Advanced Molecular Detection Clips Content (Published on 12/14/2017)
Methylation Signatures Can Distinguish Bacterial Strains in Metagenomic Samples
Heger M. GenomeWeb, Dec 13, 2017.
Urine Test for TB Yields Results in 12 Hours
Akst J. The Scientist, Dec 14, 2017.
Uganda ends Marburg virus disease outbreak
WHO, Dec 8, 2017.
Genetic tests reveal more about new H5N6 reassortant
Schnirring L. CIDRAP, Dec 13, 2017.
Virome Project Aims to Outfox Pandemics With Global Virus Atlas
Johnson M. GenomeWeb, Dec 13, 2017.
Ebola survivors still immune to virus after 40 years
Hayden EC. Nature, Dec 14, 2017.
Human Microbiome Program at MUSC Shows Early Promise
Versel N. GenomeWeb, Dec 12, 2017
EVENTS / TRAINING / WEB RESOURCES
Summer 2017 NCBI Hackathon Products
(links to software: Nastybugs, Staphviewer, Virome Sniffer) NCBI, Dec 12, 2017.
CONCEPTS / COMMENTS
METHODS / TOOLS
Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.
Beaulaurier John et al. Nature biotechnology 2017 Dec
Ten quick tips for machine learning in computational biology
Chicco D. BioData Mining, Dec 8, 2017.
EVOLUTION / ECOLOGY / POPULATIONS
Identification and genomic characterization of the emerging Senecavirus A in southeast China, 2017.
Zhang X et al. Transboundary and emerging diseases 2017 Dec
Evolutionary analysis of mumps viruses of genotype F collected in mainland China in 2001-2015.
Cui Aili et al. Scientific reports 2017 Dec (1) 17144
Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India.
Alampalli Shuba Varshini et al. PloS one 2017 (12) e0188603
Molecular evolution of types in non-polio enteroviruses.
Lukashev Alexander N et al. The Journal of general virology 2017 Dec (12) 2968-2981
The Impacts of Genome-wide Analyses on our Understanding of Human Herpesvirus Diversity and Evolution.
Renner Daniel W et al. Journal of virology 2017 Oct
Inferred father-to-son transmission of herpes simplex virus results in near-perfect preservation of viral genome identity and in vivo phenotypes.
Pandey Utsav et al. Scientific reports 2017 Oct (1) 13666
Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome.
Drees Kevin P et al. mBio 2017 Dec (6)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
Phylogeny and antimicrobial resistance in Neisseria gonorrhoeae isolates from Rio de Janeiro, Brazil.
Costa-Lourenço Ana Paula Ramalho et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Dec
Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Salmonella enterica serovars Typhi and Paratyphi.
Day Martin R et al. The Journal of antimicrobial chemotherapy 2017 Dec
Topical antibiotic use co-selects for the carriage of mobile genetic elements conferring resistance to unrelated antimicrobials in Staphylococcus aureus.
Carter Glen P et al. Antimicrobial agents and chemotherapy 2017 Dec
Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife.
Thomas Milton et al. Gut pathogens 2017 66
Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen
Gao W, et al. Current Opinion Microbiology 2018;41:76-82.
DETECTION / DIAGNOSIS
Development and Evaluation of a Loop-Mediated Isothermal Amplification Assay for the Detection of Treponema pallidum DNA in the Peripheral Blood of Secondary Syphilis Patients.
Xiao Yongjian et al. The American journal of tropical medicine and hygiene 2017 Dec (6) 1673-1678
Molecular Methods for Detection of Antimicrobial Resistance.
Anjum Muna F et al. Microbiology spectrum 2017 Dec (6)
Low cost, low tech SNP genotyping tools for resource-limited areas: Plague in Madagascar as a model.
Mitchell Cedar L et al. PLoS neglected tropical diseases 2017 Dec (12) e0006077
Comparison of sequential multiplex PCR, sequetyping and whole genome sequencing for serotyping of Streptococcus pneumoniae.
Mauffrey Florian et al. PloS one 2017 (12) e0189163
Molecular typing of methicillin-resistant Staphylococcus aureus: Comparison of PCR-based open reading frame typing, multilocus sequence typing, and Staphylococcus protein A gene typing.
Ogihara Shinji et al. Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy 2017 Dec
Genetic analysis and CRISPR typing of Salmonella enterica serovar Enteritidis from different sources revealed potential transmission from poultry and pig to human.
Li Qiuchun et al. International journal of food microbiology 2017 Nov 119-125
Advances in Serodiagnostic Testing for Lyme Disease Are at Hand.
Branda John A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Dec
Integration of molecular typing results into tuberculosis surveillance in Germany-A pilot study.
Andrés Marta et al. PloS one 2017 (11) e0188356
Diagnostic Assay Development for Poliovirus Eradication.
Gerloff Nancy et al. Journal of clinical microbiology 2017 Dec
Yeast identification by sequencing, biochemical kits, MALDI-TOF MS and rep-PCR DNA fingerprinting.
Zhao Ying et al. Medical mycology 2017 Dec
Identification of clinical isolates of Aspergillus, including cryptic species, by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).
Vidal-Acuña M Reyes et al. Medical mycology 2017 Dec
Direct genetic characterization of Toxoplasma gondii from clinical samples from Denmark: not only genotypes II and III.
Jokelainen P et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2017 Dec
Passively versus Actively Detected Malaria: Similar Genetic Diversity but Different Complexity of Infection.
Pava Zuleima et al. The American journal of tropical medicine and hygiene 2017 Dec (6) 1788-1796
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
Investigation using whole genome sequencing of a prolonged restaurant outbreak of Salmonella Typhimurium linked to the building drainage system, England, February 2015 to March 2016
Mair-Jenkins J, et al. Eurosurveillance, Dec 7, 2017.
Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania.
Phan H T T et al. The Journal of antimicrobial chemotherapy 2017 Dec
Pseudomonas aeruginosa intensive care unit outbreak: winnowing of transmissions with molecular and genomic typing.
Parcell Benjamin J et al. The Journal of hospital infection 2017 Dec
Burkholderia stabilis outbreak associated with contaminated commercially-available washing gloves, Switzerland, May 2015 to August 2016.
Sommerstein Rami et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Dec (49)
ANTIMICROBIALS / VACCINES / INTERVENTIONS
Safety, tolerability, and immunogenicity of two Zika virus DNA vaccine candidates in healthy adults: randomised, open-label, phase 1 clinical trials.
Gaudinski Martin R et al. Lancet (London, England) 2017 Dec
Meningococcal Carriage Following a Vaccination Campaign With MenB-4C and MenB-FHbp in Response to a University Serogroup B Meningococcal Disease Outbreak-Oregon, 2015-2016.
McNamara Lucy A et al. The Journal of infectious diseases 2017 Nov (9) 1130-1140
Association of heterozygous CCR5Δ32 deletion with survival in HIV-infection: A cohort study.
Ruiz-Mateos Ezequiel et al. Antiviral research 2017 Dec 15-19
Genetic Susceptibility to Hemolytic-Uremic Syndrome after Shiga Toxin-Producing Escherichia Coli (STEC) Infection: a Centers for Disease Control and Prevention (CDC) FoodNet Study.
Kallianpur Asha R et al. The Journal of infectious diseases 2017 Dec
Utilization of genomic sequencing for population screening of immunodeficiencies in the newborn.
Pavey Ashleigh R et al. Genetics in medicine : official journal of the American College of Medical Genetics 2017 Dec (12) 1367-1375
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