Spotlight
Collaborative Effort for a Centralized Worldwide Tuberculosis Relational Sequencing Data Platform. Continued progress in addressing challenges associated with detection and management of tuberculosis requires new diagnostic tools. These tools must be able to provide rapid and accurate information for detecting resistance to guide selection of the treatment regimen for each patient. To achieve this goal, globally representative genotypic, phenotypic, and clinical data are needed in a standardized and curated data platform. A global partnership of academic institutions, public health agencies, and nongovernmental organizations has been established to develop a tuberculosis relational sequencing data platform (ReSeqTB) that seeks to increase understanding of the genetic basis of resistance by correlating molecular data with results from drug susceptibility testing and, optimally, associated patient outcomes. These data will inform development of new diagnostics, facilitate clinical decision making, and improve surveillance for drug resistance. ReSeqTB offers an opportunity for collaboration to achieve improved patient outcomes and to advance efforts to prevent and control this devastating disease.
Advanced Molecular Detection Clips Content
NEWS
- The Rising Risk of a Contaminated Blood Supply
Landro L. Wall Street Journal, Sep 27, 2015. - The National Infection Service: a first step to an integrated and system wide approach to implementing genomics?
Luheshi L. PHG Foundation, Sep 25, 2015. - Columbia University Team Develops NGS Method to Screen for Viruses From Clinical Samples
Heger M. GenomeWeb, Sep 25, 2015. - Scientists find way to disarm deadly bacteria without destroying the good ones in your gut
Sun LH. Washington Post, Sep 23, 2015. - Another Frontier in Microbiome Research: Preterm Birth
Jacob JA. JAMA, Sep 29, 2015. - Mislabeled Genomes to be Fixed
Grens K. The Scientist, Sep 29, 2015.
CONCEPTS / COMMENTS
- A phylogenomic data-driven exploration of viral origins and evolution
Nasir A, Caetano-Anolles G. Science Advances 2015; 1:e1500527. - Analysis of Viral, Cellular Proteomes Indicates Ancient Cellular Origin for Viruses
GenomeWeb, Sep 25, 2015. - Host genetic architecture and the landscape of microbiome composition: humans weigh in.
Benson Andrew K et al. Genome biology 2015 (1) 203 - Data sharing: Why it's all "mine"
Yoho R. Nature Jobs, Sep 25, 2015. - Adeno-associated virus finds its disease
Russell DW, Grompe M. Nat Genet, Sep 29, 2015. - A Blueprint to Address Research Gaps in the Development of Biomarkers for Pediatric Tuberculosis.
Nicol Mark Patrick et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Oct (suppl 3) S164-S172 (CDC Author) - Collaborative Effort for a Centralized Worldwide Tuberculosis Relational Sequencing Data Platform.
Starks Angela M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Oct S141-6 (CDC Author) - Genetic tuning of avian influenza A (H7N9) virus promotes viral fitness within different species.
Zhu Wenfei et al. Microbes and infection / Institut Pasteur 2015 Feb (2) 118-22 - Rapid molecular diagnostic tests in patients with bacteremia: evaluation of their impact on decision making and clinical outcomes.
Vardakas K Z et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2015 Sep - IDSA and Gain-of-Function Experiments with Pathogens having Pandemic Potential1.
Frank Gregory M et al. The Journal of infectious diseases 2015 Sep - The main challenges that remain in applying high-throughput sequencing to clinical diagnostics.
Loeffelholz Michael et al. Expert review of molecular diagnostics 2015 Sep 1-4 - Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management
Woolhouse ME, et al. Sci Transl Med, Sep 30, 2015.
METHODS / TOOLS
- Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data.
Liu Yang et al. BMC bioinformatics 2015 202 - RDTs as a source of DNA to study Plasmodium falciparum drug resistance in isolates from Senegal and the Comoros Islands.
Papa Mze Nasserdine et al. Malaria journal 2015 (1) 373 - Targeted Proteomics of Human Metapneumovirus in Clinical Samples and Viral Cultures.
Foster Matthew W et al. Analytical chemistry 2015 Sep - PanFP: pangenome-based functional profiles for microbial communities.
Jun Se-Ran et al. BMC research notes 2015 (1) 479
EVOLUTION / ECOLOGY / POPULATIONS
- Genotypes of the Enterovirus Causing Hand Foot and Mouth Disease in Shanghai, China, 2012-2013.
Xu Menghua et al. PloS one 2015 (9) e0138514 - Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.
Nandi Tannistha et al. Genome research 2015 Jan (1) 129-41 - Genotypic characteristics of Mycobacterium tuberculosis circulating in Xinjiang, China.
Yuan Li et al. Infectious diseases (London, England) 2015 Sep 1-8 - Molecular Signature of the Ebola Virus Associated with the Fishermen Community Outbreak in Aberdeen, Sierra Leone, in February 2015.
Capobianchi Maria R et al. Genome announcements 2015 (5) - Molecular epidemiology and distribution of serotypes, genotypes, and antibiotic resistance genes of Streptococcus agalactiae clinical isolates from Guelma, Algeria and Marseille, France.
Bergal A et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2015 Sep - The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource.
Baker Kate S et al. Genome medicine 2015 (1) 97 - Phylogenetic relationship of non-typeable Haemophilus influenzae isolated in Malaysia.
Mohd-Zain Zaini et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Sep - Phylogenetic relationship of non-typeable Haemophilus influenzae isolated in Malaysia.
Mohd-Zain Zaini et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Sep - Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal.
Cohen Keira A et al. PLoS medicine 2015 Sep (9) e1001880 - High Prevalence of HIV Low abundance Drug resistant variants in a treatment naïve population in North Rift Kenya.
Cheriro Winfrida et al. AIDS research and human retroviruses 2015 Sep
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- The Distribution of Fitness Costs of Resistance-Conferring Mutations Is a Key Determinant for the Future Burden of Drug-Resistant Tuberculosis: A Model-Based Analysis.
Knight Gwenan M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Oct S147-54 - Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages.
Yin Shuang et al. BMC genomics 2015 (1) 733 - Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033.
Liu Canying et al. BMC genomics 2015 (1) 717 - Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris.
Chatterjee Sharanya et al. BMC genomics 2015 (1) 686 - Improved Detection by Next-Generation Sequencing of Pyrazinamide Resistance in Mycobacterium tuberculosis Isolates.
Maningi Nontuthuko E et al. Journal of clinical microbiology 2015 Sep - Genomic analysis, phenotype, and virulence of the historical Brazilian smallpox vaccine strain IOC: Implications for the origins and evolutionary relationships of vaccinia virus.
Medaglia Maria Luiza G et al. Journal of virology 2015 Sep
DETECTION / DIAGNOSIS
- A core genome MLST scheme for high-resolution typing of Enterococcus faecium.
de Been Mark et al. Journal of clinical microbiology 2015 Sep - Rapid Molecular Diagnostics, Antibiotic Treatment Decisions, and Developing Approaches to Inform Empiric Therapy: PRIMERS I and II.
Evans Scott R et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Sep - A novel cluster of Mycobacterium abscessus complex revealed by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS).
Suzuki Hiromichi et al. Diagnostic microbiology and infectious disease 2015 Aug - Rapid detection of carbapenemase activity: benefits and weaknesses of MALDI-TOF MS.
Mirande C et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2015 Sep - Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.
Greninger Alexander L et al. Genome medicine 2015 (1) 99 - Rapid Detection of Subtype H10N8 Influenza Virus by One-Step Reverse-Transcription Loop-Mediated Isothermal Amplification Methods.
Bao Hongmei et al. Journal of clinical microbiology 2015 Sep - Metabolomic Profiling of Plasma from Patients with Tuberculosis Using Untargeted Mass Spectrometry Reveals Novel Biomarkers for Diagnosis.
Lau Susanna K P et al. Journal of clinical microbiology 2015 Sep - Air and Surface Detection of Measles Virus RNA in a Hospital Setting.
Bischoff Werner E et al. The Journal of infectious diseases 2015 Sep - Application of Metagenomic Sequencing to Food Safety: Detection of Shiga Toxin-producing Escherichia coli on Fresh Bagged Spinach.
Leonard Susan R et al. Applied and environmental microbiology 2015 Sep - Reevaluation of an Acanthamoeba Molecular Diagnostic Algorithm following an Atypical Case of Amoebic Keratitis.
Lau Rachel et al. Journal of clinical microbiology 2015 Oct (10) 3213-8 (CDC Author)
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Genome sequencing reveals strain dynamics of methicillin-resistant Staphylococcus aureus in the same household in the context of clinical disease in a person and a dog.
Davis Meghan F et al. Veterinary microbiology 2015 Sep - An Outbreak of Lymphocutaneous Sporotrichosis among Mine-Workers in South Africa.
Govender Nelesh P et al. PLoS neglected tropical diseases 2015 Sep (9) e0004096 - Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting.
Tong Steven Y C et al. Genome research 2015 Jan (1) 111-8 - Genomic Surveillance elucidates Persistent Wild Poliovirus Transmission during 2013-2015 in Major Reservoir Areas of Pakistan.
Alam Muhammad Masroor et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Sep
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence.
Norling Martin et al. BMC genomics 2015 (1) 729
HOST-MICROBE INTERACTIONS
- Frequent detection of high human papillomavirus DNA loads in oral potentially malignant disorders.
Pierangeli Alessandra et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2015 Sep - Vaginal microbiome and metabolome highlight specific signatures of bacterial vaginosis.
Vitali B et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2015 Sep - Contribution of IL6 -174 G>C and IL1B +3954 C>T polymorphisms to congenital infection with Toxoplasma gondii.
Wujcicka W et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2015 Sep - CCR2, CCR5, and CXCL12 variation and HIV/AIDS in Papua New Guinea.
Mehlotra Rajeev K et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Sep - Is Campylobacter to esophageal adenocarcinoma as Helicobacter is to gastric adenocarcinoma?
Kaakoush Nadeem O et al. Trends in microbiology 2015 Aug (8) 455-62 - A novel locus of resistance to severe malaria in a region of ancient balancing selection.
et al. Nature 2015 Sep - Intestinal microbial communities associated with acute enteric infections and disease recovery.
Singh Pallavi et al. Microbiome 2015 (1) 45 - Dormant phages of Helicobacter pylori reveal distinct populations in Europe.
Vale F F et al. Scientific reports 2015 14333
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