Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Mar 23, 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

• Tiny genetic change lets bird flu leap to humans  
   BBC, Mar 21, 2017
• Genomic Analysis Traces Transplant Recipient Infection Back to Donor  
   GenomeWeb, Mar 17, 2017.
• Inflammation Drives Gut Bacteria Evolution  
   Williams R. The Scientist, Mar 16, 2017.

EVENTS / TRAINING / WEB RESOURCES

• I Contain Multitudes – The Microbes Within Us and a Grander View of Life  
  (video lecture) Yong E. Scripps Translational Science Institute, Mar 22, 2017.
• Applied Computational Genomics Course at UU  
  (online course) Quinlan A. Univ of Utah, Spring 2017.

CONCEPTS / COMMENTS

• Tuberculosis is changing.  
  Walker Timothy M et al. The Lancet. Infectious diseases 2017 Mar
• A human judgment approach to epidemiological forecasting.  
  Farrow David C et al. PLoS computational biology 2017 Mar (3) e1005248

METHODS / TOOLS

• OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units.  
  Westcott Sarah L et al. mSphere (2)
• Phandango: an interactive viewer for bacterial population genomics.  
  Hadfield J, et al. bioRxiv, Mar 22, 2017.
• Comparison Of Multi-locus Sequence Typing Software For Next Generation Sequencing Data  
  Page AJ, et al. bioRxiv, Mar 17, 2017. 
• ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads  
  Hunt M, et al. bioRxiv, Mar 18, 2017.
• HINGE: Long-read assembly achieves optimal repeat resolution.  
  Kamath Govinda M et al. Genome research 2017 Mar
• TreeToReads - a pipeline for simulating raw reads from phylogenies.  
  McTavish Emily Jane et al. BMC bioinformatics 2017 Mar (1) 178
• Multi-Locus And Ultra-Long Amplicon Sequencing Approach To Study Microbial Diversity At Species Level Using The MinION™ Portable Nanopore Sequencer  
  Benitez-Paez A, Sanz Y. Mar 15, 2017.
• Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets.  
  Washburne Alex D et al. PeerJ 2017 e2969
• Evaluation of reference genes at different developmental stages for quantitative real-time PCR in Aedes aegypti.  
  Dzaki Najat et al. Scientific reports 2017 Mar 43618
• Complete mapping of viral escape from neutralizing antibodies.  
  Doud Michael B et al. PLoS pathogens 2017 Mar (3) e1006271

EVOLUTION / ECOLOGY / POPULATIONS

• High-Quality Genome Sequence of an Escherichia coli O157 Strain Carrying an mcr-1 Resistance Gene Isolated from a Patient in the United States.
  Lindsey Rebecca L et al. Genome announcements 2017 Mar (11) 
• Stenotrophomonas maltophilia healthcare-associated infections: identification of two main pathogenic genetic backgrounds.
  Corlouer C et al. The Journal of hospital infection 2017 Feb
• A Few Pseudomonas Oligotypes Dominate in the Meat and Dairy Processing Environment.
  Stellato Giuseppina et al. Frontiers in microbiology 2017 264
• Molecular Sequence Typing Reveals Genotypic Diversity among Escherichia coli Isolates Recovered from a Cantaloupe Packinghouse in Northwestern Mexico.
  Quiñones Beatriz et al. Letters in applied microbiology 2017 Mar
• Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway.
  Muñoz-Ramírez Zilia Y et al. Frontiers in cellular and infection microbiology 2017 50
• Whole-Genome Analysis of Bartonella ancashensis, a Novel Pathogen Causing Verruga Peruana, Rural Ancash Region, Peru.
  Mullins Kristin E et al. Emerging infectious diseases 2017 Mar (3) 430-438
• New Mycobacterium tuberculosis Complex Sublineage, Brazzaville, Congo.
  Malm Sven et al. Emerging infectious diseases 2017 Mar (3) 423-429
• Bayesian inference reveals ancient origin of simian foamy virus in orangutans.
  Reid Michael J C et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Mar
• An outbreak of severe infections among Australian infants caused by a novel recombinant strain of human parechovirus type 3.
  Nelson Tiffanie M et al. Scientific reports 2017 Mar 44423
• Comparative analysis of protein evolution in the genome of pre-epidemic and epidemic Zika virus.
  Ramaiah Arunachalam et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Mar
• Increasing HIV-1 subtype diversity in seven states, United States, 2006-2013.
  Oster Alexandra M et al. Annals of epidemiology 2017 Feb 
• Global Distribution and Evolutionary History of Enterovirus D68, with Emphasis on the 2014 Outbreak in Ontario, Canada.
  Eshaghi Alireza et al. Frontiers in microbiology 2017 257
• Molecular Verification of New World Mansonella perstans Parasitemias.
  Tavares da Silva Lucyane Bastos et al. Emerging infectious diseases 2017 Mar (3) 545-547

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Comparative subproteomic analysis of clinically acquired fluoroquinolone resistance and ciprofloxacin stress in Salmonella Typhimurium DT104B.  
  Correia Susana et al. Proteomics. Clinical applications 2017 Mar
• Identification of antibiotic resistance genes in the multidrug-resistant Acinetobacter baumannii strain, MDR-SHH02, using whole-genome sequencing.  
  Wang Hualiang et al. International journal of molecular medicine 2017 Feb (2) 364-372
• Molecular characteristics of ofloxacin mono-resistant Mycobacterium tuberculosis isolates from new and previously treated tuberculosis patients.  
  Wang Zhirui et al. Journal of clinical laboratory analysis 2017 Mar
• pncA Gene Mutations Associated with Pyrazinamide Resistance in Drug-Resistant Tuberculosis, South Africa and Georgia.  
  Allana Salim et al. Emerging infectious diseases 2017 Mar (3) 491-495 
• Emerging highly pathogenic H5 avian influenza viruses in France during winter 2015/16: phylogenetic analyses and markers for zoonotic potential.  
  Briand François-Xavier et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Mar (9)
• Functional mutations in spike glycoprotein of Zaire ebolavirus associated with an increase in infection efficiency.  
  Ueda Mahoko Takahashi et al. Genes to cells : devoted to molecular & cellular mechanisms 2017 Feb (2) 148-159
• Molecular Evidence of Drug Resistance in Asymptomatic Malaria Infections, Myanmar, 2015.  
  Nyunt Myat Htut et al. Emerging infectious diseases 2017 Mar (3) 517-520 
• Low prevalence of DHFR and DHPS mutations in Pneumocystis jirovecii strains obtained from a German cohort.  
  Suárez Isabelle et al. Infection 2017 Mar

DETECTION / DIAGNOSIS

• Distribution and phylogeny of Brachyspira spp. in human intestinal spirochetosis revealed by FISH and 16S rRNA-gene analysis.  
  Rojas Pablo et al. Anaerobe 2017 Mar
• Laboratory Identification of Leptotrichia Species Isolated From Bacteremia Patients at a Single Institution.  
  Cho Eun Hye et al. Annals of laboratory medicine 2017 May (3) 272-276
• Real-time sequencing of Mycobacterium tuberculosis: are we there yet?  
  Lee Robyn S et al. Journal of clinical microbiology 2017 Mar
• Deep sequencing and variant analysis of an Italian pathogenic field strain of equine infectious anaemia virus.  
  Cappelli K et al. Transboundary and emerging diseases 2017 Mar
• Molecular detection of airborne Coccidioides in Tucson, Arizona.  
  Chow Nancy A et al. Medical mycology 2016 Aug (6) 584-92 
• Non-invasive diagnosis of cutaneous leishmaniasis by the direct boil loop-mediated isothermal amplification method and MinION™ nanopore sequencing.  
  Imai Kazuo et al. Parasitology international 2017 Mar
• Multiplex PCR as a tool for the diagnosis of Leishmania spp. kDNA and the gapdh housekeeping gene of mammal hosts.  
  de Cássia-Pires Renata et al. PloS one 2017 (3) e0173922

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient.  
  Bashir Ali et al. PloS one 2017 (3) e0170449
• Mycobacterium tuberculosis Infection among Asian Elephants in Captivity.  
  Simpson Gary et al. Emerging infectious diseases 2017 Mar (3) 513-516
• A large outbreak of acute gastroenteritis in Shippensburg, Pennsylvania, 1972 revisited: evidence for common source exposure to a recombinant GII.Pg/GII.3 norovirus.  
  Johnson J A et al. Epidemiology and infection 2017 Mar 1-6

HOST-MICROBE INTERACTIONS

• Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study. 
  Boutin Sébastien et al. Frontiers in microbiology 2017 340
• Severe infections emerge from the microbiome by adaptive evolution  
  Young BC, et al. bioRxiv, Mar 14, 2017.
• Enhanced understanding of the host-pathogen interaction in sepsis: new opportunities for omic approaches.  
  Goh Cyndi et al. The Lancet. Respiratory medicine 2017 Mar (3) 212-223

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