Publication Date: Jan 26, 2017
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.
Advanced Molecular Detection Clips Content
NEWS
- Toward a Virus-Free Polio Vaccine
Taylor AP. The Scientist, Jan 19, 2017. - New organisms have been formed using the first ever 6-letter genetic code
Crew B. Science Alert, Jan 24, 2017. - Ebola Survivors Have Different Transcriptome Profiles From Those Who Die
GenomeWeb, Jan 19, 2017. - Microbiome as complex as previously thought
J Harris, PHG Foundation, January 24, 2017. - NSF, USDA Award Microbiome Research Grants
Macron D. GenomeWeb, Jan 24, 2017. - FDA Releases Discussion Paper on LDT Regulation After Gathering Stakeholder Feedback
Ray T. GenomeWeb, Jan 17, 2017.
EVENTS / TRAINING / WEB RESOURCES
- The Future of Machine Learning
(webcast) National Academies of Science, Sackler Forum, Jan 31-Feb 1, 2017.
CONCEPTS / COMMENTS
- The Case for Adopting the "Species Complex" Nomenclature for the Etiologic Agents of Cryptococcosis.
Kwon-Chung Kyung J et al. mSphere (1) - Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing.
Boland Mary Regina et al. PLoS computational biology 2017 Jan (1) e1005278
METHODS / TOOLS
- Baseline Practices for the Application of Genomic Data Supporting Regulatory Food Safety.
Lambert Dominic et al. Journal of AOAC International 2017 Jan - Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms.
Zhang Qiang et al. Scientific reports 2017 Jan 41192 - Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks.
Didelot Xavier et al. Molecular biology and evolution 2017 Jan - FIND Tuberculosis Strain Bank: a resource for researchers and developers working on tests to detect Mycobacterium tuberculosis and related drug resistance.
Tessema Belay et al. Journal of clinical microbiology 2017 Jan - Haemagglutinin and neuraminidase sequencing delineate nosocomial influenza outbreaks with accuracy equivalent to whole genome sequencing.
Houghton Rebecca et al. The Journal of infection 2017 Jan - Inference of Transmission Network Structure from HIV Phylogenetic Trees.
Giardina Federica et al. PLoS computational biology 2017 Jan (1) e1005316 - VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.
Zhao Guoyan et al. Virology 2017 Jan 21-30 - Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya.
Levitt Brandt et al. Scientific reports 2017 Jan 41108 - Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies.
Borner Janus et al. BMC genomics 2017 Jan (1) 100 - Laboratory Testing of Donors and Stool for Fecal Microbiota Transplantation for Recurrent C. difficile Infection.
Woodworth Michael H et al. Journal of clinical microbiology 2017 Jan - Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes.
Saeedghalati Mohammadkarim et al. PLoS computational biology 2017 Jan (1) e1005362
EVOLUTION / ECOLOGY / POPULATIONS
- Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand.
Siriphap Achiraya et al. PloS one 2017 (1) e0169324 - Global and regional dissemination and evolution of Burkholderia pseudomallei.
Chewapreecha Claire et al. Nature microbiology 2017 Jan 16263 - Genomic epidemiology of penicillin non-susceptible pneumococci with non-vaccine serotypes causing invasive disease in the USA.
Andam Cheryl P et al. Journal of clinical microbiology 2017 Jan
- Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae.
Runcharoen Chakkaphan et al. Genome medicine 2017 Jan (1) 6 - High diversity of picornaviruses in rats from different continents revealed by deep sequencing.
Hansen Thomas Arn et al. Emerging microbes & infections 2016 Aug (8) e90 - New bunya-like viruses: Highlighting their relations.
Guterres Alexandro et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Jan - 15 year fulminant hepatitis B follow-up in Belgium: Viral evolution and signature of demographic change
Mina T, et al. Infect Genet Evol, Jan 21, 2017. - Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution.
Rutledge Gavin G et al. Nature 2017 Jan - Culture adaptation of malaria parasites selects for convergent loss-of-function mutants.
Claessens Antoine et al. Scientific reports 2017 Jan 41303
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Molecular characterisations of integrons in clinical isolates of Klebsiella pneumoniae in a Chinese tertiary hospital.
Xu Xuan et al. Microbial pathogenesis 2017 Jan - Fluoroquinolone, Macrolide, and Ketolide Resistance in Haemophilus parainfluenzae from South Africa.
Abotsi Regina Esinam et al. Microbial drug resistance (Larchmont, N.Y.) 2017 Jan - Antimicrobial susceptibility and body site distribution of community isolates of coagulase-negative staphylococci.
Cavanagh Jorunn Pauline et al. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2016 Nov (11) 973-978 - Comparative Genomics of H. pylori and Non-Pylori Helicobacter Species to Identify New Regions Associated with Its Pathogenicity and Adaptability.
Cao De-Min et al. BioMed research international 2016 6106029 - Molecular surveillance of Plasmodium falciparum drug resistance markers reveals partial recovery of chloroquine susceptibility but sustained sulfadoxine-pyrimethamine resistance at two sites of different malaria transmission intensities in Rwanda.
Kateera Fredrick et al. Acta tropica 2016 Dec 329-336
DETECTION / DIAGNOSIS
- Rapid detection of high-risk Enterococcus faecium clones by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.
Freitas Ana R et al. Diagnostic microbiology and infectious disease 2016 Dec - Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality.
Lee Elvina et al. PloS one 2017 (1) e0170008 - Comparison of 16S ribosomal RNA gene sequence analysis and conventional culture in the environmental survey of a hospital.
Manaka Akihiro et al. Journal of pharmaceutical health care and sciences 2017 8 - The additional yield of GeneXpert MTB/RIF test in the diagnosis of pulmonary tuberculosis among household contacts of smear positive TB cases.
Habte Dereje et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2016 Aug 179-84 - Detection and Differentiation of Norovirus Genogroups I and II from Clinical Stool Specimens using Real-time PCR
Ramanan P, et al. Diagn Microbiol Infect Dis, Jan 20, 2017. - National molecular surveillance of recently acquired HIV infections in Germany, 2013 to 2014.
Hauser Andrea et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Jan (2) - Development of a microarray-based assay for rapid monitoring of genetic variants of West Nile virus circulating in the United States.
Grinev Andriyan et al. Journal of virological methods 2017 Jan 17-25 - Fast preparation of a long chimeric armored RNA as controls for external quality assessment for molecular detection of Zika virus.
Lin Guigao et al. Clinica chimica acta; international journal of clinical chemistry 2017 Jan
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname.
Sabat Artur J et al. Scientific reports 2017 Jan 41050 - Notes from the Field: Multistate Outbreak of Escherichia coli O157:H7 Infections Linked to Dough Mix — United States, 2016
Gieraltowski L, et al. MMWR, Jan 27, 2017. - Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study.
Dheda Keertan et al. The Lancet. Respiratory medicine 2017 Jan - A joint cross-border investigation of a cluster of multidrug-resistant tuberculosis in Austria, Romania and Germany in 2014 using classic, genotyping and whole genome sequencing methods: lessons learnt.
Fiebig Lena et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Jan (2) - Molecular epidemiology of HIV-1 in Iceland: Early introductions, transmission dynamics and recent outbreaks among injection drug users.
Sallam Malik et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Jan - Detection of neonatal unit clusters of Candida parapsilosis fungaemia by microsatellite genotyping: Results from laboratory-based sentinel surveillance, South Africa, 2009-2010.
Magobo Rindidzani E et al. Mycoses 2017 Jan - Investigation of a Candida guilliermondii pseudo-outbreak reveals a novel source of laboratory contamination.
Kirby James E et al. Journal of clinical microbiology 2017 Jan - Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal.
Wong Wesley et al. Genome medicine 2017 Jan (1) 5
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Reverse Genetics Approaches for the Development of Influenza Vaccines.
Nogales Aitor et al. International journal of molecular sciences 2016 Dec (1)
HOST-MICROBE INTERACTIONS
- Conjunctival Microbiome Changes Associated With Soft Contact Lens and Orthokeratology Lens Wearing.
Zhang Haikun et al. Investigative ophthalmology & visual science 2017 Jan (1) 128-136 - The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia.
Zakharkina Tetyana et al. Thorax 2017 Jan - Associations of the vaginal microbiota with HIV infection, bacterial vaginosis and demographic factors.
Chehoud Christel et al. AIDS (London, England) 2017 Jan - Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus.
Liu Xuan et al. Genome biology 2017 Jan (1) 4 - Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels.
Doekes Hilje M et al. PLoS computational biology 2017 Jan (1) e1005228 - Alteration of Human Papillomavirus Type 16 Genetic and Epigenetic Profiles in Cervical Cancer Patients Is Indicative of Poor Disease Prognosis: A Cohort Analysis.
Dutta Sankhadeep et al. International journal of gynecological cancer : official journal of the International Gynecological Cancer Society 2016 May (4) 750-7 - Characterisation of microbial communities within aggressive prostate cancer tissues.
Yow Melissa A et al. Infectious agents and cancer 2017 4 - Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data.
Robinson Kelly M et al. Microbiome 2017 Jan (1) 9
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)
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