Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Feb 27, 2020

Advanced Molecular Detection Clips Content

• News
• Events / Training / Web Resources
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• New Algorithms Unlock Targeted Sequencing on Nanopore Platforms
  Han AP. GenomeWeb, Feb 11, 2020.
• New Genomic Tests Aim to Diagnose Deadly Infections Faster
  Jacobs A. New York Times, Feb 24, 2020.
• Ancient Salmonella Genomes Reveal Human Lifestyle-Related Host Adaptations
  GenomeWeb, Feb 24, 2020.
• Artificial Intelligence Discovers Potent Antibiotic
  Schleunes A. The Scientist, Feb 22, 2020.
• The fix is in
  Bentley S. Nat Microbiol, Feb 26, 2020.
• Coronavirus's Genetics Reveal Its Global Travels
  Yeager A. The Scientist, Feb 25, 2020.
• Coronavirus and the race to distribute reliable diagnostics
  Sheridan C. Nature, Feb 19, 2020.
• Mystery deepens over animal source of coronavirus
  Cyranoski D. Nature, Feb 26, 2020.
• Newer Vaccine Technologies Deployed to Develop COVID-19 Shot
  Olena A. The Scientist, Feb 21, 2020.
• Preprints bring "firehose" of outbreak data
  Kupferschmidt K. Science, Feb 28, 2020.

EVENTS / TRAINING / WEB RESOURCES

• The entire corpus of the Sequence Read Archive (SRA) now live on two cloud platforms!
  (announcement) NCBI, Feb 24, 2020.

CONCEPTS / COMMENTS

• We shouldn't worry when a virus mutates during disease outbreaks.
  Grubaugh Nathan D et al. Nature microbiology 2020 Feb
• Invest 5% of research funds in ensuring data are reusable.
  Mons Barend et al. Nature 2020 Feb (7796) 491
• How to build a genome.
  Eisenstein Michael et al. Nature 2020 Feb (7796) 633-635

METHODS / TOOLS

• NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads.
  Khelik Ksenia et al. BMC bioinformatics 2020 Feb (1) 66
• Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (mSNV) analysis during an influenza A/H5N8 outbreak.
  Poen Marjolein J et al. PloS one 2020 (2) e0229326 
• Estimating Pangenomes with Roary.
  Sitto Farrah et al. Molecular biology and evolution 2020 Mar (3) 933-939
• A Universal, Genomewide GuideFinder for CRISPR/Cas9 Targeting in Microbial Genomes.
  Spoto Michelle et al. mSphere 2020 Feb (1)
• Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED
  Kovaca S, et al. bioRxiv, Feb 3, 2020.
• Why do we need training? - A "Training school on molecular methods used for foodborne parasite diagnostics in different matrices" is a example of knowledge transfer to foster research quality in EU.
  Deksne Gunita et al. Experimental parasitology 2020 Feb 107863 

EVOLUTION / ECOLOGY / POPULATIONS

• Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region.
  Giovanetti Marta et al. Cell reports 2020 Feb 
• Molecular genetic analysis and clinical characterization of Rickettsia species isolated from the Republic of Korea in 2017.
  Kim Yeon-Sook et al. Transboundary and emerging diseases 2020 Feb
• Prevalence of torque viruses in HIV-infected and non-HIV-infected Nigerian subjects: analysis of near-full-length genome sequences.
  Elesinnla Abosede Ruth et al. Archives of virology 2020 Mar (3) 571-582
• Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain.
  van Dorp Lucy et al. Molecular biology and evolution 2020 Mar (3) 773-785

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Genomic epidemiology of complex, multi-species, plasmid-borne bla KPC carbapenemase in Enterobacterales in the UK, 2009-2014.
  Stoesser N et al. Antimicrobial agents and chemotherapy 2020 Feb
• Genomic and Phenotypic Variability in Neisseria gonorrhoeae Antimicrobial Susceptibility, England.
  Town Katy et al. Emerging infectious diseases 2020 Mar (3) 505-515
• Using comparative genomics to understand molecular features of carbapenem-resistant Acinetobacter baumannii from South Korea causing invasive infections and their clinical implications.
  Kim Min Hyung et al. PloS one 2020 (2) e0229416
• Multidrug- and Extensively Drug-Resistant Mycobacterium tuberculosis Beijing Clades, Ukraine, 2015.
  Merker Matthias et al. Emerging infectious diseases 2020 Mar (3) 481-490 
• Summer outbreak of severe RSV-B disease, Minnesota, 2017 associated with emergence of a genetically distinct viral lineage.
  Thielen Beth K et al. The Journal of infectious diseases 2020 Feb

DETECTION / DIAGNOSIS

• Evaluation of direct 16S rRNA PCR from clinical samples for bacterial detection in normally sterile body sites.
  Satilmis Serife et al. Journal of infection in developing countries 2019 Nov (11) 978-983
• Rapid and Accurate Species Identification of Mitis Group Streptococci Using the MinION Nanopore Sequencer.
  Imai Kazuo et al. Frontiers in cellular and infection microbiology 2020 11
• DNA extraction of microbial DNA directly from infected tissue: an optimized protocol for use in nanopore sequencing.
  Helmersen Karin et al. Scientific reports 2020 Feb (1) 2985
• Bioinformatics Approaches to the Understanding of Molecular Mechanisms in Antimicrobial Resistance.
  Van Camp Pieter-Jan et al. International journal of molecular sciences 2020 Feb (4) 
• miRNA Expression Profiles and Potential as Biomarkers in Nontuberculous Mycobacterial Pulmonary Disease.
  Han Sun Ae et al. Scientific reports 2020 Feb (1) 3178
• Exhaled Mycobacterium tuberculosis output and detection of subclinical disease by face-mask sampling: prospective observational studies.
  Williams Caroline M et al. The Lancet. Infectious diseases 2020 Feb
• Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania.
  Katale Bugwesa Z et al. BMC genomics 2020 Feb (1) 174
• Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.
  Brunker Kirstyn et al. Wellcome open research 2020 3 
• Outbreak of Saprochaete clavata Sepsis in Hematology Patients: Combined Use of MALDI-TOF and Sequencing Strategy to Identify and Correlate the Episodes.
  Lo Cascio Giuliana et al. Frontiers in microbiology 2020 84

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Whole-genome sequencing to explore nosocomial transmission and virulence in neonatal methicillin-susceptible Staphylococcus aureus bacteremia.
  Slingerland Bibi C G C et al. Antimicrobial resistance and infection control 2020 Feb (1) 39
• Whole-Genome Sequencing to Detect Numerous Campylobacter jejuni Outbreaks and Match Patient Isolates to Sources, Denmark, 2015-2017.
  Joensen Katrine G et al. Emerging infectious diseases 2020 Mar (3) 523-532
• Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria.
  Ajogbasile Fehintola V et al. Scientific reports 2020 Feb (1) 3180 
• Genomic variations of COVID-19 suggest multiple outbreak sources of transmission
  Zhang L, et al. medRxiv, Feb 26, 2020.
• Cross-Continental Dispersal of Major HIV-1 CRF01_AE Clusters in China.
  An Minghui et al. Frontiers in microbiology 2020 61
• Nanopore metagenomic sequencing to investigate nosocomial transmission of human metapneumovirus from a unique genetic group among haematology patients in the United Kingdom.
  Xu Yifei et al. The Journal of infection 2020 Feb

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Venezuelan equine encephalitis vaccine with rearranged genome resists reversion and protects non-human primates from viremia after aerosol challenge.
  Tretyakova Irina et al. Vaccine 2020 Feb

HOST-MICROBE INTERACTIONS

• MicroRNA expression profiling of peripheral blood mononuclear cells associated with syphilis.
  Huang Tao et al. BMC infectious diseases 2020 Feb (1) 165
• Human papillomavirus genotypes and P16INK4A expression in squamous penile carcinoma in Mexican patients.
  Martínez-Bailón Cecilia et al. BMC infectious diseases 2019 Dec (1) 1068

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.