Advanced Molecular Detection Clips Content (Published on 10/19/2017)
NEWS
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New Specification Simplifies Communication of NGS Data Analysis, Results for FDA Regulatory Review
Thomas UG. GenomeWeb, Oct 16, 2017. -
At ASHG, Bill Gates and Francis Collins Discuss Global Health and Genetics in the Computational Age
Karow J. GenomeWeb, Oct 19, 2017. -
New diarrhea guidelines stress implications of molecular tests
Roos R. CIDRAP, Oct 19, 2017. -
Global antibiotic resistance tracking project launched
Dall C. CIDRAP, Oct 13, 2017. -
'Digital' Nucleic Acid Amplification Shows Promise for Rapid Antibiotic Susceptibility Testing
Johnson M. 360dx, Oct 13, 2017. -
Going live with a live Ebola assay
Dupnik K. Sci Transl Med, Oct 18, 2017. -
H7N9 study finds virus poised to become more lethal, resistant to treatment
Schnirring L. CIDRAP, Oct 19, 2017. -
Bacteria Found in Womens Upper Reproductive Tracts
Kwon D. The Scientist, Oct 17, 2017.
POLICY
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2017 Infectious Diseases Society of America Clinical Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea.
Shane Andi L et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Nov (12) e45-e80
CONCEPTS / COMMENTS
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Molecular evolution: No escape from the tangled bank
Plotkin JB. Nature, Oct 18, 2017. -
An ace in the hole for DNA sequencing
Eisenstein M. Nature, Oct 11, 2017. -
The future of DNA sequencing.
Green Eric D et al. Nature 2017 Oct (7675) 179-181 -
Improving tuberculosis diagnosis: Better tests or better healthcare?
Datta Sumona et al. PLoS medicine 2017 Oct (10) e1002406 -
Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases.
Simner Patricia J et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Oct -
2017 Infectious Diseases Society of America Infectious Diarrhea Guidelines: A View From the Clinical Laboratory
Fang FC, Patel R. Clin Infect Dis, Oct 19, 2017. -
Investigation of Human Immunodeficiency Virus Outbreaks Among People Who Inject Drugs: Timely Diagnosis and Molecular Surveillance are Crucial.
Paraskevis Dimitrios et al. The Journal of infectious diseases 2017 Oct -
Hypothesis: RNA and DNA Viral Sequence Integration into the Mammalian Host Genome Supports Long-Term B Cell and T Cell Adaptive Immunity.
Hurwitz Julia L et al. Viral immunology 2017 Oct
METHODS / TOOLS
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DNA sequencing at 40: past, present and future.
Shendure Jay et al. Nature 2017 Oct -
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.
Noyes Noelle R et al. Microbiome 2017 Oct (1) 142 -
Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches.
George Sophie et al. Microbial genomics 2017 Aug (8) e000118 -
SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology.
Petkau Aaron et al. Microbial genomics 2017 Jun (6) e000116 -
Phylotyper: in silico predictor of gene subtypes.
Whiteside Matthew D et al. Bioinformatics (Oxford, England) 2017 Jul -
Panoptes: web-based exploration of large scale genome variation data
Vauterin P, et al. Bioinformatics, Oct 15, 2017. -
PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies.
Mallet Ludovic et al. Bioinformatics (Oxford, England) 2017 Oct (20) 3283-3285 -
BioQueue: a novel pipeline framework to accelerate bioinformatics analysis.
Yao Li et al. Bioinformatics (Oxford, England) 2017 Oct (20) 3286-3288 -
Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling.
Vrancken Bram et al. Virus evolution 2017 Jul (2) vex028 -
Reverse genetic system, genetically stable reporter viruses and packaged subgenomic replicon based on a Brazilian Zika virus isolate.
Mutso Margit et al. The Journal of general virology 2017 Oct -
Recommendations for Laboratory Containment and Management of Gene Drive Systems in Arthropods.
Benedict Mark Q et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2017 Oct -
Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results
Alterovitz G, et al. bioRxiv, Oct 9, 2017.
EVOLUTION / ECOLOGY / POPULATIONS
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Emergence and genomic diversification of a virulent serogroup W:ST-2881(CC175) Neisseria meningitidis clone in the African meningitis belt.
Lamelas Araceli et al. Microbial genomics 2017 Aug (8) e000120 -
A comparison of extended spectrum β-lactamase producing Escherichia coli from clinical, recreational water and wastewater samples associated in time and location.
Jørgensen Silje B et al. PloS one 2017 (10) e0186576 -
The new phylogeny of the genus Mycobacterium: The old and the news.
Tortoli Enrico et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Oct -
Assessing the Diversity of Rodent-Borne Viruses: Exploring of High-Throughput Sequencing and Classical Amplification/Sequencing Approaches.
Drewes Stephan et al. Advances in virus research 2017 61-108 -
Molecular Evolution of MERS Coronavirus: Dromedaries as a Recent Intermediate Host or Long-Time Animal Reservoir?
Lau Susanna K P et al. International journal of molecular sciences 2017 Oct (10) -
Impact of Clinical Parameters in the Intrahost Evolution of HIV-1 Subtype B in Pediatric Patients: A Machine Learning Approach.
Rojas Sánchez Patricia et al. Genome biology and evolution 2017 Oct (10) 2715-2726 -
Genome-wide SNPs reveal the drivers of gene flow in an urban population of the Asian Tiger Mosquito, Aedes albopictus.
Schmidt Thomas L et al. PLoS neglected tropical diseases 2017 Oct (10) e0006009 -
Population genomics reveals that an anthropophilic population of Aedes aegypti mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector.
Crawford Jacob E et al. BMC biology 2017 Feb (1) 16
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing.
Ludden Catherine et al. Microbial genomics 2017 Jul (7) e000114 -
The Role of Phylogenetics as a Tool to Predict the Spread of Resistance.
Zhukova Anna et al. The Journal of infectious diseases 2017 Oct -
High rates of human fecal carriage of mcr-1-positive multi-drug resistant Enterobacteriaceae isolates emerge in China in association with successful plasmid families.
Zhong Lan-Lan et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Oct -
Molecular epidemiology of multi- and extensively-drug-resistant mycobacterium tuberculosis in ireland, 2001-2014.
Roycroft E et al. The Journal of infection 2017 Oct -
Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients.
Vasilijevic Jasmina et al. PLoS pathogens 2017 Oct (10) e1006650
DETECTION / DIAGNOSIS
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Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates.
Lemon Jamie K et al. Journal of clinical microbiology 2017 Oct -
A rapid bio-optical sensor for diagnosing Q fever in clinical specimens.
Koo Bonhan et al. Journal of biophotonics 2017 Oct -
Diagnosing antimicrobial resistance.
Burnham Carey-Ann D et al. Nature reviews. Microbiology 2017 Oct (11) 697-703 -
Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases
Simner PJ, et al. Clin Infect Dis, Oct 12, 2017. -
Diagnostics for yaws eradication: insights from direct next generation sequencing of cutaneous strains of Treponema pallidum.
Marks Michael et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Oct -
Rapid Clearance and Frequent Reinfection With Enteric Pathogens Among Children With Acute Diarrhea in Zanzibar.
Andersson Maria Eva et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 10 (8) 1371-1377 -
Fluoroquinolone Resistance Mutation Detection Is Equivalent to Culture-Based Drug Sensitivity Testing for Predicting Multidrug-Resistant Tuberculosis Treatment Outcome: A Retrospective Cohort Study.
Farhat Maha R et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Oct (8) 1364-1370 -
Turnaround time of whole genome sequencing for mycobacterial identification and drug susceptibility testing in routine practice.
Olaru Ioana D et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2017 Oct -
An Efficient, Large-Scale Survey of Hepatitis C Viremia in the Democratic Republic of the Congo Using Dried Blood Spots
Parr JB, et al. Clin Infect Dis, Oct 18, 2017. -
Lineage-Specific Real-Time RT-PCR for Yellow Fever Virus Outbreak Surveillance, Brazil.
Fischer Carlo et al. Emerging infectious diseases 2017 Nov (11) -
Update: Interim Guidance for the Diagnosis, Evaluation, and Management of Infants with Possible Congenital Zika Virus Infection - United States, October 2017.
Tolulope Adebanjo et al. MMWR Morb Mortal Wkly Rep 2017 10 (41) 1089-1099 -
A novel Next Generation Sequencing assay as an alternative to currently available methods for Hepatitis C virus genotyping.
Dirani G et al. Journal of virological methods 2017 Oct -
Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification.
Kurosaki Yohei et al. Scientific reports 2017 Oct (1) 13503 -
Evaluation of multiplex real-time PCR for identifying dermatophytes in clinical samples - a multicentre study.
Sherman Shany et al. Mycoses 2017 Oct -
Survey of laboratory practices for diagnosis of fungal infection in seven Asian countries: An Asia Fungal Working Group (AFWG) initiative.
Chindamporn Ariya et al. Medical mycology 2017 Sep -
Droplet digital PCR diagnosis of human schistosomiasis: parasite cell-free DNA detection in diverse clinical samples.
Weerakoon Kosala G et al. The Journal of infectious diseases 2017 Sep
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island.
Sarovich Derek S et al. Microbial genomics 2017 Aug (8) e000117 -
Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns.
Donker Tjibbe et al. Microbial genomics 2017 Jul (7) e000113 -
Multi-provincial Salmonellosis Outbreak Related to Newly Hatched Chicks and Poults: A Genomics Perspective.
Croxen Matthew A et al. PLoS currents 2017 Aug -
Whole genome sequencing of Neisseria gonorrhoeae reveals transmission clusters involving patients of mixed HIV serostatus.
Peters Joanna et al. Sexually transmitted infections 2017 Oct -
Detailed molecular epidemiology of Chlamydia trachomatis in the population of Southampton attending the genitourinary medicine clinic in 2012-13 reveals the presence of long established genotypes and transitory sexual networks.
Labiran Clare et al. PloS one 2017 (9) e0185059 -
Impact of Public Safety Policies on HIV Transmission Dynamics in Tijuana, Mexico.
Mehta Sanjay R et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Oct -
No Substantial Evidence for Sexual Transmission of Minority HIV Drug Resistance Mutations in Men Who Have Sex with Men.
Chaillon Antoine et al. Journal of virology 2017 Nov (21) -
Chikungunya fever outbreak identified in North Bali, Indonesia.
Sari Kartika et al. Transactions of the Royal Society of Tropical Medicine and Hygiene 2017 Oct 1-3 -
Detailed Transmission Network Analysis of a Large Opiate-Driven Outbreak of HIV Infection in the United States.
Ellsworth M Campbell et al. J Infect Dis 2017 10 (9) 1053-1062 -
Japanese Encephalitis Virus Transmitted Via Blood Transfusion, Hong Kong, China.
Cheng Vincent C C et al. Emerging infectious diseases 2018 Jan (1)
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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An Early American Smallpox Vaccine Based on Horsepox.
Schrick Livia et al. The New England journal of medicine 2017 10 (15) 1491-1492 -
Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK.
Gladstone Rebecca A et al. Microbial genomics 2017 Jun (6) e000119 -
Beyond antigenic match: possible agent-host and immuno-epidemiological influences on influenza vaccine effectiveness during the 2015-16 season in Canada.
Skowronski Danuta M et al. The Journal of infectious diseases 2017 Oct -
Adenovirus vector-based multi-epitope vaccine provides partial protection against H5, H7, and H9 avian influenza viruses.
Hassan Ahmed O et al. PloS one 2017 (10) e0186244 -
Should We Be Testing for Baseline Integrase Resistance in Patients Newly Diagnosed With Human Immunodeficiency Virus?
Koullias Yiannis et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 10 (8) 1274-1281 -
Antimicrobial resistance gene acquisition and depletion following fecal microbiota transplantation (FMT) for recurrent Clostridium difficile infection.
Leung Victor et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Sep -
The Female Genital Tract Microbiome Is Associated With Vaginal Antiretroviral Drug Concentrations in Human Immunodeficiency Virus-Infected Women on Antiretroviral Therapy.
Donahue Carlson Renee et al. The Journal of infectious diseases 2017 Oct
HOST-MICROBE INTERACTIONS
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Ratio of Klebsiella/Bifidobacterium in early life correlates with later development of paediatric allergy.
Low J S Y et al. Beneficial microbes 2017 Oct (5) 681-695 -
The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases
Chen C, et al. Nat Commun, Oct 17, 2017. -
Gut bacterial communities of diarrheic patients with indications of Clostridioides difficile infection.
Schneider Dominik et al. Scientific data 2017 Oct 170152 -
Viral Load and Cytokine Response Profile Does Not Support Antibody-Dependent Enhancement in Dengue-Primed Zika Virus-Infected Patients.
Terzian Ana Carolina Bernardes et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 10 (8) 1260-1265 -
Whole genome next generation sequencing to study within-host evolution of chronic norovirus infection among immunocompromised patients.
van Beek J et al. The Journal of infectious diseases 2017 Sep
Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by Public Health Genomics Branch to provide current awareness of the scientific literature and news. Inclusion in the clips does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the Clips, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.
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