July 28 - August 4, 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.
Advanced Molecular Detection Clips Content
- New Genome Editing Tool Elicits Interest, Concern About Reproducibility
Han AP. GenomeWeb, Jul 26, 2016.
- Engineers design programmable RNA vaccines
Trafton A. MIT News, Jul 4, 2016.
- Nanopore Sequencing 'Read Until' Feature May Be Useful in Metagenomics, Haplotyping, Pathogen Dx
Heger M. GenomeWeb, Jul 25, 2016.
- Beyond Lead: Flint Water Strongly Tied to Legionnaire's Disease
Pelley J. Sci Am, Jul 25, 2016.
- Genomics tracking gonorrhoea across borders
Burbidge R. PHG Foundation, Jul 14, 2016.
- Gut microbiome supplement could reduce food cravings
Harris J. PHG Foundation, Jul 4, 2016.
- Hominids Underwent Co-Speciation With Some of Their Gut Microbes
GenomeWeb, Jul 21, 2016.
- Vaginal microbiome affects HIV risk
Cohen J. Science, Jul 22, 2016.
EVENTS / TRAINING / WEB RESOURCES
- NCBI Targeted Loci: RefSeq Ribosomal RNA Sequences for Identification and Phylogenetic Analysis
(webinar) NCBI, Aug 3, 2016.
- innateDB: A knowledge resource for innate immunity interactions & pathways
- Unique Device Identification System: Form and Content of the Unique Device Identifier (UDI)/ Draft Guidance for Industry and Food and Drug Administration Staff
FDA, Jul 25, 2016.
- FDA clarifies medical device tracking rule
Chacko S. The Hill, Jul 25, 2016.
CONCEPTS / COMMENTS
- What Is a Genome?
Goldman Aaron David et al. PLoS genetics 2016 Jul (7) e1006181
- Microbiology: Antibiotics right under our nose
Lewis K, Strandwitz P. Nature, July 27, 2016.
- European Open Science Cloud
(editorial) Nat Genet, Jul 27, 2016.
- Transferable resistance to colistin: a new but old threat.
Schwarz Stefan et al. The Journal of antimicrobial chemotherapy 2016 Jun
- Virus genomics and evolution: the transformative effect of new technologies and multidisciplinary collaboration on virus research and outbreak management.
Ip Camilla L C et al. Genome biology 2016 (1) 159
- Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing.
Jee Justin et al. Nature 2016 Jun (7609) 693-6
- Listeria monocytogenes cross-contamination of cheese: risk throughout the food supply chain.
Sauders B D et al. Epidemiology and infection 2016 Jul 1-5
- Cultivation of Staphylococcus epidermidis in the Human Spaceflight Environment Leads to Alterations in the Frequency and Spectrum of Spontaneous Rifampicin-Resistance Mutations in the rpoB Gene.
Fajardo-Cavazos Patricia et al. Frontiers in microbiology 2016 999
- An unsettling picture emerges from population genomic studies of Plasmodium vivax
Kissinger JC. Nat Genet, Jul 27, 2016.
- Hominid superorganisms.
Segre Julia A et al. Science (New York, N.Y.) 2016 Jul (6297) 350-351
- You Can Edit a Pig, but It Will Still Be a Pig.
Brouillette Monique et al. Scientific American 2016 Mar (3) A22
METHODS / TOOLS
- Characterization of Viral Populations using Circular Sequencing.
Whitfield Zachary J et al. Journal of virology 2016 Jul
- Real-time selective sequencing using nanopore technology
Loose M, et al. Nat Methods, Jul 25, 2016.
- Third generation sequencing technologies applied to diagnostic microbiology: benefits and challenges in applications and data analysis.
Lavezzo Enrico et al. Expert review of molecular diagnostics 2016 Jul
- Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION(TM) sequencing.
Cao Minh Duc et al. GigaScience 2016 (1) 32
- Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules.
Nyberg Lena K et al. Scientific reports 2016 30410
- Linking genomics and population genetics with R.
Paradis Emmanuel et al. Molecular ecology resources 2016 Jul
- A novel algorithm for detecting multiple covariance and clustering of biological sequences.
Shen Wei et al. Scientific reports 2016 30425
- Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2015.
Janda J Michael et al. Diagnostic microbiology and infectious disease 2016 Jul
- EbolaID: An Online Database of Informative Genomic Regions for Ebola Identification and Treatment.
Carneiro João et al. PLoS neglected tropical diseases 2016 Jul (7) e0004757
- A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes.
Avraham Roi et al. Nature protocols 2016 Aug (8) 1477-91
- The effect of DNA extraction methodology on gut microbiota research applications.
Gerasimidis Konstantinos et al. BMC research notes 2016 (1) 365
- Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies.
Gohl Daryl M et al. Nature biotechnology 2016 Jul
EVOLUTION / ECOLOGY / POPULATIONS
- Complete Genome Sequences of Three Outbreak-Associated Legionella pneumophila Isolates.
Morrison Shatavia S et al. Genome announcements 2016 (4)
- Flow Cytometric and 16S Sequencing Methodologies for Monitoring the Physiological Status of the Microbiome in Powdered Infant Formula Production.
Anvarian Amir H P et al. Frontiers in microbiology 2016 968
- The use of comparative genomics to characterize the diversity of Acinetobacter baumannii surveillance isolates in a health care institution.
Wallace Lalena et al. Antimicrobial agents and chemotherapy 2016 Jul
- Spatiotemporal Co-existence of Two Mycobacterium ulcerans Clonal Complexes in the Offin River Valley of Ghana.
Lamelas Araceli et al. PLoS neglected tropical diseases 2016 Jul (7) e0004856
- Molecular characterization of H6 subtype influenza viruses in southern China from 2009 to 2011.
Zou Shumei et al. Emerging microbes & infections 2016 (7) e73
- Distinct Zika Virus Lineage in Salvador, Bahia, Brazil.
Naccache Samia N et al. Emerging infectious diseases 2016 Oct (10)
- Outbreak of Zika virus infection, Chiapas State, Mexico, 2015, and first confirmed transmission by Aedes aegypti mosquitoes in the Americas.
Guerbois Mathilde et al. The Journal of infectious diseases 2016 Jul
- Whole genomic analysis of human and bovine G8P rotavirus strains isolated in Nigeria provides evidence for direct bovine-to-human interspecies transmission.
Komoto Satoshi et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Sep 424-33
- Novel avian influenza A (H5N6) viruses isolated in migratory waterfowl before the first human case reported in China, 2014.
Bi Yuhai et al. Scientific reports 2016 29888
- Plasmodium falciparum Drug-Resistant Haplotypes and Population Structure in Postearthquake Haiti, 2010.
Morton Lindsay Carol et al. The American journal of tropical medicine and hygiene 2016 Jul
- Historical environmental change in Africa drives divergence and admixture of Aedes aegypti mosquitoes: a precursor to successful worldwide colonisation?
Bennett Kelly Louise et al. Molecular ecology 2016 Jul
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Population Genomics of Reduced Vancomycin Susceptibility in Staphylococcus aureus.
Rishishwar Lavanya et al. mSphere (4)
- Phenotypic and Molecular Characterization of Antimicrobial Resistance in Klebsiella spp. Isolates from Companion Animals in Japan: Clonal Dissemination of Multidrug-Resistant Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae.
Harada Kazuki et al. Frontiers in microbiology 2016 1021
- Mycoplasmas and Their Antibiotic Resistance: The Problems and Prospects in Controlling Infections.
Chernova O A et al. Acta naturae (2) 24-34
- Molecular Epidemiological Interpretation of the Epidemic of Extensively Drug-Resistant Tuberculosis in South Africa.
Streicher E M et al. Journal of clinical microbiology 2015 Nov (11) 3650-3
- Molecular analysis of genetic mutations among cross-resistant second-line injectable drugs reveals a new resistant mutation in Mycobacterium tuberculosis.
Malinga Lesibana et al. Diagnostic microbiology and infectious disease 2016 Aug (4) 433-7
- Polymorphisms in Pfcrt and Pfmdr-1 genes after five years withdrawal of chloroquine for the treatment of Plasmodium falciparum malaria in West Bengal, India.
Chatterjee Moytrey et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Jul 281-285
DETECTION / DIAGNOSIS
- Real-time PCR for detection of plasmid-mediated polymyxin resistance (mcr-1) from cultured bacteria and stools.
Bontron Séverine et al. The Journal of antimicrobial chemotherapy 2016 Apr
- Detection of the plasmid-mediated colistin-resistance gene mcr-1 in clinical isolates and stool specimens obtained from hospitalized patients using a newly developed real-time PCR assay.
Nijhuis R H T et al. The Journal of antimicrobial chemotherapy 2016 Jun
- Rapid and Sensitive Multiplex Detection of Burkholderia pseudomallei-Specific Antibodies in Melioidosis Patients Based on a Protein Microarray Approach.
Kohler Christian et al. PLoS neglected tropical diseases 2016 Jul (7) e0004847
- Multiplexed Molecular Diagnostics for Respiratory, Gastrointestinal and Central Nervous System Infections.
Hanson Kimberly E et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Jul
- Challenges in laboratory diagnosis of acute viral central nervous system infections in the era of emerging infectious diseases: the syndromic approach.
Papa Anna et al. Expert review of anti-infective therapy 2016 Jul
- Sensitive and specific nested PCR assay for detection of rotavirus A in samples with a low viral load.
Mijatovic-Rustempasic Slavica et al. Journal of virological methods 2016 Jul 41-46
- Multilocus Sequence Typing Tool for Cyclospora cayetanensis.
Guo Yaqiong et al. Emerging infectious diseases 2016 Aug (8) 1464-7
- Diagnosis of Strongyloides stercoralis: detection of parasite-derived DNA in urine.
Lodh Nilanjan et al. Acta tropica 2016 Jul
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Tick-Borne Relapsing Fever Outbreak Among a High School Football Team at an Outdoor Education Camping Trip, Arizona, 2014.
Jones Jefferson M et al. The American journal of tropical medicine and hygiene 2016 Jul
- Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks.
Rusconi Brigida et al. Frontiers in microbiology 2016 985
- Whole-Genome Sequencing Detection of Ongoing Listeria Contamination at a Restaurant, Rhode Island, USA, 2014.
Barkley Jonathan S et al. Emerging infectious diseases 2016 Aug (8) 1474-6
- Legionella DNA Markers in Tap Water Coincident with a Spike in Legionnaires Disease in Flint, MI
Schwake DO, et al. Environ Sci Technol Lett, Jul 8, 2016.
- Molecular and Epidemiological Analysis of a Campylobacter jejuni Outbreak in Northern Italy in November 2013.
Lucarelli Claudia et al. Foodborne pathogens and disease 2016 Jul
- New genotyping method discovers sustained nosocomial Pseudomonas aeruginosa outbreak in an intensive care burn unit.
Tissot F et al. The Journal of hospital infection 2016 May
- Enterovirus D68 Infection in Children with Acute Flaccid Myelitis, Colorado, USA, 2014.
Aliabadi Negar et al. Emerging infectious diseases 2016 Aug (8) 1387-94
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Reversion of Cold-adapted Live Attenuated Influenza Vaccine into a Pathogenic Virus.
Zhou Bin et al. Journal of virology 2016 Jul
- Delayed Time-to-Treatment of an Antisense Morpholino Oligomer Is Effective against Lethal Marburg Virus Infection in Cynomolgus Macaques.
Warren Travis K et al. PLoS neglected tropical diseases 2016 Feb (2) e0004456
- Whole genome sequencing to evaluate the resistance landscape following antimalarial treatment failure with fosmidomycin-clindamycin.
Guggisberg Ann M et al. The Journal of infectious diseases 2016 Jul
- The Legacy of Past Pandemics: Common Human Mutations That Protect against Infectious Disease.
Pittman Kelly J et al. PLoS pathogens 2016 Jul (7) e1005680
- Human Cytomegalovirus DNA Quantification and Gene Expression in Gliomas of Different Grades.
Stangherlin Lucas Matheus et al. PloS one 2016 (7) e0159604
- Tracking the Antigenic Evolution of Foot-and-Mouth Disease Virus.
Reeve Richard et al. PloS one 2016 (7) e0159360
- An integrated genomic and transcriptomic survey of mucormycosis-causing fungi.
Chibucos Marcus C et al. Nature communications 2016 12218
- Association Analysis Suggests SOD2 as a Newly Identified Candidate Gene Associated With Leprosy Susceptibility.
Ramos Geovana Brotto et al. The Journal of infectious diseases 2016 Aug (3) 475-8
- Host Polymorphisms in TLR9 and IL10 Are Associated With the Outcomes of Experimental Haemophilus ducreyi Infection in Human Volunteers.
Singer Martin et al. The Journal of infectious diseases 2016 Aug (3) 489-95
- Analysis of TLR4 (Asp299Gly and Thr399Ile) gene polymorphisms and mRNA level in patients with dengue infection: A case-control study.
Sharma Swati et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Sep 412-7
- Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome
Dickson RP, et al. Nat Microbiol, Jul 18, 2016.
- The Gut Microbiota in Immune-Mediated Inflammatory Diseases.
Forbes Jessica D et al. Frontiers in microbiology 2016 1081
- Maternal HIV infection influences the microbiome of HIV-uninfected infants
Bender J, et al. Sci Transl Med, Jul 27, 2016.
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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