Advanced Molecular Detection Clips
July 7-14, 2016
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
- CDC Awards $26 Million to Academic Medical Centers, Drives Innovation to Protect Patients
(press release) CDC, Jun 27, 2016. - PrecisionFDA Announces Truth Challenge Winners
Bio-IT World, Jun 29, 2016. - Portable, Rapid Zika Test
Lewis T. The Scientist, Jun 30, 2016. - NIH to study 10,000 pregnant women in Zika-affected areas
Healio, Jun 25, 2016. - NIH funds Zika virus study involving U.S. Olympic team
(press release) NIH, Jul 5, 2016. - A Blood Test To Determine When Antibiotics Are Warranted
Takemura AF. The Scientist, Jul 7, 2016. - Wellcome Trust launches open-access publishing venture
Butler D. Nature, Jul 6, 2016. - Gene editing could destroy herpes viruses living inside you
Barras C. New Scientist, Jun 30, 2016. - A nose for trouble: Superbug sniffing dog starts work in Vancouver hospital
Fayerman P. Vancouver Sun, Jul 5, 2016.
CONCEPTS / COMMENTS
- Roots, Not Parachutes: Research Collaborations Combat Outbreaks.
Yozwiak Nathan L et al. Cell 2016 Jun (1) 5-8 - HIV-1 immune evasion-a threat to effective vaccines?
Rolland Morgane et al. Nature medicine 2016 Jun (6) 580-1
METHODS / TOOLS
- Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe.
Aanensen David M et al. mBio 2016 (3) - Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling.
Lau Jennifer T et al. Genome medicine 2016 (1) 72 - Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing.
Aigrain Louise et al. BMC genomics 2016 (1) 458 - Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data.
O'Brien John D et al. PLoS computational biology 2016 Jun (6) e1004824 - Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates.
Gill Mandev S et al. Systematic biology 2016 Jul - Genetic analysis of infectious diseases: estimating gene effects for susceptibility and infectivity.
Anche Mahlet T et al. Genetics, selection, evolution : GSE 2015 85 - Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes.
Shao Wei et al. Retrovirology (1) 47
EVOLUTION / ECOLOGY / POPULATIONS
- High-Quality Draft Genome Sequences for Five Non-O157 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing and Optical Maps.
Lindsey Rebecca L et al. Genome announcements 2016 (3)
- A small number of phylogenetically distinct clonal complexes dominate a coastal Vibrio cholerae population.
Kirchberger Paul C et al. Applied and environmental microbiology 2016 Jul - Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae.
Peeters Charlotte et al. Frontiers in microbiology 2016 877 - Deciphering the recent phylogenetic expansion of the originally deeply rooted Mycobacterium tuberculosis lineage 7.
Yimer Solomon A et al. BMC evolutionary biology 2016 (1) 146 - Evidence of an Exponential Decay Pattern of the Hepatitis Delta Virus Evolution Rate and Fluctuations in Quasispecies Complexity in Long-Term Studies of Chronic Delta Infection.
Homs Maria et al. PloS one 2016 (6) e0158557 - Newly identified Enterovirus-C genotypes, identified in the Netherlands through routine sequencing of all enteroviruses detected in clinical materials from 2008 to 2015.
Van Leer-Buter Coretta C et al. Journal of clinical microbiology 2016 Jun - Analysis of an echovirus 18 outbreak in Thuringia, Germany: insights into the molecular epidemiology and evolution of several enterovirus species B members.
Krumbholz Andi et al. Medical microbiology and immunology 2016 Jul - A next generation sequencing-based method to study the intra-host genetic diversity of norovirus in patients with acute and chronic infection.
Hasing Maria E et al. BMC genomics 2016 (1) 480 - Highly Pathogenic Avian Influenza Viruses and Generation of Novel Reassortants, United States, 2014-2015.
Lee Dong-Hun et al. Emerging infectious diseases 2016 Jul (7) 1283-5 - Analysis of single nucleotide polymorphism among Varicella-Zoster Virus and identification of vaccine-specific sites.
Jeon Jeong Seon et al. Virology 2016 Jul 277-286
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Molecular and Growth-Based Drug Susceptibility Testing of Mycobacterium tuberculosis Complex for Ethambutol Resistance in the United States.
Yakrus Mitchell A et al. Tuberculosis research and treatment 2016 3404860 
- Virus fitness differences observed between two naturally occurring isolates of Ebola virus Makona variant using a reverse genetics approach.
Albariño César G et al. Virology 2016 Jun 237-243 - Differences among HIV-1 subtypes indrug resistance against integrase inhibitors.
Han Ying-Shan et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Jun
DETECTION / DIAGNOSIS
- Next-generation sequencing diagnostics of bacteremia in septic patients.
Grumaz Silke et al. Genome medicine (1) 73 - Identification of Raoultella terrigena as a Rare Causative Agent of Subungual Abscess Based on 16S rRNA and Housekeeping Gene Sequencing.
Wang Yu et al. The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale 3879635 - Separating Putative Pathogens from Background Contamination with Principal Orthogonal Decomposition: Evidence for Leptospira in the Ugandan Neonatal Septisome.
Schiff Steven J et al. Frontiers in medicine 22 - Diagnosis of Nocardia paucivorans central nervous system infection by DNA sequencing from paraffin-embedded tissue.
Schiaroli Elisabetta et al. Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive 2016 Jun (2) 147-52 - Robust classification of bacterial and viral infections via integrated host gene expression diagnostics
Sweeney TE, et al. Sci Transl Med, Jul 6, 2016. - Underdiagnosing of Mycoplasma pneumoniae infections as revealed by use of a respiratory multiplex PCR panel.
Dalpke Alexander et al. Diagnostic microbiology and infectious disease 2016 Jun - Dual Combined Real-Time Reverse Transcription Polymerase Chain Reaction Assay for the Diagnosis of Lyssavirus Infection.
Dacheux Laurent et al. PLoS neglected tropical diseases 2016 Jul (7) e0004812 - Multiplex assay for subtyping avian influenza A viruses by cDNA hybridization and adapter-mediated amplification.
Yang Genyan et al. Applied microbiology and biotechnology 2016 Jul - Quantitative Real-time PCR Assays for Detection and Type-Specific Identification of the Endemic Species C Human Adenoviruses.
Lu Xiaoyan et al. Journal of virological methods 2016 Jun - Rapid and Non-destructive Detection and Identification of Two Strains of Wolbachia in Aedes aegypti by Near-Infrared Spectroscopy.
Sikulu-Lord Maggy T et al. PLoS neglected tropical diseases 2016 Jun (6) e0004759
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005-2009.
Miller Ruth R et al. The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie me´dicale 2016 5381871 - Epidemiological and Microbiological Investigation of an Outbreak of Severe Disease from Shiga Toxin-Producing Escherichia coli O157 Infection Associated with Consumption of a Slaw Garnish.
Byrne Lisa et al. Journal of food protection 2016 Jul (7) 1161-8 - Whole Genome Sequencing Elucidates the Epidemiology of Nosocomial Clusters of Acinetobacter baumannii.
Willems Stefanie et al. Journal of clinical microbiology 2016 Jun - Ebola Virus Epidemiology and Evolution in Nigeria.
Folarin Onikepe A et al. The Journal of infectious diseases 2016 Jul
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Antisense antimicrobial therapeutics.
Sully Erin K et al. Current opinion in microbiology 2016 Jun 47-55 - How Can Vaccines Contribute to Solving the Antimicrobial Resistance Problem?
Lipsitch Marc et al. mBio 2016 (3) - Programming Native CRISPR Arrays for the Generation of Targeted Immunity.
Hynes Alexander P et al. mBio 2016 (3) - CRISPR/Cas9-Mediated Genome Editing of Herpesviruses Limits Productive and Latent Infections.
van Diemen Ferdy R et al. PLoS pathogens 2016 Jun (6) e1005701
HOST-MICROBE INTERACTIONS
- The microbiome and innate immunity
Thaiss CA, et al. Nature, Jul 6, 2016. - Microbiome-wide association studies link dynamic microbial consortia to disease
Gilbert JA, et al. Nature, Jul 6, 2016. - Familial Clustering of Staphylococcus aureus Bacteremia in First-Degree Relatives: A Danish Nationwide Cohort Study.
Oestergaard Louise B et al. Annals of internal medicine 2016 Jul - Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi.
Li Yang et al. Nature medicine 2016 Jul - Impact of pre-adapted HIV transmission.
Carlson Jonathan M et al. Nature medicine 2016 Jun (6) 606-13 - Type I Interferons in Newborns-Neurotoxicity versus Antiviral Defense.
Bogunovic Dusan et al. mBio 2016 (3) - Genomic Modifiers of Natural Killer Cells, Immune Responsiveness and Lymphoid Tissue Remodeling Together Increase Host Resistance to Viral Infection.
Gillespie Alyssa Lundgren et al. PLoS pathogens 2016 Feb (2) e1005419
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.
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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