Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Sep 7, 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. View Data Selection Criteria

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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

• Massive Ebola data site planned to combat outbreaks  
  Maxmen A. Nature, Sep 1, 2017.
• University of New Mexico Spinout Aims to Develop Nanopore Sequencing Technology  
  Heger M. GenomeWEb, Sep 6, 2017.
• GenePattern Notebook Environment Needs Only A Web Browser To Run Analyses  
  Proffitt A. Bio-IT World, Aug 31, 2017.
• Madagascar's Plague Phylogeography Points to Ongoing Local Transmission  
  GenomeWeb, Sep 6, 2017.
• New hypervirulent superbug kills 5 in Chinese ICU, alarming experts  
  Healio, Sep 1, 2017.
• Outpatient antibiotic use declines by 9% in US  
  Healio, Sep 6, 2017.
• Do Microbes Trigger Alzheimer’s Disease?  
  Adams JU. The Scientist, Sep 1, 2017.

EVENTS / TRAINING / WEB RESOURCES

• Microbiomes of the Built Environment: A Research Agenda for Indoor Microbiology, Human Health, and Buildings  
  (report) NASEM, Aug 16, 2017.
• Two new videos on YouTube: SRA RunSelector & NCBI Hackathons  
  NCBI Insights, Sep 6, 2017.

CONCEPTS / COMMENTS

• Convergence of carbapenem-resistance and hypervirulence in Klebsiella pneumoniae.  
  Chen Liang et al. The Lancet. Infectious diseases 2017 Aug
• Dengue, West Nile virus, chikungunya, Zika—and now Mayaro?  
  Hotez PJ, Murray KO. PLoS Negl Trop Dis, Aug 31, 2017.
• Scientists Look to Epigenetics to Thwart Viruses  
  Williams S. The Scientist, Sep 1, 2017.
• Queuing up for resistance testing  
  Dupnik K. Sci Transl Med, Sep 6, 2017.

METHODS / TOOLS

• The GenePattern Notebook Environment.  
  Reich Michael et al. Cell systems 2017 Aug (2) 149-151.e1
• Biased phylodynamic inferences from analysing clusters of viral sequences.  
  Dearlove Bethany L et al. Virus evolution 2017 Jul (2) vex020
• SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data  
  Epping L, et al. bioRxiv, Sep 5, 2017.
• ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota  
  Batut B, et al. bioRxiv, Sep 1, 2017.

EVOLUTION / ECOLOGY / POPULATIONS

• High-Quality Draft Genome Sequences for Four Drug-Resistant or Outbreak-Associated Shigella sonnei Strains Generated with PacBio Sequencing and Whole-Genome Maps.  
  Lindsey Rebecca L et al. Genome announcements 2017 Aug (35) 
• Complete Genome Sequence of Vibrio sp. Strain 2521-89, a Close Relative of Vibrio cholerae Isolated from Lake Water in New Mexico, USA.  
  Liang Kevin et al. Genome announcements 2017 Aug (35) 
• Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov.  
  Nicholson Ainsley C et al. Antonie van Leeuwenhoek 2017 Aug 
• Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague.  
  Vogler Amy J et al. PLoS neglected tropical diseases 2017 Sep (9) e0005887
• The genomic evolution of H1 influenza A viruses from swine detected in the United States between 2009 and 2016.  
  Gao Shibo et al. The Journal of general virology 2017 Aug (8) 2001-2010
• Molecular characterization and epidemic history of hepatitis C virus using core sequences of isolates from Central Province, Saudi Arabia.  
  Shier Medhat K et al. PloS one 2017 (9) e0184163
• Population diversity and collective interactions during influenza virus replication and evolution.  
  Brooke Christopher B et al. Journal of virology 2017 Aug
• The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution.  
  Ormond Louise et al. Genome biology and evolution 2017 Jul (7) 1913-1924
• Phylogeography of Coxsackievirus A16 Reveals Global Transmission Pathways and Recent Emergence and Spread of a Recombinant Genogroup.  
  Hassel Chervin et al. Journal of virology 2017 09 (18)
• Spread of Canine Influenza A(H3N2) Virus, United States.  
  Voorhees Ian E H et al. Emerging infectious diseases 2017 Dec (12)
• Toward the Drug Factory Microbiome: Microbial Community Variations in Antibiotic-Producing Clean Rooms.  
  Hamdy Amal M et al. Omics : a journal of integrative biology 2017 Sep

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• OXA-427, a new plasmid-borne carbapenem-hydrolysing class D β-lactamase in Enterobacteriaceae.  
  Bogaerts Pierre et al. The Journal of antimicrobial chemotherapy 2017 Sep (9) 2469-2477
• A fatal outbreak of ST11 carbapenem-resistant hypervirulent Klebsiella pneumoniae in a Chinese hospital: a molecular epidemiological study.  
  Gu Danxia et al. The Lancet. Infectious diseases 2017 Aug
• Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events.  
  Jamrozy Dorota et al. BMC genomics 2017 Sep (1) 684
• Genetic epidemiology of dengue viruses in phase III trials of the CYD tetravalent dengue vaccine and implications for efficacy.  
  Rabaa Maia A et al. eLife 2017 Sep
• Effect of the fourth nucleotide at the 3' end of neuraminidase and matrix viral genomic RNA on the pathogenicity of influenza virus A/PR/8/34.  
  Lee Chung-Young et al. Journal of veterinary science 2017 Aug (S1) 307-313 

DETECTION / DIAGNOSIS

• Review: Molecular detection of extended spectrum-β-lactamase- and carbapenemase-producing Enterobacteriaceae in a clinical setting.  
  Rood Ineke Gh et al. Diagnostic microbiology and infectious disease 2017 Aug 
• Development of a real-time PCR for detection of Staphylococcus pseudintermedius using a novel automated comparison of whole-genome sequences.  
  Verstappen Koen M et al. PloS one 2017 (8) e0183925
• Development of a qualitative assay for screening of Bordetella pertussis isolates for pertussis toxin production.  
  Gates Irina et al. PloS one 2017 (4) e0175326 
• Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol  
  Russell JA, et al. bioRxiv, Sep 4, 2017.
• Comparison of algorithms for the detection of enteroviruses in stool specimens from children diagnosed with Acute Flaccid Paralysis  
  Adeniji AJ, et al. bioRxiv, Aug 23, 2017.
• Determining the Seasonality of Respiratory Syncytial Virus in the United States: The Impact of Increased Molecular Testing.  
  Midgley Claire M et al. The Journal of infectious diseases 2017 Aug (3) 345-355 
• Diagnostic Accuracy of Novel and Traditional Rapid Tests for Influenza Infection Compared With Reverse Transcriptase Polymerase Chain Reaction: A Systematic Review and Meta-analysis.  
  Merckx Joanna et al. Annals of internal medicine 2017 Sep 
• Molecular detection of Trypanosoma cruzi in acai pulp and sugarcane juice.  
  de Mattos Elaine Cristina et al. Acta tropica 2017 Aug
• Molecular identification of cestodes and nematodes by cox1 gene real-time PCR and sequencing.  
  Poon Rosana W S et al. Diagnostic microbiology and infectious disease 2017 Jul
• Many More Microbes in Humans: Enlarging the Microbiome Repertoire.  
  Lagier Jean-Christophe et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Aug (suppl_1) S20-S29

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis.  
  Quainoo Scott et al. Clinical microbiology reviews 2017 Oct (4) 1015-1063
• An outbreak in intravenous drug users due to USA300 Latin-American variant community-acquired methicillin-resistant Staphylococcus aureus in France as early as 2007.  
  Sassi M et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2017 Sep
• Genomic Characterization Helps Dissecting an Outbreak of Listeriosis in Northern Italy.  
  Comandatore Francesco et al. PLoS currents 2017 Jul
• Quantifying perinatal transmission of Hepatitis B viral quasispecies by tag linkage deep sequencing.  
  Du Yushen et al. Scientific reports 2017 Aug (1) 10168
• Outbreak of human malaria caused by Plasmodium simium in the Atlantic Forest in Rio de Janeiro: a molecular epidemiological investigation.  
  Brasil Patrícia et al. The Lancet. Global health 2017 Aug

HOST-MICROBE INTERACTIONS

• Parvovirus B19 Infection in Children With Arterial Ischemic Stroke.  
  Fullerton Heather J et al. Stroke 2017 Sep
• The Influence of Different Maternal Microbial Communities on the Development of Infant Gut and Oral Microbiota.  
  Drell Tiina et al. Scientific reports 2017 Aug (1) 9940

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.

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB