Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Nov 29, 2018

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. View Data Selection Criteria

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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

• Even on the Space Station
  GeomeWeb, Nov 29, 2018.
• Nanopore Platform Developers Aim to Bring Multiplex MDx Testing to Point of Care
  GenomeWeb, Nov 29, 2018.
• Metagenomic Sequencing Approach Proposed for Respiratory Tract Infection Detection
  GenomeWeb, Nov 28, 2018.
• Johns Hopkins Researchers Working on Tool to Combat C. Difficile Overtesting
  Johnson M. GenomeWeb, Nov 28, 2018.
• Protein Profiles Could ID Zika-Infected Pregnant Women at High Risk of Abnormal Births
  GenomeWeb, Nov 5, 2018.
• Rethinking vaccination with RNA vaccines
  Blackburn L. PHG Foundation, Nov 13, 2018.
• The Era of Cheap and Easy STD Treatment Is Over. What Went Wrong?
  McKenna M. Wired, Nov 28, 2018.

EVENTS / TRAINING / WEB RESOURCES

• RNA Vaccines: An Introduction
  (policy briefing) PHG Foundation, Oct 17, 2018.
• Long read sequencing technologies
  (policy briefings) PHG Foundation, Oct 29, 2018.

POLICY

• A data citation roadmap for scientific publishers.
  Cousijn Helena et al. Scientific data 2018 Nov 180259

CONCEPTS / COMMENTS

• Cryptic connections illuminate pathogen transmission within community networks.
  Hoyt Joseph R et al. Nature 2018 Nov

METHODS / TOOLS

• TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data.
  Sheppard Anna E et al. Microbial genomics 2018 Nov
• A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms.
  Banos Stefanos et al. BMC microbiology 2018 Nov (1) 190
• An Excel Macro for Determining Allelic and Sequence Types of Bacterial Clones in Multilocus Sequence Typing.
  Park Yu Jin et al. Annals of laboratory medicine 2019 Mar (2) 183-189
• PANINI: Pangenome Neighbour Identification for Bacterial Populations.
  Abudahab Khalil et al. Microbial genomics 2018 Nov
• A statistical method to identify recombination in bacterial genomes based on SNP incompatibility.
  Lai Yi-Pin et al. BMC bioinformatics 2018 Nov (1) 450
• The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities.
  Baldini Federico et al. Bioinformatics (Oxford, England) 2018 Nov
• BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files.
  Payne Alexander et al. Bioinformatics (Oxford, England) 2018 Nov
• Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.
  Wick Ryan R et al. PLoS computational biology 2018 Nov (11) e1006583
• Estimating epidemic incidence and prevalence from genomic data
  Vaughan TG, et al. bioRxiv, Nov 19, 2018.
• DNA Extraction Method Optimized for Nontuberculous Mycobacteria Long-Read Whole Genome Sequencing
  Bouso JM, Planet PM. bioRxiv, Nov 14, 2018.
• Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing.
  Ring Natalie et al. Microbial genomics 2018 Nov
• ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses.
  Tokuyama Maria et al. Proceedings of the National Academy of Sciences of the United States of America 2018 Nov
• Detection of HIV transmission clusters from phylogenetic trees using a multi-state birth-death model.
  Barido-Sottani Joëlle et al. Journal of the Royal Society, Interface 2018 Sep (146)
• Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes.
  Tu Shin-Lin et al. Viruses 2018 Nov (11)
• Mycobiome diversity: high-throughput sequencing and identification of fungi.
  Nilsson R Henrik et al. Nature reviews. Microbiology 2018 Nov
• Backpack PCR: A point-of-collection diagnostic platform for the rapid detection of Brugia parasites in mosquitoes.
  Zaky Weam I et al. PLoS neglected tropical diseases 2018 Nov (11) e0006962

EVOLUTION / ECOLOGY / POPULATIONS

• Evidence for positive selection of hepatitis A virus antigenic variants in vaccinated men-having-sex-with men patients: Implications for immunization policies.
  Sabrià Aurora et al. EBioMedicine 2018 Nov 
• Reemergence of St. Louis Encephalitis Virus in the Americas.
  Diaz Adrián et al. Emerging infectious diseases 2018 Dec (12)
• Investigating the Role of Easter Island in Migration of Zika Virus from South Pacific to Americas.
  Delatorre Edson et al. Emerging infectious diseases 2018 Nov (11) 2119-2121
• Spatiotemporal Distribution and Evolution of the A/H1N1 2009 Pandemic Influenza Virus in Pigs in France from 2009 to 2017: Identification of a Potential Swine-Specific Lineage.
  Chastagner Amélie et al. Journal of virology 2018 Dec (24)
• Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique.
  Petronella Nicholas et al. BMC infectious diseases 2018 Oct (1) 521
• Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest.
  Hepp Crystal M et al. PloS one 2018 (11) e0205801
• Multistate Infestation with the Exotic Disease–Vector Tick Haemaphysalis longicornis — United States, August 2017–September 2018
  Beard CB, et al. MMWR, Nov 30, 2018.  

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis.
  Johnning Anna et al. Microbial genomics 2018 Nov
• Highly Pathogenic Clone of Shiga Toxin-Producing Escherichia coli O157:H7, England and Wales.
  Byrne Lisa et al. Emerging infectious diseases 2018 Dec (12) 2303-2308
• Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci.
  Azarian Taj et al. PLoS pathogens 2018 Nov (11) e1007438 
• Multi-drug resistant Enterobacter bugandensis species isolated from the International Space Station and comparative genomic analyses with human pathogenic strains.
  Singh Nitin K et al. BMC microbiology 2018 Nov (1) 175
• Genomics of Klebsiella pneumoniae ST16 producing NDM-1, CTX-M-15 and OXA-232.
  Espinal Paula et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2018 Nov
• Moderate to high levels of pre-treatment HIV drug resistance in KwaZulu-Natal Province, South Africa.
  Chimukangara Benjamin et al. AIDS research and human retroviruses 2018 Nov

DETECTION / DIAGNOSIS

• Evaluation of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for identifying Burkholderia pseudomallei and Burkholderia thailandensis isolates.
  Li Jin et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2018 Nov
• Genotyping of Salmonella spp. on the basis of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats).
  Jiksing C, et al. bioRxiv, Nov 19, 2018.
• Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults
  Langelier C, et al. Proc Nat Acad Sci, Nov 27, 2018.
• Discrimination of Mycobacterium leprae and Mycobacterium haemophilum in clinical isolates/specimens by multiple PCR assay and prediction of drug susceptibility.
  Kitaoka Naoya et al. Journal of clinical microbiology 2018 Nov
• A Novel, 5-Transcript, Whole-blood Gene-expression Signature for Tuberculosis Screening Among People Living With Human Immunodeficiency Virus.
  Rajan Jayant V et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Nov
• Massively parallel profiling of HIV-1 resistance to the fusion inhibitor enfuvirtide
  Dingen A, et al. bioRxiv, Nov 19, 2018.
• Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches.
  Williams Simon H et al. mSphere 2018 08 (4)
• The utility of real-time polymerase chain reaction in detecting Coccidioides immitis among clinical specimens in the Central California San Joaquin Valley.
  Dizon Dominic et al. Medical mycology 2018 Nov

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Investigation of a Carbapenemase-producing Acinetobacter baumannii outbreak using whole genome sequencing versus a standard epidemiologic investigation.
  Bogaty Chloe et al. Antimicrobial resistance and infection control 2018 140
• Outbreak of Tattoo-Associated Nontuberculous Mycobacterial Skin Infections.
  Griffin Isabel et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Nov  
• A large HCV transmission network enabled a fast-growing HIV outbreak in rural Indiana, 2015.
  Ramachandran Sumathi et al. EBioMedicine 2018 Nov 
• Completeness of HIV nucleotide sequence ascertainment and its potential impact on understanding HIV transmission - Maryland, 2011-2013.
  Brooks Richard B et al. AIDS care 2018 Nov 1-8  
• Outbreak of HIV Infection Linked to Nosocomial Transmission, China, 2016-2017.
  Pan Xiaohong et al. Emerging infectious diseases 2018 Dec (12) 2141-2149

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Inhibiting the Evolution of Antibiotic Resistance.
  Ragheb Mark N et al. Molecular cell 2018 Nov
• The use of proteomics to understand antiviral immunity.
  Woon Amanda P et al. Seminars in cell & developmental biology 2018 Dec 22-29

HOST-MICROBE INTERACTIONS

• Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome.
  Hannigan Geoffrey D et al. mBio 2018 Nov (6)
• Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial.
  Wei Shaodong et al. EBioMedicine 2018 Nov

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.