Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jun 1, 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

• How a Usually Harmless Bacteria Ended Up Killing 18 People in Wisconsin  
   Zhang S. Atlantic, May 24, 2017.
• Scientists Link a Gene Mutation to Rheumatic Heart Disease  
   McNeil DG Jr. New York Times, May 29, 2017.
• Floating in microgravity gives bacteria permanent genetic boost  
   Crane L. New Scientist, May 31, 2017.
• Ebola Virus: Lessons from a Unique Survivor  
   Collins F. NIH Director's Blog, May 30, 2017.
• Genetic Testing Underway on Virus Behind New Ebola Outbreak  
   Halake S. VOA News, May 26, 2017.
• Could pigs be involved in Congo's new Ebola outbreak?  
   Kupferschmidt K, Cohen J. Science, May 26, 2017.
• H7N9 cases ebb in China as CDC creates vaccine virus  
   Schnirring L. CIDRAP News, May 26, 2017.
• Multi-Center Collaboration Defends Against Tick-borne Diseases  
   Bahn C. Mayo Clinic, May 31, 2017.
• Girls have genetic edge in fighting infections, study shows  
   O'Sullivan K. Irish Times, May 25, 2017.

POLICY

• Nations Press for International Restrictions to Govern Genetic Sequence Data  
  Manheim BS. GEN, May 10, 2017.
• Lab Group Backs Draft Bill Proposing Dx Regulatory Reform; Finds Points of Agreement With FDA Paper  
  Ray T. GenomeWeb, Jun 1, 2017.

CONCEPTS / COMMENTS

• Finding useful data across multiple biomedical data repositories using DataMed.  
  Ohno-Machado Lucila et al. Nature genetics 2017 May (6) 816-819
• Why is scientific research on 'data-poor' microorganisms being ignored?  
  Hays John P et al. Future microbiology 2017 May
• Unexpected mutations after CRISPR-Cas9 editing in vivo.  
  Schaefer Kellie A et al. Nature methods 2017 May (6) 547-548
• The multi-omics promise in context: from sequence to microbial isolate.  
  Gutleben Johanna et al. Critical reviews in microbiology 2017 May 1-18
• Diagnostics and laboratory role in outbreaks.  
  Lee Francesca et al. Current opinion in infectious diseases 2017 May
• Salivary Diagnostics in Pediatrics: Applicability, Translatability, and Limitations.  
  Hassaneen Mona et al. Frontiers in public health 2017 83
• Salmonella typhi Genomics: Envisaging the Future of Typhoid Eradication.  
  Yap Kien-Pong et al. Tropical medicine & international health : TM & IH 2017 May

METHODS / TOOLS

• Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.  
  Quick Joshua et al. Nature protocols 2017 Jun (6) 1261-1276
• Measuring changes in transmission of neglected tropical diseases, malaria, and enteric pathogens from quantitative antibody levels.  
  Arnold Benjamin F et al. PLoS neglected tropical diseases 2017 May (5) e0005616
• PhredEM: a phred-score-informed genotype-calling approach for next-generation sequencing studies.  
  Liao Peizhou et al. Genetic epidemiology 2017 May 
• Co-infecting microorganisms dramatically alter pathogen gene essentiality during polymicrobial infection.  
  Ibberson Carolyn B et al. Nature microbiology 2017 May 17079
• Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks.  
  Klinkenberg Don et al. PLoS computational biology 2017 May (5) e1005495
• HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.  
  Ratmann Oliver et al. AIDS research and human retroviruses 2017 May
• Applications of Digital PCR for Clinical Microbiology.  
  Kuypers Jane et al. Journal of clinical microbiology 2017 Jun (6) 1621-1628
• Genome-wide Association Studies in Infectious Diseases.  
  Seaby Eleanor G et al. The Pediatric infectious disease journal 2016 07 (7) 802-4

EVOLUTION / ECOLOGY / POPULATIONS

• Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain.
  Perrin Amandine et al. Nature communications 2017 May 15483 
• Comparative Analysis of Extended Spectrum Beta- Lactamase CTX-M-65-Producing Salmonella Infantis Isolates from Humans, Food Animals, and Retail Chickens in the United States.
  Tate Heather et al. Antimicrobial agents and chemotherapy 2017 May 
• Finished Whole-Genome Sequences of Two Clostridium botulinum Type A(B) Isolates.
  Halpin Jessica L et al. Genome announcements 2017 May (21) 
• Finished Whole-Genome Sequence of Clostridium argentinense Producing Botulinum Neurotoxin Type G.
  Halpin Jessica L et al. Genome announcements 2017 May (21) 
• Lost in plasmids: next generation sequencing and the complex genome of the tick-borne pathogen Borrelia burgdorferi.
  Margos G et al. BMC genomics 2017 May (1) 422
• Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia.
  Bårnes Guro K et al. BMC genomics 2017 May (1) 407
• Quasispecies composition and evolution of a typical Zika virus clinical isolate from Suriname.
  van Boheemen Sander et al. Scientific reports 2017 May (1) 2368
• Establishment and cryptic transmission of Zika virus in Brazil and the Americas.
  Faria N R et al. Nature 2017 May
• Genomic epidemiology reveals multiple introductions of Zika virus into the United States.
  Grubaugh Nathan D et al. Nature 2017 May
• Sequence-Independent, Single-Primer Amplification Next-Generation Sequencing of Hantaan Virus Cell Culture-Based Isolates.
  Song Dong Hyun et al. The American journal of tropical medicine and hygiene 2017 Feb (2) 389-394
• Insights into Reston virus spillovers and adaption from virus whole genome sequences.
  Albariño César G et al. PloS one 2017 (5) e0178224 
• Molecular epidemiology of hepatitis B virus infection in Tanzania.
  Forbi Joseph C et al. The Journal of general virology 2017 May 
• Molecular Evolution and Emergence of H5N6 Avian Influenza Virus in Central China.
  Du Yingying et al. Journal of virology 2017 Jun (12)
• Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses.
  Bào Yimíng et al. Viruses 2017 May (5) 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Azithromycin Resistance and Decreased Ceftriaxone Susceptibility in Neisseria gonorrhoeae, Hawaii, USA.  
  Papp John R et al. Emerging infectious diseases 2017 May (5) 830-832 
• Cluster of Neisseria gonorrhoeae isolates with high-level azithromycin resistance and decreased ceftriaxone susceptibility, Hawaii, 2016.  
  Katz Alan R et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 May 
• Antimicrobial susceptibility of Neisseria gonorrhoeae isolates from Hefei (2014-2015): genetic characteristics of antimicrobial resistance.  
  Jiang Fa-Xing et al. BMC infectious diseases 2017 May (1) 366
• Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis.  
  Skwark Marcin J et al. PLoS genetics 2017 Feb (2) e1006508
• Clonal replacement of epidemic KPC-producing Klebsiella pneumoniae in a hospital in China.  
  Liang Yuying et al. BMC infectious diseases 2017 May (1) 363
• Differential carriage of virulence-associated loci in the New Zealand Rangipo outbreak strain of Mycobacterium tuberculosis.  
  Gautam Sanjay S et al. Infectious diseases (London, England) 2017 May 1-9
• Whole Genome Analysis Reveals New Insights into Macrolide Resistance in Mycoplasma pneumoniae.  
  Li Shao Li et al. Biomedical and environmental sciences : BES 2017 May (5) 343-350
• Prevalence and extent of heteroresistance by next generation sequencing of multidrug-resistant tuberculosis.  
  Operario Darwin J et al. PloS one 2017 (5) e0176522

DETECTION / DIAGNOSIS

• Development and Validation of a Novel Real-time Assay for the Detection and Quantification of Vibrio cholerae  
  Bin Rashid R, et al. Front Public Health, May 19, 2017.
• A critical review on ultrasensitive, spectroscopic-based methods for high-throughput monitoring of bacteria during infection treatment.  
  Dina Nicoleta Elena et al. Critical reviews in analytical chemistry 2017 May 0
• Notes from the Field: Veillonella Misidentified as Francisella tularensis — Idaho, 2016
  Carter KK, et al. MMWR, Jun 2, 2017. 
• Sensitive diagnostics confirm that influenza C is an uncommon cause of medically attended respiratory illness in adults.  
  Nesmith Natalie et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 May
• XMRV and Public Health: The Retroviral Genome Is Not a Suitable Template for Diagnostic PCR, and Its Association with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Appears Unreliable  
  Panelli S, et la. Front Public Health, May 22, 2017.
• Detection of HPV subtypes by mass spectrometry in FFPE tissue specimens: a reliable tool for routine diagnostics.  
  Kriegsmann Mark et al. Journal of clinical pathology 2017 May (5) 417-423
• Rapid and accurate molecular identification of the emerging multidrug resistant pathogen Candida auris.  
  Kordalewska Milena et al. Journal of clinical microbiology 2017 May 
• High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology.  
  Nag Sidsel et al. Scientific reports 2017 May (1) 2398

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 S, et al. Eurosurveillance, May 25, 2017.
• Whole genome and core genome multilocus sequence typing and single nucleotide polymorphism analyses of Listeria monocytogenes associated with an outbreak linked to cheese, United States, 2013.  
  Chen Yi et al. Applied and environmental microbiology 2017 May 
• Mycoplasma hominis Infections Transmitted through Amniotic Tissue Product  
  Novosad SA, et al. Clin Infect Dis, May 31, 2017.
• Multiple Introductions and Onward Transmission of HIV-1 Subtype B Strains in Shanghai, China.  
  Li Xiaoshan et al. The Journal of infection 2017 May
• Outbreak of Pneumocystis jirovecii Infection among Heart Transplant Recipients: Molecular Investigation and Management of an Inter-human Transmission.  
  Vindrios William et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 May

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Virologic Monitoring of Poliovirus Type 2 after Oral Poliovirus Vaccine Type 2 Withdrawal in April 2016 - Worldwide, 2016-2017.  
  Diop Ousmane M et al. MMWR. Morbidity and mortality weekly report 2017 May (20) 538-542 

HOST-MICROBE INTERACTIONS

• Association between a common immunoglobulin heavy chain allele and rheumatic heart disease risk in Oceania.  
  Parks Tom et al. Nature communications 2017 May 14946
• Polymorphism of TLR5 rs5744174 is associated with disease progression in Chinese patients with chronic HBV infection.  
  Cao Lina et al. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2017 May
• Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome.  
  Zuo Tao et al. Gut 2017 May
• Early pregnancy vaginal microbiome trends and preterm birth.  
  Stout Molly J et al. American journal of obstetrics and gynecology 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.

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