Advanced Molecular Detection Clips Content (Published on 05/02/2019)
European Project Aims to Develop Tools, Guidelines to Improve Data Sharing, Access
Petrone J. GenomeWeb, Apr 26, 2019.
Method to Improve Nanopore Sequencing Accuracy Developed by University of Washington Team
Heger M. GenomeWeb, Apr 30, 2019
Microbiology Meets Machine Learning
Williams R. The Scientist, May 1, 2019.
CONCEPTS / COMMENTS
Candida auris: An emerging pathogen "incognito"?
Nett Jeniel E et al. PLoS pathogens 2019 04 (4) e1007638
Using Machine Learning to Battle Antibiotic Resistance
Dance A. The Scientist, May 1, 2019.
METHODS / TOOLS
DNAscan: personal computer compatible NGS analysis, annotation and visualisation.
Iacoangeli A et al. BMC bioinformatics 2019 Apr (1) 213
BHap: a novel approach for bacterial haplotype reconstruction.
Li Xin et al. Bioinformatics (Oxford, England) 2019 Apr
ORCA: A Comprehensive Bioinformatics Container Environment for Education and Research.
Jackman Shaun D et al. Bioinformatics (Oxford, England) 2019 Apr
Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage.
Noakes Matthew T et al. Nature biotechnology 2019 Apr
The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences.
Tapinos Avraam et al. Viruses 2019 Apr (5)
Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology - A systematic literature review.
Mintzer Vered et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Apr
A Comparison of Three Different Bioinformatics Analyses of the 16S-23S rRNA Encoding Region for Bacterial Identification.
Peker Nilay et al. Frontiers in microbiology 2019 620
Rapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory.
Blane Beth et al. The Journal of antimicrobial chemotherapy 2019 Apr
Whole-genome and targeted sequencing of drug-resistant Mycobacterium tuberculosis on the iSeq100 and MiSeq: A performance, ease-of-use, and cost evaluation.
Colman Rebecca E et al. PLoS medicine 2019 Apr (4) e1002794
EVOLUTION / ECOLOGY / POPULATIONS
Defining the core essential genome of Pseudomonas aeruginosa
Poulsen BE, et al. Proc Nat Acad Sci, Apr 29, 2019.
Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing.
Dyrdak Robert et al. Virus evolution 2019 Jan (1) vez007
Combination of surveillance tools reveals that Yellow Fever virus can remain in the same Atlantic Forest area at least for three transmission seasons.
Abreu Filipe Vieira Santos de et al. Memorias do Instituto Oswaldo Cruz 2019 e190076
Local Epidemics Gone Viral: Evolution and Diffusion of the Italian HIV-1 Recombinant Form CRF60_BC.
Lai Alessia et al. Frontiers in microbiology 2019 769
Genetic landscape and macro-evolution of co-circulating Coxsackieviruses A and Vaccine-derived Polioviruses in the Democratic Republic of Congo, 2008-2013.
Sadeuh-Mba Serge Alain et al. PLoS neglected tropical diseases 2019 Apr (4) e0007335
Microbiome analysis of Ixodes scapularis ticks from New York and Connecticut.
Tokarz Rafal et al. Ticks and tick-borne diseases 2019 Apr
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
CRISPR tracking reveals global spreading of antimicrobial resistance genes by Staphylococcus of canine origin.
Rossi Ciro César et al. Veterinary microbiology 2019 May 65-69
Global Spread of Mutant PfCRT and Its Pleiotropic Impact on Plasmodium falciparum Multidrug Resistance and Fitness.
Dhingra Satish K et al. mBio 2019 04 (2)
DETECTION / DIAGNOSIS
Preliminary Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food - Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2015-2018.
Tack Danielle M et al. MMWR. Morbidity and mortality weekly report 2019 Apr (16) 369-373
Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors.
Heinz Eva et al. Microbial genomics 2019 Apr
Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance.
Guglielmini Julien et al. PLoS neglected tropical diseases 2019 Apr (4) e0007374
Design and validation of transcription-mediated amplification nucleic acid amplification tests for Mycoplasma genitalium .
Kirkconnell Brett et al. Journal of clinical microbiology 2019 Apr
Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples.
Kamaraj Uma Sangumathi et al. PLoS neglected tropical diseases 2019 Apr (4) e0007184
Using the Plasmodium mitochondrial genome for classifying mixed-species infections and inferring the geographical origin of P. falciparum parasites imported to the U.S.
Schmedes Sarah E et al. PloS one 2019 (4) e0215754
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
Whole genome sequencing uses for foodborne contamination and compliance: Discovery of an emerging contamination event in an ice cream facility using whole genome sequencing.
Allard Marc W et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Apr
Notes from the Field: Outbreak of Multidrug-Resistant Shigella sonnei Infections in a Retirement Community Vermont, OctoberNovember 2018
Strysko J, et al. MMWR, May 3, 2019.
Prevalence and detection of drug resistant mutations in Mycobacterium tuberculosis among drug naïve patients in Nairobi, Kenya.
Ogari Collins Otieno et al. BMC infectious diseases 2019 Mar (1) 279
Hepatitis C Virus Potentially Transmitted by Opioid Drug Diversion from a Nurse - Washington, August 2017-March 2018.
Njuguna Henry N et al. MMWR. Morbidity and mortality weekly report 2019 Apr (16) 374-376
A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation.
Järvenpää Marko et al. PLoS computational biology 2019 Apr (4) e1006534
Host immune markers distinguish C. difficile infection from asymptomatic carriage and non-C. difficile diarrhea
Kelly CP, et al. Clin Infect Dis, Apr 26, 2019.
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