Publication Date: Mar 5, 2020
Advanced Molecular Detection Clips Content
NEWS
- FDA Provides SARS-CoV-2 Test Validation Guidance for High-Complexity Labs Seeking EUA
Johnson M. GenomeWeb, Mar 3, 2020. - CDC Revises SARS-CoV-2 Assay Protocol; Surveillance Testing on Track to Start Next Week
Johnson M. GenomeWeb, Feb 28, 2020. - How SARS-CoV-2 Tests Work and What's Next in COVID-19 Diagnostics
Nogrady B. The Scientist, Mar 3, 2020. - EU notes rising resistance in common foodborne pathogens
Dall, C. CIDRAP, Mar 4, 2020. - Gene sleuths are tracking the coronavirus outbreak as it happens
Regalado A. MIT Tech Review, Mar 4, 2020. - One gene to rule them all in a chronic brain infection
Frickel EM. Nature, Mar 2, 2020.
EVENTS / TRAINING / WEB RESOURCES
- Open peer-review platform for COVID-19 preprints
Johansson MA, Saderi D. Nature, Mar 3, 2020.
POLICY
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2.
et al. Nature microbiology 2020 Mar - Screening for Hepatitis C Virus Infection in Adolescents and Adults: US Preventive Services Task Force Recommendation Statement.
et al. JAMA 2020 Mar - White House Requests National Academies Standing Committee on Emerging Infectious Diseases and Health Threats in Response to Spread of Coronavirus
NASEM, Mar 2, 2020.
CONCEPTS / COMMENTS
- RNA-Sequencing Analyses of Small Bacterial RNAs and their Emergence as Virulence Factors in Host-Pathogen Interactions.
Diallo Idrissa et al. International journal of molecular sciences 2020 Feb (5) - Responding to Covid-19 - A Once-in-a-Century Pandemic?
Gates Bill et al. The New England journal of medicine 2020 Feb - Covid-19 - Navigating the Uncharted.
Fauci Anthony S et al. The New England journal of medicine 2020 Feb
METHODS / TOOLS
- NG-Tax 2.0: A Semantic Framework for High-Throughput Amplicon Analysis.
Poncheewin Wasin et al. Frontiers in genetics 2019 1366 - Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction.
Gill Mandev S et al. Molecular biology and evolution 2020 Feb - Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes.
Saber Morteza M et al. Microbial genomics 2020 Feb - Coinfinder: detecting significant associations and dissociations in pangenomes.
Whelan Fiona Jane et al. Microbial genomics 2020 Feb - RootDigger: a root placement program for phylogenetic trees
Bettisworth B, Stamatakis A. bioRxiv, Mar 5, 2020. - Benchmarking of computational error-correction methods for next-generation sequencing data
Mitchell K, et al. bioRxiv, Mar 5, 2020. - yacrd and fpa: upstream tools for long-read genome assembly
Marijon P, et al. bioRxiv, Mar 2, 2020. - Bactopia: a flexible pipeline for complete analysis of bacterial genomes
Petit III RA, Read TD. - Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods.
Munck Nanna et al. Scientific data 2020 Mar (1) 75 - Concordance of SNP- and allele-based typing workflows in the context of a large-scale international Salmonella Enteritidis outbreak investigation.
Coipan Claudia E et al. Microbial genomics 2020 Feb
- Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.
Cleemput Sara et al. Bioinformatics (Oxford, England) 2020 Feb - The 2019 novel coronavirus resource.
Zhao Wen-Ming et al. Yi chuan = Hereditas 2020 Feb (2) 212-221
EVOLUTION / ECOLOGY / POPULATIONS
- Meningococcal carriage in young adults six years after meningococcal C conjugate (MCC) vaccine catch-up campaign in Salvador, Brazil.
Ferreira Viviane Matos et al. Vaccine 2020 Feb
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Surveillance of Enterococcus spp. reveals distinct species and antimicrobial resistance diversity across a One-Health continuum.
Zaheer Rahat et al. Scientific reports 2020 Mar (1) 3937 - Association between vancomycin-resistant Enterococcus faecium colonization and subsequent infection: a retrospective WGS study.
Rubin Ingrid Maria Cecilia et al. The Journal of antimicrobial chemotherapy 2020 Mar - Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producing Escherichia coli O157:H7 in the UK.
Yara Daniel A et al. Microbial genomics 2020 Feb - High prevalence of integrase mutation L74I in West African HIV-1 subtypes prior to integrase inhibitor treatment.
El Bouzidi Kate et al. The Journal of antimicrobial chemotherapy 2020 Feb - Fluconazole-resistant Candida parapsilosis strains with a Y132F substitution in the ERG11 gene causing invasive infections in a neonatal unit, South Africa.
Magobo Rindidzani E et al. Mycoses 2020 Mar - Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity.
Rokas Antonis et al. PLoS pathogens 2020 Feb (2) e1008315 - Metagenomic analysis reveals the microbiome and resistome in migratory birds.
Cao Jian et al. Microbiome 2020 Mar (1) 26
DETECTION / DIAGNOSIS
- Detection of Rickettsia asembonensis in Fleas (Siphonaptera: Pulicidae, Ceratophyllidae) Collected in Five Counties in Georgia, United States.
Eremeeva Marina E et al. Journal of medical entomology 2020 Mar - Systematic review of whole genome sequencing data to predict phenotypic drug resistance and susceptibility in Swedish Mycobacterium tuberculosis isolates 2016-2018.
Enkirch Theresa et al. Antimicrobial agents and chemotherapy 2020 Mar - Differential diagnosis of illness in patients under investigation for the novel coronavirus (SARS-CoV-2), Italy, February 2020.
Bordi Licia et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 Feb (8) - Evaluation of a PCR-electrospray ionization mass spectrometry platform for detection and identification of fungal pathogens directly from prospectively collected bronchoalveolar lavage specimens.
Jia Bei et al. Diagnostic microbiology and infectious disease 2020 Jan 114988 - Loop mediated isothermal amplification (LAMP) of Toxoplasma DNA from dried blood spots.
Hegazy Mona K et al. Experimental parasitology 2020 Feb 107869 - Loop-mediated isothermal amplification methods for diagnosis of visceral leishmaniasis ( kala-azar ) - a systematic review.
Silva Nunes Bezerra Gilberto et al. Expert review of molecular diagnostics 2020 Feb
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Klebsiella variicola causing nosocomial transmission among neonates - an emerging pathogen?
Piepenbrock Ellen et al. Journal of medical microbiology 2020 Mar - Importation of extensively drug resistant (XDR) Salmonella Typhi cases in Ontario, Canada.
Eshaghi Alireza et al. Antimicrobial agents and chemotherapy 2020 Mar - Distinct mechanisms of dissemination of NDM-1 metallo- β-lactamase in Acinetobacter spp. in Argentina.
Adams Mark D et al. Antimicrobial agents and chemotherapy 2020 Mar - In-depth Study of a Nosocomial Outbreak Caused by XDR-Pseudomonas aeruginosa Using Whole Genome Sequencing Coupled with a PCR Targeting Strain-Specific SNPs.
Acosta Fermín et al. American journal of epidemiology 2020 Mar - Using genomics to understand inter- and intra- outbreak diversity of Pasteurella multocida isolates associated with fowl cholera in meat chickens.
Omaleki Lida et al. Microbial genomics 2020 Mar - Genomic investigation reveals contaminated detergent as the source of an ESBL-producing Klebsiella michiganensis outbreak in a neonatal unit.
Chapman Paul et al. Journal of clinical microbiology 2020 Feb - Detection of dengue virus type 2 of Indian origin in acute febrile patients in rural Kenya.
Masika Moses Muia et al. PLoS neglected tropical diseases 2020 Mar (3) e0008099
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Inhibition of Nipah Virus by Defective Interfering Particles.
Welch Stephen R et al. The Journal of infectious diseases 2020 Feb - VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage.
Shen Chen-Hsiang et al. Cell host & microbe 2020 Mar - Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus in China (SARS-CoV-2)
Feng Y, et al. bioRxiv, Mar 5, 2020.
HOST-MICROBE INTERACTIONS
- Antimicrobial Resistance Gene Prevalence in a Population of Patients with Advanced Dementia Is Related to Specific Pathobionts.
Rowan-Nash Aislinn D et al. iScience 2020 Feb (3) 100905
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
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