Public Health Genomics Knowledge Base (beta version) || Advanced Molecular Detection Clips Content

Public Health Genomics Knowledge Base (beta version)

Published Date: Sep 24, 2015

Advanced Molecular Detection Clips Content

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

NEWS

• Fighting Ebola With a Palm-Sized DNA Sequencer 
  Yong E. Atlantic, Sep 16, 2015.
• People Emit Unique Microbial Clouds 
  Zusi K. The Scientist, Sep 23, 2015.
• PacBio Unveils Plans to Use BAM Format for Sequence Data; User Community Weighs in 
  Thomas UG. GenomeWeb, Sep 16, 2015.
• Metagenomic Sequencing Shows Changes in Healthy Gut Microbiome Pre- and Post-Antibiotics 
  GenomeWeb, Sep 23, 2015.
• New Virus Discovered in Human Blood 
  Akst J. The Scientist, Sep 23, 2015.

CONCEPTS / COMMENTS

• The Human Microbiome and the Future Practice of Medicine. 
  Relman David A et al. JAMA 2015 Sep 15. (11) 1127-8
• United States FDA's emergency use authorization of Ebola virus diagnostics: current impact and lessons for the future. 
  Whitehouse Chris A et al. Expert Rev. Mol. Diagn. 2015 Oct (10) 1231-5
• Genomics of HIV infection. 
  Telenti Amalio et al. Curr Opin HIV AIDS 2015 Mar (2) 77-8
• Aptamers against pathogenic microorganisms. 
  Davydova Anna et al. Crit. Rev. Microbiol. 2015 Aug 10. 1-19
• Adaptive Landscapes of Resistance Genes Change as Antibiotic Concentrations Change. 
  Mira Portia M et al. Mol. Biol. Evol. 2015 Oct (10) 2707-15

METHODS / TOOLS

• NanoOK: Multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. 
  Leggett Richard M et al. Bioinformatics 2015 Sep 17.
• Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data. 
  Daly Gordon M et al. PLoS ONE 2015 (6) e0129059
• Identifying personal microbiomes using metagenomic codes. 
  Franzosa Eric A et al. Proc. Natl. Acad. Sci. U.S.A. 2015 Jun 2. (22) E2930-8
• Complete assembly of novel environmental bacterial genomes by MinION sequencing 
  Turner DJ, et al. bioRxiv, Sep 19, 2015.
• Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis. 
  Briese Thomas et al. MBio 2015 (5)
• Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology. 
  Yu Jinsheng et al. BMC Genomics 2015 (1) 710
• FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program. 
  Lefort Vincent et al. Mol. Biol. Evol. 2015 Oct (10) 2798-800

EVOLUTION / ECOLOGY / POPULATIONS

• Genomic Epidemiology of Hypervirulent Serogroup W, ST-11 Neisseria meningitidis 
  Mustapha MM, et al. eBiomedicine, Sep 8, 2015. (CDC Author)
• Introduction and evolution of dengue virus type 2 in Pakistan: a phylogeographic analysis. 
  Akram Madiha et al. Virol. J. 2015 (1) 148
• Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2. 
  Huang Hui-Wen et al. BMC Bioinformatics 2015 (1) 302
• Comparative genomic analysis of Leishmania (Viannia) peruviana and Leishmania (Viannia) braziliensis. 
  Valdivia Hugo O et al. BMC Genomics 2015 (1) 715
• Molecular and Phylogenetic analysis revealed new genotypes of Theileria annulata parasites from India. 
  George Neena et al. Parasit Vectors 2015 (1) 468
• Limited genomic divergence between intraspecific forms of Culex pipiens under different ecological pressures. 
  Gomes Bruno et al. BMC Evol. Biol. 2015 (1) 197 (CDC Author)

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• In Vivo Evolution of Bacterial Resistance in Two Cases of Enterobacter aerogenes Infections during Treatment with Imipenem. 
  Philippe Nadège et al. PLoS ONE 2015 (9) e0138828
• The Widespread Multidrug-Resistant Serotype O12 Pseudomonas aeruginosa Clone Emerged through Concomitant Horizontal Transfer of Serotype Antigen and Antibiotic Resistance Gene Clusters. 
  Thrane Sandra Wingaard et al. MBio 2015 (5)
• In vitro and molecular surveillance for antimalarial drug resistance in Plasmodium falciparum parasites in western Kenya reveals sustained artemisinin sensitivity and increased chloroquine sensitivity. 
  Lucchi Naomi W et al. Antimicrob. Agents Chemother. 2015 Sep 21. (CDC Author)
• Evidence for Reduced Drug Susceptibility without Emergence of Major Protease Mutations following Protease Inhibitor Monotherapy Failure in the SARA Trial. 
  Sutherland Katherine A et al. PLoS ONE 2015 (9) e0137834
• A naturally occurring single amino acid replacement in multiple gene regulator of group A Streptococcus significantly increases virulence. 
  Sanson Misu et al. Am. J. Pathol. 2015 Feb (2) 462-71

DETECTION / DIAGNOSIS

• Molecular Testing for Plasmodium falciparum using Serum or Plasma and Comparison with Microscopy and Rapid Diagnostic Testing in Febrile Nigerian Patients. 
  Waggoner Jesse J et al. J. Clin. Microbiol. 2015 Sep 9.
• Virome Analysis of Transfusion Recipients Reveals a Novel Human Virus That Shares Genomic Features with Hepaciviruses and Pegiviruses 
  Kapoor A, et al. 2015 mBio 2015; 6: e01466-15.
• Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire: a proof-of-concept study. 
  Schneeberger Pierre H H et al. Infect. Genet. Evol. 2015 Sep 18.
• Discrimination between E. granulosus sensu stricto, E. multilocularis and E. shiquicus Using a Multiplex PCR Assay. 
  Liu Cong-Nuan et al. PLoS Negl Trop Dis 2015 Sep (9) e0004084

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• HIV-1 Transmission During Recent Infection and During Treatment Interruptions as Major Drivers of New Infections in the Swiss HIV Cohort Study.
  Marzel Alex et al. Clin. Infect. Dis. 2015 Sep 19.
• HIV-1 Thai B strain has spread out of former plasma donors into general population through sexual contact in Henan, China. 
  Li Lin et al. J. Med. Virol. 2015 Sep 18.
• The molecular epidemiology of incident methicillin-resistant Staphylococcus aureus cases among hospitalized patients in Alberta, Canada: a retrospective cohort study. 
  Bush Kathryn et al. Antimicrob Resist Infect Control 2015 35
• Molecular Epidemiology of Hospital Outbreak of Middle East Respiratory Syndrome, Riyadh, Saudi Arabia, 2014 
  Fagbo SF, et al. Emerg Infect Dis, Nov 2015.

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Dengue viruses cluster antigenically but not as discrete serotypes. 
  Katzelnick Leah C et al. Science 2015 Sep 18. (6254) 1338-43
• Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance. 
  Nichol Daniel et al. PLoS Comput. Biol. 2015 Sep (9) e1004493

HOST-MICROBE INTERACTIONS

• Host genetic variation impacts microbiome composition across human body sites. 
  Blekhman Ran et al. Genome Biol. 2015 191
• Single nucleotide polymorphisms in IL28B, but not in TNF-alpha, are associated with the severity of the disease caused by Andes virus 
  Angulo J. Clin Infect Dis, Sep 22, 2015.
• Extremely High Mutation Rate of HIV-1 In Vivo. 
  Cuevas José M et al. PLoS Biol. 2015 Sep (9) e1002251
• No Major Host Genetic Risk Factor Contributed to A(H1N1)2009 Influenza Severity. 
  Garcia-Etxebarria Koldo et al. PLoS ONE 2015 (9) e0135983
• New insights on the viral and host factors contributing to the airway pathogenesis caused by the respiratory syncytial virus. 
  Lay Margarita K et al. Crit. Rev. Microbiol. 2015 Jun 29. 1-13

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.