About Advanced Molecular Detection Clips ► Public Health Genomics Knowledge Base (v1.0)

Public Health Genomics Knowledge Base (v1.0)

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

NEWS

• Infectious Disease Sequencing Dx Devices to Be Regulated by FDA 
  GenomeWeb, May 13, 2016.
• Researchers decry consent proposal 
  Kaiser J. Science, May 20, 2016.
• Culture clash: New diagnostics complicate public health surveillance 
  Healio, May 19, 2016.
• Announcing the US Microbiome Initiative
  US White House, May 13, 2016.
• DNA Sequencing Proving Useful in Virus ID, Say Clinical Virology Symposium Presenters 
  Rizk C. GenomeWeb, May 23, 2016.
• Cape Verde Zika virus matches Americas' strain, threatening Africa 
  Schnirring L. CIDRAP, May 20, 2016.
• Scientists clone Zika for vaccine race 
  BBC News, May 16, 2016.
• WHO recommends shorter regimen, new diagnostic test for MDR-TB 
  Healio, May 13, 2016.
• Sequencing of Ebola Samples Finds Cases Transmitted by Sex, Breast Feeding 
  GenomeWeb, May 19, 2016.
• Polio-free world? Not if scientists refuse to destroy their research specimens 
  Branswell H. STAT, May 26, 2016.
• Amyloid Thwarts Microbial Invaders 
  Azvolinsky A. The Scientist, May 25, 2016.

EVENTS / TRAINING / WEB RESOURCES

• Translating the microbiome: health and disease 
  (special issue) Genome Med, May 20, 2016.
• CDC expanding groundbreaking disease identification tool 
  (press release) More info at http://www.cdc.gov/microbenet/
• Fast Sequence Inspection with ORFfinder + SmartBLAST 
  (blog post) NCBI, May 16, 2016.
• Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee). 
  Welch Lonnie et al. PLoS computational biology 2016 May (5) e1004943

POLICY

• Infectious Disease Next Generation Sequencing Based Diagnostic Devices: Microbial Identification and Detection of Antimicrobial Resistance and Virulence Markers
  (draft guidance) FDA, May 13, 2016.
• Antimicrobial animal drug sales and distribution reporting. 
  FDA, May 11, 2016.
• Maintaining Life-saving Testing for Patients With Infectious Diseases: Infectious Diseases Society of America, American Society for Microbiology, and Pan American Society for Clinical Virology Recommendations on the Regulation of Laboratory-developed Tests. 
  Caliendo Angela M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Apr
• US reviews plan to infect mosquitoes with bacteria to stop disease 
  Waltz E. Nature, May 24, 2016.
• Public health: Use open data to curb Zika virus 
  Kieny MP, et al. Nature, May 25, 2016.

CONCEPTS / COMMENTS

• Further Evidence that Life Might Have Started with RNA 
  Offord C. The Scientist, May 13, 2016.
• Suddenly everyone is a microbiota specialist! 
  Boers Stefan A et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 May
• Coming of age: ten years of next-generation sequencing technologies. 
  Goodwin Sara et al. Nature reviews. Genetics 2016 May (6) 333-51
• Dumpster Diving in the Gut: Bacterial Microcompartments as Part of a Host-Associated Lifestyle. 
  Jakobson Christopher M et al. PLoS pathogens 2016 May (5) e1005558
• Antibiotic-Resistant Neisseria gonorrhoeae Spread Faster with More Treatment, Not More Sexual Partners. 
  Fingerhuth Stephanie M et al. PLoS pathogens 2016 May (5) e1005611
• Sensors for All: A versatile modular strategy for detecting small molecules in eukaryotes 
  Williams R. The Scientist, May 1, 2016.

METHODS / TOOLS

• An adaptive association test for microbiome data 
  Wu C, et al. Genome Medicine 2016; 8:56.
• Measurements of intrahost viral diversity are extremely sensitive to systematic errors in variant calling. 
  McCrone John T et al. Journal of virology 2016 May
• Badges to Acknowledge Open Practices: A Simple, Low-Cost, Effective Method for Increasing Transparency. 
  Kidwell Mallory C et al. PLoS biology 2016 May (5) e1002456
• Diagnosis and management of Ebola samples in the laboratory. 
  de La Vega Marc-Antoine et al. Expert review of anti-infective therapy 2016 May 1-11
• Standard finishing categories for high-throughput sequencing of viral genomes. 
  Ladner J T et al. Revue scientifique et technique (International Office of Epizootics) 2016 Apr (1) 43-52
• MS-REDUCE: an ultrafast technique for reduction of big mass spectrometry data for high-throughput processing. 
  Awan Muaaz Gul et al. Bioinformatics (Oxford, England) 2016 May (10) 1518-26
• Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web. 
  Robinson Oscar et al. Molecular biology and evolution 2016 Apr
• Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. 
  Gu W et al. Genome biology 2016 41
• Targeted isolation and cloning of 100-kb microbial genomic sequences by Cas9-assisted targeting of chromosome segments. 
  Jiang Wenjun et al. Nature protocols 2016 May (5) 960-75

EVOLUTION / ECOLOGY / POPULATIONS

• Multi locus sequence typing of pathogenic treponemes isolated from cloven hoofed animals and their comparison to human isolates. 
  Clegg Simon R et al. Applied and environmental microbiology 2016 May
• Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing. 
  Kim Won-Keun et al. Scientific reports 2016 26017
• Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses. 
  Lam Tommy T-Y et al. Annual review of genomics and human genetics 2016 May
• Novel Avian Influenza A(H5N8) Viruses in Migratory Birds, China, 2013-2014. 
  Zhou Li-Chen et al. Emerging infectious diseases 2016 Jun (6) 1121-3
• Whole genome sequencing-based molecular epidemiologic analysis of autochthonous dengue virus type 1 strains circulating in Japan in 2014. 
  Tajima Shigeru et al. Japanese journal of infectious diseases 2016 May
• Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides 
  Teixeira MM, Barker BM. Emerg Infect Dis, Jun 2016.
• Whole-Genome Analysis of Cryptococcus gattii, Southeastern United States. 
  Lockhart Shawn R et al. Emerging infectious diseases 2016 Jun (6) 1098-101
• Microsatellite genotyping and genome-wide single nucleotide polymorphism-based indices of Plasmodium falciparum diversity within clinical infections. 
  Murray Lee et al. Malaria journal 2016 (1) 275
• Population and Evolutionary Genomics of Amblyomma americanum, an Expanding Arthropod Disease Vector. 
  Monzón Javier D et al. Genome biology and evolution 2016 (5) 1351-60

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• The Challenges of Implementing Next Generation Sequencing Across a Large Healthcare System, and the Molecular Epidemiology and Antibiotic Susceptibilities of Carbapenemase-Producing Bacteria in the Healthcare System of the U.S. Department of Defense. 
  Lesho Emil et al. PloS one 2016 (5) e0155770 
• Antimicrobial Susceptibility Profiles of Human Campylobacter jejuni Isolates and Association with Phylogenetic Lineages. 
  Cha Wonhee et al. Frontiers in microbiology 2016 589
• DNA microarray analysis of Staphylococcus aureus causing bloodstream infection: bacterial genes associated with mortality? 
  Blomfeldt A et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2016 May
• Genotypic and phenotypic characterization of methicillin-resistant Staphylococcus aureus (MRSA) clones with high-level mupirocin resistance. 
  González-Domínguez María et al. Diagnostic microbiology and infectious disease 2016 Jun (2) 213-7
• Genome-based characterization of hospital-adapted Enterococcus faecalis lineages. 
  Raven Kathy E et al. Nature microbiology 2016 Mar (3)
• Genetic analysis of Vibrio parahaemolyticus intestinal colonization. 
  Hubbard Troy P et al. Proceedings of the National Academy of Sciences of the United States of America 2016 May
• Whole transcriptome expression analysis and comparison of two different strains of Plasmodium falciparum using RNA-Seq. 
  Antony Hiasindh Ashmi et al. Genomics data 2016 Jun 110-2

DETECTION / DIAGNOSIS

• Advances in Molecular Serotyping and Subtyping of Escherichia coli. 
  Fratamico Pina M et al. Frontiers in microbiology 2016 644
• The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives. 
  Endimiani Andrea et al. Infectious disease clinics of North America 2016 Jun (2) 323-45
• Utility of 16S rDNA Sequencing for Identification of Rare Pathogenic Bacteria. 
  Loong Shih Keng et al. Journal of clinical laboratory analysis 2016 May
• Deep sequencing approach for investigating infectious agents causing fever. 
  Susilawati T N et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2016 May
• An Innovative Method for Rapid Identification and Detection of Vibrio alginolyticus in Different Infection Models. 
  Fu Kaifei et al. Frontiers in microbiology 2016 651
• Evaluation of Techniques for Measuring Microbial Hazards in Bathing Waters: A Comparative Study. 
  Schang Christelle et al. PloS one 2016 (5) e0155848
• Next-Generation Sequencing of Mycobacterium tuberculosis. 
  Mokrousov Igor et al. Emerging infectious diseases 2016 Jun (6) 1127-9
• Comparison of Test Results for Zika Virus RNA in Urine, Serum, and Saliva Specimens from Persons with Travel-Associated Zika Virus Disease - Florida, 2016. 
  Bingham Andrea M et al. MMWR. Morbidity and mortality weekly report 2016 (18) 475-8 
• Use of Unamplified RNA/cDNA-Hybrid Nanopore Sequencing for Rapid Detection and Characterization of RNA Viruses. 
  Kilianski Andy et al. Emerging infectious diseases 2016 Aug (8)
• Rapid detection of measles virus using reverse transcription loop-mediated isothermal amplification coupled with a disposable lateral flow device. 
  Xu Changping et al. Diagnostic microbiology and infectious disease 2016 Jun (2) 168-73
• Programmatic Use of Molecular Xenomonitoring at the Level of Evaluation Units to Assess Persistence of Lymphatic Filariasis in Sri Lanka. 
  Rao Ramakrishna U et al. PLoS neglected tropical diseases 2016 May (5) e0004722 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Integration of Genomic and Other Epidemiologic Data to Investigate and Control a Cross-Institutional Outbreak of Streptococcus pyogenes. 
  Chalker Victoria J et al. Emerging infectious diseases 2016 Jun (6) 973-80
• Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time? 
  McGann Patrick et al. Diagnostic microbiology and infectious disease 2016 Apr 
• Whole-genome sequencing as standard practice for the analysis of clonality in outbreaks of meticillin-resistant Staphylococcus aureus in a paediatric setting. 
  Ugolotti E et al. The Journal of hospital infection 2016 Apr
• The 2002 Chandigarh cholera outbreak revisited: utility of MALDI-TOF as a molecular epidemiology tool. 
  Taneja N et al. Letters in applied microbiology 2016 Jun (6) 452-8
• Extensively drug-resistant Acinetobacter baumannii outbreak cross-transmitted in an intensive care unit and respiratory intensive care unit. 
  Lei Jin'e et al. American journal of infection control 2016 May
• Standard genotyping overestimates transmission of Mycobacterium tuberculosis among immigrants in a low incidence country. 
  Stucki David et al. Journal of clinical microbiology 2016 May
• Origin and spread of HIV-1 in persons who inject drugs in Bulgaria. 
  Alexiev Ivailo et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 May
• Genomics and outbreaks: foot and mouth disease. 
  Freimanis G L et al. Revue scientifique et technique (International Office of Epizootics) 2016 Apr (1) 175-89
• Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.
  Arias A, et al. Virus Evol, May 2016. 
• Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California. 
  Mehta Sanjay R et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 May 
• Reemergence of Dengue in Southern Texas, 2013. 
  Thomas Dana L et al. Emerging infectious diseases 2016 Jun (6) 1002-7 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Enhanced genetic characterization of influenza A(H3N2) viruses and vaccine effectiveness by genetic group, 2014-2015. 
  Flannery Brendan et al. The Journal of infectious diseases 2016 May 

HOST-MICROBE INTERACTIONS

• Interconnected microbiomes and resistomes in low-income human habitats. 
  Pehrsson Erica C et al. Nature 2016 May (7602) 212-6
• Intricacies of assessing the human microbiome in epidemiologic studies. 
  Robinson Courtney K et al. Annals of epidemiology 2016 Apr
• The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review. 
  Leung Marcus H Y et al. Microbiome 2016 (1) 21
• Potential Pitfalls in Estimating Viral Load Heritability. 
  Leventhal Gabriel E et al. Trends in microbiology 2016 May
• Genomic African and Native American Ancestry and Chagas Disease: The Bambui (Brazil) Epigen Cohort Study of Aging. 
  Lima-Costa M Fernanda et al. PLoS neglected tropical diseases 2016 May (5) e0004724

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 (v1.0)