Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Oct 5, 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
• Policy
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• FDA, GWU Push Data Sharing With New 'BioCompute Object' Standard  
  GenomeWeb, Sep 29, 2017.
• FDA’s Scott Gottlieb: LDTs are no longer a “mom-and-pop” industry and need legislative approach  
  Parmar A. MedCity News, Sep 26, 2017.
• MIT-Led Team Develops Rapid Dipstick Test for Zika, Dengue  
  360dx, Sep 27, 2017.
• The Zika Virus Grew Deadlier With a Small Mutation, Study Suggests  
  Belluck P, McNeil DG Jr. New York Times, Sep 28, 2017.
• DNA-Delivered Antibodies Fight Off Lethal Bacterial Infection  
  Offord C. The Scientist, Oct 3, 2017.
• Do Pathogens Gain Virulence as Hosts Become More Resistant?  
  Read AF, Kerr PJ. The Scientist, Oct 1, 2017.
• Genetically modified approaches to fighting malaria succeed in new tests  
  Wan S. Washington Post, Sep 28, 2017.
• The microbes in a mosquito’s gut may help fight malaria  
  Servick K. Science, Sep 28, 2017.
• Researchers discover new animal hosts for Chagas disease vectors  
  Healio, Sep 27, 2017.
• International Team Suggests Standardized DNA Extraction Method for Fecal Microbiome Studies  
  GenomeWeb, Oct 2, 2017.
• New Data on Microbiome Triples Number of Identified Bacterial Genes  
  Clinical Omics, Oct 3, 2017

EVENTS / TRAINING / WEB RESOURCES

• The rise of whole genome microbial sequencing: A new era for human microbiome analysis  
  (on-demand webinar) Segre J, Pollard K. Science, Sep 29, 2017.

POLICY

• Science in Emergency Response at CDC: Structure and Functions.  
  Iskander John et al. American journal of public health 2017 Sep (S2) S122-S125 

CONCEPTS / COMMENTS

• Ethical challenges for international collaborative research partnerships in the context of the Zika outbreak in the Dominican Republic: a qualitative case study.  
  Canario Guzmán Julio Arturo et al. Health research policy and systems 2017 Sep (1) 82
• Conducting Science in Disasters: Recommendations from the NIEHS Working Group for Special IRB Considerations in the Review of Disaster Related Research.  
  Packenham Joan P et al. Environmental health perspectives 2017 Sep (9) 094503
• The preprint dilemma  
  Kaiser J. Science, Sep 29, 2017.

METHODS / TOOLS

• Towards standards for human fecal sample processing in metagenomic studies.  
  Costea Paul I et al. Nature biotechnology 2017 Oct
• Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.  
  Sczyrba Alexander et al. Nature methods 2017 Oct
• PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context.  
  Libin Pieter et al. Bioinformatics (Oxford, England) 2017 Aug
• Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing.  
  Orenstein Yaron et al. PLoS computational biology 2017 Oct (10) e1005777
• Epidemiology of transmissible diseases: Array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools.  
  Michael Dunne W et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Sep
• Ten simple rules for structuring papers.  
  Mensh Brett et al. PLoS computational biology 2017 Sep (9) e1005619

EVOLUTION / ECOLOGY / POPULATIONS

• Mutation and recombination in pathogen evolution: Relevance, methods and controversies.  
  Arenas Miguel et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Sep
• Evolutionary genotypes of influenza A (H7N9) viruses over five epidemic waves in China.  
  Ding Xiao et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Sep 269-276
• Assessment of Molecular, Antigenic, and Pathological Features of Canine Influenza A(H3N2) Viruses That Emerged in the United States.  
  Pulit-Penaloza Joanna A et al. The Journal of infectious diseases 2017 Sep (suppl_4) S499-S507 
• High-resolution phylogeny providing insights towards the epidemiology, zoonotic aspects and taxonomy of sapoviruses.  
  Barry A F et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Sep
• The diversity of the Chagas parasite, Trypanosoma cruzi, infecting the main Central American vector, Triatoma dimidiata, from Mexico to Colombia.  
  Dorn Patricia L et al. PLoS neglected tropical diseases 2017 Sep (9) e0005878
• Genomic analyses of African Trypanozoon strains to assess evolutionary relationships and identify markers for strain identification.  
  Richardson Joshua Brian et al. PLoS neglected tropical diseases 2017 Sep (9) e0005949
• Accurate identification of Anopheles gambiae Giles trophic preferences by MALDI-TOF MS.  
  Niare Sirama et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Sep

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Identification and characterization of the novel colonization factor CS30 based on whole genome sequencing in enterotoxigenic Escherichia coli (ETEC).  
  Mentzer Astrid von et al. Scientific reports 2017 Oct (1) 12514
• Comparative genomic analysis and in vivo modelling of Streptococcus pneumoniae ST3081 and ST618 isolates reveal key genetic and phenotypic differences contributing to clonal replacement of serotype 1 in The Gambia.  
  Bricio-Moreno Laura et al. The Journal of infectious diseases 2017 Sep
• Novel multiresistance cfr plasmids in linezolid-resistant methicillin-resistant Staphylococcus epidermidis and vancomycin-resistant Enterococcus faecium (VRE) from a hospital outbreak: co-location of cfr and optrA in VRE.  
  Lazaris Alexandros et al. The Journal of antimicrobial chemotherapy 2017 Aug
• Food poisoning outbreak in Tokyo, Japan caused by Staphylococcus argenteus.  
  Suzuki Yasunori et al. International journal of food microbiology 2017 Sep 31-37
• Drug Susceptibility Evaluation of an Influenza A(H7N9) Virus by Analyzing Recombinant Neuraminidase Proteins.  
  Gubareva Larisa V et al. The Journal of infectious diseases 2017 Sep (suppl_4) S566-S574 

DETECTION / DIAGNOSIS

• Potential testing of reprocessing procedures by real-time polymerase chain reaction: A multicenter study of colonoscopy devices.  
  Valeriani Federica et al. American journal of infection control 2017 Sep 
• Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples  
  Schoepp NG, et al. Sci Transl Med, Oct 4, 2017.
• Comparison of three multiplex gastrointestinal platforms for the detection of gastroenteritis viruses.  
  Chhabra Preeti et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 Oct 66-71 
• Rapid antigen tests for dengue virus serotypes and Zika virus in patient serum.  
  Bosch Irene et al. Science translational medicine 2017 Sep (409)
• Rhinovirus Viremia in Patients Hospitalized with Community Acquired Pneumonia.  
  Lu Xiaoyan et al. The Journal of infectious diseases 2017 Aug 
• O-5S quantitative real-time PCR: a new diagnostic tool for laboratory confirmation of human onchocerciasis.  
  Mekonnen Solomon A et al. Parasites & vectors 2017 Oct (1) 451

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Epidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing.  
  Woksepp Hanna et al. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2017 Sep
• Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission.  
  Martin Jessica et al. The Journal of antimicrobial chemotherapy 2017 Aug
• Estimating time of HIV-1 infection from next-generation sequence diversity.  
  Puller Vadim et al. PLoS computational biology 2017 Oct (10) e1005775

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Safety and Immunogenicity of an Anti-Zika Virus DNA Vaccine - Preliminary Report.  
  Tebas Pablo et al. The New England journal of medicine 2017 Oct

HOST-MICROBE INTERACTIONS

• Genetic susceptibility to infectious diseases: Current status and future perspectives from genome-wide approaches.  
  Mozzi Alessandra et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Sep
• Pathogen lineage-based genome-wide association study identified CD53 as susceptible locus in tuberculosis.  
  Omae Yosuke et al. Journal of human genetics 2017 Sep
• Evaluating the impact of functional genetic variation on HIV-1 control.  
  McLaren Paul J et al. The Journal of infectious diseases 2017 Sep
• Toll like receptor7 polymorphisms in relation to disease susceptibility and progression in Chinese patients with chronic HBV infection.  
  Zhu Junping et al. Scientific reports 2017 Sep (1) 12417
• Marked variation in prevalence of malaria-protective human genetic polymorphisms across Uganda.  
  Walakira Andrew et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Sep
• Changes in the microbiota cause genetically modified Anopheles to spread in a population.  
  Pike Andrew et al. Science (New York, N.Y.) 2017 Sep (6358) 1396-1399
• A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children.  
  Salter Susannah J et al. PLoS neglected tropical diseases 2017 Oct (10) e0005975

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