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.
Advanced Molecular Detection Clips Content
NEWS
- FDA approves Xpert Carba-R assay for detection of carbapenem resistance genes
Healio, Mar 19, 2016. - Fecal Transplants Transmit Viruses, Too
Offord C. The Scientist, Mar 29, 2016. - Know Your Mosquito Enemy
GenomeWeb, Mar 30, 2016. - Microbiology: Fungus produces a toxic surprise
Mitchell AP. Nature, Mar 30, 2016. - State Lab Overseer NYSDOH Issues Plan for LDT Pre-Market Approval
GenomeWeb, Mar 28, 2016. - NIH Funds Research to Sequence Malaria Parasite Transcriptome, Proteome
Newbern E. GenomeWeb, Mar 31, 2016.
POLICY
- Point-Counterpoint: The FDA Has a Role in Regulation of Laboratory-Developed Tests.
Caliendo Angela M et al. Journal of clinical microbiology 2016 Apr (4) 829-33 - FDA allows use of investigational test to screen blood donations for Zika virus
(news release) FDA, Mar 30, 2016. - The Neglected Dimension of Global Security - A Framework for Countering Infectious-Disease Crises.
Sands Peter et al. The New England journal of medicine 2016 Mar (13) 1281-1287
CONCEPTS / COMMENTS
- FAIR principles for data stewardship
(editorial) Nature, Mar 29, 2016. - Delivering an effective infectious disease genomics service
Rands C. PHGFoundation, Mar 2016.
- The real cost of sequencing: scaling computation to keep pace with data generation.
Muir Paul et al. Genome biology 2016 (1) 53 - Ethics review for international data-intensive research
Dove ES, et al. Science, Mar 25, 2016. - Synthetic microbe has fewest genes, but many mysteries
Service RF. Science, Mar 25, 2016. - Uniting to end the TB epidemic: advances in disease control from prevention to better diagnosis and treatment.
Abubakar Ibrahim et al. BMC medicine 2016 (1) 47 - Pediatric Norovirus in Developing Countries: A Picture Slowly Comes Into Focus.
Lopman Benjamin A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Mar
- Zika Virus.
Petersen Lyle R et al. The New England journal of medicine 2016 Mar
METHODS / TOOLS
- Design and synthesis of a minimal bacterial genome
Hutchison III CA, et al. Science, Mar 25, 2016. - Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis.
Yang Bo et al. BMC bioinformatics 2016 (1) 135 - Application of Molecular Typing Results in Source Attribution Models: The Case of Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) of Salmonella Isolates Obtained from Integrated Surveillance in Denmark.
de Knegt Leonardo V et al. Risk analysis : an official publication of the Society for Risk Analysis 2016 Mar (3) 571-88 - Large-scale machine learning for metagenomics sequence classification.
Vervier Kévin et al. Bioinformatics (Oxford, England) 2015 Nov - MetaQUAST: evaluation of metagenome assemblies.
Mikheenko Alla et al. Bioinformatics (Oxford, England) 2015 Nov - CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries.
Heigwer Florian et al. Genome biology 2016 (1) 55
EVOLUTION / ECOLOGY / POPULATIONS
- Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131.
Stoesser Nicole et al. mBio 2016 (2) - Whole-genome sequencing used to investigate a nationwide outbreak of listeriosis caused by ready-to-eat delicatessen meat, Denmark, 2014.
Jensen Anne Kvistholm et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Mar - Profile and Fate of Bacterial Pathogens in Sewage Treatment Plants Revealed by High-Throughput Metagenomic Approach.
Li Bing et al. Environmental science & technology 2015 Sep (17) 10492-502 - Molecular and Phenotypic Characterization of a Highly Evolved Type 2 Vaccine-Derived Poliovirus Isolated from Seawater in Brazil, 2014.
Cassemiro Klécia Marília S de Melo et al. PloS one 2016 (3) e0152251 - Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh.
Gerloff Nancy A et al. PloS one 2016 (3) e0152131 - Molecular characterization of Nipah virus from Pteropus hypomelanus in Southern Thailand.
Wacharapluesadee Supaporn et al. Virology journal 2016 (1) 53 - Genetic diversity amongst human parainfluenza virus type 2 isolated in Croatia between 2011 and 2014.
Šantak Maja et al. Journal of medical virology 2016 Mar - Microsatellite Genotyping of Plasmodium vivax Isolates from Pregnant Women in Four Malaria Endemic Countries.
Menegon Michela et al. PloS one 2016 (3) e0152447 - Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria.
Sundararaman Sesh A et al. Nature communications 2016 11078 - Molecular detection and genetic diversity of Babesia gibsoni in dogs in India.
Singh M N et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Mar - Phylogeography of Rhipicephalus sanguineus sensu lato and its relationships with climatic factors.
Zemtsova Galina E et al. Experimental & applied acarology 2016 Mar
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Genomic Insights into a New Citrobacter koseri Strain Revealed Gene Exchanges with the Virulence-Associated Yersinia pestis pPCP1 Plasmid.
Armougom Fabrice et al. Frontiers in microbiology 2016 340 - Carriage of Extended-Spectrum Beta-Lactamase-Plasmids Does Not Reduce Fitness but Enhances Virulence in Some Strains of Pandemic E. coli Lineages.
Schaufler Katharina et al. Frontiers in microbiology 2016 336 - Antimicrobial resistance in faecal Escherichia coli isolates from farmed red deer and wild small mammals. Detection of a multiresistant E. coli producing extended-spectrum beta-lactamase.
Alonso C A et al. Comparative immunology, microbiology and infectious diseases 2016 Apr 34-9 - Molecular Characterization of Clostridium difficile Isolates from Human Subjects and the Environment.
Tian Tian-Tian et al. PloS one 2016 (3) e0151964 - The Molecular Epidemiology of Resistance in Cefotaximase-Producing Escherichia coli Clinical Isolates from Dublin, Ireland.
Burke Liam et al. Microbial drug resistance (Larchmont, N.Y.) 2016 Mar - Early emergence of mcr-1 in Escherichia coli from food-producing animals.
Shen Zhangqi et al. The Lancet. Infectious diseases 2016 Mar (3) 293 - Analysis of β-Lactamase Resistance Determinants in Enterobacteriaceae from Chicago Children: A Multicenter Survey.
Logan Latania K et al. Antimicrobial agents and chemotherapy 2016 Mar - Virological factors that increase the transmissibility of emerging human viruses.
Geoghegan Jemma L et al. Proceedings of the National Academy of Sciences of the United States of America 2016 Mar - Genome-wide siRNA Screening at Biosafety Level 4 Reveals a Crucial Role for Fibrillarin in Henipavirus Infection.
Deffrasnes Celine et al. PLoS pathogens 2016 Mar (3) e1005478 - Increasing HIV-1 drug resistance between 2010 and 2012 in adults participating in population-based HIV surveillance in rural KwaZulu-Natal South Africa.
Manasa Justen et al. AIDS research and human retroviruses 2016 Mar - Low Frequency Drug Resistance in HIV-infected Ugandans on Antiretroviral Treatment is Associated with Regimen Failure.
Kyeyune Fred et al. Antimicrobial agents and chemotherapy 2016 Mar
DETECTION / DIAGNOSIS
- the PRACTICAL value of Food Pathogen Traceability through BUILDING a Whole-Genome Sequencing Network and database.
Allard Marc W et al. Journal of clinical microbiology 2016 Mar - Investigation of Recurrent Melioidosis in Lao People's Democratic Republic by Multilocus Sequence Typing.
Rachlin Audrey et al. The American journal of tropical medicine and hygiene 2016 Mar - Evaluation of a multiplex polymerase chain reaction for early diagnosis of ventriculostomy-related infections.
Gordon Claire L et al. Journal of neurosurgery 2015 Dec (6) 1586-92 - Development of Point-of-Care Testing for Disaster-Related Infectious Diseases.
Hattori Toshio et al. The Tohoku journal of experimental medicine 2016 (4) 287-93 - Validation of a mycoplasma molecular diagnostic test and distribution of mycoplasma species in bovine milk among New York dairy farms.
Gioia G et al. Journal of dairy science 2016 Mar - Clinical use of whole genome sequencing for Mycobacterium tuberculosis.
Witney Adam A et al. BMC medicine 2016 (1) 46 - The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae.
Diaz Maureen H et al. Frontiers in microbiology 2016 232 - Diagnostic strategies for Ebola virus detection.
Su Shuo et al. The Lancet. Infectious diseases 2016 Mar (3) 294-5 - Performance of the GeneXpert Ebola Assay for Diagnosis of Ebola Virus Disease in Sierra Leone: A Field Evaluation Study.
Semper Amanda E et al. PLoS medicine 2016 Mar (3) e1001980 - Optimisation of a droplet digital PCR assay for the diagnosis of Schistosoma japonicum infection: A duplex approach with DNA binding dye chemistry.
Weerakoon Kosala G et al. Journal of microbiological methods 2016 Mar - Advanced molecular detection of malarone resistance.
Talundzic Eldin et al. Antimicrobial agents and chemotherapy 2016 Mar - A method for amplicon deep sequencing of drug resistance genes in Plasmodium falciparum clinical isolates from India.
Rao Pavitra N et al. Journal of clinical microbiology 2016 Mar
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Multistate Outbreak of Respiratory Infections among Unaccompanied Children, June-July 2014.
Tomczyk Sara et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Mar - Application of Whole-Genome Sequencing to an Unusual Outbreak of Invasive Group A Streptococcal Disease.
Galloway-Peña Jessica et al. Open forum infectious diseases 2016 Jan (1) ofw042 - Investigation Into an Outbreak of Dengue-like Illness in Pernambuco, Brazil, Revealed a Cocirculation of Zika, Chikungunya, and Dengue Virus Type 1.
Pessôa Rodrigo et al. Medicine 2016 Mar (12) e3201
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation
Chehoud C, et al. mBio, Mar 29, 2016. - Baseline HIV-1 resistance, virological outcomes, and emergent resistance in the SECOND-LINE trial: an exploratory analysis.
Boyd Mark A et al. The lancet. HIV 2015 Feb (2) e42-51
HOST-MICROBE INTERACTIONS
- Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling.
Ilott Nicholas Edward et al. The ISME journal 2016 Mar - Modeling the integration of bacterial rRNA fragments into the human cancer genome.
Sieber Karsten B et al. BMC bioinformatics 2016 (1) 134 - Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance.
Moya Andrés et al. Trends in microbiology 2016 Feb - Oscillospira: a Central, Enigmatic Component of the Human Gut Microbiota.
Konikoff Tom et al. Trends in microbiology 2016 Mar - The Gastrointestinal Tract Microbiota and Allergic Diseases.
Kyburz Andreas et al. Digestive diseases (Basel, Switzerland) 2016 Mar (3) 230-243 - Incidence of Hepatocellular Carcinoma According to Hepatitis B Virus Genotype in Alaska Native People.
Ching Lance K et al. Liver international : official journal of the International Association for the Study of the Liver 2016 Mar - A blood RNA signature for tuberculosis disease risk: a prospective cohort study.
Zak Daniel E et al. Lancet (London, England) 2016 Mar - RAD51 G135C genetic polymorphism and their potential role in gastric cancer induced by Helicobacter pylori infection in Bhutan.
Trang T T H et al. Epidemiology and infection 2016 Jan (2) 234-40
indicates that at least one CDC-affiliated author; indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice.
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