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.
Advanced Molecular Detection Clips Content
EVENTS / TRAINING / WEB RESOURCES
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
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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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