Public Health Genomics Knowledge Base (v1.0)
June 9-16, 2016
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.
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Advanced Molecular Detection Clips Content
News
Events / Training / Web Resources
Policy
Concepts / Comments
Methods / Tools
Evolution / Ecology / Populations
Pathogenicity / Antimicrobial Resistance
Detection / Diagnosis
Epidemiology / Outbreaks / Transmission
Antimicrobials / Vaccines / Interventions
Host-Microbe Interactions
NEWS
Behind the scenes of a U.S. superbug discovery that made headlines around the world
Sun LH. Washington Post, Jun 6, 2016.
Fast-spreading genetic mutations pose ecological risk
Ledford H. Nature, Jun 8, 2016.
Species-wide gene editing, applauded and feared, gets a push.
Harmon A. New York Times, Jun 8, 2016.
To halt the spread of Lyme, Nantucket residents consider genetically engineered mice
Swet;itz I. STAT, Jun 7, 2016.
Mobile laboratories help track Zika spread across Brazil
(press release) Univ of Birmingham (UK), Jun 8, 2016.
Testing limitations may leave 20% to 80% of Zika patients undiagnosed
Healio, Jun 6, 2016.
Novel method may lead to more precise influenza vaccine
Healio, May 31, 2016.
Researchers create genetic blueprint of cunning tuberculosis bacteria
MedicalXpress, Jun 6, 2016.
EVENTS / TRAINING / WEB RESOURCES
The Secret World Inside You
(exhibition) American Museum of Natural History, through Aug 14, 2016.
Infectious Disease News Outbreak Tracker
(website) Infectious Disease News, healio.com.
POLICY
Gene Drive Research in Non-Human Organisms: Recommendations for Responsible Conduct
The National Academies of Sciences, Engineering, and Medicine. June 8, 2016.
Precision Medicine Initiative: Data Security Policy Principles and Framework
White House, May 25, 2016.
CONCEPTS / COMMENTS
Will integrated surveillance systems for vectors and vector-borne diseases be the future of controlling vector-borne diseases? A practical example from China.
Wu Y et al. Epidemiology and infection 2016 Jul (9) 1895-903
Bacterial GWAS: not just gilding the lily
Lees JA, Bentley SD. Nat Rev Microbiol, May 31, 2016.
Metagenomics: Pathogen diagnostics for the masses.
Koch Linda et al. Nature reviews. Genetics 2016 Jun
Microbiome Data Science: Understanding Our Microbial Planet.
Kyrpides Nikos C et al. Trends in microbiology 2016 Jun (6) 425-7
Host-microbe interaction: Rules of the game for microbiota
Faust K, Raes J. Nature, Jun 8, 2016.
Trypanosoma cruzi: Time for International Recognition as a Foodborne Parasite.
Robertson Lucy J et al. PLoS neglected tropical diseases 2016 Jun (6) e0004656
The Future of Antibiotics: Emerging Technologies and Stewardship.
Fortman Jeffrey L et al. Trends in microbiology 2016 May
METHODS / TOOLS
Droplet microfluidics for microbiology: techniques, applications and challenges.
Kaminski Tomasz S et al. Lab on a chip 2016 May
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics.
Escobar-Zepeda Alejandra et al. Frontiers in genetics 2015 348
An Infectious cDNA Clone of Zika Virus to Study Viral Virulence, Mosquito Transmission, and Antiviral Inhibitors.
Shan Chao et al. Cell host & microbe 2016 May
Genetically Engineered Phages: a Review of Advances over the Last Decade.
Pires Diana P et al. Microbiology and molecular biology reviews : MMBR 2016 Sep (3) 523-43
Controlling for phylogenetic relatedness and evolutionary rates improves the discovery of associations between species' phenotypic and genomic differences.
Prudent Xavier et al. Molecular biology and evolution 2016 May
Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.
Kühnert Denise et al. Molecular biology and evolution 2016 Apr
Integrating molecular epidemiology and social network analysis to study infectious diseases: towards a socio-molecular era for public health.
Vasylyeva Tetyana I et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Jun
RepeatAnalyzer: a tool for analysing and managing short-sequence repeat data.
Catanese Helen N et al. BMC genomics 2016 (1) 422
MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses.
Bucci Vanni et al. Genome biology 2016 (1) 121
EVOLUTION / ECOLOGY / POPULATIONS
Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics
Spyrou MA, et al. Cell Host Microbe, Jun 8, 2016.
New insights into the hepatitis E virus genotype 3 phylodynamics and evolutionary history.
Mirazo Santiago et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Jun
Genetic diversity and population structure of Plasmodium falciparum over space and time in an African archipelago.
Salgueiro Patrícia et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Jun
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
Phylogenetic analysis of enteroaggregative Escherichia coli (EAEC) isolated in Japan revealed the emergence of CTX-M-14-producing EAEC O25:H4 clones related to ST131.
Imuta Naoko et al. Journal of clinical microbiology 2016 Jun
Impact of Pathogen Population Heterogeneity and Stress-Resistant Variants on Food Safety.
Abee T et al. Annual review of food science and technology 2016 439-56
The pathogenicity and host adaptation of livestock-associated MRSA CC398.
Ballhausen Britta et al. Veterinary microbiology 2016 May
DETECTION / DIAGNOSIS
Rapid identification of health care associated infections with an integrated fluorescence anisotropy system
Park KS, et al. Sci Adv, May 6, 2016.
sesC as a genetic marker for easy identification of Staphylococcus epidermidis from other isolates.
Khodaparast Ladan et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 May
The Use of a Dengue Rapid Diagnostic Test During Suspected Dengue Outbreaks in Resource Limited Regions.
Hunsperger Elizabeth A et al. Journal of clinical microbiology 2016 May
Impact of Early Detection of Respiratory Viruses by Multiplex PCR on Clinical Outcomes in Adult Patients.
Rappo Urania et al. Journal of clinical microbiology 2016 May
A computationally-designed serological assay for the porcine epidemic diarrhea virus.
Song Yunfeng et al. Journal of clinical microbiology 2016 May
Clinical comparison, standardization and optimization of Zika virus molecular detection
Corman VM, et al. Bull World Health Organ 2016;doi:10.2471/BLT.16.175950.
Performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry for the identification of Aspergillus, Scedosporium, and Fusarium spp. in the Australian clinical setting.
Sleiman Sue et al. Journal of clinical microbiology 2016 Jun
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
Colonization with methicillin-resistant Staphylococcus pseudintermedius in multi-dog households: A longitudinal study using whole genome sequencing.
Windahl Ulrika et al. Veterinary microbiology 2016 Jun 8-14
Whole Genome DNA Sequence Analysis of Salmonella subspecies enterica serotype Tennessee obtained from related peanut butter foodborne outbreaks.
Wilson Mark R et al. PloS one (6) e0146929
Declaring a tuberculosis outbreak over with genomic epidemiology
Hatherell HA, et al. Open Microbiol, Jun 2016.
Investigating Salmonella Eko from Various Sources in Nigeria by Whole Genome Sequencing to Identify the Source of Human Infections.
Leekitcharoenphon Pimlapas et al. PloS one 2016 (5) e0156212
Evidence of Sexual Transmission of Zika Virus.
D'Ortenzio Eric et al. The New England journal of medicine 2016 Jun (22) 2195-8
Investigation of an unrecognized large-scale outbreak of Candida parapsilosis sensu stricto fungaemia in a tertiary-care hospital in China.
Wang He et al. Scientific reports 2016 27099
ANTIMICROBIALS / VACCINES / INTERVENTIONS
Selection of antigenically advanced variants of seasonal influenza viruses
Li C, et al. Nat Microbiol, May 23, 2016.
Low pathogenic avian influenza (H9N2) in chicken: Evaluation of an ancestral H9-MVA vaccine.
Ducatez Mariette F et al. Veterinary microbiology 2016 Jun 59-67
Evidence of susceptibility to lamivudine-based HAART and genetic stability of hepatitis B virus (HBV) in HIV co-infected patients: A South African longitudinal HBV whole genome study.
Amponsah-Dacosta Edina et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 May 232-238
Genetically Modified (GM) Mosquito Use to Reduce Mosquito-Transmitted Disease in the US: A Community Opinion Survey
Adalja A, et al. PLoS Currents Outbreaks, May 25, 2016.
HOST-MICROBE INTERACTIONS
A Cellular GWAS Approach to Define Human Variation in Cellular Pathways Important to Inflammation.
Miller Samuel I et al. Pathogens (Basel, Switzerland) 2016 (2)
TLR1 Variant H305L Associated with Protection from Pulmonary Tuberculosis.
Meyer Christian G et al. PloS one 2016 (5) e0156046
Accounting for reciprocal host– microbiome interactions in experimental science
Stappenbeck TS, Virgin HW. Nature, Jun 9, 2016.
Complete Genome Sequence of Germline Chromosomally Integrated Human Herpesvirus 6A and Analyses Integration Sites Define a New Human Endogenous Virus with Potential to Reactivate as an Emerging Infection.
Tweedy Joshua et al. Viruses 2016 Jan (1)
The Telomeric Repeats of Human Herpesvirus 6A (HHV-6A) Are Required for Efficient Virus Integration.
Wallaschek Nina et al. PLoS pathogens 2016 May (5) e1005666
Making Bunyaviruses Talk: Interrogation Tactics to Identify Host Factors Required for Infection.
Riblett Amber M et al. Viruses 2016 (5)
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.
Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by the CDC Office of Public Health Genomics 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.