ACTUALIZACIÓN MÉDICO-CONTINUADA EN GENÓMICA Y SU IMPACTO EN LA SALUD PÚBLICA || TRATADO CONTINUO DE ENFERMEDADES USUALMENTE "COMUNICABLES" - Public Health Genomics Knowledge Base (v1.2) | 21 de AGOSTO de 2016

Public Health Genomics Knowledge Base (v1.2)





ACTUALIZACIÓN MÉDICO-CONTINUADA EN GENÓMICA Y SU IMPACTO EN LA SALUD PÚBLICA || TRATADO CONTINUO DE ENFERMEDADES USUALMENTE "COMUNICABLES" - Public Health Genomics Knowledge Base (v1.2) | 21 de AGOSTO de 2016



ACTUALIZACIÓN QUE COMPRENDE desde el 18 de AGOSTO al 24 de AGOSTO de 2016

Advanced Molecular Detection Clips

About Advanced Molecular Detection Clips

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 infectious disease 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. Items marked I&E address aspects of implementation or evaluation in clinical or public health practice.

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Advanced Molecular Detection Clips Content

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

NEWS

• NIAID launches trial testing Zika vaccine for humans 
  Healio, Aug 13, 2016.
• As New York Fights Zika Virus, Officials Turn Their Focus to Sex 
  Santora M, Schmidt S. New York Times, Aug 12, 2016.
• Zika strains nation's blood-collection industry 
  Cranford S. Crain's, Aug 12, 2016.
• Current Methods for Counting HIV Proviruses May Be Inaccurate 
  GenomeWeb, Aug 9, 2016.
• WPV1 resurges in Nigeria 
  Healio, Aug 11, 2016.
• Canadian and UK Researchers Team on Genomic Tuberculosis Testing, Reporting Infrastructure 
  Thomas UG. GenomeWeb, Aug 16, 2016.
• Microbial Identification and Tracking: the Next Generation 
  (blog post) mBiosphere, Aug 16, 2016.
• Team Develops Consensus Sequencing Method to Improve Accuracy of Oxford Nanopore's MinIon 
  Heger M. GenomeWeb, Aug 11, 2016.
• Brazilian Researchers Profile Microbiome of Rio Before, During, After Olympic Games 
  Curtin C. GenomeWeb, Aug 16, 2016.

POLICY

• FDA Seeks Input on OTC Infectious Disease Testing 
  Walker M. MedPage Today, Aug 15, 2016.
• Ebola. Zika. Could a rapid-response fund help the US address crises faster? 
  Nather D. STAT, Aug 15, 2016.
• Make Data Sharing Routine to Prepare for Public Health Emergencies 
  Chretien JP, et al. PLoS Med, Aug 16, 2016.
• U.N. Admits Role in Cholera Epidemic in Haiti 
  Katz JM. New York Times, Aug 17, 2016.

CONCEPTS / COMMENTS

• Pains and Gains from China's Experiences with Emerging Epidemics: From SARS to H7N9. 
  Wei Pengfei et al. BioMed research international 5717108
• Expansion of Microbial Forensics. 
  Schmedes Sarah E et al. Journal of clinical microbiology 2016 Aug (8) 1964-74
• Preclinical studies and prospective clinical applications for bacteria-targeted imaging: the future is bright. 
  Heuker Marjolein et al. Clinical and translational imaging 253-264

METHODS / TOOLS

• Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories. 
  Gargis Amy S et al. Journal of clinical microbiology 2016 Aug 
• KlebSeq: A Diagnostic Tool for Surveillance, Detection, and Monitoring of Klebsiella pneumoniae. 
  Bowers Jolene R et al. Journal of clinical microbiology 2016 Aug
• LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes. 
  Hanson Niels W et al. Bioinformatics (Oxford, England) 2016 Aug
• Analysis of Metagenomics Next Generation Sequence Data for Fungal ITS Barcoding: Do You Need Advance Bioinformatics Experience? 
  Ahmed Abdalla et al. Frontiers in microbiology 2016 1061
• SARS-like WIV1-CoV poised for human emergence. 
  Menachery Vineet D et al. Proceedings of the National Academy of Sciences of the United States of America 2016 Mar (11) 3048-53
• INC-Seq: accurate single molecule reads using nanopore sequencing. 
  Li Chenhao et al. GigaScience 2016 (1) 34
• Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights. 
  Pasolli Edoardo et al. PLoS computational biology 2016 Jul (7) e1004977

EVOLUTION / ECOLOGY / POPULATIONS

• A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland 
  Raven KE, et al. Genome Res, Aug 16, 2016.
• A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet? 
  Garrity George M et al. Journal of clinical microbiology 2016 Aug (8) 1956-63
• Increase in pertussis cases along with high prevalence of two emerging genotypes of Bordetella pertussis in Perú, 2012. 
  Bailon H et al. BMC infectious diseases (1) 422
• Multilevel population genetic analysis of vanA and vanB Enterococcus faecium causing nosocomial outbreaks in 27 countries (1986-2012). 
  Freitas Ana R et al. The Journal of antimicrobial chemotherapy 2016 Aug
• Genomic insights into the emergence and spread of international clones of healthcare-, community- and livestock-associated meticillin-resistant Staphylococcus aureus: Blurring of the traditional definitions. 
  Bal A M et al. Journal of global antimicrobial resistance 2016 May 95-101
• Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria. 
  Boritsch Eva C et al. Proceedings of the National Academy of Sciences of the United States of America 2016 Aug
• Impact of HIV co-infection on the evolution and transmission of multidrug-resistant tuberculosis. 
  Eldholm Vegard et al. eLife 2016
• Link of a ubiquitous human coronavirus to dromedary camels 
  Corman VM, et al. PNAS, Aug 15, 2015.
• First NGS full genome characterization of a hepatitis C virus genotype 7 divergent subtype. 
  Salmona Maud et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 Aug
• Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. 
  Mena Ignacio et al. eLife 2016
• Defective proviruses rapidly accumulate during acute HIV-1 infection. 
  Bruner Katherine M et al. Nature medicine 2016 Aug
• Uncovering Earth’s virome 
  Paez-Espino D, et al. Nature, Aug 17, 2016.
• Molecular Evolution and Spatial Transmission of Severe Fever with Thrombocytopenia Syndrome Virus Based on Complete Genome Sequences. 
  Liu Jian-Wei et al. PloS one 2016 (3) e0151677
• Analysis of HCV-6 isolates among Asian-born immigrants in North America reveals their high genetic diversity and a new subtype. 
  Lu Ling et al. Virology 2016 May 25-31
• Population Genetic Analysis Reveals a High Genetic Diversity in the Brazilian Cryptococcus gattii VGII Population and Shifts the Global Origin from the Amazon Rainforest to the Semi-arid Desert in the Northeast of Brazil. 
  Souto Ana C P et al. PLoS neglected tropical diseases 2016 Aug (8) e0004885 
• Metagenomic analysis of fungal taxa inhabiting Mecca region, Saudi Arabia. 
  Moussa Tarek A A et al. Genomics data 2016 Sep 126-7

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• First Report of the Globally Disseminated IncX4 Plasmid Carrying the mcr-1 Gene in a Colistin-Resistant Escherichia coli ST101 isolated from a Human Infection in Brazil. 
  Fernandes Miriam R et al. Antimicrobial agents and chemotherapy 2016 Aug
• Molecular epidemiology of drug-resistant Neisseria gonorrhoeae in Russia (Current Status, 2015). 
  Kubanov Alexey et al. BMC infectious diseases 2016 389
• High prevalence of the PER-1 gene among carbapenem-resistant Acinetobacter baumannii in Riyadh, Saudi Arabia. 
  Aly M M et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2016 Aug
• Multidrug Intrinsic Resistance Factors in Staphylococcus aureus Identified by Profiling Fitness within High-Diversity Transposon Libraries. 
  Rajagopal Mithila et al. mBio (4)
• Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients. 
  Jitwasinkul Tossawan et al. Journal of global antimicrobial resistance 2016 Apr 57-66
• Whole-genome sequencing of multidrug-resistant Mycobacterium tuberculosis isolates from Myanmar. 
  Aung Htin Lin et al. Journal of global antimicrobial resistance 2016 May 113-117
• Genetic variation in Mycobacterium tuberculosis isolates from a London outbreak associated with isoniazid resistance. 
  Satta Giovanni et al. BMC medicine (1) 117
• Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. 
  Phelan Jody et al. BMC medicine 2016 31
• Whole-Genome Sequencing Analysis of Serially Isolated Multi-Drug and Extensively Drug Resistant Mycobacterium tuberculosis from Thai Patients.
  Faksri Kiatichai et al. PloS one (8) e0160992
• Preliminary Evaluation of the Effect of Investigational Ebola Virus Disease Treatments on Viral Genome Sequences. 
  Whitmer Shannon L M et al. The Journal of infectious diseases 2016 Aug  
• HCV NS3 naturally occurring variants in HIV/HCV coinfected DAA-naïve patients: consideration for HCV genotyping resistance testing. 
  Ruggiero T et al. Infection 2016 Aug

DETECTION / DIAGNOSIS

• Streptococcus dysgalactiae subsp. equisimilis Isolated From Infections in Dogs and Humans: Are Current Subspecies Identification Criteria accurate?
  Ciszewski Marcin et al. Current microbiology 2016 Aug
• Imaging bacteria with radiolabelled quinolones, cephalosporins and siderophores for imaging infection: a systematic review. 
  Auletta S et al. Clinical and translational imaging 229-252
• Staphylococcus aureus Regulatory RNAs as Potential Biomarkers for Bloodstream Infections. 
  Bordeau Valérie et al. Emerging infectious diseases 2016 Sep (9) 1570-1578
• Evaluation of Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) for identification of KPC-producing K. pneumoniae. 
  Gaibani Paolo et al. Journal of clinical microbiology 2016 Jul
• Combined approach to the identification of clinically infrequent non-tuberculous mycobacteria in Argentina. 
  Monteserin J et al. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 2016 Sep (9) 1257-62
• Background review for diagnostic test development for Zika virus infection. 
  Charrel Rémi N et al. Bulletin of the World Health Organization 2016 Aug (8) 574-584D
• Prolonged Detection of Zika Virus RNA in Pregnant Women. 
  Meaney-Delman Dana et al. Obstetrics and gynecology 2016 Jul 
• Is "dried stool spots on filter paper method (DSSFP)" more sensitive and effective for detecting Blastocystis spp. and their subtypes by PCR and sequencing? 
  Seyer Ayse et al. Parasitology research 2016 Aug
• High-resolution molecular typing of two large outbreaks of acute Chagas disease in Colombia. 
  Hernández Carolina et al. The Journal of infectious diseases 2016 Aug

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Whole genome sequencing analysis of Salmonella Enteritidis isolated in Chile provides insights about possible transmission between gulls, poultry and humans. 
  Toro Magaly et al. Applied and environmental microbiology 2016 Aug
• MRSA CC398 in humans and pigs in Norway: A "One Health" perspective on introduction and transmission. 
  Grøntvedt Carl Andreas et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Aug
• Travel- and Community-Based Transmission of Multidrug-Resistant Shigella sonnei Lineage among International Orthodox Jewish Communities 
  Baker KS, et al. Emerg Infect Dis, Sep 2016.
• An Outbreak of Clostridium difficile Ribotype 027 Associated with Length of Stay in the Intensive Care Unit and Use of Selective Decontamination of the Digestive Tract: A Case Control Study. 
  van Beurden Yvette H et al. PloS one (8) e0160778
• Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium. 
  Carter Glen P et al. The Journal of antimicrobial chemotherapy 2016 Aug
• Treatment as Prevention: Characterization of partner infections in the HIV Prevention Trials Network 052 trial. 
  Eshleman Susan H et al. Journal of acquired immune deficiency syndromes (1999) 2016 Aug  

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Design of the FemCure study: prospective multicentre study on the transmission of genital and extra-genital Chlamydia trachomatis infections in women receiving routine care. 
  Dukers-Muijrers Nicole H T M et al. BMC infectious diseases 2016 381 
• Negative Feedback Regulation of HIV-1 by Gene Editing Strategy. 
  Kaminski Rafal et al. Scientific reports 31527

HOST-MICROBE INTERACTIONS

• Gut Microbiome Associates With Lifetime Cardiovascular Disease Risk Profile Among Bogalusa Heart Study Participants. 
  Kelly Tanika N et al. Circulation research 2016 Aug
• Gut microbiome predictors of treatment response and recurrence in primary Clostridium difficile infection. 
  Khanna S et al. Alimentary pharmacology & therapeutics 2016 Aug
• A community-based prospective cohort study of dengue viral infection in Malaysia: the study protocol. 
  Jahan Nowrozy Kamar et al. Infectious diseases of poverty 2016 (1) 76

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.

Public Health Genomics Knowledge Base (v1.2)