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Public Health Genomics Knowledge Base (v1.0)

Advanced Molecular Detection Clips

los capítulos incluidos en esta sección, se actualizarán semanalmente, incorporando documentos y accesos a nuevas bases de datos que actualmente están en desarrollo... los contenidos, como es costumbre en secciones avanzadas, están únicamente en idioma inglés y reflejan los últimos contenidos editados en cada materia en todo el mundo...

About Advanced Molecular Detection Clips

Advanced Molecular Detection(AMD) Clips are selected weekly from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in public health surveillance, investigation, and development of new diagnostics and interventions. The collection is not comprehensive but aims to capture highlights, while surveying a wide range of topics. CDC-authored articles are flagged.

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Spotlight

Twenty years of bacterial genome sequencing. Twenty years ago, the publication of the first bacterial genome sequence, from Haemophilus influenzae, shook the world of bacteriology. In this Timeline, we review the first two decades of bacterial genome sequencing, which have been marked by three revolutions: whole-genome shotgun sequencing, high-throughput sequencing and single-molecule long-read sequencing. We summarize the social history of sequencing and its impact on our understanding of the biology, diversity and evolution of bacteria, while also highlighting spin-offs and translational impact in the clinic. We look forward to a 'sequencing singularity', where sequencing becomes the method of choice for as-yet unthinkable applications in bacteriology and beyond.

Advanced Molecular Detection Clips Content

• News
• Events / Training / Web Resources
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• New Sepsis Detector Shrinks the Diagnosis from Days to Hours 
  Orcutt M. MIT Tech Rev, Nov 4, 2015.
• Fecal Transplants Made (Somewhat) More Palatable 
  Smith PA. New York Times, Nov 9, 2015.
• Nanotrap Lyme Antigen Test clinical study published 
  Outbreak News Today, Nov 11, 2015.
• Geneticist Craig Venter helped sequence the human genome. Now he wants yours. 
  Zimmer C. STAT, Nov 5, 2015.

EVENTS / TRAINING / WEB RESOURCES

• Apply to Attend the Winter 2016 Online Class "Fundamentals of Bioinformatics and Searching" 
  (training) Majewski K. NLM Tech Bull. 2015 Nov-Dec;(407):e2.

CONCEPTS / COMMENTS

• Twenty years of bacterial genome sequencing. 
  Loman Nicholas J et al. Nature reviews. Microbiology 2015 Nov
• A century of the phage: past, present and future. 
  Salmond George P C et al. Nature reviews. Microbiology 2015 Nov
• Typing of Neisseria meningitidis by whole-genome analysis. 
  Tsang Raymond S W et al. The Lancet. Infectious diseases 2015 Oct
• Microbiomes in light of traits: A phylogenetic perspective 
  Martiny JB, et al. Science, Nov 6, 2015.
• The ecology of the microbiome: Networks, competition, and stability 
  Coyte KZ, et al. Science, Nov 6, 2015.
• Mammoth 2.0: will genome engineering resurrect extinct species? 
  Shapiro Beth et al. Genome biology 2015 (1) 228

METHODS / TOOLS

• Pseudoalignment for metagenomic read assignment 
  Schaeffer L, et al. bioRxiv, Oct 26, 2015.
• Analysis of Minor Populations of Human Immunodeficiency Virus by Primer Identification and Insertion-Deletion and Carry Forward Correction Pipelines. 
  Hughes Paul et al. AIDS research and human retroviruses 2015 Nov
• Spaced seeds improve k-mer-based metagenomic classification. 
  Brinda Karel et al. Bioinformatics (Oxford, England) 2015 Nov (22) 3584-92
• Mobile diagnostics in outbreak response, not only for Ebola: a blueprint for a modular and robust field laboratory 
  Wolfel R, et al. Euro Surveill 2015;20(44):pii=30055.
• Improving control of antibiotic resistant gonorrhea by integrating research agendas across disciplines: key questions arising from mathematical modeling. 
  Grad Yonatan H et al. The Journal of infectious diseases 2015 Oct

EVOLUTION / ECOLOGY / POPULATIONS

• Characterisation of an emergent clone of Enteroinvasive Escherichia coli circulating in Europe. 
  Michelacci V et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2015 Nov
• High genetic similarity of ciprofloxacin-resistant Campylobacter jejuni in central Europe. 
  Kovac Jasna et al. Frontiers in microbiology 2015 1169
• Urogenital Chlamydia trachomatis strain types, defined by high-resolution multilocus sequence typing, in relation to ethnicity and urogenital symptoms among a young screening population in Amsterdam, The Netherlands. 
  Versteeg Bart et al. Sexually transmitted infections 2015 Sep (6) 415-22
• Incidence, Antimicrobial Resistance, and Molecular Characteristics of Nontyphoidal Salmonella Including Extended-Spectrum β-Lactamase Producers in Retail Chicken Meat. 
  Choi Dasom et al. Journal of food protection 2015 Nov (11) 1932-7
• Evidence for an Ancestral Association of Human Coronavirus 229E with Bats. 
  Corman Victor Max et al. Journal of virology 2015 Dec (23) 11858-70
• From lesions to viral clones: biological and molecular diversity amongst autochthonous Brazilian vaccinia virus. 
  Oliveira Graziele et al. Viruses 2015 Mar (3) 1218-37
• Genetic diversity of the Korean field strains of porcine reproductive and respiratory syndrome virus. 
  Lee Jung-Ah et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Nov
• Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data. 
  Lewis Nicola S et al. The Journal of general virology 2015 Aug (8) 2050-60
• Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin. 
  Wu Guangxi et al. PLoS genetics 2015 Nov (11) e1005614
• The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships. 
  Valdivia Hugo O et al. BMC genomics 2015 (1) 887

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes. 
  Chewapreecha Claire et al. PLoS genetics 2014 Aug (8) e1004547
• Specific genetic features of Campylobacter jejuni strain G1 revealed by genome sequencing. 
  Lehri Burhan et al. FEMS microbiology letters 2015 Feb (4)
• Evidence for the critical role of a secondary site rpoB mutation in the compensatory evolution and successful transmission of an MDR tuberculosis outbreak strain. 
  Meftahi Nedra et al. The Journal of antimicrobial chemotherapy 2015 Nov
• Multiple Origins of Mutations in the mdr1 Gene-A Putative Marker of Chloroquine Resistance in P. vivax. 
  Schousboe Mette L et al. PLoS neglected tropical diseases 2015 Nov (11) e0004196
• Identification of intrinsically metronidazole-resistant clades of Gardnerella vaginalis. 
  Schuyler Jessica A et al. Diagnostic microbiology and infectious disease 2015 Oct

DETECTION / DIAGNOSIS

• A real-time PCR assay for direct characterization of the Neisseria gonorrhoeae GyrA 91 locus associated with ciprofloxacin susceptibility. 
  Buckley Cameron et al. The Journal of antimicrobial chemotherapy 2015 Nov
• A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing. 
  Vogler Amy J et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Oct 21-36
• Detection of the HA-33 protein in botulinum neurotoxin type G complex by mass spectrometry. 
  Kalb Suzanne R et al. BMC microbiology 2015 (1) 227 (CDC Author)
• Evaluation of Selected Borrelia burgdorferi lp54 Plasmid-Encoded Gene Products Expressed during Mammalian Infection as Antigens To Improve Serodiagnostic Testing for Early Lyme Disease. 
  Weiner Zachary P et al. Clinical and vaccine immunology : CVI 2015 Nov (11) 1176-86 (CDC Author)
• Application of Nanotrap technology for high sensitivity measurement of urinary outer surface protein A carboxyl-terminus domain in early stage Lyme borreliosis. 
  Magni Ruben et al. Journal of translational medicine 2015 (1) 346
• Metagenomic profiling of the viromes of plasma collected from blood donors with elevated serum alanine aminotransferase levels. 
  Furuta Rika A et al. Transfusion 2015 Aug (8) 1889-99
• Molecular genotyping and quantitation assay for rotavirus surveillance. 
  Liu Jie et al. Journal of virological methods 2015 Mar 157-63 (CDC Author)
• Sequence-independent amplification coupled with DNA microarray analysis for detection and genotyping of noroviruses. 
  Hu Yuan et al. AMB Express 2015 Dec (1) 69
• Probing the Viromic Frontiers. 
  Rasmussen Angela L et al. mBio (6)
• Implementation of next-generation sequencing for hepatitis B resistance and genotyping in a clinical microbiology laboratory. 
  Lowe Christopher F et al. Journal of clinical microbiology 2015 Nov
• Molecular genotyping and sub-genotyping of Cryptosporidium spp. isolates from symptomatic individuals attending two major public hospitals in Madrid, Spain. 
  de Lucio Aida et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Oct 49-56
• Evidence of genotypic diversity among Candida auris isolates by multilocus sequence typing, matrix-assisted laser desorption ionization-time of flight mass spectrometry and amplified fragment length polymorphism. 
  Prakash Anupam et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2015 Nov
• Type-specific PCR assays for babesia bovis msa-1 genotypes in Asia: Revisiting the genetic diversity in Sri Lanka, Mongolia, and Vietnam. 
  Liyanagunawardena Nilukshi et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Oct

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Whole genome sequencing identifies circulating Beijing-lineage Mycobacterium tuberculosis strains in Guatemala and an associated urban outbreak.
  Saelens Joseph W et al. Tuberculosis (Edinburgh, Scotland) 2015 Sep
• Molecular Epidemiology of Invasive Listeriosis due to Listeria monocytogenes in a Spanish Hospital over a Nine-Year Study Period, 2006-2014. 
  Ariza-Miguel Jaime et al. BioMed research international 2015 191409
• Hospital-wide Eradication of a Nosocomial Legionella pneumophila Serogroup 1 Outbreak. 
  Bartley Paul B et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Oct
• Molecular epidemiology of genogroup II norovirus infection among hospitalized children with acute gastroenteritis in Suzhou (Jiangsu, China) from 2010 to 2013. 
  Fu Jian-Guang et al. Journal of medical virology 2015 Nov
• Epidemiological and genomic characteristics of a very large outbreak of Dengue in Guangdong, China. 
  Sun Jiufeng et al. The Journal of infection 2015 Nov

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• A gene deletion that up-regulates viral gene expression yields an attenuated RSV vaccine with improved antibody responses in children. 
  Karron Ruth A et al. Science translational medicine 2015 Nov (312) 312ra175
• RSV vaccine: Beating the virus at its own game. 
  Moscona Anne et al. Science translational medicine 2015 Nov (312) 312fs44
• Reversion of methicillin-susceptible Staphylococcus aureus to methicillin-resistant Staphylococcus aureus during treatment of bacteremia. 
  Proulx Megan K et al. The Journal of infectious diseases 2015 Oct

HOST-MICROBE INTERACTIONS

• Gut biogeography of the bacterial microbiota. 
  Donaldson Gregory P et al. Nature reviews. Microbiology 2015 Oct
• Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis. 
  Shelburne Samuel A et al. PloS one (11) e0139851