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
Advanced Molecular Detection Clips Content
NEWS
- UCSF-led Team IDs Blood Expression Signature in Individuals With Acute Lyme Disease
Anderson A. GenomeWeb, Feb 12, 2016. - New cause for Lyme disease complicates already murky diagnosis
Moyer MW. Nature (via Scientific American), Feb 16, 2016. - A new method to dramatically improve the sequencing of metagenomes
phys.org, Feb 16, 2016. - Search technique helps researchers find DNA sequences in minutes rather than days
phys.org, Feb 8, 2016. - Novel herpes virus isolated from bat cells
Eurekalert, Feb 17, 2016. - Can CRISPR help edit out female mosquitos?
phys.org, Feb 17, 2016.
EVENTS / TRAINING / WEB RESOURCES
- New video on the NCBI YouTube channel: Viral resources at NCBI
(video) NCBI, Feb 11, 2016.
CONCEPTS / COMMENTS
- Ten Simple Rules for Selecting a Bio-ontology.
Malone James et al. PLoS computational biology 2016 Feb (2) e1004743 - Single-cell genome sequencing: current state of the science.
Gawad Charles et al. Nature reviews. Genetics 2016 Jan - Sharing Data for Global Infectious Disease Surveillance and Outbreak Detection.
Aarestrup Frank M et al. Trends in microbiology 2016 Feb - Zika Virus in the Americas - Yet Another Arbovirus Threat.
Fauci Anthony S et al. The New England journal of medicine 2016 Feb (7) 601-604 - Viruses Causing Gastroenteritis: The Known, The New and Those Beyond.
Munnink Bas B Oude et al. Viruses 2016 (2) - Genetically-modified insects to combat vector-borne diseases — curtain rise or fall?
(editorial) Nat Rev Genet, Feb 8, 2016. - Immunoinformatics and epitope prediction in the age of genomic medicine
Backert L, Kohlbacher O. Genome Med 2015; 7:119.
METHODS / TOOLS
- Practical Approaches for Detecting Selection in Microbial Genomes.
Hedge Jessica et al. PLoS computational biology 2016 Feb (2) e1004739 - SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
Xia E, et al. Genome Med, Feb 17, 2016. - Ten years of maintaining and expanding a microbial genome and metagenome analysis system.
Markowitz Victor M et al. Trends in microbiology 2015 Nov (11) 730-41 - Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution.
Corel Eduardo et al. Trends in microbiology 2016 Jan - SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
Page AJ, et al. bioRxiv, Jan 29, 2016. - MetaFlow: Metagenomic profiling based on whole-genome coverage analysis with min-cost flows
Sobih A, et al. bioRxiv, Jan 29, 2016. - TruSPAdes: barcode assembly of TruSeq synthetic long reads.
Bankevich Anton et al. Nature methods 2016 Feb - Fast search of thousands of short-read sequencing experiments.
Solomon Brad et al. Nature biotechnology 2016 Feb
EVOLUTION / ECOLOGY / POPULATIONS
- A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions.
Makendi Carine et al. PLoS neglected tropical diseases 2016 Feb (2) e0004446 - Two Distinct Yersinia pestis Populations Causing Plague among Humans in the West Nile Region of Uganda.
Respicio-Kingry Laurel B et al. PLoS neglected tropical diseases 2016 Feb (2) e0004360 - Global epidemiology of capsular group W meningococcal disease (1970-2015): Multifocal emergence and persistence of hypervirulent sequence type (ST)-11 clonal complex.
Mustapha Mustapha M et al. Vaccine 2016 Feb - Applications of Bayesian Phylodynamic Methods in a Recent U.S. Porcine Reproductive and Respiratory Syndrome Virus Outbreak.
Alkhamis Mohammad A et al. Frontiers in microbiology 2016 67 - Reconstruction of the Evolutionary History and Dispersal of Usutu Virus, a Neglected Emerging Arbovirus in Europe and Africa.
Engel Dimitri et al. mBio 2016 (1) - Complete genome sequence of mumps viruses isolated from patients with parotitis, pancreatitis and encephalitis in India.
Vaidya Sunil R et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Feb - High genetic diversity and frequent genetic reassortment of avian influenza A(H9N2) viruses along the East Asian-Australian migratory flyway.
Wang Haiming et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Feb - Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection
Crellen T, et al. Sci Rep, Feb 16, 2016.
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Linezolid resistance in clinical isolates of Staphylococcus epidermidis from German hospitals and characterization of two cfr-carrying plasmids.
Bender Jennifer et al. The Journal of antimicrobial chemotherapy 2015 (6) 1630-8 - CTX-M-27- and CTX-M-14-producing, ciprofloxacin-resistant Escherichia coli of the H30 subclonal group within ST131 drive a Japanese regional ESBL epidemic.
Matsumura Yasufumi et al. The Journal of antimicrobial chemotherapy 2015 (6) 1639-49 - Relevance of spontaneous fabT mutations to a streptococcal toxic shock syndrome to non-streptococcal toxic shock syndrome transition in the novel-type Streptococcus pyogenes isolates that lost a salRK.
Tatsuno Ichiro et al. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2016 Feb - Mechanisms of cephalosporin resistance in indicator Escherichia coli isolated from food animals.
Lalak Anna et al. Veterinary microbiology 2016 Feb
DETECTION / DIAGNOSIS
- Evaluation of a Labelled Bacteriophage with 99mTc as a Potential Agent for Infection Diagnosis.
Elena Cardoso María et al. Current radiopharmaceuticals 2016 Feb - Genetic Variability of HIV-1 for Drug Resistance Assay Development.
Clutter Dana S et al. Viruses 2016 (2) - Viremia Frequencies of a Novel Human Pegivirus Evaluated by using Bioinformatic Screening and PCR
Bonsall D, et al. Emerg Infect Dis, Apr 2016. - Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study
Calvet G, et al. Lancet Infect Dis, Feb 17, 2016. - Ultradeep sequencing in the therapeutic management of HIV-1 infection at treatment initiation.
Todesco Eve et al. The Journal of antimicrobial chemotherapy 2015 (6) 1919-20 - Identification of blood meal sources in the main African malaria mosquito vector by MALDI-TOF MS.
Niare Sirama et al. Malaria journal 2016 (1) 87
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Whole Genome Analysis of Injectional Anthrax Identifies Two Disease Clusters Spanning More Than 13 Years.
Keim Paul et al. EBioMedicine 2015 Nov (11) 1613-8 - Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae.
Zhou Kai et al. Scientific reports 2016 20840 - Microbiological diagnosis and molecular typing of Legionella strains during an outbreak of legionellosis in Southern Germany.
Essig Andreas et al. International journal of medical microbiology : IJMM 2016 Jan - Tracing melioidosis back to the source: using whole-genome sequencing to investigate an outbreak originating from a contaminated domestic water supply.
McRobb Evan et al. Journal of clinical microbiology 2015 Apr (4) 1144-8 - Delineating community outbreaks of Salmonella enterica serovar Typhimurium by use of whole-genome sequencing: insights into genomic variability within an outbreak.
Octavia Sophie et al. Journal of clinical microbiology 2015 Apr (4) 1063-71 - Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus
Chang HH, et al. Genome Med, Feb 13, 2016. - Hepatitis C Virus Subtype and Evolution Characteristic Among Drug Users, Men Who Have Sex With Men, and the General Population in Beijing, China.
Jiao Yang et al. Medicine 2016 Feb (6) e2688 - Molecular Epidemiology and Transmission Dynamics of Recent and Long-Term HIV-1 Infections in Rural Western Kenya.
Zeh Clement et al. PloS one 2016 (2) e0147436
- Whole-Genome Sequencing to Determine Origin of Multinational Outbreak of Sarocladium kiliense Bloodstream Infections
Etienne KA, et al. Emerg Infect Dis, Mar 2016.
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Cheating evolution: engineering gene drives to manipulate the fate of wild populations.
Champer Jackson et al. Nature reviews. Genetics 2016 Feb
HOST-MICROBE INTERACTIONS
- Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease.
Bouquet Jerome et al. mBio 2015 (1) - Gene control of tyrosine kinase TIE2 and vascular manifestations of infections
Ghosh CC, et al. Proc Nat Acad Sci, Feb 18, 2016. - Polymorphisms in HLA Class II Genes Are Associated With Susceptibility to Staphylococcus aureus Infection in a White Population.
DeLorenze Gerald N et al. The Journal of infectious diseases 2015 Oct - Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism.
Tisoncik-Go Jennifer et al. Cell host & microbe 2016 Feb (2) 254-66 - Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing.
Païssé Sandrine et al. Transfusion 2016 Feb - On the Origins and Control of Community Types in the Human Microbiome.
Gibson Travis E et al. PLoS computational biology 2016 Feb (2) e1004688 - A necrotizing enterocolitis-associated gut microbiota is already present in the meconium: results of a prospective study.
Heida Fardou H et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Jan - Composition and dynamics of the respiratory tract microbiome in intubated patients.
Kelly Brendan J et al. Microbiome 2016 (1) 7 - Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes
Yassour M, et al. Genome Med, Feb 17, 2016.
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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