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

Public Health Genomics Knowledge Base (v1.2)

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
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• CDC funds 34 innovative projects to combat antibiotic resistance 
  (news release) CDC, Oct 6, 2016.
• Florida’s Feud Over Zika-Fighting GMO Mosquitoes 
  Kolker J. Bloomberg, Oct 6, 2016.
• Who is immune to Zika? 
  Keener AB. The Scientist, Oct 11, 2016.
• Point-of-Care Diagnostic Promising for Detection of Chikungunya Virus 
  Larkin M. Medscape, Oct 5, 2016.
• Got Zika? Lab Constraints Mean It's Often Hard to Know 
  Luthra S. Medscape, Oct 7, 2016.
• NIST Team Explores Alternative to Graphene for Nanopore Sequencing 
  Heger M. GenomeNews, Oct 11, 2016.
• Bacteria and Humans Have Been Swapping DNA for Millennia 
  Robinson K, Hotopp JD. The Scientist, Oct 1, 2016.

EVENTS / TRAINING / WEB RESOURCES

• Announcing Second Public Workshop on Promoting Semantic Interoperability of Laboratory Data
  (workshop) National Library of Medicine, NIH, Bethesda, MD. Nov 8, 8:00 - 5:00. Comments due Dec 9, 2016.

POLICY

• What Is Stopping the Use of Genetically Modified Insects for Disease Control? 
  Panjwani Anusha et al. PLoS pathogens 2016 Oct (10) e1005830

CONCEPTS / COMMENTS

• DNA Sequencing: From Tedious to Automatic 
  Offord C. The Scientist, Oct 1, 2016.

METHODS / TOOLS

• Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples. 
  Kumar Nikhil et al. Scientific reports 2016 Oct 34850
• NEAT: a framework for building fully automated NGS pipelines and analyses. 
  Schorderet Patrick et al. BMC bioinformatics 2016 Feb 53
• A Method for Bioinformatic Analysis of Transposon Insertion Sequencing (INSeq) Results for Identification of Microbial Fitness Determinants. 
  Wang Nengding et al. Methods in molecular biology (Clifton, N.J.) 2017 243-253
• SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent. 
  De Maio Nicola et al. PLoS computational biology 2016 Sep (9) e1005130
• A multicenter study benchmarks software tools for label-free proteome quantification. 
  Navarro Pedro et al. Nature biotechnology 2016 Oct
• Influenza Research Database: An integrated bioinformatics resource for influenza virus research. 
  Zhang Yun et al. Nucleic acids research 2016 Sep
• The past, present and future of microbiome analyses 
  White RA, et al. Nat Protoc, Sep 29, 2016.

EVOLUTION / ECOLOGY / POPULATIONS

• Major Shift of Toxigenic V. cholerae O1 from Ogawa to Inaba Serotype Isolated from Clinical and Environmental Samples in Haiti. 
  Alam Meer T et al. PLoS neglected tropical diseases 2016 Oct (10) e0005045
• Acquisition and loss of virulence-associated factors during genome evolution and speciation in three clades of Bordetella species. 
  Linz Bodo et al. BMC genomics 2016 Sep (1) 767
• Genomic tracks behind spread of bacteremic Group A Streptococcus type emm89 in Finland, 2004-2014. 
  Latronico Francesca et al. The Journal of infectious diseases 2016 Oct
• Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. 
  Moura Alexandra et al. Nature microbiology 2016 Oct 16185 
• Evolutionary history and spatiotemporal dynamics of DENV-1 genotype V in the Americas. 
  de Bruycker-Nogueira Fernanda et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Oct
• Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification. 
  Sobel Leonard Ashley et al. Journal of virology 2016 Oct

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Comparison by multi-locus variable-number tandem repeat analysis and antimicrobial resistance among atypical enteropathogenic Escherichia coli strains isolated from foods and human and animal faecal specimens. 
  Wang L et al. Journal of applied microbiology 2016 Oct

DETECTION / DIAGNOSIS

• Assessing Pathogens for Natural versus Laboratory Origins Using Genomic Data and Machine Learning 
  Korves T, et al. bioRxiv, Oct 6, 2016. 
• Identification of bacterial pathogens from formalin-fixed paraffin-embedded tissues by using 16S sequencing: Retrospective correlation of results to clinicians' responses. 
  Racsa Lori D et al. Human pathology 2016 Oct 
• Comparative genomic analysis of Haemophilus haemolyticus and non-typeable Haemophilus influenzae and a new testing scheme for their discrimination. 
  Hu Fang et al. Journal of clinical microbiology 2016 Oct 
• Rapid diagnostic test and use of antibiotic against methicillin-resistant Staphylococcus aureus in adult intensive care unit. 
  Dureau A-F et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2016 Oct 
• Use of a Molecular Panel to Aid in the Diagnosis of Culture-Negative Meningitis. 
  Dien Bard Jennifer et al. Journal of clinical microbiology 2016 Sep
• Clinical Utility of On-Demand Multiplex Respiratory Pathogen Testing among Adult Outpatients. 
  Green Daniel A et al. Journal of clinical microbiology 2016 Sep 
• Molecular Detection of Tick-Borne Pathogens in Humans with Tick Bites and Erythema Migrans, in the Netherlands. 
  Jahfari Setareh et al. PLoS neglected tropical diseases 2016 Oct (10) e0005042
• Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for identification of Mycobacterium abscessus subspecies according to whole genome sequencing. 
  Luo Liulin et al. Journal of clinical microbiology 2016 Sep
• Urgent implementation in a hospital setting of a strategy to rule out secondary cases caused by imported XDR tuberculosis at diagnosis. 
  Pérez-Lago Laura et al. Journal of clinical microbiology 2016 Sep 
• Development and evaluation of a molecular diagnostic method to rapidly detect Histoplasma capsulatum var. farciminosum, the causative agent of epizootic lymphangitis, in equine clinical samples. 
  Scantlebury C E et al. Journal of clinical microbiology 2016 Oct

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Use of whole-genome sequencing in the epidemiology of Campylobacter jejuni infections: state-of-knowledge 
  Llarena AK, Rossi M. bioRxiv, Oct 1, 2016.
• Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks. 
  Harrison Ewan M et al. Genome medicine 2016 Oct (1) 102
• VIRO-TypeNed, systematic molecular surveillance of enteroviruses in the Netherlands between 2010 and 2014. 
  Benschop Kimberley S M et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2016 Sep (39)
• HCV dispersal patterns among intravenous drug users (IDUs) in Athens metropolitan area. 
  Papachristou Eleni et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Oct

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Rapid development of a DNA vaccine for Zika virus. 
  Dowd Kimberly A et al. Science (New York, N.Y.) 2016 Sep

HOST-MICROBE INTERACTIONS

• Exome and genome sequencing for inborn errors of immunity. 
  Meyts Isabelle et al. The Journal of allergy and clinical immunology 2016 Oct (4) 957-969
• Large Variations in HIV-1 Viral Load Explained by Shifting-Mosaic Metapopulation Dynamics. 
  Lythgoe Katrina A et al. PLoS biology 2016 Oct (10) e1002567
• Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes. 
  Heintz-Buschart Anna et al. Nature microbiology 2016 Oct 16180
• Health Disparities and the Microbiome. 
  Findley Keisha et al. Trends in microbiology 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

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