Advanced Molecular Detection Clips ▲ Public Health Genomics Knowledge Base (v1.0)

Public Health Genomics Knowledge Base (v1.0)

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

• Rapid Zika Test Is Introduced by Researchers 
  McNeil Jr, DG. New York Times, May 5, 2016.
• New Zika Test Uses Isothermal RNA Amplification for Detection, CRISPR/Cas9 for Strain ID 
  Han AP. GenomeWeb, May 6, 2016.
• FDA Clinical Mass Spectrometry Meeting Highlights Progress and Struggles of Implementing Tech 
  Bonislawski A. GenomeWeb, May 11, 2016.
• DNA Sequencing Helps Screen for Drug Targets, Resistance in Sleeping Sickness Pathogen 
  Heger M. GenomeWeb, May 12, 2016.
• Novel orthopoxvirus discovered in Alaska patient 
  Healio Infect Dis News, May 9, 2016.
• C Diff Molecular Screening Strategy Reduces Incidence, Saves Money in Canadian Study 
  Johnson M. GenomeWeb, May 5, 2016.
• Most Gut Microbes Can Be Cultured 
  Madhusoodanan j. The Scientist, May 4, 2016.
• Extra! Extra! Microfluidic chips go to print 
  Castro C. Sci Transl Med, May 4, 2016.

EVENTS / TRAINING / WEB RESOURCES

• Real-Time Evolutionary Tracking for Pathogen Surveillance and Epidemiological Investigation 
  (announcement) Open Science Prize Winners, https://www.openscienceprize.org/, May 9, 2016.
• A roadmap to translating the microbiome 
  (special issue) Begum R. Genome Med, Apr 28, 2016.

POLICY

• Innovations for infectious disease: the need for speed 
  Brice P. PHG Foundation, May 3, 2016.
• Reminder to deposit DNA sequences 
  Blaxter M, et al. Science, May 12, 2016.
• WHO recommends new test, treatment plan for superbug strains of TB 
  Kelland K. Reuters, May 12, 2016.

CONCEPTS / COMMENTS

• Fungal Genomics Challenges the Dogma of Name-Based Biosecurity. 
  McTaggart Alistair R et al. PLoS pathogens 2016 May (5) e1005475
• How Europe exported the Black Death 
  Lawler A. Science, Apr 28, 2016.

METHODS / TOOLS

• StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform. 
  Zheng Wenning et al. PloS one 2016 (5) e0151908
• PREDAC-H3: a user-friendly platform for antigenic surveillance of human influenza a(H3N2) virus based on hemagglutinin sequences. 
  Peng Yousong et al. Bioinformatics (Oxford, England) 2016 Apr
• Single-Cell Genomics for Virology. 
  Ciuffi Angela et al. Viruses (5)
• Graph mining for next generation sequencing: leveraging the assembly graph for biological insights. 
  Warnke-Sommer Julia et al. BMC genomics 2016 (1) 340
• Phylogeny-aware identification and correction of taxonomically mislabeled sequences. 
  Kozlov Alexey M et al. Nucleic acids research 2016 May

EVOLUTION / ECOLOGY / POPULATIONS

• Three Genome Sequences of Legionella pneumophila subsp. pascullei Associated with Colonization of a Health Care Facility. 
  Kozak-Muiznieks Natalia A et al. Genome announcements 2016 (3) 
• Fluoroquinolone-Resistant Enteric Bacteria in Sub-Saharan Africa: Clones, Implications and Research Needs. 
  Chattaway Marie A et al. Frontiers in microbiology 2016 558
• Population Structure of Streptococcus pneumoniae Causing Invasive Disease in Adults in Portugal before PCV13 Availability for Adults: 2008-2011.
  Horácio Andreia N et al. PloS one (5) e0153602
• Genomic characterization and phylogenetic analysis of Zika virus circulating in the Americas. 
  Ye Qing et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 May
• Detection of Sindbis and Inkoo Virus RNA in Genetically Typed Mosquito Larvae Sampled in Northern Sweden. 
  Tingström Olov et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2016 May
• Transmission of Foot-and-Mouth Disease SAT2 Viruses at the Wildlife-Livestock Interface of Two Major Transfrontier Conservation Areas in Southern Africa. 
  Brito Barbara P et al. Frontiers in microbiology 2016 528
• Genetic characterization of Enterovirus 71 strains circulating in Vietnam in 2012. 
  Donato Celeste et al. Virology 2016 May 1-9
• Disease vectors in the era of next generation sequencing. 
  Rinker David C et al. Genome biology 2016 (1) 95

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men. 
  Taha Muhamed-Kheir et al. PloS one (5) e0154047
• Genetic features of MCR-1-producing colistin-resistant Escherichia coli isolates, South Africa. 
  Poirel Laurent et al. Antimicrobial agents and chemotherapy 2016 May
• Longitudinal whole genome analysis of pre and post drug treatment Mycobacterium tuberculosis isolates reveals progressive steps to drug resistance. 
  Datta Gargi et al. Tuberculosis (Edinburgh, Scotland) 2016 May 50-5
• A study of two separate types of macrolide-resistant Mycoplasma pneumoniae outbreaks. 
  Wang Yingshuo et al. Antimicrobial agents and chemotherapy 2016 May
• Features of Circulating Parainfluenza Virus Required for Growth in Human Airway. 
  Palermo Laura M et al. mBio 2016 (2)

DETECTION / DIAGNOSIS

• Development of a rapid diagnostic assay based on magnetic bead purification of OXA-β-lactamase mRNA. 
  Brandt Christian et al. Future microbiology 2016 May
• Identification of bacterial and viral co-detections with Mycoplasma pneumoniae using the TaqMan Array Card in patients hospitalized with community-acquired pneumonia 
  Diaz MH, et al. Open Forum Infect Dis, Mar 29, 2016. 
• Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components 
  Pardee K, et al. Cell, May 6, 2016.
• Using Rapid Diagnostic Tests as a Source of Viral RNA for Dengue Serotyping by RT-PCR - A Novel Epidemiological Tool. 
  Vongsouvath Manivanh et al. PLoS neglected tropical diseases 2016 May (5) e0004704
• Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. 
  Pardee Keith et al. Cell 2016 May
• Comparison of Test Results for Zika Virus RNA in Urine, Serum, and Saliva Specimens from Persons with Travel-Associated Zika Virus Disease — Florida, 2016 
  Bingham AM, et al. MMWR, May 13, 2016. 
• Rapid detection of fungal pathogens in bronchoalveolar lavage samples using panfungal PCR combined with high resolution melting analysis. 
  Bezdicek Matej et al. Medical mycology 2016 May

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Characterization and rapid control of a vancomycin-resistant Enterococcus faecium (VREF) outbreak in a renal transplant unit in Spain: The environment matters. 
  Herrera Sabina et al. Enfermedades infecciosas y microbiologia clinica 2016 May
• Molecular characterization and antimicrobial susceptibility of Acinetobacter baumannii isolates obtained from two hospital outbreaks in Los Angeles County, California, USA. 
  Warner Wayne A et al. BMC infectious diseases 2016 (1) 194
• Two listeria outbreaks caused by smoked fish consumption - Using whole-genome sequencing for outbreak investigations. 
  Lassen Sofie Gillesberg et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 May
• Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock. 
  Kamath Pauline L et al. Nature communications 2016 11448
• Protocol for a population-based molecular epidemiology study of tuberculosis transmission in a high HIV-burden setting: the Botswana Kopanyo study. 
  Zetola N M et al. BMJ open 2016 (5) e010046 
• Hepatitis B Reverse Seroconversion and Transmission in a Hemodialysis Center: A Public Health Investigation and Case Report. 
  Rhea Sarah et al. American journal of kidney diseases : the official journal of the National Kidney Foundation 2016 May 
• Unexpected Inter-farm Transmission Dynamics During a Highly Pathogenic Avian Influenza Epidemic. 
  Fusaro Alice et al. Journal of virology 2016 May

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Effect of Detecting and Isolating Clostridium difficile Carriers at Hospital Admission on the Incidence of C difficile Infections: A Quasi-Experimental Controlled Study. 
  Longtin Yves et al. JAMA internal medicine 2016 Apr
• Exploiting Genetic Interference for Antiviral Therapy. 
  Tanner Elizabeth J et al. PLoS genetics 2016 May (5) e1005986
• Cos-Seq for high-throughput identification of drug target and resistance mechanisms in the protozoan parasite Leishmania. 
  Gazanion Élodie et al. Proceedings of the National Academy of Sciences of the United States of America 2016 May

HOST-MICROBE INTERACTIONS

• Temporal Stability of the Human Skin Microbiome. 
  Oh Julia et al. Cell 2016 May (4) 854-66
• Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers. 
  Einarsson G G et al. Thorax 2016 May
• Long-term changes of bacterial and viral compositions in the intestine of a recovered Clostridium difficile patient after fecal microbiota transplantation. 
  Broecker Felix et al. Cold Spring Harbor molecular case studies 2016 Jan (1) a000448
• Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection. 
  Seekatz Anna Maria et al. Genome medicine 2016 (1) 47
• The healthy human microbiome. 
  Lloyd-Price Jason et al. Genome medicine 2016 (1) 51
• Interconnected microbiomes and resistomes in low-income human habitats 
  Pehrsson EC, et al. Nature, May 12, 2016.
• Spread of Mutant Middle East Respiratory Syndrome Coronavirus with Reduced Affinity to Human CD26 during the South Korean Outbreak. 
  Kim Yuri et al. mBio 2016 (2)
• Unraveling methylation changes of host macrophages in Mycobacterium tuberculosis infection. 
  Zheng Lin et al. Tuberculosis (Edinburgh, Scotland) 2016 May 139-48
• Influenza Virus Affects Intestinal Microbiota and Secondary Salmonella Infection in the Gut through Type I Interferons. 
  Deriu Elisa et al. PLoS pathogens 2016 May (5) e1005572

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.