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

Public Health Genomics Knowledge Base (v1.2)

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
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• Oxford Nanopore Develops Direct RNA Sequencing Protocol 
  Heger M. GenomeWeb, Aug 19, 2016.
• Next-Generation Sequencing of Viral Pathogens 
  CDC Connects, Aug 19, 2016.
• Streamlining the E.coli Genetic Code 
  Zusi K. The Scientist, Aug 18, 2016.
• Genomic Analysis Uncovers Three Salmonella Enteritidis Lineages 
  GenomeWeb, Aug 22, 2016.
• Slow diagnosis, malaria limited response to 2015 Zambia plague outbreak 
  Healio, Aug 19, 2016.
• Simple new test could improve diagnosis of tuberculosis in developing nations 
  phys.org, Aug 22, 2016.
• New Data Support Advancement of Gene Expression Tests for Infection in Febrile Infants 
  Ashford M. GenomeWeb, Aug 23, 2016.
• Anthrax genome reveals secrets about a Soviet bioweapons accident 
  Kupferschmidt K. Science, Aug 16, 2016.

EVENTS / TRAINING / WEB RESOURCES

• Public Health InfoVis 
  (blog) New blog launched by Jennifer Gardy's lab, Univ British Columbia, Canada.
• How to Build Bioinformatic Pipelines Using Galaxy 
  Perkel JM. The Scientist, Aug 1, 2016.

CONCEPTS / COMMENTS

• Are Microbial Politics Local? 
  Hohmann Elizabeth L et al. Annals of internal medicine 2016 Aug
• Revised Estimates for the Number of Human and Bacteria Cells in the Body. 
  Sender Ron et al. PLoS biology 2016 Aug (8) e1002533
• New Developments in Clinical Bacteriology Laboratories. 
  Patel Robin et al. Mayo Clinic proceedings 2016 Aug

METHODS / TOOLS

• msBiodat analysis tool, big data analysis for high-throughput experiments. 
  Muñoz-Torres Pau M et al. BioData mining 2016 26
• Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation 
  Koren S, et al. bioRxiv, Aug 24, 2016.
• Evaluation of library preparation methods for Illumina next generation sequencing of small amounts of DNA from foodborne parasites. 
  Nascimento Fernanda S et al. Journal of microbiological methods 2016 Aug 

EVOLUTION / ECOLOGY / POPULATIONS

• A Bacillus anthracis Genome Sequence from the Sverdlovsk 1979 Autopsy Specimens 
  Sahl JW, et al. bioRxiv,Aug 16, 2016.
• Unexpected genomic relationships between Bacillus anthracis strains from Bangladesh and Central Europe. 
  Rume Farzana Islam et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Aug
• Draft Genome Sequences of Nine Clinical Isolates of Vancomycin-Resistant Enterococci. 
  Higgins Paul G et al. Genome announcements 2016 (4)
• What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B. 
  Connor Thomas R et al. mBio 2016 (4)
• Rickettsial Infections among Ctenocephalides felis and Host Animals during a Flea-Borne Rickettsioses Outbreak in Orange County, California. 
  Maina Alice N et al. PloS one 2016 (8) e0160604
• Complete Genome Sequences of Three Historically Important, Spatiotemporally Distinct, and Genetically Divergent Strains of Zika Virus: MR-766, P6-740, and PRVABC-59. 
  Yun Sang-Im et al. Genome announcements 2016 (4)
• Hiv-2 molecular epidemiology. 
  Visseaux Benoit et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Aug
• Evidence for the introduction, reassortment and persistence of diverse influenza A viruses in Antarctica. 
  Hurt Aeron C et al. Journal of virology 2016 Aug
• The Comparative Molecular Epidemiology of GII.P7_GII.6 and GII.P7_GII.7 Norovirus Outbreaks in Victoria, Australia, 2012-2014. 
  Bruggink Leesa D et al. Intervirology 2016 Aug (1) 60-65
• A molecular epidemiological perspective of rhinovirus types circulating in Amsterdam from 2007 to 2012. 
  van der Linden Lonneke et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 Aug
• Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting. 
  Bourhy Hervé et al. PLoS pathogens 2016 Apr (4) e1005525
• Multilocus sequence typing of Dientamoeba fragilis identified a major clone with widespread geographical distribution. 
  Cacciò Simone M et al. International journal for parasitology 2016 Aug
• Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum. 
  Miles Alistair et al. Genome research 2016 Aug

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Plasmids from Shiga toxin-producing Escherichia coli of rare Enterohemolysin (ehxA) Subtypes reveal Pathogenicity Potential and display a Novel Evolutionary Path. 
  Lorenz Sandra C et al. Applied and environmental microbiology 2016 Aug
• Molecular evolution and functional divergence of Vibrio cholerae. 
  Das Bhabatosh et al. Current opinion in infectious diseases 2016 Aug
• Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States. 
  Metcalf Benjamin J et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 Aug 
• Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings. 
  Feasey Nicholas A et al. Nature genetics 2016 Aug 
• Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster. 
  Bespyatykh Julia et al. Scientific reports 2016 28985
• In-depth analysis of the genome sequence of a clinical, extensively drug-resistant Mycobacterium bovis strain. 
  Sagasti Sara et al. Tuberculosis (Edinburgh, Scotland) 2016 Sep 46-52
• West Nile Virus Temperature Sensitivity and Avian Virulence Are Modulated by NS1-2B Polymorphisms. 
  Dietrich Elizabeth A et al. PLoS neglected tropical diseases 2016 Aug (8) e0004938 
• Prevalence of K13-propeller gene polymorphisms among Plasmodium falciparum parasites isolated from adult symptomatic patients in northern Uganda. 
  Ocan Moses et al. BMC infectious diseases 2016 (1) 428

DETECTION / DIAGNOSIS

• Molecular diagnostics for human leptospirosis. 
  Waggoner Jesse J et al. Current opinion in infectious diseases 2016 Aug
• Identification of novel host biomarkers in plasma as candidates for the immunodiagnosis of tuberculosis disease and monitoring of tuberculosis treatment response. 
  Jacobs Ruschca et al. Oncotarget 2016 Aug
• A Norovirus Detection Architecture Based on Isothermal Amplification and Expanded Genetic Systems. 
  Yaren Ozlem et al. Journal of virological methods 2016 Aug
• Assessment of submicroscopic infections and gametocyte carriage of Plasmodium falciparum during peak malaria transmission season in a community-based cross-sectional survey in western Kenya, 2012. 
  Zhou Zhiyong et al. Malaria journal 2016 (1) 421 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Travel- and Community-Based Transmission of Multidrug-Resistant Shigella sonnei Lineage among International Orthodox Jewish Communities. 
  Baker Kate S et al. Emerging infectious diseases 2016 Sep (9) 1545-53

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection: A Randomized Trial. 
  Kelly Colleen R et al. Annals of internal medicine 2016 Aug
• Systematic Review: Adverse Events of Fecal Microbiota Transplantation. 
  Wang Sinan et al. PloS one 2016 (8) e0161174 
• Genetic stability of live attenuated vaccines against potentially pandemic influenza viruses. 
  Kiseleva Irina et al. Vaccine 2015 Dec (49) 7008-14
• Variability of high risk HPV genotypes among HIV infected women in Mwanza, Tanzania- the need for evaluation of current vaccine effectiveness in developing countries. 
  Mujuni Fridolin et al. Infectious agents and cancer 2016 49

HOST-MICROBE INTERACTIONS

• Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children. 
  Herberg Jethro A et al. JAMA 2016 Aug (8) 835-845
• Association of RNA Biosignatures With Bacterial Infections in Febrile Infants Aged 60 Days or Younger. 
  Mahajan Prashant et al. JAMA (8) 846-57
• Common haplotypes in CD209 promoter and susceptibility to HIV-1 infection in intravenous drug users. 
  Herrero Rocio et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Aug 20-25
• Virome characterisation from Guthrie cards in children who later developed acute lymphoblastic leukaemia. 
  Bogdanovic G et al. British journal of cancer 2016 Aug
• The role of CCR5 in Chagas disease - a systematic review. 
  de Oliveira Amanda P et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Aug

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.