Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

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

• UCSF Lab Readies Launch of Metagenomic NGS Test for Infectious Disease  
   Heger M. GenomeWeb, Feb 24, 2017.
• FDA OKs Tests for Guiding Infection Treatment  
   Kelley KJ. NEJM Journal Watch, Feb 27, 2017.
• Pathogen Surveillance System Wins NIH Open Science Prize  
   GenomeWeb, Feb 28, 2017.
• The drug-resistant bacteria that pose the greatest health threats  
   Willyard C. Nature, Feb 28, 2017.
• Human cases of bird flu are surging, alarming public health officials  
   Branswell H. STAT, Feb 28, 2017.
• WHO: H7N9 antiviral resistance likely arose after treatment  
   Schnirring L. CIDRAP, Mar 1, 2017.
• Controlling Mosquito Viruses with Transcriptomics  
   Clinical Omics, February 23, 2017
• Genome Sequences Show How Hospital-Acquired Bloodstream Infections Are Transmitted  
   GenomeWeb, Feb 24, 2017.
• Scientists Are Creating a Genetic Chainsaw to Hack Superbug DNA to Bits  
   Brown KV. Gizmodo, Feb 24, 2017.
• Helicobacter Pylori Subpopulations Evolved During Colonization of Americas  
   GenomeWeb, Feb 23, 2017.
• Biologists propose to sequence the DNA of all life on Earth  
   Pennisi E. ScienceInsider, Feb 24, 2017.
• Newfound 3.77-billion-year-old fossils could be earliest evidence of life on Earth  
   Kaplan S. Washington Post, Mar 1, 2017.

EVENTS / TRAINING / WEB RESOURCES

• Molecular Epidemiology  
  (training) New York Integrated Food Safety Center of Excellence

POLICY

• FDA allows marketing of test to identify organisms that cause bloodstream infections and provide antibiotic sensitivity results  
  (news release) FDA, Feb 23, 2017.

CONCEPTS / COMMENTS

• The role of laboratory diagnostics in emerging viral infections: the example of the Middle East respiratory syndrome epidemic.  
  Chan Jasper F W et al. Journal of microbiology (Seoul, Korea) 2017 Mar (3) 172-182
• How bioinformatics tools are bringing genetic analysis to the masses  
  Perkel JM. Nature, Feb 28, 2017.
• Ecological networks to unravel the routes to horizontal transposon transfers.  
  Venner Samuel et al. PLoS biology 2017 Feb (2) e2001536
• A new genetic tool maps how deadly viruses spread around the world in real time  
  Rathi A. Quartz, Feb 28, 2017.
• DNA vaccines against Zika virus speed into clinical trials.  
  Morrison Chris et al. Nature reviews. Drug discovery 2016 Jul (8) 521-2

METHODS / TOOLS

• A global perspective on bioinformatics training needs  
  Brazas MD, et al. bioRxiv, Feb 27, 2017.
• MetaCherchant - an algorithm for analyzing genomic environment of antibiotic resistance gene in gut microbiota  
  Olekhnovich EI, et al. bioRxiv, Feb 23, 2017.
• MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification.  
  Fiscon Giulia et al. BioData mining 2016 38
• Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research.  
  Comeau André M et al. mSystems (1)
• GMPR: A novel normalization method for microbiome sequencing data  
  Chen J, Chen L. bioRxiv, Feb 28, 2017.

EVOLUTION / ECOLOGY / POPULATIONS

• Genome Sequences of Three Brucella canis Strains Isolated from Humans and a Dog.
  Viana Marcus Vinicius Canário et al. Genome announcements 2017 Feb (8) 
• Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas.
  Thorell Kaisa et al. PLoS genetics 2017 Feb (2) e1006546
• Molecular epidemiological survey of bacterial and parasitic pathogens in hard ticks from eastern China.
  Liu Xiang-Ye et al. Acta tropica 2017 Mar 26-30
• Genomic changes associated with the evolutionary transition of an insect gut symbiont into a blood-borne pathogen.
  Segers Francisca Hid et al. The ISME journal 2017 Feb 
• Complete Genome Sequence of Mycoplasma pneumoniae Type 2 Reference Strain FH Using Single-Molecule Real-Time Sequencing Technology.
  Desai Heta P et al. Genome announcements 2017 Feb (8) 
• Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand.
  Crispell Joseph et al. BMC genomics 2017 Feb (1) 180
• Pairwise diversity and tMRCA as potential markers for HIV infection recency.
  Moyo Sikhulile et al. Medicine 2017 Feb (6) e6041
• Sensitive Next-Generation Sequencing Method Reveals Deep Genetic Diversity of HIV-1 in the Democratic Republic of the Congo 
  Rodgers MA, et al. J Virol, Jan 2017.

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Comparative and functional triatomine genomics reveals reductions and expansions in insecticide resistance-related gene families.  
  Traverso Lucila et al. PLoS neglected tropical diseases 2017 Feb (2) e0005313
• Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance.  
  Manson Abigail L et al. Nature genetics 2017 Mar (3) 395-402
• Characterization of genome sequences and clinical features of coxsackievirus A6 strains collected in Hyogo, Japan in 1999-2013.  
  Ogi Miki et al. Journal of medical virology 2017 Feb
• A polymorphism within the internal fusion loop of the Ebola virus glycoprotein modulates host cell entry.  
  Hoffmann Markus et al. Journal of virology 2017 Feb

DETECTION / DIAGNOSIS

• Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR): a novel antimicrobial resistance multilocus typing scheme for tracking the global dissemination of N. gonorrhoeae strains.  
  Demczuk W et al. Journal of clinical microbiology 2017 Feb 
• Short-Read Whole Genome Sequencing for Laboratory-Based Surveillance of Bordetella pertussis.  
  Marchand-Austin Alex et al. Journal of clinical microbiology 2017 Feb
• Use of eschar swabbing for the molecular diagnosis and genotyping of Orientia tsutsugamushi causing scrub typhus in Quang Nam province, Vietnam. 
  Le Viet Nhiem et al. PLoS neglected tropical diseases 2017 Feb (2) e0005397
• Rapid Molecular Detection of Zika Virus in Acute-Phase Urine Samples Using the Recombinase Polymerase Amplification Assay.  
  Abd El Wahed Ahmed et al. PLoS currents 2017 Jan
• First cases of Zika virus-infected US blood donors outside states with areas of active transmission.  
  Williamson Phillip C et al. Transfusion 2017 Feb
• Harmonization of nucleic acid testing for Zika virus: development of the 1(st) World Health Organization International Standard.  
  Baylis Sally A et al. Transfusion 2017 Feb
• Hepatitis E Virus Detection and Quantification by an RT-qPCR Assay calibrated to the World Health Organization Standard for HEV RNA.  
  Germer Jeffrey J et al. Journal of clinical microbiology 2017 Feb
• Fungal DNA barcoding.  
  Xu Jianping et al. Genome 2016 Nov (11) 913-932

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing  
  Raven KE, et al. Clin Infect Dis, Feb 23, 2017.
• Multinational outbreak of travel-related Salmonella Chester infections in Europe, summers 2014 and 2015.  
  Fonteneau Laure et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Feb (7)
• Characterization of HCV envelope diversification from acute to chronic infection using SMRT sequencing within a sexually-transmitted hepatitis C virus cluster.  
  Ho Cynthia K Y et al. Journal of virology 2017 Jan

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• MALDI-TOF alone versus MALDI-TOF combined with real-time antimicrobial stewardship interventions on time to optimal antimicrobial therapy in patients with positive blood cultures.  
  Beganovic Maya et al. Journal of clinical microbiology 2017 Feb 

HOST-MICROBE INTERACTIONS

• A genome wide association study identifies a lncRna as risk factor for pathological inflammatory responses in leprosy.  
  Fava Vinicius M et al. PLoS genetics 2017 Feb (2) e1006637
• Dense genotyping of immune-related loci implicates host responses to microbial exposure in Behçet's disease susceptibility.  
  Takeuchi Masaki et al. Nature genetics 2017 Mar (3) 438-443
• Intensive trapping of blood-fed Anopheles darlingi in Amazonian Peru reveals unexpectedly high proportions of avian blood-meals.  
  Moreno Marta et al. PLoS neglected tropical diseases 2017 Feb (2) e0005337

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.