Publication Date: Jan 18, 2018
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. View Data Selection Criteria
Advanced Molecular Detection Clips Content
NEWS
- Mapping How The Opioid Epidemic Sparked An HIV Outbreak
Boerner H. NPR, Jan 14, 2018. - Who will answer the call in the next outbreak? Drug makers feel burned by string of vaccine pleas
Branswell H. STAT, Jan 11, 2017. - A severe flu season is stretching hospitals thin. That is a very bad omen
Branswell H. STAT, Jan 15, 2018. - Scientists seek super-shot for flu 100 years after pandemic
Neergaard L. AP, Jan 17, 2018. - Neurons Use Virus-Like Proteins to Transmit Information
Kwon D. The Scientist, Jan 16, 2018. - Lethal malaria parasite’s weaknesses revealed - Genomic insights could inform discovery of more durable drugs.
Nature, Jan 16, 2018. - Study identifies malaria resistance genes, possible drug targets
Dall C. CIDRAP, Jan 16, 2018. - Sixteenth Century Outbreak Linked by Metagenomic DNA to Salmonella Paratyphi
GenomeWeb, Jan 15, 2018. - Could baby’s first bacteria take root before birth?
Willyard C. Nature, Jan 17, 2018. - Genome watch: Microbial diversity knows no borders
Pike LJ, et al. Nat Rev Microbiol, Jan 2, 2018.
EVENTS / TRAINING / WEB RESOURCES
- Canadian Bioinformatics Workshops: Summer 2018
(announcement) bioinformatics.ca, Jan 12, 2018. - Assessing an effective undergraduate module teaching applied bioinformatics to biology students.
Madlung Andreas et al. PLoS computational biology 2018 01 (1) e1005872 - The 2018 Nucleic Acids Research database issue and the online molecular biology database collection.
Rigden Daniel J et al. Nucleic acids research 2018 Jan (D1) D1-D7
CONCEPTS / COMMENTS
- In Pakistan, surveillance for polio reveals a paradox
Roberts L. Science, Jan 10, 2018. - 1918 influenza virus: 100 years on, are we prepared against the next influenza pandemic?
Medina Rafael A et al. Nature reviews. Microbiology 2018 Jan (2) 61-62 - How Do Infant Immune Systems Learn to Tolerate Gut Bacteria?
Kwon D. The Scientist, Jan 11, 2018. - Good Bug, Bad Bug: Breaking through Microbial Stereotypes.
Cirstea Mihai et al. Cell host & microbe 2018 Jan (1) 10-13
METHODS / TOOLS
- Database resources of the National Center for Biotechnology Information.
et al. Nucleic acids research 2018 Jan (D1) D8-D13 - RefSeq: an update on prokaryotic genome annotation and curation.
Haft Daniel H et al. Nucleic acids research 2018 Jan (D1) D851-D860 - EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.
Mitchell Alex L et al. Nucleic acids research 2018 Jan (D1) D726-D735 - Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella in silico Typing Resource (SISTR).
Robertson James et al. Microbial genomics 2018 Jan
- How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota.
Dubourg Grégory et al. Expert review of proteomics 2018 Jan - In-depth resistome analysis by targeted metagenomics.
Lanza Val F et al. Microbiome 2018 Jan (1) 11 - PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures
Krawczyk PS, et al. Proc Nat Acad Sci, Jan 13, 2018. - Moving toward rapid and low-cost point-of-care molecular diagnostics with a repurposed 3D printer and RPA.
Chan Kamfai et al. Analytical biochemistry 2018 Jan - Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory.
Crisan Anamaria et al. PeerJ 2018 e4218
EVOLUTION / ECOLOGY / POPULATIONS
- High-Quality Whole-Genome Sequences for 21 Enterotoxigenic Escherichia coli Strains Generated with PacBio Sequencing.
Smith Peyton et al. Genome announcements 2018 Jan (2)
- Survey of Parasitic Bacteria in Bat Bugs, Colorado.
McKee Clifton D et al. Journal of medical entomology 2018 Jan (1) 237-241 - Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes.
Strouhal Michal et al. BMC research notes 2018 Jan (1) 16 - HIV-1 genetic diversity, geographical linkages and antiretroviral drug resistance among individuals from Pakistan.
Khan Saeed et al. Archives of virology 2018 Jan (1) 33-40 - Isolation and complete genome analysis of neurotropic dengue virus serotype 3 from the cerebrospinal fluid of an encephalitis patient.
Dhenni Rama et al. PLoS neglected tropical diseases 2018 Jan (1) e0006198 - Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China.
Atoni Evans et al. Viruses 2018 Jan (1) - Continental synchronicity of human influenza virus epidemics despite climactic variation.
Geoghegan Jemma L et al. PLoS pathogens 2018 Jan (1) e1006780 - Etiology of invasive candidosis agents in Russia: a multicenter epidemiological survey.
Vasilyeva N V et al. Frontiers of medicine 2018 Jan - Dramatic Changes in Malaria Population Genetic Complexity in Dielmo and Ndiop, Senegal, Revealed Using Genomic Surveillance.
Bei Amy K et al. The Journal of infectious diseases 2018 Jan
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Multi-drug resistant non-typhoidal Salmonella associated with invasive disease in western Kenya.
Akullian Adam et al. PLoS neglected tropical diseases 2018 Jan (1) e0006156 - Transfer of a bla CTX-M-1-carrying plasmid between different Escherichia coli strains within the human gut explored by whole genome sequencing analyses.
Knudsen Per Kristian et al. Scientific reports 2018 Jan (1) 280 - Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces.
Urbaniak C et al. Scientific reports 2018 Jan (1) 814 - Uncovering the mechanisms of Acinetobacter baumannii virulence.
Harding Christian M et al. Nature reviews. Microbiology 2018 Feb (2) 91-102 - Scarlet Fever Epidemic in China Caused by Streptococcus pyogenes Serotype M12: Epidemiologic and Molecular Analysis.
You Yuanhai et al. EBioMedicine 2018 Jan - Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species.
Kjærbølling Inge et al. Proceedings of the National Academy of Sciences of the United States of America 2018 Jan - A multicentre study of antifungal susceptibility patterns among 350 Candida auris isolates (2009-17) in India: role of the ERG11 and FKS1 genes in azole and echinocandin resistance.
Chowdhary Anuradha et al. The Journal of antimicrobial chemotherapy 2018 Jan - Sequence variation in Plasmodium falciparum merozoite surface protein-2 is associated with virulence causing severe and cerebral malaria.
Chaorattanakawee Suwanna et al. PloS one 2018 (1) e0190418
DETECTION / DIAGNOSIS
- Survey on the Use of Whole-Genome Sequencing for Infectious Diseases Surveillance: Rapid Expansion of European National Capacities, 2015-2016.
Revez Joana et al. Frontiers in public health 2017 347 - Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae.
Nguyen Marcus et al. Scientific reports 2018 Jan (1) 421 - Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis.
Peker Nilay et al. Microorganisms 2018 Jan (1) - Tick-borne pathogen detection: what's new?
Cabezas-Cruz Alejandro et al. Microbes and infection 2018 Jan - Handheld isothermal amplification and electrochemical detection of DNA in resource-limited settings.
Tsaloglou Maria-Nefeli et al. Analytical biochemistry 2017 Dec 116-121 - Epidemiological aspects of healthcare-associated infections and microbial genomics.
Mirande C et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2018 Jan - Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing.
Li Zhigang et al. Investigative ophthalmology & visual science 2018 Jan (1) 280-288 - Incorporating Whole-Genome Sequencing into Public Health Surveillance: Lessons from Prospective Sequencing of Salmonella Typhimurium in Australia.
Ford Laura et al. Foodborne pathogens and disease 2018 Jan - Pneumococcal Community-Acquired Pneumonia Detected by Serotype-Specific Urinary Antigen Detection Assays.
Wunderink Richard G et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Jan - Detection of Apparent Cell-free M. tuberculosis DNA from Plasma.
Click E S et al. Scientific reports 2018 Jan (1) 645 - Development and evaluation of a RT-qPCR assay for fast and sensitive rabies diagnosis.
Dedkov V G et al. Diagnostic microbiology and infectious disease 2018 Jan (1) 18-25 - Updates on the molecular epidemiology of Enterovirus D68 after installation of screening test among acute flaccid paralysis patients in Taiwan.
Wei Hsin-Yi et al. Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi 2018 Jan - An Efficient, Large-Scale Survey of Hepatitis C Viremia in the Democratic Republic of the Congo Using Dried Blood Spots.
Parr Jonathan B et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Jan (2) 254-260
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital.
Gorrie Claire L et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Jan - A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study.
Walker Timothy M et al. The Lancet. Infectious diseases 2018 Jan - Continued propagation of the CRF19_cpx variant among HIV-positive MSM patients in Spain.
Pérez-Parra S et al. The Journal of antimicrobial chemotherapy 2018 Jan - Molecular epidemiology reveals the role of war in the spread of HIV in Ukraine.
Vasylyeva Tetyana I et al. Proceedings of the National Academy of Sciences of the United States of America 2018 Jan
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics.
Cowell Annie N et al. Science (New York, N.Y.) 2018 Jan (6372) 191-199
HOST-MICROBE INTERACTIONS
- Transcriptomics in Human Challenge Models.
Barton Amber J et al. Frontiers in immunology 2017 1839 - Functional horizontal gene transfer from bacteria to eukaryotes.
Husnik Filip et al. Nature reviews. Microbiology 2018 Feb (2) 67-79 - Pathogenesis of HIV-1 and Mycobacterium tuberculosis co-infection.
Bell Lucy C K et al. Nature reviews. Microbiology 2018 Feb (2) 80-90 - Composition of salivary microbiota in elderly subjects.
Ogawa Taiji et al. Scientific reports 2018 Jan (1) 414 - Maturation of the gut microbiome and risk of asthma in childhood.
Stokholm Jakob et al. Nature communications 2018 Jan (1) 141 - The human skin microbiome.
Byrd Allyson L et al. Nature reviews. Microbiology 2018 Jan - Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer.
Hayes Richard B et al. JAMA oncology 2018 Jan - Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study.
Fan Xiaozhou et al. Gut 2018 Jan (1) 120-127 - Association of genetic variants in the interleukin-18 gene promoter with risk of hepatocellular carcinoma and metastasis in patients with hepatitis c virus infection.
Bakr Noha M et al. IUBMB life 2018 Jan
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.
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