Publication Date: Feb 20, 2020
Advanced Molecular Detection Clips Content
NEWS
- HHS partners with drug makers on COVID-19 vaccine, drugs
Soucheray S. CIDRAP, Feb 19, 2020. - More than 80 clinical trials launch to test coronavirus treatments
Maxmen A. Nature, Feb 15, 2020. - Labs scramble to produce new coronavirus diagnostics
Kupferschmidt K, Cohen J. Science, Feb 14, 2020. - Studies show COVID-19 likely has multiple infection routes
Soucheray S. CIDRAP, Feb 19, 2020. - The next chapter for African genomics
Maxmen A. Nature, Feb 19, 2020. - CDC Building NGS Quality Management Tools as Public Health Labs Increase Use of Sequencing
Bonislawski A. 360dx, Feb 10, 2020. - POC Molecular Flu Tests Finding Resistance in Pediatrics Despite High Accuracy
Johnson M. GenomeWeb, Feb 13, 2020. - Ebola Virus Response Signature Emerges From Mouse Gene Expression Data
GenomeWeb, Feb 11, 2020.
EVENTS / TRAINING / WEB RESOURCES
- Ten simple rules for getting started on Twitter as a scientist
Cheplygina V, et al. PLoS Comput Biol, Feb 10, 2020.
CONCEPTS / COMMENTS
- Machine learning in the clinical microbiology laboratory: has the time come for routine practice?
Peiffer-Smadja Nathan et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Feb
- Improving the usability and comprehensiveness of microbial databases
Loeffler C, et al. bioRxiv, Feb 16, 2020. - Statement in support of the scientists, public health professionals, and medical professionals of China combatting COVID-19
Calisher C, et al. Lancet, Feb 19, 2020. - Defining the Epidemiology of Covid-19 - Studies Needed.
Lipsitch Marc et al. The New England journal of medicine 2020 Feb
- Cyber security threats in the microbial genomics era: implications for public health.
Fayans Iliya et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 Feb (6)
METHODS / TOOLS
- A pipeline for targeted metagenomics of environmental bacteria.
Grieb Anissa et al. Microbiome 2020 Feb (1) 21 - nanoMLST: accurate multilocus sequence typing using Oxford Nanopore Technologies MinION with a dual-barcode approach to multiplex large numbers of samples.
Liou Ci-Hong et al. Microbial genomics 2020 Feb - Computational methods for 16S metabarcoding studies using Nanopore sequencing data.
Santos Andres et al. Computational and structural biotechnology journal 2020 296-305 - Successful isolation of Treponema pallidum strains from patients' cryopreserved ulcer exudate using the rabbit model.
Pereira Lara E et al. PloS one 2020 (1) e0227769 - A lab-on-a-chip for free-flow electrophoretic preconcentration of viruses and gel electrophoretic DNA extraction.
Hügle Matthias et al. The Analyst 2020 Feb - Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia.
Stubbs Samuel C B et al. Virology journal 2020 Feb (1) 24
EVOLUTION / ECOLOGY / POPULATIONS
- Flies from a tertiary hospital in Rwanda carry multidrug-resistant Gram-negative pathogens including extended-spectrum beta-lactamase-producing E. coli sequence type 131.
Heiden Stefan E et al. Antimicrobial resistance and infection control 2020 Feb (1) 34 - Duplications drive diversity in Bordetella pertussis on an underestimated scale
Abrahams JS, et al. bioRxiv, Feb 10, 2020. - Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages.
Wang Haoqiu et al. PLoS neglected tropical diseases 2020 Feb (2) e0008046 - Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016-2018.
Oude Munnink B Bas et al. Scientific reports 2020 Feb (1) 2798 - Identification of a pangolin niche for a 2019-nCoV-like coronavirus through an extensive meta-metagenomic search
Wahba L, et al. bioRxiv, Feb 14, 2020. - Long-term monitoring of G1P[8] rotaviruses circulating without vaccine pressure in Nizhny Novgorod, Russia, 1984-2019.
Novikova N A et al. Archives of virology 2020 Feb
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- A three-year whole genome sequencing perspective of Enterococcus faecium sepsis in Australia.
Lee Terence et al. PloS one 2020 (2) e0228781 - Underrated Staphylococcus species and their role in antimicrobial resistance spreading.
Rossi Ciro César et al. Genetics and molecular biology 2020 (1 suppl 2) e20190065 - Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii.
Iversen Katrine Højholt et al. Scientific reports 2020 Feb (1) 2728 - Multistate, population-based distributions of candidate vaccine targets, clonal complexes, and resistance features of invasive Group B Streptococci within the US: 2015-2017.
McGee Lesley et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Feb - Genomic analysis and antimicrobial resistance of Neisseria gonorrhoeae isolates from Vietnam in 2011 and 2015-16.
Lan Pham Thi et al. The Journal of antimicrobial chemotherapy 2020 Feb - First Case of High-Level Azithromycin Resistant Neisseria gonorrhoeae in North Carolina.
Palavecino Elizabeth L et al. Sexually transmitted diseases 2020 Feb - Genomic characterization of Neisseria gonorrhoeae Strains from 2016 United States Sentinel Surveillance Displaying Reduced Susceptibility to Azithromycin
Schmerer MW, et al. Antimicrob Agents Chemother,Feb 18, 2020. - Early prediction of antigenic transitions for influenza A/H3N2.
Castro Lauren A et al. PLoS computational biology 2020 Feb (2) e1007683 - Characterization of drug resistance and the defective HIV reservoir in virally suppressed vertically infected children in Mali.
Brice Josephine et al. The Journal of antimicrobial chemotherapy 2020 Feb - Chikungunya Outbreaks in India: A Prospective Study Comparing Neutralization and Sequelae during Two Outbreaks in 2010 and 2016.
Jain Jaspreet et al. The American journal of tropical medicine and hygiene 2020 Feb - Molecular characterization and clinical outcomes of Candida auris infection: Single-center experience in Saudi Arabia.
Almaghrabi Reem S et al. Mycoses 2020 Feb
DETECTION / DIAGNOSIS
- Taxonomic classification and abundance estimation using 16S and WGS-A comparison using controlled reference samples.
Khachatryan Lusine et al. Forensic science international. Genetics 2020 Feb 102257 - Innovative and rapid antimicrobial susceptibility testing systems.
van Belkum Alex et al. Nature reviews. Microbiology 2020 Feb - Diagnostic accuracy of genetic markers and nucleic acid techniques for the detection of Leptospira in clinical samples: A meta-analysis.
Lam Jia-Yong et al. PLoS neglected tropical diseases 2020 Feb (2) e0008074 - Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing.
Brinda Karel et al. Nature microbiology 2020 Feb - Label-Free Biosensors for Laboratory-Based Diagnostics of Infections: Current Achievements and New Trends.
Andryukov Boris G et al. Biosensors 2020 Feb (2) - CRISPR-based rapid and ultra-sensitive diagnostic test for Mycobacterium tuberculosis .
Ai Jing-Wen et al. Emerging microbes & infections 2019 (1) 1361-1369 - Rickettsia felis identified in two fatal cases of acute meningoencephalitis.
Mawuntu Arthur H P et al. PLoS neglected tropical diseases 2020 Feb (2) e0007893 - 2019_nCoV: Rapid classification of betacoronaviruses and identification of traditional Chinese medicine as potential origin of zoonotic coronaviruses.
Wassenaar Trudy M et al. Letters in applied microbiology 2020 Feb - Ultra-low HIV-1 p24 detection limits with a bioelectronic sensor.
Macchia Eleonora et al. Analytical and bioanalytical chemistry 2020 Feb (4) 811-818 - Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes.
Zhang Wei et al. Emerging microbes & infections 2020 Dec (1) 386-389 - Pre-emptive genomic surveillance of emerging ebolaviruses.
Postigo-Hidalgo Ignacio et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 Jan (3) - A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria.
Diez Benavente Ernest et al. PLoS genetics 2020 Feb (2) e1008576
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Outbreak of Listeriosis in South Africa Associated with Processed Meat.
Thomas Juno et al. The New England journal of medicine 2020 02 (7) 632-643 - Disentangling outbreaks using whole-genome sequencing: concurrent multistate-outbreaks of Salmonella Kottbus in Germany, 2017.
Enkelmann J et al. Epidemiology and infection 2020 Feb 1-17 - Clostridioides difficile Whole Genome Sequencing Differentiates Relapse with the Same Strain from Reinfection with a New Strain.
Cho Janice et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Feb - Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit.
Cremers A J H et al. Scientific reports 2020 Feb (1) 2619 - Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae : evolutionary analysis for outbreak investigation.
Fontana Carla et al. Future microbiology 2020 Feb - Human surveillance and phylogeny of highly pathogenic avian influenza A(H5N8) during an outbreak in poultry in South Africa, 2017.
Valley-Omar Ziyaad et al. Influenza and other respiratory viruses 2020 Feb - Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic.
Reimering Susanne et al. PLoS computational biology 2020 Feb (2) e1007101 - Transmission of NS5A resistance associated substitutions among men-who-have-sex-with-men recently infected with hepatitis C virus genotype 1a.
Popping Stephanie et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Feb
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Safety of bacteriophage therapy in severe Staphylococcus aureus infection
Fabijan AP, et al. Nat Microbiol, Feb 17, 2020. - Designing ecologically optimized pneumococcal vaccines using population genomics.
Colijn Caroline et al. Nature microbiology 2020 Feb - Potentially highly potent drugs for 2019-nCoV
Nguyen DD, et al. bioRxiv, Feb 13, 2020.
HOST-MICROBE INTERACTIONS
- Profiling the immune vulnerability landscape of the 2019 Novel Coronavirus
Zhu J, et al. bioRxiv, Feb 12, 2020. - Changes in Microbiome Confer Multigenerational Host Resistance after Sub-toxic Pesticide Exposure.
Wang Guan-Hong et al. Cell host & microbe 2020 Feb (2) 213-224.e7
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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