Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Feb 13, 2020

Advanced Molecular Detection Clips Content

• News
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Host-Microbe Interactions

NEWS

• Coronavirus latest: WHO identifies its top research priorities
  Nature, Feb 11, 2020.
• Timetable For A Vaccine Against The New Coronavirus? Maybe This Fall
  Palca J. NPR, Feb 12, 2020.
• Scientists Compare Novel Coronavirus with SARS and MERS Viruses
  Olena A. The Scientist, Feb 11, 2020.
• Coronavirus Test Kits Encounter Quality Control Hiccup in Some States, CDC Reports
  GenomeWeb, Feb 12, 2020.
• Early Coronavirus Genetic Data May Have Forewarned Outbreak
  Gale J. Bloomberg, Feb 12, 2020.
• Easy COVID-19 test tops research priorities as cases climb
  Schnirring L. CIDRAP, Feb 12, 2020.
• Fluctuating funding and flagging interest hurt coronavirus research, leaving crucial knowledge gaps
  Branswell H. STAT, Feb 10, 2020.
• Viral Genomes Trace Spread of Mumps in Vaccinated Population
  GenomeWeb, Feb 11, 2020.
• New Clues About "Ambigram"Viruses With Strange Reversible Genes
  Cepelewicz J. Quanta, Feb 12, 2020.

CONCEPTS / COMMENTS

• Severe acute respiratory syndrome-related coronavirus: The species and its viruses, a statement of the Coronavirus Study Group
  Gorbalenya AE. bioRxiv, Feb 11, 2020.
• Antibiotic resistance: turning evolutionary principles into clinical reality.
  Andersson Dan I et al. FEMS microbiology reviews 2020 Jan
• Virus interactions with bacteria: Partners in the infectious dance.
  Neu Ursula et al. PLoS pathogens 2020 Feb (2) e1008234
• Tracing the Origin of Invasive Fungal Infections.
  Papon Nicolas et al. Trends in microbiology 2020 Feb

METHODS / TOOLS

• DeepNano-blitz: A Fast Base Caller for MinION Nanopore Sequencers
  Boza V, et al. bioRxiv, Feb 12, 2020.
• iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone
  Palatnick A, et al. bioRxiv, Feb 12, 2020.
• Mapping short reads, faithfully
  Zorita DV, et al. bioRxiv, Feb 11, 2020.
• Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.
  Bush Stephen J et al. GigaScience 2020 Feb (2) 
• Fast and accurate correction of optical mapping data via spaced seeds.
  Salmela Leena et al. Bioinformatics (Oxford, England) 2020 Feb (3) 682-689
• Emerging challenges of whole-genome-sequencing-powered epidemiological surveillance of globally distributed clonal groups of bacterial infections, giving Acinetobacter baumannii ST195 as an example.
  Jia Huiqiong et al. International journal of medical microbiology : IJMM 2019 Nov (7) 151339 
• Bacterial genetics and molecular pathogenesis in the age of high throughput DNA sequencing.
  Davey Lauren et al. Current opinion in microbiology 2020 Feb 59-66 
• FluPhenotype - a one-stop platform for early warnings of the influenza A virus.
  Lu Congyu et al. Bioinformatics (Oxford, England) 2020 Feb
• Machine learning analysis of genomic signatures provides evidence of associations between Wuhan 2019-nCoV and bat betacoronaviruses
  Randhawa GS, et al. bioRxiv, Feb 9, 2020.
• PIRD: Pan Immune Repertoire Database.
  Zhang Wei et al. Bioinformatics (Oxford, England) 2020 Feb (3) 897-903
• Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines.
  Ducarmon Q R et al. mSystems 2020 Feb (1)

EVOLUTION / ECOLOGY / POPULATIONS

• Duplications drive diversity in Bordetella pertussis on an underestimated scale
  Abrahams JS, et al. bioRxiv, Feb 7, 2020. 
• Genome Dynamics of Vibrio cholerae Isolates Linked to Seasonal Outbreaks of Cholera in Dhaka, Bangladesh.
  Baddam Ramani et al. mBio 2020 Feb (1)
• Emergence of waterfowl-originated gene cassettes in HPAI H7N9 viruses caused severe human infection in Fujian, China.
  Yang Lei et al. Influenza and other respiratory viruses 2019 09 (5) 496-503
• "Submergence" of Western equine encephalitis virus: Evidence of positive selection argues against genetic drift and fitness reductions.
  Bergren Nicholas A et al. PLoS pathogens 2020 Feb (2) e1008102 
• The global spread of 2019-nCoV: a molecular evolutionary analysis.
  Benvenuto Domenico et al. Pathogens and global health 2020 Feb 1-4
• Genetic characterization of a novel recombinant echovirus 30 strain causing a regional epidemic of aseptic meningitis in Hokkaido, Japan, 2017.
  Miyoshi Masahiro et al. Archives of virology 2020 Feb (2) 433-438
• Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China.
  Wu Aiping et al. Cell host & microbe 2020 Feb

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• A snapshot of diversity: Intraclonal variation of Escherichia coli clones as commensals and pathogens.
  Stegger Marc et al. International journal of medical microbiology : IJMM 2020 Jan 151401
• Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli.
  Patiño-Navarrete Rafael et al. Genome medicine 2020 01 (1) 10
• Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium.
  Arredondo-Alonso S et al. mBio 2020 Feb (1)
• Key Transitions in the Evolution of Rapid and Slow Growing Mycobacteria Identified by Comparative Genomics.
  Bachmann Nathan L et al. Frontiers in microbiology 2019 3019
• HIV-1 subtype C predicted co-receptor tropism in Africa: an individual sequence level meta-analysis.
  Matume Nontokozo D et al. AIDS research and therapy 2020 Feb (1) 5
• Pathogenicity and Transmissibility of 2019-nCoV-A Quick Overview and Comparison with Other Emerging Viruses.
  Chen Jieliang et al. Microbes and infection 2020 Feb

DETECTION / DIAGNOSIS

• Appropriate Use and Future Directions of Molecular Diagnostic Testing.
  Graf Erin H et al. Current infectious disease reports 2020 Feb (2) 5 
• Invasive Haemophilus influenzae Type b Disease in the Post Hexavalent Era: Ten Years of Molecular Surveillance in Tuscany.
  Ricci Silvia et al. The Pediatric infectious disease journal 2020 Feb 
• Expanding US Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole Genome Sequencing through CDC's Antibiotic Resistance Laboratory Network.
  Kersh Ellen N et al. Journal of clinical microbiology 2020 Feb  
• Evaluation of a fully automated bioinformatics tool to predict antibiotic resistance from MRSA genomes.
  Kumar Narender et al. The Journal of antimicrobial chemotherapy 2020 Feb
• Bringing phylogeny and clinical microbiology together.
  Ciotti Marco et al. Future microbiology 2020 Feb
• High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
  Sanderson ND, et al. bioRxiv, Feb 9, 2020.
• Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study.
  Doyle Ronan M et al. Microbial genomics 2020 Feb 
• Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics.
  Khaledi Ariane et al. EMBO molecular medicine 2020 Feb e10264
• Novel Cassette Assay To Quantify the Outer Membrane Permeability of Five β-Lactams Simultaneously in Carbapenem-Resistant Klebsiella pneumoniae and Enterobacter cloacae .
  Kim Tae Hwan et al. mBio 2020 Feb (1)
• Genotypic characterization of 'inferred' rifampin mutations in GenoType MTBDRplus assay and its association with phenotypic susceptibility testing of Mycobacterium tuberculosis.
  Singhal Ritu et al. Diagnostic microbiology and infectious disease 2020 Jan 114995
• Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia.
  Chu Daniel K W et al. Clinical chemistry 2020 Jan
• Genomic evidence of yellow fever virus in Aedes scapularis, southeastern Brazil, 2016.
  Cunha Mariana Sequetin et al. Acta tropica 2020 Feb 105390
• Evolving status of the 2019 novel coronavirus Infection: proposal of conventional serologic assays for disease diagnosis and infection monitoring [Commentary/Review].
  Xiao Shu-Yuan et al. Journal of medical virology 2020 Feb 
• Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand.
  Rolland Morgane et al. PLoS pathogens 2020 Feb (2) e1008179
• First Description of Seronegative HTLV-1 Carriers in Argentina.
  Gallego Sandra et al. The American journal of tropical medicine and hygiene 2020 Feb

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Transmission of Vancomycin-Resistant Enterococci in the Hospital Setting: Uncovering the Patient-Environment Interplay.
  Correa-Martinez Carlos L et al. Microorganisms 2020 Jan (2)
• Genomic epizoology of a Brucella abortus outbreak in Northern Ireland (1997-2012).
  Allen Adrian R et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Feb 104235 
• Outbreak of Listeriosis in South Africa Associated with Processed Meat
  Thomas J, et al. New Engl J Med, Feb 13, 2020.
• Combining Standard Molecular Typing and Whole Genome Sequencing to Investigate Pseudomonas aeruginosa Epidemiology in Intensive Care Units.
  Magalhães Bárbara et al. Frontiers in public health 2020 3
• Investigation and Response to an Outbreak of Dengue: Island of Hawaii, 2015-2016.
  Johnston David I et al. Public health reports (Washington, D.C. : 1974) 2020 Feb 33354920904068 
• Phylogenetic investigation of HCV-4d epidemic in Paris MSM HIV population reveals a still active outbreak and a strong link to the Netherlands.
  Visseaux Benoit et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Feb
• Combining genomics and epidemiology to track mumps virus transmission in the United States.
  Wohl Shirlee et al. PLoS biology 2020 Feb (2) e3000611 
• Influenza A Virus Field Surveillance at a Swine-Human Interface.
  Rambo-Martin Benjamin L et al. mSphere 2020 Feb (1)  

HOST-MICROBE INTERACTIONS

• Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation.
  Dirmeier Simon et al. PLoS computational biology 2020 Feb (2) e1007587
• Circulating HPV cDNA in the blood as a reliable biomarker for cervical cancer: A meta-analysis.
  Gu Yulan et al. PloS one 2020 (2) e0224001
• Separating the signal from the noise in metagenomic cell-free DNA sequencing.
  Burnham Philip et al. Microbiome 2020 Feb (1) 18
• Foes or Friends? Bacteria Enriched in the Tumor Microenvironment of Colorectal Cancer.
  Xu Siyang et al. Cancers 2020 Feb (2)

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.