Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jun 15, 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
• Events / Training / Web Resources
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Host-Microbe Interactions

NEWS

• Klebsiella pneumoniae: when a colonizer turns bad  
   Dorman MJ, Short FL. Nat Microbio., May 30, 2017.
• NIAID scientists discover rare genetic susceptibility to common cold  
   NIAID, Jun 12, 2017.
• Rapid tests for respiratory viruses show high specificity, wide range of sensitivity  
   Healio, Jun 7, 2017.
• Bats a Major Global Reservoir of Coronaviruses  
   Kwon D. The Scientist, Jun 12, 2017.
• Donor microbes persist up to two years after a fecal transplant to treat recurrent C. difficile infection  
   Hansen J. UAB News, Jun 13, 2017.

EVENTS / TRAINING / WEB RESOURCES

• Fourth Annual Rapid Detection for Food Safety: Advances in Genomics, Capture Technologies & High Throughput Detection  
  (conference) Knowledge Foundation, June 26-27, Alexandria, VA.

CONCEPTS / COMMENTS

• Epidemiology: Molecular mapping of Zika spread  
  Worobey M. Nature, Jun 15, 2017.
• Dissecting the human microbiome with single-cell genomics  
  Tolonen AC, Xavier RJ. Genome Med, Jun 14, 2017.
• Nucleic acid detection — it's elementary with SHERLOCK!  
  Clyde D. Science, 2017; 18:392-3.
• Empty rhetoric over data sharing slows science  
  (Editorial) Nature, Jun 15, 2017.

METHODS / TOOLS

• Validation and Implementation of Clinical Laboratory Improvements Act (CLIA)-Compliant Whole Genome Sequencing in Public Health Microbiology Laboratory.  
  Kozyreva Varvara K et al. Journal of clinical microbiology 2017 Jun 
• Development of a web tool for Escherichia coli sub-typing based on fimH alleles.  
  Roer Louise et al. Journal of clinical microbiology 2017 Jun
• Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinIONTM portable nanopore sequencer. 
  Benítez-Páez Alfonso et al. GigaScience 2017 Jun
• Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome.  
  Belda Eugeni et al. Scientific reports 2017 Jun (1) 3241

EVOLUTION / ECOLOGY / POPULATIONS

• Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection.
  Gordon David M et al. mSphere (3)
• Molecular Characterization of Methicillin-Resistant Staphylococcus aureus Isolated from Australian Animals and Veterinarians.
  Worthing Kate A et al. Microbial drug resistance (Larchmont, N.Y.) 2017 Jun
• Comparative Genomic and Phylogenetic Analysis of a Shiga Toxin Producing Shigella sonnei (STSS) Strain.
  Sváb Domonkos et al. Frontiers in cellular and infection microbiology 2017 229
• A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses.
  Pauly Matthew D et al. eLife 2017 Jun
• First report of naturally infected Aedes aegypti with chikungunya virus genotype ECSA in the Americas.
  Costa-da-Silva André Luis et al. PLoS neglected tropical diseases 2017 Jun (6) e0005630
• Analysis of Synonymous Codon Usage in Zika Virus.
  Hussain Snawar et al. Acta tropica 2017 Jun
• Environmental transport of emerging human-pathogenic Cryptosporidium species and subtypes through combined sewer overflow and wastewater.
  Huang Chengchen et al. Applied and environmental microbiology 2017 Jun 
• Comparative analyses of whole genome sequences of Leishmania infantum isolates from humans and dogs in northeastern Brazil.
  Teixeira D G et al. International journal for parasitology 2017 Jun
• Molecular approaches for blood meal analysis and species identification of mosquitoes (Insecta: Diptera: Culicidae) in rural locations in southern England, United Kingdom.
  Hernández-Triana Luis Miguel et al. Zootaxa 2017 Apr (1) 67-76

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• FRI-2 carbapenemase-producing Enterobacter cloacae complex in the UK.  
  Meunier Danièle et al. The Journal of antimicrobial chemotherapy 2017 Jun
• Next-generation approaches to understand and combat the antibiotic resistome.  
  Crofts Terence S et al. Nature reviews. Microbiology 2017 Apr
• Insights into enterotoxigenic Escherichia coli diversity in Bangladesh utilizing genomic epidemiology.  
  Sahl Jason W et al. Scientific reports 2017 Jun (1) 3402
• Mycoplasma genitalium Antibiotic Resistance-Mediating Mutations in Canadian Women With or Without Chlamydia Trachomatis Infection.  
  Chernesky Max A et al. Sexually transmitted diseases 2017 Jul (7) 433-435
• Cryptic Micro-heteroresistance Explains M. tuberculosis Phenotypic Resistance.  
  Metcalfe John Z et al. American journal of respiratory and critical care medicine 2017 Jun
• Deep-sequencing of Marburg virus genome during sequential mouse passaging and cell-culture adaptation reveals extensive changes over time.  
  Wei Haiyan et al. Scientific reports 2017 Jun (1) 3390
• Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.  
  Blanquart François et al. PLoS biology 2017 Jun (6) e2001855
• Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans.  
  Desjardins Christopher A et al. Genome research 2017 Jun 
• Evolution of mitosome metabolism and invasion-related proteins in Cryptosporidium.  
  Liu Shiyou et al. BMC genomics 2016 Dec (1) 1006 

DETECTION / DIAGNOSIS

• PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance  
  Nadon C, et al. Eurosurveillance, Jun 8, 2017.
• Whole genome sequencing (WGS) for food-borne pathogen surveillance and control – taking the pulse  
  Moran-Gilad J. Eurosurveillance, Jun 8, 2017
• Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii.  
  Higgins Paul G et al. PloS one 2017 (6) e0179228
• Diagnostic Bacteriology: Raman Spectroscopy.  
  Pavlicek Rebecca L et al. Methods in molecular biology (Clifton, N.J.) 2017 249-261
• Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii.  
  Lindsey Rebecca L et al. Journal of microbiological methods 2017 Jun 
• Towards diagnostic metagenomics of Campylobacter in fecal samples.  
  Andersen Sandra Christine et al. BMC microbiology 2017 Jun (1) 133
• Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species.  
  Sabat Artur J et al. Scientific reports 2017 Jun (1) 3434
• Accurate differentiation of Mycobacterium chimaera from Mycobacterium intracellulare by MALDI-TOF MS analysis.  
  Pranada Arthur B et al. Journal of medical microbiology 2017 May (5) 670-677
• Methods for Real-Time PCR-Based Diagnosis of Chlamydia pneumoniae, Chlamydia psittaci, and Chlamydia abortus Infections in an Opened Molecular Diagnostic Platform.  
  Opota Onya et al. Methods in molecular biology (Clifton, N.J.) 2017 171-181
• Whole-Genome Enrichment Using RNA Probes and Sequencing of Chlamydia trachomatis Directly from Clinical Samples.  
  Brown Amanda Claire et al. Methods in molecular biology (Clifton, N.J.) 2017 1-22
• Rapid tests for influenza, respiratory syncytial virus, and other respiratory viruses: a systematic review and meta-analysis  
  Bruning AH, et al. Clin Infect Dis, May 17, 2017. 
• Diagnostic and prognostic value of human prion detection in cerebrospinal fluid.  
  Foutz Aaron et al. Annals of neurology 2017 Jan (1) 79-92 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Ongoing haemolytic uraemic syndrome (HUS) outbreak caused by sorbitol-fermenting (SF) Shiga toxin-producing Escherichia coli (STEC) O157, Germany, December 2016 to May 2017.  
  Vygen-Bonnet Sabine et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 May (21)
• Multi-country outbreak of Salmonella enteritidis infection linked to the international ice hockey tournament.  
  Pärn T et al. Epidemiology and infection 2017 Jun 1-10
• Investigation of a food-borne outbreak of gastroenteritis in a school canteen revealed a variant of sapovirus genogroup V not detected by standard PCR, Sollentuna, Sweden, 2016.  
  Hergens Maria-Pia et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Jun (22)
• Evolutionary analysis of whole-genome sequences confirms inter-farm transmission of Aleutian mink disease virus.  
  Hagberg Emma E et al. The Journal of general virology 2017 Jun

HOST-MICROBE INTERACTIONS

• Characterization of Sinus Microbiota by 16S Sequencing from Swabs.  
  Vickery Thad W et al. Methods in molecular biology (Clifton, N.J.) 2017 23-38
• Ménage à trois in the human gut: interactions between host, bacteria and phages.  
  Mirzaei Mohammadali Khan et al. Nature reviews. Microbiology 2017 May
• Strain-based HLA association analysis identified HLA-DRB1*09:01 associated with modern strain tuberculosis.  
  Toyo-Oka L et al. HLA 2017 Jun

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.