Advanced Molecular Detection Clips :: Public Health Genomics Knowledge Base (v1.2)

Public Health Genomics Knowledge Base (v1.2)



September 15, 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
• Host-Microbe Interactions

NEWS

• Genome Canada Awards C$4M for 16 Bioinformatics, Computational Biology Projects 
  GenomeWeb, Sep 13, 2016.
• Federal prize competition seeks innovative ideas to combat antimicrobial resistance 
  NIH, Sep 8, 2016.
• One year of Zika in Brazil: what have we learned? 
  Faccini LS. PHG Foundation, Sep 8, 2016.
• Zika virus may spread through bodily fluids, study finds 
  Sun LH. Washington Post, Sep 13, 2016.
• Amid outbreak, Singapore links local Zika cases to past Asian strains 
  Healio, Sep 13, 2016.
• Ebola Vaccine Development Gets Boost From US Army Team's LC/MS Method 
  Han AP. GenomeWeb, Sep 13, 2016.
• Ebola virus lingers longer than scientists thought 
  EC Hayden. Nature News, September 14, 2016.
• Recombinant Zoster Vaccine Works Well in Older Patients 
  Zuger A. NEJM Journal Watch, Sep 15, 2016.
• Scientists use genetic analysis to forecast spatial expansion of rabies in Peru 
  Science Daily, Sep 12, 2016.
• New Anthrax-Causing Clade Uncovered by Sequencing 
  GenomeWeb, Sep 8, 2016.
• Neonatal Gut Bacteria Might Promote Asthma 
  Azvolinsky A. The Scientist, Sep 12, 2016.
• Giant Petri Dish Displays Evolution in Space and Time 
  Rood J. The Scientist, Sep 8, 2016.

EVENTS / TRAINING / WEB RESOURCES

• BCCDC publishes new findings on power of integrated health data 
  (news release) BC Centre for Disease Control, Sep 8, 2016.
• StrongNet: An International Network to Improve Diagnostics and Access to Treatment for Strongyloidiasis Control. 
  Albonico Marco et al. PLoS neglected tropical diseases 2016 Sep (9) e0004898

POLICY

• STMA presents opinion for the delay of current susceptibility tests. 
  Kircher Susan M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Aug
• Hospitalizations due to selected infections caused by opportunistic premise plumbing pathogens (OPPP) and reported drug resistance in the United States older adult population in 1991-2006. 
  Naumova Elena N et al. Journal of public health policy 2016 Sep

CONCEPTS / COMMENTS

• Linking an unchained malady 
  Sanchez-Buso L, et al. Nat Rev Microbiol, Sep 13, 2016.
• Microbial Genomics of Ancient Plagues and Outbreaks. 
  Andam Cheryl P et al. Trends in microbiology 2016 Sep
• Functional Annotations of Paralogs: A Blessing and a Curse. 
  Zallot Rémi et al. Life (Basel, Switzerland) (3)
• PITing host against bacteria in the fight for infection control 
  Rayner KJ. Sci Transl Med, Sep 14, 2016.
• Using waste water to flush out drug dealers 
  Nature (editorial), Sep 14, 2016.
• The surprising history of the war on superbugs — and what it means for the world today 
  Zimmer C. STAT, Sep 12, 2016.
• Infectious diseases epidemic threats and mass gatherings: refocusing global attention on the continuing spread of the Middle East Respiratory syndrome coronavirus (MERS-CoV). 
  Zumla Alimuddin et al. BMC medicine 2016 (1) 132
• Primary Amebic Meningoencephalitis: What Have We Learned in the Last 5 Years? 
  Cope Jennifer R et al. Current infectious disease reports 2016 Sep (10) 31 
• Biomimetic Salmonella: A Next-Generation Therapeutic Vector? 
  Felgner S, et al. Trends Microbiol, Sep 7, 2016.

METHODS / TOOLS

• stringMLST: a fast k-mer based tool for multi locus sequence typing. 
  Gupta Anuj et al. Bioinformatics (Oxford, England) 2016 Sep
• Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer. 
  Lee Hong Kai et al. Scientific reports 2016 33318

EVOLUTION / ECOLOGY / POPULATIONS

• Bacillus cereus Biovar Anthracis Causing Anthrax in Sub-Saharan Africa-Chromosomal Monophyly and Broad Geographic Distribution. 
  Antonation Kym S et al. PLoS neglected tropical diseases 2016 Sep (9) e0004923
• Typhoidal Salmonellae: Use of Multi-Locus Sequence Typing to Determine Population Structure. 
  Sharma Priyanka et al. PloS one (9) e0162530
• Typhoidal Salmonellae: Use of Multi-Locus Sequence Typing to Determine Population Structure. 
  Sharma Priyanka et al. PloS one (9) e0162530
• High Leptospira Diversity in Animals and Humans Complicates the Search for Common Reservoirs of Human Disease in Rural Ecuador. 
  Barragan Veronica et al. PLoS neglected tropical diseases 2016 Sep (9) e0004990
• Host-pathogen evolutionary signatures reveal dynamics and future invasions of vampire bat rabies. 
  Streicker Daniel G et al. Proceedings of the National Academy of Sciences of the United States of America 2016 Sep 
• Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi. 
  Weatherly D Brent et al. BMC genomics 2016 (1) 729

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome. 
  van Opijnen Tim et al. PLoS pathogens 2016 Sep (9) e1005869
• Use of bacterial whole-genome sequencing to understand and improve the management of invasive Staphylococcus aureus infections. 
  Giulieri Stefano G et al. Expert review of anti-infective therapy 2016 Sep
• Investigation of Escherichia coli Harboring the mcr-1 Resistance Gene — Connecticut, 2016 
  Vasquez AM, et al. MMWR, Sep 9, 2016. 
• Investigation of First Identified mcr-1 Gene in an Isolate from a U.S. Patient — Pennsylvania, 2016 
  Kline KE, et al. MMWR, Sep 9, 2016. 
• Twenty Years of Global Surveillance of Antituberculosis-Drug Resistance. 
  Zignol Matteo et al. The New England journal of medicine 2016 Sep (11) 1081-1089
• Pathogenesis and Molecular Mechanisms of Zika Virus. 
  Nayak Shriddha et al. Seminars in reproductive medicine 2016 Sep
• Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients. 
  Marascio Nadia et al. International journal of molecular sciences 2016 (9)
• The transfer network of bacterial mobile resistome connecting animal and human microbiome. 
  Hu Yongfei et al. Applied and environmental microbiology 2016 Sep

DETECTION / DIAGNOSIS

• A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia. 
  Wang Le et al. PloS one (9) e0162411
• Rapid Bacterial Detection via an All-Electronic CMOS Biosensor. 
  Nikkhoo Nasim et al. PloS one 2016 (9) e0162438
• Clinical Next Generation Sequencing Outperforms Standard Microbiological Culture for Characterizing Polymicrobial Samples. 
  Cummings Lisa A et al. Clinical chemistry 2016 Sep
• Simultaneous detection of Zika, Chikungunya and Dengue viruses by a multiplex real-time RT-PCR assay. 
  Pabbaraju Kanti et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2016 Sep 66-71
• Proteomic Identification of Immunodiagnostic Antigens for Trypanosoma vivax Infections in Cattle and Generation of a Proof-of-Concept Lateral Flow Test Diagnostic Device. 
  Fleming Jennifer R et al. PLoS neglected tropical diseases 2016 Sep (9) e0004977

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae: an observational study. 
  De Silva Dilrini et al. The Lancet. Infectious diseases 2016 Jul
• Genetic Studies of Vibrio cholerae in South West Cameroon-A Phylogenetic Analysis of Isolates from the 2010-2011 Epidemic. 
  Ngwa Moise C et al. PLoS currents 2016

HOST-MICROBE INTERACTIONS

• Clostridium difficile colitis: pathogenesis and host defence. 
  Abt Michael C et al. Nature reviews. Microbiology 2016 Aug
• Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. 
  Fujimura Kei E et al. Nature medicine 2016 Sep

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.