Publication Date: Jan 16, 2020
Advanced Molecular Detection Clips Content
NEWS
- China releases genetic data on new coronavirus, now deadly
Schnirring L. CIDRAP, Jan 11, 2020. - Second family cluster found in Wuhan novel coronavirus outbreak
Schnirring L. CIDRAP, Jan 15, 2020. - US veterinary hospital faces rare antibiotic-resistant E coli
Dall C. CIDRAP, Jan 10, 2020. - Evaluation of Chagas RDTs Shows High Accuracy in Endemic Region
Johnson M. 360dx, Jan 9, 2020. - The kill-switch for CRISPR that could make gene-editing safer
Dolgin E. Nature, Jan 15, 2020. - Type of Herpes Virus Tied to Multiple Sclerosis
Zimmer K. The Scientist, Jan 10, 2020.
EVENTS / TRAINING / WEB RESOURCES
- Novel coronavirus complete genome from the Wuhan outbreak now available in GenBank
NCBI Insights, Jan 13, 2020. - Recent improvements to the genome Assembly resource
NCBI Insights, Jan 9, 2020. - A Scientist's Guide to Social Media
Heemstra J. ACS Cent Sci, Jan 10, 2020.
CONCEPTS / COMMENTS
- Waiting for data: Barriers to executing data use agreements.
Mello Michelle M et al. Science (New York, N.Y.) 2020 01 (6474) 150-152 - Eleven tips for working with large data sets.
Nowogrodzki Anna et al. Nature 2020 Jan (7790) 439-440 - Determining the direction of HIV transmission: Benefits and potential harms of taking phylogenetic analysis one step further.
Taylor Barbara et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jan - Are noncommunicable diseases communicable?
Finlay BB, et al. Science, Jan 17, 2020.
METHODS / TOOLS
- Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.
Deng Xianding et al. Nature microbiology 2020 Jan - The effect of storage conditions on microbial communities in stool.
Nel Van Zyl Kristien et al. PloS one 2020 (1) e0227486 - VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning.
Kim Jiwoong et al. PLoS computational biology 2020 Jan (1) e1007511 - Designing and implementing programmable depletion in sequencing libraries with DASHit
Dynerman D, et al. bioRxiv, Jan 13, 2020. - NASQAR: A web-based platform for high-throughput sequencing data analysis and visualization
Yousif A, et al. bioRxiv, Jan 12, 2020. - Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel
Labbe G, et al. bioRxiv, Jan 11, 2020. - DNA Features Viewer, a sequence annotations formatting and plotting library for Python
Zulkower V, et al. bioXriv, Jan 9, 2020. - Full-length de novo viral quasispecies assembly through variation graph construction.
Baaijens Jasmijn A et al. Bioinformatics (Oxford, England) 2019 Dec (24) 5086-5094 - SquiggleKit: a toolkit for manipulating nanopore signal data.
Ferguson James M et al. Bioinformatics (Oxford, England) 2019 Dec (24) 5372-5373 - Evaluating accuracy of microsatellite markers for classification of recurrent infections during routine monitoring of anti-malarial drug efficacy: A computer modelling approach.
Jones Sam et al. Antimicrobial agents and chemotherapy 2020 Jan
EVOLUTION / ECOLOGY / POPULATIONS
- Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei.
Chewapreecha Claire et al. Communications biology 2019 Nov (1) 428 - Whole Genome Sequencing for Studying Bacillus anthracis from an Outbreak in the Abruzzo Region of Italy.
Chiaverini Alexandra et al. Microorganisms 2020 Jan (1) - Tuberculosis in Liberia: high multidrug-resistance burden, transmission and diversity modelled by multiple importation events.
López Mariana G et al. Microbial genomics 2020 Jan - Identification and molecular characterization of Wolbachia strains in natural populations of Aedes albopictus in China.
Hu Yaping et al. Parasites & vectors 2020 Jan (1) 28
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- IS 26 -Mediated Transfer of bla NDM-1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital.
Weber Robert E et al. Frontiers in microbiology 2019 2817 - Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 - 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content.
van Hout Denise et al. PloS one 2020 (1) e0227604 - There is no hiding if you Seq: recent breakthroughs in Pseudomonas aeruginosa research revealed by genomic and transcriptomic next-generation sequencing.
Valli Richard X E et al. Journal of medical microbiology 2020 Jan - Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28.
Nakamura Keiji et al. Microbial genomics 2020 Jan - Nipah shell disorder, modes of infection, and virulence.
Kian-Meng Goh Gerard et al. Microbial pathogenesis 2020 Jan 103976
DETECTION / DIAGNOSIS
- Development and Evaluation of a Novel Protein-Based Assay for Specific Detection of KPC β-Lactamases from Klebsiella pneumoniae Clinical Isolates.
Lu Shuo et al. mSphere 2020 Jan (1) - A Real-Time PCR Screening Assay for Rapid Detection of Listeria Monocytogenes Outbreak Strains.
Torresi Marina et al. Foods (Basel, Switzerland) 2020 Jan (1) - Clinical Utility of Universal Broad-Range PCR Amplicon Sequencing for Pathogen Identification: a retrospective cohort study.
Kerkhoff Andrew D et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jan
- A Laboratory's Guide to the Universe of Broad-Range PCRs.
Schuetz Audrey N et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jan - Transcriptional Profiling of Human Peripheral Blood Mononuclear Cells Identifies Diagnostic Biomarkers That Distinguish Active and Latent Tuberculosis.
Wang Sen et al. Frontiers in immunology 2019 2948 - Cas12a-Based On-Site and Rapid Nucleic Acid Detection of African Swine Fever.
Bai Jing et al. Frontiers in microbiology 2019 2830
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Thorough analysis of a rapid spread tuberculosis outbreak by epidemiological and whole-genome sequencing.
Comin J et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Jan 104184 - Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052.
Zhang Yinfeng et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jan - Candida blankii: an emerging yeast in an outbreak of fungemia in neonates in Delhi, India.
Chowdhary Anuradha et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Jan
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Cost-Effectiveness of a Pharmacogenomic Test for Stratified Isoniazid Dosing in Treatment of Active Tuberculosis.
Rens Neil E et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jan
HOST-MICROBE INTERACTIONS
- Instances of altered gut microbiomes among Irish cricketers over periods of travel in the lead up to the 2016 World Cup: A sequencing analysis.
O' Donovan Ciara M et al. Travel medicine and infectious disease 2020 Jan 101553 - Taxonomic Signatures of Long-Term Mortality Risk in Human Gut Microbiota
Salosensaari A, et al. medRxiv, Jan 13, 2020. - Assessment of peritoneal microbial features and tumor marker levels as potential diagnostic tools for ovarian cancer.
Miao Ruizhong et al. PloS one 2020 (1) e0227707 - Homotypic and heterotypic protection and risk of re-infection following natural norovirus infection in a highly endemic setting.
Chhabra Preeti et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jan - Acute enterovirus infections significantly alter host cellular DNA methylation status.
Zhu Zheng et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Jan 104190 - Genetic Variation on TNF/LTA and TNFRSF1A Genes is Associated with Outcomes of Hepatitis C Virus Infection.
Yue Ming et al. Immunological investigations 2020 Jan 1-11
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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