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.
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Spotlight
Notes from the Field: Hepatitis C Outbreak in a Dialysis Clinic - Tennessee, 2014. Quasispecies (HCV intra-genotype variants) analysis was performed from serum specimens collected from all nine patients found to be HCV positive. Patients A, B, and C were infected with genotype 1a; less than 5% nucleotide variation among intra-host HCV sequences was detected among the three patients, suggesting epidemiologic linkage of these infections (Figure).
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
Fight against superbugs gets dramatic funding boost under congressional budget plan
Sun LH. Washington Post, Dec 17, 2015.
Outbreak Tracking, Infectious Disease Diagnostics Becoming Key Applications for NGS
Heger M. GenomeWeb, Dec 28, 2015.
Viral Soldiers: Phage therapy to combat bacterial infections
Madhusoodanan J. The Scientist, Jan 1, 2016.
The unsung heroes of scientific software
Chawla DS. Nature, Jan 4, 2016.
Funding for key data resources in jeopardy
Kaiser J. Science, Jan 1, 2016.
Dogs thwart effort to eradicate Guinea worm
Callaway E. Nature, Jan 5, 2015.
First Dengue Fever Vaccine Gets Green Light in 3 Countries
Maron DF. Scientific American, Dec 30, 2015.
Updating the Polio Vaccine
Akst J. The Scientist, Jan 4, 2016.
Genetic Diversity of Influenza Underscores Presence, Transmission of Minor Variants
GenomeWeb, Jan 4, 2015.
MERS Vax Tested in Camels
Azvolinsky A. The Scientist, Dec 17, 2015.
Diagnostics Group Refutes FDA’s Concerns
Grens K. The Scientist, Dec 17, 2015.
Canadian Research Team Wins $7.3M to Develop New Vaccines for Cattle
Petrone J. GenomeWeb, Dec 17, 2015.
EVENTS / TRAINING / WEB RESOURCES
HIV mutation browser
(website) Last updated Dec 31, 2015.
POLICY
PLOS Genetics Data Sharing Policy: In Pursuit of Functional Utility.
Barsh Gregory S et al. PLoS genetics 2015 Dec (12) e1005716
Controlled Access under Review: Improving the Governance of Genomic Data Access.
Shabani Mahsa et al. PLoS biology 2015 Dec (12) e1002339
Developing Global Norms for Sharing Data and Results during Public Health Emergencies.
Modjarrad Kayvon et al. PLoS medicine 2016 Jan (1) e1001935
CONCEPTS / COMMENTS
Precision Diagnosis Is a Team Sport.
Zehnbauer Barbara A et al. The Journal of molecular diagnostics : JMD 2016 Jan (1) 1-2 (CDC Author)
Genomic perspectives on the evolution and spread of bacterial pathogens.
Bentley Stephen D et al. Proceedings. Biological sciences / The Royal Society 2015 Dec (1821)
Moving pathogen genomics out of the lab and into the clinic: what will it take?
Luheshi Leila M et al. Genome medicine 2015 (1) 132
Whole Genome Sequencing of Clostridium difficile: Exquisitely Sensitive but Not Yet Optimally Applied.
Gerding Dale N et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Dec
As Ebola epidemic draws to a close, a thin scientific harvest.
Cohen Jon et al. Science (New York, N.Y.) 2016 Jan (6268) 12-3
Unfilled Vials.
Cohen Jon et al. Science (New York, N.Y.) 2016 Jan (6268) 16-9
Peaks of Promise and Peril: Screening for Antibiotic Resistance by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.
Anderson Neil W et al. Journal of clinical microbiology 2016 Jan (1) 5-6
What role can metabolomics play in the discovery and development of new medicines for infectious diseases?
Kim Dong-Hyun et al. Bioanalysis 2015 (6) 629-31
Expanding the role of diagnostic and prognostic tools for infectious diseases in resource-poor settings.
Ghani Azra C et al. Nature 2015 Dec (7580) S50-2
METHODS / TOOLS
FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis.
Parente Eugenio et al. International journal of food microbiology 2015 Dec 28-37
MyGene.info and MyVariant.info: Gene and Variant Annotation Query Services
Xin J, et al. bioRxiv, Dec 30, 2015.
High-throughput pipeline for de-novo assembly and drug resistance mutations identification from Next-Generation Sequencing viral data of residual diagnostic samples
Cassarino TG, et al. bioRxiv, Dec 24, 2015.
Interactive Analytics for Very Large Scale Genomic Data
Pan C, et al. bioRxiv, Dec 24, 2015.
Practical Guidelines for Secure Cloud Computing using Genomic Data
Datta S, et al. bioRxiv, Dec 20, 2015.
Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set.
Hall Matthew et al. PLoS computational biology 2015 Dec (12) e1004613
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome.
Kuleshov Volodymyr et al. Nature biotechnology 2015 Dec
Prediction of Missing Sequences and Branch Lengths in Phylogenomic Data.
Darriba Diego et al. Bioinformatics (Oxford, England) 2016 Jan
Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform.
Kilianski Andy et al. BMC bioinformatics 2015 (1) 416
Circlator: automated circularization of genome assemblies using long sequencing reads.
Hunt Martin et al. Genome biology 2015 (1) 294
SPMM: estimating infection duration of multi-variant HIV-1 infections.
Love Tanzy M T et al. Bioinformatics (Oxford, England) 2015 Dec
Swarm v2: highly-scalable and high-resolution amplicon clustering.
Mahé Frédéric et al. PeerJ 2015 e1420
Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology.
Zhu Lingxiang et al. Nucleic acids research 2015 Dec
EVOLUTION / ECOLOGY / POPULATIONS
Complete Genome Sequences of Two Shiga Toxin-Producing Escherichia coli Strains from Serotypes O119:H4 and O165:H25.
Lindsey Rebecca L et al. Genome announcements 2015 (6) (CDC Author)
Genome Sequences of Oblitimonas alkaliphila gen. nov. sp. nov. (Proposed), a Novel Bacterium of the Pseudomonadaceae Family.
Lauer Ana C et al. Genome announcements 2015 (6) (CDC Author)
Intraclonal genome diversity of the major Pseudomonas aeruginosa clones C and PA14.
Fischer Sebastian et al. Environmental microbiology reports 2015 Dec
Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana.
Forbi Joseph C et al. PloS one 2015 (12) e0145530 (CDC Author)
Evolutionary and Ecological Dynamics of Transboundary Disease Caused by H5N1 Virus in Southeast Asia.
Wei K et al. Transboundary and emerging diseases 2015 Jun (3) 315-27
Multiregion Deep Sequencing of Hepatitis C Virus: An improved Approach for Genetic Relatedness Studies.
Rossi Livia Maria Gonçalves et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Dec
Sequencing of emerging canine distemper virus strain reveals new distinct genetic lineage in the United States associated with disease in wildlife and domestic canine populations.
Riley Matthew C et al. Virology journal 2015 (1) 219
Evolution and molecular epidemiology of Classical swine fever virus during a multi-annual outbreak among European wild boar.
Goller Katja V et al. The Journal of general virology 2015 Dec
Porcine epidemic diarrhea virus: An emerging and re-emerging epizootic swine virus.
Lee Changhee et al. Virology journal 2015 (1) 193
Molecular characterisation of Porcine rubulavirus (PorPV) isolates from different outbreaks in Mexico.
Cuevas-Romero S et al. Virus genes 2016 Jan
Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia.
Winter David J et al. PLoS neglected tropical diseases 2015 Dec (12) e0004252
Phylogenomic reconstruction supports supercontinent origins for Leishmania.
Harkins Kelly M et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Dec
Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium.
Pajuelo Mónica J et al. PLoS neglected tropical diseases 2015 Dec (12) e0004316 (CDC Author)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.
Bradley Phelim et al. Nature communications 2015 10063
Comprehensive Characterization of Escherichia coli O104:H4 Isolated from Patients in the Netherlands.
Ferdous Mithila et al. Frontiers in microbiology 2015 1348
Comparative genomics to delineate pathogenic potential in non-O157 Shiga toxin-producing Escherichia coli (STEC) from patients with and without haemolytic uremic syndrome (HUS) in Norway.
Haugum Kjersti et al. PloS one 2014 (10) e111788
Genomic Comparison of two O111:H- Enterohemorrhagic Escherichia coli Isolates from a Historic Hemolytic Uremic Syndrome Outbreak in Australia.
McAllister Lauren J et al. Infection and immunity 2016 Jan
2015 Update of the Drug Resistance Mutations in HIV-1.
Wensing Annemarie M et al. Topics in antiviral medicine (4) 132-41
Network analysis of the chronic Hepatitis C virome defines HVR1 evolutionary phenotypes in the context of humoral immune responses.
Palmer Brendan A et al. Journal of virology 2015 Dec (CDC Author)
Study of viremic profile in febrile specimens of chikungunya in Bandung, Indonesia.
Riswari S F et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2016 Jan 61-5
Post treatment antifungal resistance among colonizing Candida isolates in candidemia patients: results from a systematic multicenter study.
Jensen R H et al. Antimicrobial agents and chemotherapy 2015 Dec
First Detection of TR34 L98H and TR46 Y121F T289A Cyp51 Mutations in Aspergillus fumigatus Isolates in the United States.
Wiederhold Nathan P et al. Journal of clinical microbiology 2016 Jan (1) 168-71
Independent Emergence of the Plasmodium Falciparum Kelch Propeller Domain Mutant Allele C580Y in Guyana.
Chenet Stella M et al. The Journal of infectious diseases 2015 Dec (CDC Author)
Decreasing pfmdr1 copy number suggests that Plasmodium falciparum in Western Cambodia is regaining in vitro susceptibility to mefloquine.
Lim Pharath et al. Antimicrobial agents and chemotherapy 2015 May (5) 2934-7
DETECTION / DIAGNOSIS
Usefulness of a novel multiplex real-time PCR assay for the diagnosis of sexually-transmitted infections.
Fernández Gema et al. Enfermedades infecciosas y microbiologia clinica 2015 Dec
Clustered Regularly Interspaced Short Palindromic Repeats Are emm Type-Specific in Highly Prevalent Group A Streptococci.
Zheng Po-Xing et al. PloS one 2015 (12) e0145223
Rapid and Accurate Determination of Lipopolysaccharide O-Antigen Types in Klebsiella pneumoniae with a Novel PCR-Based O-Genotyping Method.
Fang Chi-Tai et al. Journal of clinical microbiology 2015 Dec
Preclinical Assessment of a Fully Automated Multiplex PCR Panel for the Detection of Central Nervous System Pathogens.
Hanson K E et al. Journal of clinical microbiology 2015 Dec
MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal (West Africa).
Lo Cheikh I et al. PloS one (12) e0145889
Practical Utility and Accuracy of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Corynebacterium Species and Other Medically Relevant Coryneform-Like Bacteria.
Suwantarat Nuntra et al. American journal of clinical pathology 2016 Jan (1) 22-8
Rapid Identification of Emerging Human-Pathogenic Sporothrix Species with Rolling Circle Amplification.
Rodrigues Anderson M et al. Frontiers in microbiology 2015 1385
Direct Screening of Blood by PCR and Pyrosequencing for a 16S rRNA Gene Target from Emergency Department and Intensive Care Unit Patients Being Evaluated for Bloodstream Infection.
Moore M S et al. Journal of clinical microbiology 2016 Jan (1) 99-105
Evaluation in Cameroon of a Novel, Simplified Methodology to Assist Molecular Microbiological Analysis of V. cholerae in Resource-Limited Settings.
Debes Amanda K et al. PLoS neglected tropical diseases 2016 Jan (1) e0004307
Approaching a diagnostic point-of-care test for pediatric tuberculosis through evaluation of immune biomarkers across the clinical disease spectrum.
Jenum Synne et al. Scientific reports 2016 18520
Estimation of Rickettsia rickettsii copy number in the blood of patients 1 with Rocky Mountain spotted fever suggests cyclic diurnal trends in bacteremia.
Cecilia Kato et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2015 Dec (CDC Author)
A polymerase chain reaction-based algorithm to detect and prevent transmission of adenoviral conjunctivitis in hospital employees.
Kuo Irene C et al. American journal of ophthalmology 2015 Dec
Complex Genotype Mixtures Analyzed by Deep Sequencing in Two Different Regions of Hepatitis B Virus.
Caballero Andrea et al. PloS one 2015 (12) e0144816
Mycobacterium genavense infection in a solid organ recipient: a diagnostic and therapeutic challenge.
Ombelet S et al. Transplant infectious disease : an official journal of the Transplantation Society 2015 Dec
Concise gene signature for point-of-care classification of tuberculosis.
Maertzdorf Jeroen et al. EMBO molecular medicine 2015 Dec
External quality assessment for the molecular detection of MERS-CoV in China.
Zhang Lei et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2015 Dec 5-9
Pulmonary toxoplasmosis in immunocompromised patients with interstitial pneumonia: a single-centre prospective study assessing PCR-based diagnosis.
Desoubeaux Guillaume et al. Journal of clinical pathology 2016 Jan
Molecular Identification of Zoonotic Tissue-Invasive Tapeworm Larvae Other than Taenia solium in Suspected Human Cysticercosis Cases.
Tappe Dennis et al. Journal of clinical microbiology 2016 Jan (1) 172-4
Molecular Detection of Schistosome Infections with a Disposable Microfluidic Cassette.
Song Jinzhao et al. PLoS neglected tropical diseases 2015 Dec (12) e0004318
Novel PCRs for differential diagnosis of Cestodes.
Roelfsema Jeroen H et al. Experimental parasitology 2015 Dec
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
The utility of whole genome sequencing in characterizing Acinetobacter epidemiology and analyzing hospital outbreaks.
Fitzpatrick Margaret A et al. Journal of clinical microbiology 2015 Dec
Ongoing outbreak of invasive listeriosis, Germany, 2012 to 2015.
Ruppitsch Werner et al. Euro surveillance : bulletin Europe´en sur les maladies transmissibles = European communicable disease bulletin 2015 Dec (50)
Escherichia coli and UTI: the role of poultry-meat.
Manges Amee R et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2015 Dec
Outbreak of a beta-lactam resistant non-typeable Haemophilus influenzae sequence type 14 associated with severe clinical outcomes.
Andersson Madelen et al. BMC infectious diseases 2015 (1) 581
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