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
- Sandia Researchers Developing Multiplex Assay Differentiating Viral Febrile Illnesses, Malaria
Johnson M. GenomeWeb, Jan 13, 2016.
- Simultaneous Analysis of Host, Pathogen Transcripts Highlights Infection Features
GenomeWeb, Jan 20, 2016.
- Study Describes Gene Expression Model to Distinguish Viral, Bacterial Infections in Clinical Setting
Curtin C. GenomeWeb, Jan 22, 2016.
- NIST Team Aims to Develop Graphene Nanopore Sequencing Tech
Heger M. GenomeWeb, Jan 21, 2016.
- A Scary New Superbug Gene Has Reached at Least 19 Countries
Tozzi J. Bloomberg News, Jan 22, 2016.
- New Tests for Zika in the Works
Grens K. The Scientist, Jan 25, 2016.
- New light-activated nanoparticles kill over 90% of antibiotic-resistant bacteria
Dockrill P. Science Alert, Jan 19, 2016.
- Nanopore Trap Sucks In DNA for Rapid Sequencing of Genetic Material
medGadget, Jan 25, 2016.
- Individuals genes provide innate resilience to infection
Healio, Jan 22, 2016.
- Data Sharing, Data Scientists, and 'Parasites'
GenomeWeb, Jan 25, 2016.
- More evidence emerges for 'transmissible Alzheimer's' theory
Abbott A. Nature, Jan 26, 2016.
- Zika virus: US scientists say vaccine '10 years away'
Cook J. BBC News, Jan 27, 2016.
- U.S. deploys newly minted bird flu plan to protect humans, poultry
Reuters, Jan 21, 2016.
CONCEPTS / COMMENTS
- Data Sharing.
Longo Dan L et al. The New England journal of medicine 2016 Jan (3) 276-7
- Data Scientists = Research Parasites?
Shaywitz D. Forbes, Jan 21, 2016.
- Can Data Sharing Become the Path of Least Resistance?
(editorial) PLoS Med, Jan 26, 2016.
- Adapting Koch's postulates.
Byrd Allyson L et al. Science (New York, N.Y.) 2016 Jan (6270) 224-226
- HIV whole genome sequencing now - answering still open questions.
Metzner Karin J et al. Journal of clinical microbiology 2016 Jan
- Survival proteomes: the emerging proteotype of antimicrobial resistance.
Park Amber J et al. FEMS microbiology reviews 2016 Jan
- A call for biological data mining approaches in epidemiology.
Lynch Shannon M et al. BioData mining 2016 1
METHODS / TOOLS
- A Quick Introduction to Version Control with Git and GitHub.
Blischak John D et al. PLoS computational biology 2016 Jan (1) e1004668
- The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries.
Barquist Lars et al. Bioinformatics (Oxford, England) 2016 Jan
- The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies.
Yoshida Catherine E et al. PloS one (1) e0147101
- Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering.
Novitsky Vlad et al. AIDS research and human retroviruses 2015 May (5) 531-42
- A PAN-HIV STRATEGY FOR COMPLETE GENOME SEQUENCING.
Berg Michael G et al. Journal of clinical microbiology 2015 Dec
- Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping.
Fraley Stephanie I et al. Scientific reports 2016 19218
- Depletion of human DNA in spiked clinical specimens to improve the sensitivity of pathogen detection by next generation sequencing.
Hasan Mohammad R et al. Journal of clinical microbiology 2016 Jan
- A survey of best practices for RNA-seq data analysis.
Conesa Ana et al. Genome biology 2016 (1) 13
- Bayesian molecular clock dating of species divergences in the genomics era.
Dos Reis Mario et al. Nature reviews. Genetics 2016 Feb (2) 71-80
- Harnessing the power of RADseq for ecological and evolutionary genomics.
Andrews Kimberly R et al. Nature reviews. Genetics 2016 Feb (2) 81-92
EVOLUTION / ECOLOGY / POPULATIONS
- Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis.
Tyx Robert E et al. PloS one 2016 (1) e0146939
- Phenotypic, genotypic, and antimicrobial characteristics of Streptococcus halichoeri isolated from humans and proposal to rename Streptococcus halichoeri as Streptococcus halichoeri subsp. halichoeri and description of Streptococcus halichoeri subsp. hominis subsp. nov., a bacterium associated with human clinical infections.
Shewmaker P L et al. Journal of clinical microbiology 2016 Jan
- The 5300-year-old Helicobacter pylori genome of the Iceman.
Maixner Frank et al. Science (New York, N.Y.) 2016 Jan (6269) 162-5
- Genetic Diversity and Phylogeny of Aedes aegypti, the Main Arbovirus Vector in the Pacific.
Calvez Elodie et al. PLoS neglected tropical diseases 2016 Jan (1) e0004374
- First Report of Rickettsia Identical to R. slovaca in Colony-Originated D. variabilis in the United States: Detection, Laboratory Animal Model, and Vector Competence of Ticks.
Zemtsova Galina E et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2016 Jan
- High-resolution multilocus sequence typing reveals novel urogenital Chlamydia trachomatis strains in women in Mopani district, South Africa.
Versteeg Bart et al. Sexually transmitted infections 2015 Nov (7) 510-2
- Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis.
Bryant Josephine M et al. BMC genomics 2016 (1) 79
- Microevolution of Outbreak-Associated Middle East Respiratory Syndrome Coronavirus, South Korea, 2015.
Seong Moon-Woo et al. Emerging infectious diseases 2016 Feb (2)
- Whole-Genome Sequencing Analysis from the Chikungunya Virus Caribbean Outbreak Reveals Novel Evolutionary Genomic Elements.
Stapleford Kenneth A et al. PLoS neglected tropical diseases 2016 Jan (1) e0004402
- Epidemic history and iatrogenic transmission of blood-borne viruses in mid-20th century Kinshasa.
Hogan Catherine et al. The Journal of infectious diseases 2016 Jan
- Out of the Reservoir: Phenotypic and Genotypic Characterization of a Novel Cowpox Virus Isolated from a Common Vole.
Hoffmann Donata et al. Journal of virology 2015 Nov (21) 10959-69
- Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia.
Sabir Jamal S M et al. Science (New York, N.Y.) 2016 Jan (6268) 81-4
- Clinical surveillance for human astrovirus in Monastir region, Tunisia.
Monastiri Abir et al. BMC public health 2016 (1) 57
- The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin.
Phan Tung Gia et al. Archives of virology 2016 Jan
- Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak.
Meyer Austin G et al. Virus evolution 2015 Jan (1)
- Multilocus sequence typing analysis reveals that Cryptococcus neoformans var. neoformans is a recombinant population.
Cogliati Massimo et al. Fungal genetics and biology : FG & B 2016 Jan 22-29
- Molecular Characterization Reveals Diverse and Unknown Malaria Vectors in the Western Kenyan Highlands.
St Laurent Brandyce et al. The American journal of tropical medicine and hygiene 2016 Jan
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Using whole-genome sequencing to determine appropriate streptomycin epidemiological cutoffs for Salmonella and Escherichia coli.
Tyson Gregory H et al. FEMS microbiology letters 2016 Jan
- Methicillin-resistant Staphylococcus aureus carrying the new mecC gene-a meta-analysis.
Diaz Raquel et al. Diagnostic microbiology and infectious disease 2016 Feb (2) 135-40
- Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires.
Burstein David et al. Nature genetics 2016 Jan
- Bordetella pertussis Strain Lacking Pertactin and Pertussis Toxin.
Williams Margaret M et al. Emerging infectious diseases 2016 Feb (2) 319-22
- Emergence of Escherichia coli Sequence Type 131 (ST131) and ST3948 with KPC-2, KPC-3 and KPC-8 carbapenemases from a Long-Term Care and Rehabilitation Facility (LTCRF) in Northern Italy.
Piazza Aurora et al. Advances in experimental medicine and biology 2016 Jan
- Molecular Epidemiology of Ampicillin-Resistant Haemophilus influenzae Causing Acute Otitis Media in Japanese Infants and Young Children.
Kakuta Risako et al. The Pediatric infectious disease journal 2016 Jan
- Outbreak of NDM-1-producing Klebsiella pneumoniae ST76 and ST37 isolates in neonates.
Zhu J et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2016 Jan
- Multidrug evolutionary strategies to reverse antibiotic resistance.
Baym Michael et al. Science (New York, N.Y.) 2016 Jan (6268) aad3292
- Unique Determinants of Neuraminidase Inhibitor Resistance among N3, N7, and N9 Avian Influenza Viruses.
Song Min-Suk et al. Journal of virology 2015 Nov (21) 10891-900
- Phenotype, Genotype, and Drug Resistance in Subtype C HIV-1 Infection.
Derache Anne et al. The Journal of infectious diseases 2016 Jan (2) 250-6
DETECTION / DIAGNOSIS
- Whole genome multilocus sequence typing as an epidemiologic tool for Yersinia pestis.
Kingry Luke C et al. Diagnostic microbiology and infectious disease 2015 Dec
- Diagnosis of Helicobacter pylori recurrence: relapse or reinfection? Usefulness of molecular tools.
Raymond Josette et al. Scandinavian journal of gastroenterology 2016 Jan 1-7
- Combined use of real-time PCR and nested sequence-based typing in survey of human Legionella infection.
Qin T et al. Epidemiology and infection 2016 Jan 1-5
- Detection of Zika virus in urine.
Gourinat Ann-Claire et al. Emerging infectious diseases 2015 Jan (1) 84-6
- Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia.
Gadsby Naomi J et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Jan
- Bruker matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of Neisseria gonorrhoeae is improved by a database extension.
Schweitzer Valentijn A et al. Journal of clinical microbiology 2016 Jan
- Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study.
Pankhurst Louise J et al. The Lancet. Respiratory medicine 2016 Jan (1) 49-58
- Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool.
Hoenen Thomas et al. Emerging infectious diseases 2016 Feb (2)
- Loop mediated isothermal amplification (LAMP) for the detection and subtyping of human papillomaviruses (HPV) in oropharyngeal squamous cell carcinoma (OPSCC).
Livingstone D M et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2016 Jan 37-41
- Costs per Diagnosis of Acute HIV Infection in Community-based Screening Strategies: A Comparative Analysis of Four Screening Algorithms.
Hoenigl Martin et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Feb (4) 501-11
- DNA barcoding of fungi causing infections in humans and animals.
Irinyi Laszlo et al. Fungal biology 2016 Feb (2) 125-36
- The Merits of Malaria Diagnostics during an Ebola Virus Disease Outbreak.
de Wit Emmie et al. Emerging infectious diseases 2016 Feb (2)
- Development and Evaluation of Loop-Mediated Isothermal Amplification Method for Rapid Detection of Aspergillus fumigatus.
Tang Qing et al. Journal of clinical microbiology 2016 Jan
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage in Maintaining a Long-Term Hospital Outbreak of ST228 Methicillin-Resistant Staphylococcus aureus.
Senn Laurence et al. mBio 2016 (1)
- Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens.
Deng Xiangyu et al. Annual review of food science and technology 2016 Jan
- Molecular characterisation and epidemiological investigation of an outbreak of blaOXA-181 carbapenemase-producing isolates of Klebsiella pneumoniae in South Africa.
Jacobson Rachael Kiera et al. South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde 2015 Dec (12) 1030-5
- Descriptive Epidemiology and Whole Genome Sequencing Analysis for an Outbreak of Bovine Tuberculosis in Beef Cattle and White-Tailed Deer in Northwestern Minnesota.
Glaser Linda et al. PloS one 2016 (1) e0145735
- Prolonged Post-procedural Outbreak of Mycobacterium massiliense Infections Associated with Ultrasound Transmission Gel.
Cheng Aristine et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 Jan
- Dogs and Opossums Positive for Vaccinia Virus during Outbreak Affecting Cattle and Humans, São Paulo State, Brazil.
Peres Marina G et al. Emerging infectious diseases 2016 Feb (2) 271-3
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Treatment Options for Infections Caused by Carbapenem-resistant Enterobacteriaceae: Can We Apply "Precision Medicine" to Antimicrobial Chemotherapy?
Perez Federico et al. Expert opinion on pharmacotherapy 2016 Jan
- Platform technology to generate broadly cross-reactive antibodies to α-helical epitopes in hemagglutinin proteins from influenza a viruses.
Jiang Ziqing et al. Biopolymers 2016 Jan
- SNP rs7770370 in HLA-DPB1 loci as a major genetic determinant of response to booster hepatitis B vaccination: results of a genome-wide association study.
Wu Tzu-Wei et al. Journal of gastroenterology and hepatology 2015 May (5) 891-9
- Impact of Bacterial and Human Genetic Variation on Staphylococcus aureus Infections.
Messina Julia A et al. PLoS pathogens 2016 Jan (1) e1005330
- Host gene expression classifiers diagnose acute respiratory illness etiology
Science Translational Medicine 20 Jan 2016: Vol. 8, Issue 322, pp. 322ra11
- Transcriptomic Analysis of the Host Response and Innate Resilience to Enterotoxigenic Escherichia coli Infection in Humans.
Yang William E et al. The Journal of infectious diseases 2016 Jan
- Changes in Colonic Bile Acid Composition following Fecal Microbiota Transplantation Are Sufficient to Control Clostridium difficile Germination and Growth.
Weingarden Alexa R et al. PloS one 2016 (1) e0147210
- Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.
Korpela Katri et al. Nature communications 2016 10410
- Association between human leukocyte antigen class II and pulmonary tuberculosis due to mycobacterium tuberculosis in Uganda.
Wamala Dan et al. BMC infectious diseases 2016 (1) 23
- The role of HPV RNA transcription, immune response-related gene expression and disruptive TP53 mutations in diagnostic and prognostic profiling of head and neck cancer.
Wichmann Gunnar et al. International journal of cancer. Journal international du cancer 2015 Dec (12) 2846-57
- Associations of Oral Alpha-, Beta-, and Gamma-Human Papillomavirus Types With Risk of Incident Head and Neck Cancer
Agalliu I, et al. JAMA Oncology, Jan 21, 2016.
- Causality of Chlamydiae in Arthritis and Spondyloarthritis: a Plea for Increased Translational Research.
Zeidler Henning et al. Current rheumatology reports 2016 Jan (2) 9
- Quantifying prion disease penetrance using large population control cohorts.
Minikel Eric Vallabh et al. Science translational medicine 2016 Jan (322) 322ra9
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