Advanced Molecular Detection Clips
About Advanced Molecular Detection Clips
Clips are selected weekly from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in infectious disease public health surveillance, investigation, and development of new diagnostics and interventions. The collection is not comprehensive but aims to capture highlights, while surveying a wide range of topics. CDC-authored articles are flagged. Items marked I&E address aspects of implementation or evaluation in clinical or public health practice.
Advanced Molecular Detection Clips Content
NEWS
- JGI Researchers Use PacBio Sequencing to Create High-Resolution Phylogenetic Profiles for Microbes
Newbern E. GenomeWeb, Feb 19, 2016. - Pocket DNA sequencers make real-time diagnostics a reality
Pennisi E. Science, Feb 19, 2016. - NIAID's Nephele Offers Free Compute Power, Software for Microbial Genome Analysis
Thomas UG. GenomeWeb, Feb 23, 2016. - Virus-Mimicking Drug Boosts Resistance to Antibiotic-Resistant Bacteria
Offord C. The Scientist, Feb 24, 2016. - Leptospira Genome Project Yields Clues to Pathogenesis
GenomeWeb, Feb 18, 2016. - Analysis of Blood Fluke Genomes Indicates Parasite Arrived in New World With Slave Trade
GenomeWeb, Feb 17, 2016.
EVENTS / TRAINING / WEB RESOURCES
- Applications of Clinical Microbial Next-Generation Sequencing
(report) American Academy of Microbiology / American Society for Microbiology, Feb 19, 2016. - Rapid Medical Countermeasure Response to Infectious Diseases
(workshop summary) IOM, 2016. - Rotavirus resource uses standardized metadata and annotations, suite of tools to make it easier to search, download and analyze sequences
(web resource) NCBI, Feb 19, 2016.
POLICY
- Tackling infectious diseases - lessons from emergencies
(blog post) Raza S. PHG Foundation, Jan 29, 2016. - Analysis of five years of controlled access and data sharing compliance at the International Cancer Genome Consortium
Joly Y, et al. Nat Genet, Feb 24, 2016.
CONCEPTS / COMMENTS
- SeXX Matters in Infectious Disease Pathogenesis.
Vom Steeg Landon G et al. PLoS pathogens 2016 Feb (2) e1005374 - The Epigenomic Landscape of Prokaryotes.
Blow Matthew J et al. PLoS genetics 2016 Feb (2) e1005854 - A systems biology approach for diagnostic and vaccine antigen discovery in tropical infectious diseases.
Liang Li et al. Current opinion in infectious diseases 2015 Oct (5) 438-45 - A Guide to Scientific Crowdfunding
Vachelard J, et al. PLoS Biol, Feb 17, 2016.
METHODS / TOOLS
- High-resolution phylogenetic microbial community profiling.
Singer Esther et al. The ISME journal 2016 Feb - The Impact of Missing Data on Species Tree Estimation.
Xi Zhenxiang et al. Molecular biology and evolution 2016 Mar (3) 838-60 - A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing.
Zhang Tian-Hao et al. BMC genomics 2016 (1) 108 - Advances in time estimation methods for molecular data.
Kumar Sudhir et al. Molecular biology and evolution 2016 Feb - Phylogenetically resolving epidemiologic linkage
Romero-Severson EO, et al. Proc Nat Acad Sci, Feb 2016. - Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web
Robinson O. arXiv:1602.04258, Feb 12, 2016. - Random amplified polymorphic DNA PCR in the teaching of molecular epidemiology.
Reinoso Elina B et al. Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology 2016 Feb - SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor
de Man TJ, Limbago BM. mSphere 2016; 1(1)
- Open-Source Sequence Clustering Methods Improve the State Of the Art
Kopylova E, et al. mSystems 2016; 1(1) - cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
Chase JH, et al. mSystems 2016; 1(1)
EVOLUTION / ECOLOGY / POPULATIONS
- Demography and Intercontinental Spread of the USA300 Community-Acquired Methicillin-Resistant Staphylococcus aureus Lineage.
Glaser Philippe et al. mBio 2015 (1) - Evidence for Host-Genotype Associations of Borrelia burgdorferi Sensu Stricto.
Mechai Samir et al. PloS one (2) e0149345 - Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications.
Sapriel Guillaume et al. BMC genomics 2016 (1) 118 - Reassortment of Avian Influenza A/H6N6 Viruses from Live Poultry Markets in Guangdong, China.
Yuan Runyu et al. Frontiers in microbiology 65 - Highly Pathogenic Avian Influenza A(H5N8) Viruses Reintroduced into South Korea by Migratory Waterfowl, 2014-2015.
Kwon Jung-Hoon et al. Emerging infectious diseases 2016 Mar (3) - Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection.
Crellen Thomas et al. Scientific reports 2016 20954 - Population Structure Shapes Copy Number Variation in Malaria Parasites.
Cheeseman Ian H et al. Molecular biology and evolution 2016 Mar (3) 603-20 - Genomic insights into the Ixodes scapularis tick vector of Lyme disease.
Gulia-Nuss Monika et al. Nature communications 2016 10507
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Far East Scarlet-Like Fever Caused by a Few Related Genotypes of Yersinia pseudotuberculosis, Russia.
Timchenko Nelly F et al. Emerging infectious diseases 2016 Mar (3) - Identification of Novel Zoonotic Activity of Bartonella spp., France.
Vayssier-Taussat Muriel et al. Emerging infectious diseases 2016 Mar (3) 457-62 - What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.
Fouts Derrick E et al. PLoS neglected tropical diseases 2016 Feb (2) e0004403 - Tissue tropisms in group A Streptococcus: what virulence factors distinguish pharyngitis from impetigo strains?
Bessen Debra E et al. Current opinion in infectious diseases 2016 Feb - Biodiversity and hypervirulence of Listeria monocytogenes
Grad YH, Fortune SM. Nat Genet, Feb 24, 2016. - Detection of translocatable units in a blaCTX-M-15 extended-spectrum β-lactamase-producing ST131 Escherichia coli isolate using a hybrid sequencing approach.
Ghosh Hiren et al. International journal of antimicrobial agents 2016 Feb - Multiple ESBL-Producing Escherichia coli Sequence Types Carrying Quinolone and Aminoglycoside Resistance Genes Circulating in Companion and Domestic Farm Animals in Mwanza, Tanzania, Harbor Commonly Occurring Plasmids.
Seni Jeremiah et al. Frontiers in microbiology 142 - Differences in the epidemiology and virology of mild, severe and fatal human infections with avian influenza A (H7N9) virus.
Sha Jianping et al. Archives of virology 2016 Feb - The genomic basis of parasitism in the Strongyloides clade of nematodes.
Hunt Vicky L et al. Nature genetics 2016 Feb
DETECTION / DIAGNOSIS
- How Recent Advances in Molecular Tests Could Impact the Diagnosis of Pneumonia.
Murdoch David R et al. Expert review of molecular diagnostics 2016 Feb - State-of-the-Art Microbiologic Testing for Community-acquired Meningitis and Encephalitis.
Polage Christopher R et al. Journal of clinical microbiology 2016 Feb - Verification of a MALDI-TOF mass spectrometry method for diagnostic identification of high-consequence bacterial pathogens.
Tracz Dobryan M et al. Journal of clinical microbiology 2015 Dec - Novel SNP-based assay for genotyping Mycobacterium avium subsp. paratuberculosis.
Leão Celia et al. Journal of clinical microbiology 2015 Dec - Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis
Sweeney TE, et al. Lancet Resp Med, Feb 19, 2016. - Zika Virus: Diagnostics for an Emerging Pandemic Threat.
Waggoner Jesse J et al. Journal of clinical microbiology 2016 Feb - Survey of influenza and other respiratory viruses diagnostic testing in US hospitals, 2012-2013.
Su Su et al. Influenza and other respiratory viruses 2016 Mar (2) 86-90 
- Nonculture Diagnostics in Fungal Disease.
Powers-Fletcher Margaret V et al. Infectious disease clinics of North America 2016 Mar (1) 37-49 - Detection and identification of Trichophyton tonsurans from clinical isolates and hairbrush samples by loop-mediated isothermal amplification system.
Yo Ayaka et al. The Journal of dermatology 2016 Feb
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Benchtop Whole-Genome Sequencing for Identification of Nosocomial Outbreaks in Tanzania.
Sonda Tolbert et al. Infection control and hospital epidemiology 2016 Feb 1-2 - Pan-genome multilocus sequence typing and outbreak-specific reference-based SNP analysis to resolve two concurrent Staphylococcus aureus outbreaks in neonatal services.
Roisin S et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 Feb - Two Listeria monocytogenes pseudo-outbreaks caused by contaminated laboratory culture media.
Matanock Almea et al. Journal of clinical microbiology 2015 Dec - Molecular Detection of Rickettsia felis in Humans, Cats, and Cat Fleas in Bangladesh, 2013-2014.
Ahmed Rajib et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2016 Feb - Declaring a tuberculosis outbreak over with genomic epidemiology
Hatherell HA, et al. bioRxiv, Feb 22, 2016. - Key Role of Sequencing to Trace Hepatitis A Viruses Circulating in Italy During a Large Multi-Country European Foodborne Outbreak in 2013.
Bruni Roberto et al. PloS one (2) e0149642 - Cluster of HIV Infections Attributed to Unsafe Injection Practices - Cambodia, December 1, 2014-February 28, 2015.
Vun Mean Chhi et al. MMWR. Morbidity and mortality weekly report 2016 (6) 142-5 - Laboratory-Based Surveillance and Molecular Characterization of Dengue Viruses in Taiwan, 2014.
Chang Shu-Fen et al. The American journal of tropical medicine and hygiene 2016 Feb - Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study.
Calvet Guilherme et al. The Lancet. Infectious diseases 2016 Feb - Newcastle Disease Viruses Causing Recent Outbreaks Worldwide Show Unexpectedly High Genetic Similarity with Historical Virulent Isolates from the 1940's.
Dimitrov Kiril M et al. Journal of clinical microbiology 2016 Feb
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Decreased Time to Treatment Initiation for Multidrug-Resistant Tuberculosis Patients after Use of Xpert MTB/RIF Test, Latvia.
Stagg Helen R et al. Emerging infectious diseases 2016 Mar (3)
HOST-MICROBE INTERACTIONS
- Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.
Yassour Moran et al. Genome medicine 2016 (1) 17 - Asymtomatic Bacteriuria as a Model to Study the Coevolution of Hosts and Bacteria.
Dobrindt Ulrich et al. Pathogens (Basel, Switzerland) 2016 (1) - Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis
Zackular JP, et al. mSphere 2016; 1(1)
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