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
- Oxford Nanopore Developing Smartphone-Powered Device, Launches New Pore
GenomeWeb, May 27, 2016. - Smartphone-Based Genetic Testing Identifies Hospital Pathogens
Harrison L. Medscape, May 30, 2016. - UK grants support novel methods of combating resistant infections
Healio, May 21, 2016. - First discovery in United States of colistin resistance in a human E. coli infection
The U.S. Military HIV Research Program (MHRP), EurekAlert, May 26, 2016. - Nanopore Sequencing Assembly Method Could Help Unravel Antibiotic Resistance
Heger M. GenomeWeb, May 26, 2016. - The global battle against AMR - can technology lead the way?
Blackburn L. PHG Foundation, May 20, 2016 - Searching for Superbugs: The Lab Looking for the Next Big Threat
Fox M. NBC News, May 31, 2016. - DNA Sequencing Proving Useful for Virus ID, Say Clinical Virology Symposium Presenters
Rizk C. GenomeWeb, May 23, 2016. - Novel method may lead to more precise influenza vaccine
Healio, May 31, 2016. - Metagenomic Techniques Can Profile Individual Microbe Strains
GenomeWeb, May 27, 2016. - Stanford Group Publishes Field Evaluation of Zika, Chikungunya, Dengue Triplex Assay
Johnson M. GenomeWeb, Jun 2, 2016. - The First DNA Sequencing in Space Could Happen This Summer
Hackett J. Sci Am, Jun 1, 2016.
EVENTS / TRAINING / WEB RESOURCES
- Public Health Ethics: Cases Spanning the Globe
(open access book) Barrett D, et al. Springer, May 2016.
POLICY
- Review on Antimicrobial Resistance. Tackling Drug-Resistant Infections Globally: Final Report and Recommendations
O'Neill J, et al. United Kingdom, Wellcome Trust. May 2016. - E.U. Pushes for Open Access by 2020
Grant B. The Scientist, Jun 1, 2016.
CONCEPTS / COMMENTS
- For Rapid Molecular Detection, Why Not A Whole Genome Approach?
Lesho Emil P et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 May - Benefit-Risk Evaluation for Diagnostics: A Framework (BED-FRAME).
Evans Scott R et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 May - Multidrug-resistant opportunistic pathogens challenging veterinary infection control
Walther B, et al. Vet Microbiol, May 27, 2016.
METHODS / TOOLS
- Scaffolding and Completing Genome Assemblies in Real-time with Nanopore Sequencing
Cao MD, et al. bioRxiv, May 22, 2016. - Multiplex, Rapid, and Sensitive Isothermal Detection of Nucleic-Acid Sequence by Endonuclease Restriction-Mediated Real-Time Multiple Cross Displacement Amplification.
Wang Yi et al. Frontiers in microbiology 2016 753 - Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling.
Flygare Steven et al. Genome biology 2016 (1) 111 - Galaxy Portal: interacting with the galaxy platform through mobile devices.
Børnich Claus et al. Bioinformatics (Oxford, England) 2016 Jun (11) 1743-5 - HIV-1 Protease, Reverse Transcriptase, and Integrase Variation.
Rhee Soo-Yon et al. Journal of virology 2016 Apr - A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria.
Peters Jason M et al. Cell 2016 May - Molecular clock of HIV-1 envelope genes under early immune selection.
Park Sung Yong et al. Retrovirology 2016 (1) 38 - An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples.
Bag Satyabrata et al. Scientific reports 2016 26775 - Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples.
Glassing Angela et al. Gut pathogens 2016 24
EVOLUTION / ECOLOGY / POPULATIONS
- Transcriptome Remodeling Contributes to Epidemic Disease Caused by the Human Pathogen Streptococcus pyogenes.
Beres Stephen B et al. mBio 2016 (3) - Detailed phylogenetic analysis of primate T-lymphotropic virus type 1 (PTLV-1) sequences from orangutans (Pongo pygmaeus) reveals new insights into the evolutionary history of PTLV-1 in Asia.
Reid Michael J C et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 May
- Two Outbreak Sources of Influenza A (H7N9) Viruses Have Been Established in China.
Wang Dayan et al. Journal of virology 2016 Jun (12) 5561-73 - Molecular characterization of the first G24P[14] rotavirus strain detected in humans.
Ward M Leanne et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 May - Deep Sequencing of the HIV-1 env Gene Reveals Discrete X4 Lineages and Linkage Disequilibrium Between X4 and R5 Viruses In the V1/V2 and V3 Variable Regions.
Zhou Shuntai et al. Journal of virology 2016 May - Phylodynamics of DENV-1 reveals the spatiotemporal co-circulation of two distinct lineages in 2013 and multiple introductions of dengue virus in Goiás, Brazil.
Cunha Marielton Dos Passos et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 May 130-134 - Genome sequence analysis of Ebola virus in clinical samples from three British healthcare workers, August 2014 to March 2015
Bell A, et al. Euro Surveill 2015;20(20):pii=21131. - Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides.
Teixeira Marcus M et al. Emerging infectious diseases 2016 Jun (6) 1022-30 - Worldwide Phylogenetic Distributions and Population Dynamics of the Genus Histoplasma.
Teixeira Marcus de M et al. PLoS neglected tropical diseases 2016 Jun (6) e0004732 - Mitochondrial population genomic analyses reveal population structure and demography of Indian Plasmodium falciparum.
Tyagi Suchi et al. Mitochondrion 2015 Sep 9-21
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Escherichia coli Harboring mcr-1 and blaCTX-M on a Novel IncF Plasmid: First report of mcr-1 in the USA
McGann P, et al. Antimicrob Agents Chemother, May 26, 2016. PMID: 27230792 - Genomic and Phenotypic Analysis Reveal the Emergence of an Atypical Salmonella Senftenberg Variant in China.
Abd El Ghany Moataz et al. Journal of clinical microbiology 2016 May - Host-specific patterns of genetic diversity among IncI1-Iγ and IncK plasmids encoding CMY-2 β-lactamase in Escherichia coli isolates from humans, poultry meat, poultry and dogs in Denmark.
Hansen Katrine Hartung et al. Applied and environmental microbiology 2016 May - Genetic Characterization of Carbapenem-Resistant Enterobacteriaceae and the Spread of Carbapenem-Resistant Klebsiella pneumonia ST340 at a University Hospital in Thailand.
Netikul Thidarat et al. PloS one 2015 (9) e0139116 - Emergence and evolution of an international cluster of MDR Bacteroides fragilis isolates.
Sóki József et al. The Journal of antimicrobial chemotherapy 2016 May - Phenotypic and genetic changes in the life cycle of small colony variants of Salmonella enterica serotype Typhimurium induced by streptomycin.
Li Wanli et al. Annals of clinical microbiology and antimicrobials 2016 (1) 37 - Paradoxical Hypersusceptibility of Drug-Resistant M. tuberculosis to beta-Lactam Antibiotics
Cohen KA, et al. EBioMedicine, Jun 1, 2016. - Distinctive Drug-resistant Mutation Profiles and Interpretations of HIV-1 Proviral DNA Revealed by Deep Sequencing in Reverse Transcriptase.
Yin Qian Qian et al. Biomedical and environmental sciences : BES 2016 Apr (4) 239-47
DETECTION / DIAGNOSIS
- Molecular characterization and phylogeny of Shiga toxin-producing E. coli (STEC) from imported beef meat in Malaysia.
Abuelhassan Nawal Nouridaim et al. Environmental science and pollution research international 2016 May - A Multiplex Real-Time PCR with High Resolution Melting Analysis for the Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae.
Donà Valentina et al. Journal of clinical microbiology 2016 May - Implementation of Whole Genome Sequencing (WGS) for Identification and Characterization of Shiga Toxin-Producing Escherichia coli (STEC) in the United States.
Lindsey Rebecca L et al. Frontiers in microbiology 2016 766 
- Rapid Drug Susceptibility Testing of Drug Resistant Mycobacterium tuberculosis Directly from Clinical Samples using Amplicon Sequencing: A Proof of Concept Study.
Colman Rebecca E et al. Journal of clinical microbiology 2016 May - Molecular Epidemiology of Chikungunya Virus by Sequencing.
Thayan Ravindran et al. Methods in molecular biology (Clifton, N.J.) 2016 11-9 - Virus and Host Testing to Manage Chronic Hepatitis B.
Wong Grace Lai-Hung et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Jun S298-305 - Development, Evaluation, and Integration of a Quantitative Reverse-Transcription Polymerase Chain Reaction Diagnostic Test for Ebola Virus on a Molecular Diagnostics Platform.
Cnops Lieselotte et al. The Journal of infectious diseases 2016 May - Single-Reaction Multiplex Reverse Transcription PCR for Detection of Zika, Chikungunya, and Dengue Viruses.
Waggoner Jesse J et al. Emerging infectious diseases 2016 Jul (7)
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Genome-based study of a spatio-temporal cluster of invasive meningococcal disease due to Neisseria meningitidis serogroup C, clonal complex 11.
Stefanelli P et al. The Journal of infection 2016 May - Molecular Epidemiology and Antibiotic Susceptibility of Vibrio cholerae Associated with a Large Cholera Outbreak in Ghana in 2014.
Eibach Daniel et al. PLoS neglected tropical diseases 2016 May (5) e0004751 - Genetic diversity and transmission networks of HIV-1 strains among men having sex with men (MSM) in Lomé, Togo.
Konou Abla A et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 May
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Protocols for Developing Novel Chikungunya Virus DNA Vaccines.
Chung Christopher et al. Methods in molecular biology (Clifton, N.J.) 2016 311-32 - Selection of antigenically advanced variants of seasonal influenza viruses
Li C, et al. Nat Microbiol, May 23, 2016.
HOST-MICROBE INTERACTIONS
- Uncovering oral Neisseria tropism and persistence using metagenomic sequencing
Donati C, et al. Nat Microbiol, May 27, 2016. - Polymorphism in a lincRNA Associates with a Doubled Risk of Pneumococcal Bacteremia in Kenyan Children.
et al. American journal of human genetics 2016 May - Pauci- and Multibacillary Leprosy: Two Distinct, Genetically Neglected Diseases.
Gaschignard Jean et al. PLoS neglected tropical diseases 2016 May (5) e0004345 - Polymorphisms on IFNG, IL12B and IL12RB1 genes and paracoccidioidomycosis in the Brazilian population.
Holanda F M C et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 May - Familial aggregation and heritability of Wuchereria bancrofti infection.
Chesnais Cédric B et al. The Journal of infectious diseases 2016 May - Heterozygous mutants of TIRAP (S180L) polymorphism protect adult patients with Plasmodium falciparum infection against severe disease and mortality.
Panda Aditya K et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 May 146-150 - Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease.
Chu Hiutung et al. Science (New York, N.Y.) 2016 May (6289) 1116-20 - Note: indicates that at least one CDC-affiliated author; indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice.
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