About Advanced Molecular Detection Clips
Advanced Molecular Detection(AMD) 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 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.
Advanced Molecular Detection Clips Content
NEWS
- The plague's deadly pedigree goes back 3,000 years earlier than thought
Khan A. Los Angeles Times, Oct 22, 2015. - Opinion: Biodefense Innovation Needed
Lieberman J, Ridge T. The Scientist, Oct 27, 2015. - Lack of coordination during Ebola outbreak was a lost opportunity to test therapies
Gulland A. BMJ 2015;351:h5644 - The Lettuce, Tomatoes, or Cilantro?
GenomeWeb, Nov 4, 2015. - We Need You to Design the Systems that Help Save Lives.
Braun P. HHS Idea Lab, Oct 26, 2015. - Powerful 'Gene Drive' Can Quickly Change An Entire Species
Stein R. NPR News, Nov 5, 2015. - Novel assay detects TB in early stages of disease
healio.com, Oct 13, 2015 - NIH Announces Funding Opportunities for Novel Genomic Technology Development
GenomeWeb, Oct 27, 2015. - One Codex Launches First Version of Metagenomics Classification Platform
Thomas UG. GenomeWeb, Oct 22, 2015. - UMass Scientists Lead Effort to Excise Latent HIV With CRISPR/Cas9
Han AP. GenomeWeb, Oct 28, 2015. - Clinical Evaluation of Molecular CRE Test Spurs Concerns About Potential Use in Screening
Johnson M. GenomeWeb, Oct 30, 2015. - JPL Researchers Characterize International Space Station Microbiome
GenomeWeb, Oct 27, 2015
EVENTS / TRAINING / WEB RESOURCES
- treevis.net - A Visual Bibliography of Tree Visualization 2.0
(website) Shulz HJ. - Cross Validated
(website) Stack Exchange Q&A site on statistics, machine learning, data analysis, data mining, and data visualization.
POLICY
- A National Biosafety and Biosecurity System in the United States
(blog post) Monaco LO, Holdren JP. www.whitehouse.gov, Oct 29, 2015. - SHATTUCK LECTURE: The Future of Public Health.
Frieden Thomas R et al. The New England journal of medicine 2015 Oct (18) 1748-54 (CDC Author) - Bringing the Common Rule into the 21st Century.
Hudson Kathy L et al. The New England journal of medicine 2015 Oct
CONCEPTS / COMMENTS
- Microbiology: Create a global microbiome effort.
Dubilier Nicole et al. Nature 2015 Oct (7575) 631-4 - MICROBIOME. A unified initiative to harness Earth's microbiomes.
Alivisatos A P et al. Science (New York, N.Y.) 2015 Oct (6260) 507-8 - Microbesity
Rood J. The Scientist, Nov 1, 2015. - Bringing foodborne diseases under control with WGS
Luheshi L. PHG Foundation, Oct 23, 2015. - Molecular epidemiology tools in the management of healthcare-associated infections: towards the definition of recommendations.
Boccia Stefania et al. Epidemiologia e prevenzione (4 Suppl 1) 21-26
METHODS / TOOLS
- One Codex: A Sensitive and Accurate Data Platform for Genomic Microbial Identification
Minot SS, et al. bioRxiv, Sep 28, 2015. - BioDB extractor: customized data extraction system for commonly used bioinformatics databases.
Karbhal Rajiv et al. BioData mining 2015 31 - Teaser: Individualized benchmarking and optimization of read mapping results for NGS data.
Smolka Moritz et al. Genome biology 2015 (1) 235 - Infectious cause of death determination using minimally invasive autopsies in developing countries.
Martínez Miguel J et al. Diagnostic microbiology and infectious disease 2015 Oct - Biomarker identification from next-generation sequencing data for pathogen bacteria characterization and surveillance.
Zhao Weizhong et al. Biomarkers in medicine 2015 Oct - Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study.
Hill Dorothea M C et al. The Lancet. Infectious diseases 2015 Oct - Metagenomic insights into the dynamics of microbial communities in food.
Kergourlay Gilles et al. International journal of food microbiology 2015 Nov 31-9 - Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community.
Bowers Robert M et al. BMC genomics 2015 (1) 856 - Library preparation methodology can influence genomic and functional predictions in human microbiome research.
Jones Marcus B et al. Proceedings of the National Academy of Sciences of the United States of America 2015 Oct
EVOLUTION / ECOLOGY / POPULATIONS
- Dimensions of Horizontal Gene Transfer in Eukaryotic Microbial Pathogens.
Gluck-Thaler Emile et al. PLoS pathogens 2015 Oct (10) e1005156 - Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago.
Rasmussen Simon et al. Cell 2015 Oct (3) 571-82 - Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities.
Checinska Aleksandra et al. Microbiome 2015 (1) 50 - Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae.
Croucher Nicholas J et al. Scientific data 2015 150058 - Prevalence and genetic diversity of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in nursing homes in Bavaria, Germany.
Valenza Giuseppe et al. Veterinary microbiology 2015 Oct - Molecular epidemiology of tuberculosis in Sicily, Italy: what has changed after a decade?
Bonura Celestino et al. BMC infectious diseases 2014 602 - The High Prevalence and Diversity of Chlamydiales DNA within Ixodes ricinus Ticks Suggest a Role for Ticks as Reservoirs and Vectors of Chlamydia-Related Bacteria.
Pilloux Ludovic et al. Applied and environmental microbiology 2015 Dec (23) 8177-82 - Molecular epidemiology and evolution of porcine parvoviruses.
Streck André Felipe et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Oct 300-306 - Phylogenetic analysis of Indian rabies virus isolates targeting the complete glycoprotein gene.
Cherian Susan et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Sep 333-338 - Successive Respiratory Syncytial Virus Epidemics in Local Populations Arise from Multiple Variant Introductions, Providing Insights into Virus Persistence.
Agoti Charles N et al. Journal of virology 2015 Nov (22) 11630-42 - Genetic analysis of Giardia and Cryptosporidium from people in Northern Australia using PCR-based tools.
Ebner Janine et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Aug 389-395 - Rediscovery of Trypanosoma (Pycnomonas) suis, a tsetse-transmitted trypanosome closely related to T. brucei.
Hutchinson Rachel et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Oct 381-388 - A comparative study on worldwide genetic diversity and population structure analysis of Plasmodium vivax thrombospondin-related adhesive protein (PvTRAP) and its implications for the vivax vaccine design.
Nazeri Saeed et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Oct 410-423 - Molecular detection and genetic identification of Babesia bigemina, Theileria annulata, Theileria orientalis and Anaplasma marginale in Turkey.
Zhou Mo et al. Ticks and tick-borne diseases 2015 Sep - Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.
Farrer Rhys A et al. mBio 2015 (5)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Genetic import and phenotype specific alleles associated with hyper-invasion in Campylobacter jejuni.
Baig Abiyad et al. BMC genomics 2015 (1) 852 - Whole Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter.
Zhao S et al. Applied and environmental microbiology 2015 Oct (CDC Author) - Transfer of scarlet fever-associated elements into the group A Streptococcus M1T1 clone.
Ben Zakour Nouri L et al. Scientific reports 2015 15877 - Comparative whole genome sequencing of community-associated methicillin-resistant Staphylococcus aureus sequence type 8 from primary care clinics in a Texas community.
Lee Grace C et al. Pharmacotherapy 2015 Feb (2) 220-8 - The spread of bla OXA-48 and bla OXA-244 carbapenemase genes among Klebsiella pneumoniae, Proteus mirabilis and Enterobacter spp. isolated in Moscow, Russia.
Fursova Nadezhda K et al. Annals of clinical microbiology and antimicrobials 2015 (1) 46 - Intrinsic Antimicrobial Resistance Determinants in the Superbug Pseudomonas aeruginosa.
Murray Justine L et al. mBio 2015 (6) - Epidemiological Study of Erythromycin-Resistant Streptococcus pyogenes From Korea and Japan by emm Genotyping and Multilocus Sequence Typing.
Takahashi Takashi et al. Annals of laboratory medicine 2016 Jan (1) 9-14 - HIV-1 tropism dynamics and phylogenetic analysis from longitudinal ultra-deep sequencing data of CCR5- and CXCR4-using variants.
Sede Mariano M et al. PloS one 2014 (7) e102857 - Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates.
Black P A et al. BMC genomics 2015 (1) 857 - Comparative Genomic Analysis of Classical and Variant Virulent Parental/Attenuated Strains of Porcine Epidemic Diarrhea Virus.
Chen Fangzhou et al. Viruses 2015 (10) 5525-38
DETECTION / DIAGNOSIS
- Clinical Performance of Check-Direct CPE, a Multiplex PCR for Direct Detection of blaKPC, blaNDM/VIM, and blaOXA48 from Perirectal Swabs.
Lau Anna F et al. Journal of clinical microbiology 2015 Sep - Impact of rapid screening for discontinuation of methicillin-resistant Staphylococcus aureus contact precautions.
Shenoy Erica S et al. American journal of infection control 2015 Oct - What to expect from molecular tools for non-documented pediatric infectious diseases.
Filleron Anne et al. Expert review of molecular diagnostics 2015 Oct 1-12 - Development of a Gene Expression Assay for the Diagnosis of Mycobacterium bovis Infection in African Lions (Panthera leo).
Olivier T T et al. Transboundary and emerging diseases 2015 Oct - Development of a TaqMan Array Card for Acute Febrile Illness Outbreak Investigation and Surveillance of Emerging Pathogens including Ebola Virus.
Liu Jie et al. Journal of clinical microbiology 2015 Oct (CDC Author) - Whole genome sequencing of fecal samples as a tool for the diagnosis and genetic characterization of norovirus.
Bavelaar Herjan H J et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2015 Oct 122-125 - Real-Time Polymerase Chain Reaction Detection of Angiostrongylus cantonensis DNA in Cerebrospinal Fluid from Patients with Eosinophilic Meningitis.
Qvarnstrom Yvonne et al. The American journal of tropical medicine and hygiene 2015 Nov (CDC Author)
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Outbreak Breakthrough: Using Whole-Genome Sequencing to Control Hospital Infection.
Arnold Carrie et al. Environmental health perspectives 2015 Nov (11) A281-A286 - A Field-Validated Approach Using Surveillance and Genotyping Data to Estimate Tuberculosis Attributable to Recent Transmission in the United States.
France Anne Marie et al. American journal of epidemiology 2015 Nov (9) 799-807 (CDC Author) - Spatiotemporal Reconstruction of the Introduction of Hepatitis C Virus into Scotland and Its Subsequent Regional Transmission.
McNaughton Anna L et al. Journal of virology 2015 Nov (22) 11223-32 - Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis.
Bezemer Daniela et al. PLoS medicine 2015 Nov (11) e1001898 - Molecular Investigation into a Malaria Outbreak in Cusco, Peru: Plasmodium falciparum BV1 Lineage is Linked to a Second Outbreak in Recent Times.
Okoth Sheila Akinyi et al. The American journal of tropical medicine and hygiene 2015 Oct (CDC Author) - Healthcare-Associated Transmission of Plasmodium falciparum in New York City.
Lee Ellen H et al. Infection control and hospital epidemiology 2015 Oct 1-3 (CDC Author)
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Identification of the Mechanisms Causing Reversion to Virulence in an Attenuated SARS-CoV for the Design of a Genetically Stable Vaccine.
Jimenez-Guardeño Jose M et al. PLoS pathogens 2015 Oct (10) e1005215 - The potential of a multiplex high-throughput molecular assay for early detection of first and second line tuberculosis drug resistance mutations to improve infection control and reduce costs: a decision analytical modeling study.
Van't Hoog A H et al. BMC infectious diseases 2015 473 - A gene deletion that up-regulates viral gene expression yields an attenuated RSV vaccine with improved antibody responses in children
Karron RA, et al. Sci Transl Med 2015; 7: 312ra175. - RSV vaccine: Beating the virus at its own game
Moscona A. Sci Transl Med 2015; 7: 312fs44.
HOST-MICROBE INTERACTIONS
- Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers.
Esterhuyse Maria M et al. mBio 2015 (5) - The Microbiome and the Respiratory Tract.
Dickson Robert P et al. Annual review of physiology 2015 Nov - Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes.
Wang Mingjie et al. Genome biology 2015 243 - The new world of the urinary microbiota in women.
Brubaker Linda et al. American journal of obstetrics and gynecology 2015 Nov (5) 644-9 - Malignant Transformation of Hymenolepis nana in a Human Host.
Muehlenbachs Atis et al. The New England journal of medicine 2015 Nov (19) 1845-1852 (CDC Author) - Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition.
Quince Christopher et al. The American journal of gastroenterology 2015 Nov - The Toxin-Producing Pathobiont Klebsiella oxytoca Is Not Associated with Flares of Inflammatory Bowel Diseases.
Zollner-Schwetz Ines et al. Digestive diseases and sciences 2015 Nov (11) 3393-8 - Prevalence of Mycobacterium avium subsp. paratuberculosis and Escherichia coli in blood samples from patients with inflammatory bowel disease.
Nazareth Nair et al. Medical microbiology and immunology 2015 Dec (6) 681-92 - Human papillomavirus oncogenic mRNA testing for cervical cancer screening: baseline and longitudinal results from the CLEAR study.
Reid Jennifer L et al. American journal of clinical pathology 2015 Sep (3) 473-83 - Host Genetic Susceptibility to Enteric Viruses: A Systematic Review and Metaanalysis.
Kambhampati Anita et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Oct (CDC Author) - Limits and patterns of cytomegalovirus genomic diversity in humans.
Renzette Nicholas et al. Proceedings of the National Academy of Sciences of the United States of America 2015 Jul (30) E4120-8
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