Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jun 29, 2017

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
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Host-Microbe Interactions

NEWS

• Tests for Lyme disease miss many early cases — but a new approach could help  
  Caruso C. STAT, Jun 28, 2017.
• Modified viruses deliver death to antibiotic-resistant bacteria  
  Reardon S. Nature, Jun 21, 2017.
• New colistin resistance gene identified in China  
  Dall C. CIDRAP, Jun 28, 2017.
• Consortium Builds Tuberculosis Genome Database in Move Toward NGS-Based Diagnostics  
  Heger M. GenomeWeb, Jun 23, 2017.
• Study Validates Single-Gene Biomarker That Discriminates Between Influenza and Bacterial Infections  
  GenomeWeb, Jun 28, 2017.
• Genetic analysis of H7N9 finds adaptations, clade patterns  
  Schnirring L. CIDRAP, Jun 26, 2017.
• USDA: Environmental spread, multiple entries likely fueled US H7N9 outbreaks  
  Schnirring L. CIDRAP, Jun 23, 2017.
• 2015 measles outbreak in Canada traced to unique genotype  
  Healio, Jun 26, 2017.
• Avoiding CRISPR-Mediated Gene-Drive–Evolved Resistance in Mosquitoes  
  GEN News, Jun 28, 2017.

EVENTS / TRAINING / WEB RESOURCES

• Applications open for the August 2017 NCBI-NLM Bioinformatics Hackathon  
  (event) NCBI, Bethesda MD, Aug 14-16, 2017. Applications due Jul 11, 2017.

CONCEPTS / COMMENTS

• Bioinformatics: indispensable, yet hidden in plain sight?  
  Bartlett Andrew et al. BMC bioinformatics 2017 Jun (1) 311
• Computing patient data in the cloud: practical and legal considerations for genetics and genomics research in Europe and internationally.  
  Molnár-Gábor Fruzsina et al. Genome medicine 2017 Jun (1) 58
• Emergence of a Urogenital Pathotype of Neisseria meningitidis.  
  Kahler Charlene M et al. Trends in microbiology 2017 Jul (7) 510-512
• A billion-year arms race against viruses shaped our evolution  
  Maxmen A. Nature, Jun 28, 2017.
• The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals  
  Franco-Obregon A, Gilbert JA. mSystems 2017; 2:e00018-17.

METHODS / TOOLS

• Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus.  
  Sobel Leonard Ashley et al. Journal of virology 2017 May
• 25 years of serving the community with ribosomal RNA gene reference databases and tools.  
  Glöckner Frank Oliver et al. Journal of biotechnology 2017 Jun
• sourceR: Classification and source attribution of infectious agents among heterogeneous populations.  
  Miller Poppy et al. PLoS computational biology 2017 May (5) e1005564
• Preliminary Validation of a Method Combining Cultivation and Cloning-Based Approaches to Monitor Airborne Bacteria.  
  Schäfer Jenny et al. Annals of work exposures and health 2017 Jun

EVOLUTION / ECOLOGY / POPULATIONS

• Parallel evolution of influenza across multiple spatiotemporal scales.  
  Xue Katherine S et al. eLife 2017 Jun
• Global emergence of the widespread Pseudomonas aeruginosa ST235 clone.  
  Treepong Panisa et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2017 Jun
• Milk-originated Bacillus cereus sensu lato strains harbouring Bacillus anthracis-like plasmids are genetically and phenotypically diverse.  
  Bartoszewicz Marek et al. Food microbiology 2017 Oct 23-30
• Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila.  
  David Sophia et al. PLoS genetics 2017 Jun (6) e1006855
• Prevalence, diversity, and host associations of Bartonella strains in bats from Georgia (Caucasus).  
  Urushadze Lela et al. PLoS neglected tropical diseases 2017 Apr (4) e0005428 
• Genetic diversity of environmental Vibrio cholerae O1 strains isolated in Northern Vietnam.  
  Takemura Taichiro et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Jun
• Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing.  
  Garrine Marcelino et al. PLoS neglected tropical diseases 2017 Jun (6) e0005671
• Whole genome analysis of selected human and animal rotaviruses identified in Uganda from 2012 to 2014 reveals complex genome reassortment events between human, bovine, caprine and porcine strains.  
  Bwogi Josephine et al. PloS one 2017 (6) e0178855
• A New Bat-HKU2-like Coronavirus in Swine, China, 2017.  
  Gong Lang et al. Emerging infectious diseases 2017 Sep (9)
• Tiger on the prowl: Invasion history and spatio-temporal genetic structure of the Asian tiger mosquito Aedes albopictus (Skuse 1894) in the Indo-Pacific.  
  Maynard Andrew J et al. PLoS neglected tropical diseases 2017 Apr (4) e0005546
• High Resolution Meta-Transcriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia.  
  Shi Mang et al. Journal of virology 2017 Jun

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Molecular epidemiology and resistome analysis of multidrug-resistant ST11 Klebsiella pneumoniae strain containing multiple copies of extended-spectrum β-lactamase genes using whole-genome sequencing.  
  DSouza Roshan et al. The new microbiologica 2017 Jan (1) 38-44
• Vibrio cholerae O1 with ctxB7 variant genotype acquired qnrVC mediated ciprofloxacin resistance in Yavatmal, India.  
  Kumar Pramod et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2017 Jun
• Novel Plasmid-Mediated Colistin Resistance Gene mcr-3 in Escherichia coli.  
  Yin Wenjuan et al. mBio 2017 Jun (3)

DETECTION / DIAGNOSIS

• Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review.  
  Tagini F et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2017 Jun 
• Added diagnostic value and impact on antimicrobial therapy of 16S rRNA PCR and Amplicon Sequencing on resected heart valves in infective endocarditis: a prospective cohort study.  
  Peeters Bart et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2017 Jun
• Development of a real-time loop-mediated isothermal amplification assay for detection of Burkholderia mallei.  
  Pal V et al. Transboundary and emerging diseases 2017 Jun
• Real-Time Whole-Genome Sequencing for Surveillance of Listeria monocytogenes, France.  
  Moura Alexandra et al. Emerging infectious diseases 2017 Sep (9)
• Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station  
  Venkateswaran K, et al. mSystems 2017; 2:e00021-17.
• A novel immune biomarker IFI27 discriminates between influenza and bacteria in patients with suspected respiratory infection.  
  Tang Benjamin M et al. The European respiratory journal 2017 Jun (6)
• Comparison of Zika virus (ZIKV) RNA detection in plasma, whole blood and urine - case series of travel-associated ZIKV infection imported to Italy, 2016.  
  Rossini Giada et al. The Journal of infection 2017 Jun
• Online identification of fungi using MALDI-TOF mass spectrometry: validation of a new web application.  
  Normand A C et al. Journal of clinical microbiology 2017 Jun
• Evidence of non-Plasmodium falciparum malaria infection in Kédougou, Sénégal.  
  Daniels Rachel F et al. Malaria journal 2017 Jan (1) 9

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Environmental sampling coupled with real-time PCR and genotyping to investigate the source of a Q fever outbreak in a work setting.  
  Hurtado A et al. Epidemiology and infection 2017 Jul (9) 1834-1842
• A nationwide outbreak of listeriosis associated with cold-cuts, Sweden 2013-2014.  
  Dahl Viktor et al. Infection ecology & epidemiology 2017 (1) 1324232
• Genomic investigation of a suspected outbreak of Legionella pneumophila ST82 reveals undetected heterogeneity by the present gold-standard methods, Denmark, July to November 2014  
  Schjørring S, et al. Eurosurveillance, Jun 22, 2017.
• Multistate Outbreak of Salmonella Anatum Infections Linked to Imported Hot Peppers — United States, May–July 2016
  Hassan R, et al. MMWR, Jun 30, 2017. 
• Late-Onset Infant Group B Streptococcus Infection Associated with Maternal Consumption of Capsules Containing Dehydrated Placenta — Oregon, 2016
  Busers GL, et al. MMWR, Jun 30, 2017. 

HOST-MICROBE INTERACTIONS

• Influenza-Omics and the Host Response: Recent Advances and Future Prospects.  
  Powell Joshua D et al. Pathogens (Basel, Switzerland) 2017 Jun (2)
• Microbial Genetic Composition Tunes Host Longevity.  
  Han Bing et al. Cell 2017 Jun (7) 1249-1262.e13

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.