Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: May 25, 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.

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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

• Single mosquito bite might be enough to transmit multiple viruses, study finds  
   Hassanali A. ABC News, May 19, 2017.
• Genomic Studies Untangle Zika Virus Introduction, Spread Across Americas  
   GenomeWeb, May 24, 2017.
• Microbiome Study Maps How Bacteria Spread in New Chicago Hospital Over a Year  
   Karow J. GenomeWeb, May 24, 2017.
• Gonorrhea drug-resistance: UCLA researchers develop test to identify best treatment  
   Outbreak News, May 23, 2017.
• New resistance gene found in Salmonella isolated from chickens  
   Dall C. CIDRAP News, May 23, 2017.
• Some Species May Have Variants That Confer Immunity to Gene Drives  
   GenomeWeb, May 19, 2017.
• Population Genomic Data Leads to CNVs Related to Severe Malaria Risk  
   GenomeWeb, May 18, 2017.

POLICY

• GAO says diagnostics, mosquito control key in Zika efforts  
  Soucheray S. CIDRAP, May 24, 2017.

CONCEPTS / COMMENTS

• The potential economic burden of Zika in the continental United States  
  Lee BY, et al. PLoS Negl Trop Dis. 2017 Apr; 11(4): e0005531.
• Unforeseen Consequences: Culture-Independent Diagnostic Tests and Epidemiologic Tracking of Foodborne Pathogens.  
  McAdam Alexander J et al. Journal of clinical microbiology 2017 May
• Antiviral Goes Viral: Harnessing CRISPR/Cas9 to Combat Viruses in Humans.  
  Soppe Jasper Adriaan et al. Trends in microbiology 2017 May

METHODS / TOOLS

• Rapid deployment of a mobile biosafety level-3 laboratory in Sierra Leone during the 2014 Ebola virus epidemic.  
  Zhang Yi et al. PLoS neglected tropical diseases 2017 May (5) e0005622
• Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples  
  Quick J, et al. Nat Protoc, May 24, 2017.
• TimeTree: A resource for timelines, timetrees, and divergence times.  
  Kumar Sudhir et al. Molecular biology and evolution 2017 Apr
• Virulence factor activity relationships (VFARs): a bioinformatics perspective.  
  Waseem Hassan et al. Environmental science. Processes & impacts 2017 Mar (3) 247-260
• Minimizing Next-Generation Sequencing Errors for HIV Drug Resistance Testing.  
  Fernández-Caballero José A et al. AIDS reviews 2017 May (2)
• StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.  
  Roosaare Märt et al. PeerJ 2017 e3353
• A diverse community to study communities: integration of experiments and mathematical models to study microbial consortia.  
  Succurro Antonella et al. Journal of bacteriology 2017 May
• A CRISPR toolbox to study virus-host interactions.  
  Puschnik Andreas S et al. Nature reviews. Microbiology 2017 Jun (6) 351-364
• Requirements for Driving Antipathogen Effector Genes into Populations of Disease Vectors by Homing.  
  Beaghton Andrea et al. Genetics 2017 Apr (4) 1587-1596

EVOLUTION / ECOLOGY / POPULATIONS

• Environmental contamination with Staphylococcus aureus at a large, Midwestern university campus.
  Thapaliya Dipendra et al. The Science of the total environment 2017 May 1363-1368
• Genomic Analysis of Salmonella enterica Serovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998-2012.
  Bloomfield Samuel J et al. Emerging infectious diseases 2017 Jun (6) 906-913
• Bacterial colonization and succession in a newly opened hospital
  Lax S, et al. Sci Transl Med, May 24, 2017.
• Characterization of Mycobacterium chelonae-Like Strains by Comparative Genomics.
  Nogueira Christiane L et al. Frontiers in microbiology 2017 789
• Zika virus evolution and spread in the Americas
  Metsky HC, et al. Nature, May 24, 2017.
• Establishment and cryptic transmission of Zika virus in Brazil and the Americas
  Faria NR, et al. Nature, May 24, 2017.
• Genomic epidemiology reveals multiple introductions of Zika virus into the United States
  Grubaugh ND, et al. Nature, May 24, 2017.
• Emergence of Babesia canis in southern England.
  de Marco Maria Del Mar Fernández et al. Parasites & vectors 2017 May (1) 241
• High-Throughput Sequencing of Transposable Element Insertions Suggests Adaptive Evolution of the Invasive Asian Tiger Mosquito Towards Temperate Environments.
  Goubert Clément et al. Molecular ecology 2017 May

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing. 
  Demczuk Walter H B et al. PloS one 2017 (5) e0178040
• Characterization of the novel In1059 harbouring VIM gene cassette.  
  Wang Dongguo et al. Antimicrobial resistance and infection control 2017 50
• De Novo Generation and Characterization of New Zika Virus Isolate Using Sequence Data from a Microcephaly Case.  
  Setoh Yin Xiang et al. mSphere (3)

DETECTION / DIAGNOSIS

• 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome.  
  Almonacid Daniel E et al. PloS one 2017 (5) e0176555
• A Novel stool PCR Test for Helicobacter pylori may Predict Clarithromycin Resistance and Patient Eradication at a High Rate.  
  Beckman Erin et al. Journal of clinical microbiology 2017 May
• Malaria Surveillance — United States, 2014
  Mace KE, Arguin PM. MMWR, May 24, 2017. 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• An outbreak of NDM-1 producing Klebsiella pneumoniae in a Dutch hospital with interspecies transfer of the resistance plasmid and unexpected occurrence in unrelated healthcare centers.  
  Bosch Thijs et al. Journal of clinical microbiology 2017 May
• The role of next generation sequencing in infection prevention in human parainfluenza virus 3 infections in immunocompromised patients.  
  Kothari Atul et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 May 53-55
• Outbreak of Zika virus infection in Singapore: an epidemiological, entomological, virological, and clinical analysis.  
  et al. The Lancet. Infectious diseases 2017 May
• Phylogenetic analysis of an epidemic outbreak of acute hepatitis C in HIV-infected patients by ultra-deep pyrosequencing.  
  Caro-Pérez Noelia et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 May 42-47

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Weekly screening supports terminating nosocomial transmissions of vancomycin-resistant enterococci on an oncologic ward - a retrospective analysis.  
  Kampmeier Stefanie et al. Antimicrobial resistance and infection control 2017 48
• Methods and Reporting Studies Assessing Fecal Microbiota Transplantation: A Systematic Review.  
  Bafeta Aïda et al. Annals of internal medicine 2017 May 
• Virologic Monitoring of Poliovirus Type 2 after Oral Poliovirus Vaccine Type 2 Withdrawal in April 2016 — Worldwide, 2016–2017
  Diop OM, et al. MMWR, May 26, 2017.

HOST-MICROBE INTERACTIONS

• Resistance to malaria through structural variation of red blood cell invasion receptors.  
  Leffler Ellen M et al. Science (New York, N.Y.) 2017 May
• Changes in microbiome during and after travellers' diarrhea: what we know and what we do not.  
  Rasko David A et al. Journal of travel medicine 2017 Apr (suppl_1) S52-S56
• The effects of micronutrient deficiencies on bacterial species from the human gut microbiota.  
  Hibberd Matthew C et al. Science translational medicine 2017 May (390)
• Anticancer effects of the microbiome and its products.  
  Zitvogel Laurence et al. Nature reviews. Microbiology 2017 May
• Associations of Nasopharyngeal Metabolome and Microbiome with Severity Among Infants with Bronchiolitis: A Multi-omic Analysis.  
  Stewart Christopher J et al. American journal of respiratory and critical care medicine 2017 May

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.

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB