês Portela Lobato
Bovine vaccinia (BV), caused by Vaccinia virus (VACV), is a zoonosis characterized by exanthematous lesions on the teats of dairy cows and the milkers' hands. Since 1999, due to the occurrence of many BV outbreaks in dairy farms across all Brazilian regions, there is a need to improve the control and prevention measures of the disease. Vaccination is one of the major tools to prevent viral diseases, and it could be an alternative for BV prevention. The main objective of this study was the development of vaccine formulations against BV using the inactivated VACV strain GP2 as antigen combined with different adjuvants...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28532787/evolution-of-avian-encephalomyelitis-virus-during-embryo-adaptation
#19
Rüdiger Hauck, C Gabriel Sentíes-Cué, Ying Wang, Colin Kern, H L Shivaprasad, Huaijun Zhou, Rodrigo A Gallardo
Wild-type avian encephalomyelitis virus (AEV) causes neurological signs in young chicks but no disease in pullets after oral or intracutaneous infection. However, if the virus gets embryo-adapted by serial passaging in chicken embryos, it will cause AE after intracutaneous infection in chickens of all ages. Recently, several cases of AE in layer pullets occurring shortly after intracutaneous vaccination were described. The present investigation was initiated to determine if vaccines that had inadvertently been embryo-adapted were responsible for these outbreaks...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28532667/evaluation-of-three-recombinant-outer-membrane-proteins-ompa1-tdr-and-tbpa-as-potential-vaccine-antigens-against-virulent-aeromonas-hydrophila-infection-in-channel-catfish-ictalurus-punctatus
#20
Hossam Abdelhamed, Iman Ibrahim, Seong Won Nho, Michelle M Banes, Robert W Wills, Attila Karsi, Mark L Lawrence
A virulent clonal population of Aeromonas hydrophila (VAh) is recognized as the etiological agent in outbreaks of motile aeromonas septicemia (MAS) in catfish aquaculture in the southeastern United States since 2009. Genomic subtraction revealed three outer membrane proteins present in VAh strain ML09-119 but not in low virulence reference A. hydrophila strains: major outer membrane protein OmpA1, TonB-dependent receptor (Tdr), and transferrin-binding protein A (TbpA). Here, the genes encoding ompA1, tdr, and tbpA were cloned from A...
May 19, 2017: Fish & Shellfish Immunology
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