Public Health Genomics Knowledge Base (v1.2)
August 11-18, 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
US approves GMO mosquito test, but no release imminent
Kay J. Washington Post, Aug 5, 2016.
Three vaccines prevent Zika infection in monkeys; vaccine trial in humans gets underway
Kaplan K. Los Angeles Times, Aug 4, 2016.
Unpacking the innards of Theranos’s new Zika-detection box
Buhr S. Tech Crunch, Aug 5, 2016.
INFECTIOUS DISEASE. Zika vaccine has a good shot.
Cohen Jon et al. Science (New York, N.Y.) 2016 Aug (6299) 529-30
BC researchers collaborate with Oxford University and Public Health England to make TB genomic data quick and easy to read for clinicians
(news release) Genome British Columbia, Aug 9, 2016.
Diagnostics at Home: Mately Uses Blood Spots to Track STDs
McCann R. Diagnostics World, Aug 4, 2016.
HHS, international partners launch antibiotic research accelerator
Healio, Jul 31, 2016.
Beyond CRISPR: A guide to the many other ways to edit a genome
Ledford H. Nature, Aug 8, 2016.
Garvan Team Uses Synthetic DNA to Create Spike-In Method for NGS Assay Validation
Heger M. GenomeWeb, Aug 8, 2016.
Not your momma's microbe lab: a new genetic engineering machine takes microbial design to the masses
Gilman C. philly.com, Aug 9, 2016.
MIT researchers are sending robots into sewers to help predict disease outbreaks
Nguyen C. Business Insider, Aug 4, 2016.
EVENTS / TRAINING / WEB RESOURCES
Consultation on Report from the EUCAST Subcommittee on the Role of Whole Genome Sequencing (WGS) in Antimicrobial Susceptibility Testing of Bacteria
(report) European Committee on Antimicrobial Susceptibility Testing (EUCAST), May 2016.
CLIMB – a timely resource for microbial genomics
(blog post) Raza S. PHG Foundation, Aug 11, 2016.
CLIMB - Cloud Infrastructure for Microbial Informatics
(web site) CLIMB (UK)
POLICY
FDA Releases Final Environmental Assessment for Genetically Engineered Mosquito
(announcement) FDA, Aug 5, 2016.
A Step Forward to Empower Global Microbiome Research Through Local Leadership.
Pylro Victor S et al. Trends in microbiology 2016 Aug
Toward Fairness in Data Sharing
The International Consortium of Investigators for Fairness in Trial Data Sharing, New Engl J Med, Aug 4, 2016.
NEJM editorial doubles down on resistance to data sharing
Oransky I, Marcus A. STAT, Aug 10, 2016.
CONCEPTS / COMMENTS
How The Microbes Inside Us Went From Enemies To Purported Superhealers
(blog post) Beans C. NPR, August 9, 2016
Zika Virus 6 Months Later
Frieden TF, et al. JAMA, August 9, 2016
The Virtuous Cycle of a Data Ecosystem.
Voytek Bradley et al. PLoS computational biology 2016 Aug (8) e1005037
METHODS / TOOLS
From clinical sample to complete genome: comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing.
Cornelissen Marion et al. Virus research 2016 Aug
Norovirus whole genome sequencing by SureSelect target enrichment: a robust and sensitive method.
Brown Julianne R et al. Journal of clinical microbiology 2016 Aug
FARAO - The Flexible All-Round Annotation Organizer.
Hammarén Rickard et al. Bioinformatics (Oxford, England) 2016 Aug
Bayesian identification of bacterial strains from sequencing data
Sankar A, et al. Microb Genom, Jun 27, 2016.
Robust high throughput prokaryote de novo assembly and improvement pipeline for Illumina data
Page AJ, et al. Microb Genom, Aug 8, 2016.
Using genomics data to reconstruct transmission trees during disease outbreaks.
Hall M D et al. Revue scientifique et technique (International Office of Epizootics) 2016 Apr (1) 287-96
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.
Wheeler Nicole E et al. Bioinformatics (Oxford, England) 2016 Aug
EVOLUTION / ECOLOGY / POPULATIONS
Evolution and Diversity of Listeria monocytogenes from Clinical and Food Samples in Shanghai, China.
Zhang Jianmin et al. Frontiers in microbiology 2016 1138
Taxonomic reassessment of the genus Elizabethkingia using whole genome sequencing: Elizabethkingia endophytica Kämpfer et al. 2015 is a later subjective synonym of Elizabethkingia anophelis Kämpfer et al. 2011.
Doijad Swapnil et al. International journal of systematic and evolutionary microbiology 2016 Aug
Epidemiological Investigation of Legionella pneumophila serogroups 2-14 Isolates from Water Samples by Amplified Fragment Length Polymorphism and Sequence-Based Typing and Detection of Virulence Traits.
Katsiaflaka Anna et al. Applied and environmental microbiology 2016 Aug
Population structure of invasive Streptococcus pneumoniae isolates among Alaskan children in the conjugate vaccine era, 2001 to 2013.
Miernyk Karen M et al. Diagnostic microbiology and infectious disease 2016 Jul
Recombination-driven genome evolution and stability of bacterial species
Dixit PD, et al. bioRxiv, Aug 4, 2016.
Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA.
Ward Melissa J et al. Genome biology 2016 (1) 160
Short term evolution of Shiga toxin producing Escherichia coli O157:H7 between two food-borne outbreaks
Cowley LA, et al. Microb Genom, Aug 9, 2016.
Massive dispersal of Coxiella burnetii among cattle across the United States
Olivas S, et al. Microb Genom, Aug 1, 2016.
Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients.
Ssengooba Willy et al. BMC infectious diseases 2016 371
Different Variants in Reverse Transcriptase Domain Determined by Ultra-deep Sequencing in Treatment-naïve and Treated Indonesian Patients Infected with Hepatitis B Virus.
Wasityastuti Widya et al. The Kobe journal of medical sciences 2016 (1) E1-8
Complete Genome Sequence of Zika Virus Isolated in Mexico, 2016.
Díaz-Quiñonez José Alberto et al. Genome announcements 2016 (4)
Diversity and Tropism of HIV-1 Rebound Virus Populations in Plasma Level After Treatment Discontinuation.
Bednar Maria M et al. The Journal of infectious diseases 2016 Aug (3) 403-7
Genotypes of rubella virus and the epidemiology of rubella infections in the Democratic Republic of the Congo, 2004-2013.
Pukuta Elizabeth et al. Journal of medical virology 2016 Oct (10) 1677-84
Molecular evolution and the global reemergence of enterovirus D68 by genome-wide analysis.
Gong Yu-Nong et al. Medicine 2016 Aug (31) e4416
MLST and Whole-Genome-Based Population Analysis of Cryptococcus gattii VGIII Links Clinical, Veterinary and Environmental Strains, and Reveals Divergent Serotype Specific Sub-populations and Distant Ancestors.
Firacative Carolina et al. PLoS neglected tropical diseases 2016 Aug (8) e0004861
Onchocerciasis transmission in Ghana: the human blood index of sibling species of the Simulium damnosum complex.
Lamberton Poppy H L et al. Parasites & vectors 2016 (1) 432
Animal genomics in natural reservoirs of infectious diseases.
Cowled C et al. Revue scientifique et technique (International Office of Epizootics) 2016 Apr (1) 159-74
Extensive genetic diversity among populations of the malaria mosquito Anopheles moucheti revealed by population genomics
Fouet C, et al. bioRxiv, Aug 6, 2016.
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
Emergence of Plasmid-Borne dfrA14 Trimethoprim Resistance Gene in Shigella sonnei.
Miranda Alfonso et al. Frontiers in cellular and infection microbiology 2016 77
Tracking inter-institutional spread of NDM and identification of a novel NDM-positive plasmid, pSg1-NDM, using next-generation sequencing approaches.
Khong Wei Xin et al. The Journal of antimicrobial chemotherapy 2016 Aug
Survival and evolution of a large multidrug resistance plasmid in new clinical bacterial hosts.
Porse Andreas et al. Molecular biology and evolution 2016 Aug
Prevalence of transmitted HIV-1 drug resistance among young adults attending HIV counselling and testing clinics in Kigali, Rwanda.
Mutagoma Mwumvaneza et al. Antiviral therapy 2016 (3) 247-51
DETECTION / DIAGNOSIS
Real-time PCR detection of Neisseria gonorrhoeae susceptibility to penicillin.
Buckley Cameron et al. The Journal of antimicrobial chemotherapy 2016 Jul
A novel SimpleProbe PCR for detection of mutations in the 23S rRNA gene associated with macrolide resistance in Mycoplasma genitalium in clinical samples.
Gossé M et al. Journal of clinical microbiology 2016 Aug
A molecular platform for the diagnosis of multidrug-resistant and pre-extensively drug-resistant tuberculosis based on single nucleotide polymorphism mutations present in Colombian isolates of Mycobacterium tuberculosis.
Martínez Luz Maira Wintaco et al. Memo´rias do Instituto Oswaldo Cruz 2016 Feb (2) 93-100
The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis.
Devonshire Alison S et al. BMC infectious diseases 2016 366
Identification of a dominant Chlamydia trachomatis strain in patients attending sexual transmitted infection clinic and female sex workers in Tunisia using a high resolution typing method.
Gharsallah Houda et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Aug
Easy and inexpensive molecular detection of dengue, chikungunya and zika viruses in febrile patients.
Calvo Eliana P et al. Acta tropica 2016 Jul 32-37
Privacy-preserving genomic testing in the clinic: a model using HIV treatment.
McLaren Paul J et al. Genetics in medicine : official journal of the American College of Medical Genetics 2016 Aug (8) 814-22
Detection of Zika virus in Brazilian patients during the first five days of infection - urine versus plasma.
Pessôa Rodrigo et al. Euro surveillance : bulletin Europe´en sur les maladies transmissibles = European communicable disease bulletin 2016 Jul (30)
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
Nosocomial Outbreak of OXA-48-Producing Klebsiella pneumoniae in a Chinese Hospital: Clonal Transmission of ST147 and ST383.
Guo Ling et al. PloS one 2016 (8) e0160754
Simultaneous occurrence of MRSA and ESBL-producing Enterobacteriaceae on pig farms and in nasal and stool samples from farmers.
Fischer Julia et al. Veterinary microbiology 2016 Jun
HIV Infection Linked to Injection Use of Oxymorphone in Indiana, 2014-2015.
Peters Philip J et al. The New England journal of medicine 2016 Jul (3) 229-39
Genomic Analysis of Viral Outbreaks.
Wohl Shirlee et al. Annual review of virology 2016 Aug
ANTIMICROBIALS / VACCINES / INTERVENTIONS
Protective efficacy of multiple vaccine platforms against Zika virus challenge in rhesus monkeys.
Abbink Peter et al. Science (New York, N.Y.) 2016 Aug
Induction of systemic IFITM3 expression does not effectively control foot-and-mouth disease viral infection in transgenic pigs.
Zhang Huawei et al. Veterinary microbiology 2016 Aug 20-6
HOST-MICROBE INTERACTIONS
A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition.
Li Dalin et al. Gastroenterology 2016 Aug
IFITM3 and severe influenza virus infection. No evidence of genetic association.
López-Rodríguez M et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2016 Aug
The early infant gut microbiome varies in association with a maternal high-fat diet.
Chu Derrick M et al. Genome medicine 2016 (1) 77
A Primate APOL1 Variant That Kills Trypanosoma brucei gambiense.
Cooper Anneli et al. PLoS neglected tropical diseases 2016 Aug (8) e0004903
Microbiomic and Posttranslational Modifications as Preludes to Autoimmune Diseases.
Opdenakker Ghislain et al. Trends in molecular medicine 2016 Aug
Viruses within animal genomes.
De Brognier A et al. Revue scientifique et technique (International Office of Epizootics) 2016 Apr (1) 133-42
Bioinformatic analysis reveals the expression of unique transcriptomic signatures in Zika virus infected human neural stem cells.
Rolfe Alyssa J et al. Cell & bioscience 2016 42
Animal genomics and infectious disease resistance in poultry.
Smith J et al. Revue scientifique et technique (International Office of Epizootics) 2016 Apr (1) 105-19
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.
Public Health Genomics Knowledge Base (v1.2)