Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Nov 1, 2018

Advanced Molecular Detection Clips Content

• News
• Events / Training / Web Resources
• Policy
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• Push to change genetic materials treaty over disease pandemic fears
  Cosmos, Oct 26, 2018.
• With machine learning, researchers get new clues in the hunt for the source of mysterious viruses
  Joseph A. STAT, Nov 1, 2018.
• EV-D68 steps up its neurotropism
  Hofer U. Nature, Oct 29, 2018.
• Don’t just blame the hospital, bloodborne pathogens were hiding inside the whole time
  Cohen LJ. Sci Transl Med, Oct 31, 2018.
• Improving outbreak response
  (book review)Pewen WF. Science, Nov 2, 2018.
• Llama antibodies inspire gene spray to prevent all flus
  Cohen J. Science, Nov 2, 2018.
• Flu mutations in a single cell help to predict immune response: Genetic diversity of the virus may explain variability in how well a cell fights back. 
  Arnold C. Nature, Oct 29, 2018.
• FDA says it will consider approval of first dengue vaccine, despite controversy
  Branswell H. STAT, Oct 30, 2018.
• Gutted about opioids
  Yan W. Nature, Oct 30, 2018.
• Doctors Test Bacterial Smear After Cesarean Sections To Bolster Babies' Microbiomes
  Stein R. NPR, Oct 30, 2018.
• Microbiome conservancy stores global fecal samples
  Rabesandratana T. Science, Nov 2, 2018.
• There’s a jungle in your bed
  (book review) Foster W. Nature, Oct 29, 2018.

EVENTS / TRAINING / WEB RESOURCES

• Why Jupyter is data scientists' computational notebook of choice.
  Perkel Jeffrey M et al. Nature 2018 Nov (7729) 145-146

POLICY

• Threats to timely sharing of pathogen sequence data.
  Dos S Ribeiro Carolina et al. Science (New York, N.Y.) 2018 10 (6413) 404-406

CONCEPTS / COMMENTS

• Developmental roadmap for antimicrobial susceptibility testing systems.
  van Belkum Alex et al. Nature reviews. Microbiology 2018 Oct
• Next-Generation Sequencing for Biodefense: Biothreat Detection, Forensics, and the Clinic.
  Minogue Timothy D et al. Clinical chemistry 2018 Oct
• Targeting the microbiome: from probiotics to fecal microbiota transplantation
  Khoruts A. Genome Med, Oct 301, 2018.
• Sources of human viruses
  Woolhouse M. Science, Nov 2, 2018.

METHODS / TOOLS

• Bioinformatics tools to assess metagenomic data for applied microbiology.
  Almeida Otávio G G et al. Applied microbiology and biotechnology 2018 Oct
• Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection.
  Gu Wei et al. Annual review of pathology 2018 Oct
• Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples.
  Zhang Dan et al. BMC genomics 2018 Oct (1) 773
• How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis.
  Terranova Leonardo et al. International journal of molecular sciences 2018 Oct (10)
• Isolation and Whole-Genome Sequencing of Environmental Campylobacter.
  Kelley Brittni R et al. Current protocols in microbiology 2018 Nov (1) e64
• Purification of Cyclospora cayetanensis oocysts obtained from human stool specimens for whole genome sequencing.
  Qvarnstrom Yvonne et al. Gut pathogens 2018 45 
• Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains.
  Shrivastava Susmita et al. Scientific reports 2018 Oct (1) 15843
• PhasomeIt: an 'omics' approach to cataloguing the potential breadth of phase variation in the genus Campylobacter.
  Aidley Jack et al. Microbial genomics 2018 Oct
• PoSE: visualization of patterns of sequence evolution using PAML and MATLAB.
  Zhao Kun et al. BMC bioinformatics 2018 Oct (Suppl 11) 364 
• Victors: a web-based knowledge base of virulence factors in human and animal pathogens.
  Sayers Samantha et al. Nucleic acids research 2018 Oct
• SENSE: Siamese neural network for sequence embedding and alignment-free comparison.
  Zheng Wei et al. Bioinformatics (Oxford, England) 2018 Oct
• Automated quality control for a molecular surveillance system.
  Sims Seth et al. BMC bioinformatics 2018 Oct (Suppl 11) 358  
• Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus.
  Ji Hezhao et al. Journal of the International AIDS Society 2018 Oct (10) e25193 
• Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants.
  Tsyvina Viachaslau et al. BMC bioinformatics 2018 Oct (Suppl 11) 360 
• Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase.
  Ezewudo Matthew et al. Scientific reports 2018 Oct (1) 15382 
• The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology.
  Meehan Conor J et al. EBioMedicine 2018 Oct
• Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes
  Babayan SA, et al. Science, Nov 2, 2018.
• Tracing Antibody Repertoire Evolution by Systems Phylogeny.
  Yermanos Alexander Dimitri et al. Frontiers in immunology 2018 2149

EVOLUTION / ECOLOGY / POPULATIONS

• Phylogeographic analysis reveals multiple international transmission events have driven the global emergence of Escherichia coli O157:H7.
  Franz Eelco et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Oct
• Whole genome sequencing of toxigenic C. difficile in asymptomatic carriers: insights into possible role in transmission.
  Halstead Fenella D et al. The Journal of hospital infection 2018 Oct
• Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.
  Mercante Jeffrey W et al. PloS one 2018 (10) e0206110 
• Complete genome sequencing of sixteen Francisella noatunensis subsp. orientalis isolates: A genomic approach for molecular characterization and spread dynamics of this clonal population.
  Pereira Felipe Luiz et al. Genomics 2018 Oct
• Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation.
  Brynildsrud Ola B et al. Science advances 2018 Oct (10) eaat5869
• Emergence of dengue virus type 1 and type 3 as dominant serotypes during 2017 in Pune and Nashik regions of Maharashtra, Western India.
  Patil J A et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Oct
• Continuous Invasion by Respiratory Viruses Observed in Rural Households During a Respiratory Syncytial Virus Seasonal Outbreak in Coastal Kenya.
  Munywoki Patrick K et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Oct (10) 1559-1567
• New Insights into the Evolutionary and Genomic Landscape of Molluscum Contagiosum Virus (MCV) based on Nine MCV1 and Six MCV2 Complete Genome Sequences.
  Zorec Tomaž M et al. Viruses 2018 Oct (11) 
• Multiple introductions and antigenic mismatch with vaccines may contribute to increased predominance of G12P[8] rotaviruses in the United States.
  Ogden Kristen M et al. Journal of virology 2018 Oct 
• Genetic characterization of human metapneumovirus (hMPV) identified through community and facility-based surveillance of infants in Dhaka, Bangladesh.
  Rahman M Z et al. Journal of medical virology 2018 Oct
• Time to Harmonize Dengue Nomenclature and Classification.
  Cuypers Lize et al. Viruses 2018 Oct (10) 
• Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.
  Vesth Tammi C et al. Nature genetics 2018 Oct
• Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development.
  Duffy Craig W et al. Scientific reports 2018 Oct (1) 15763
• Timing the Origin of Cryptococcus gattii sensu stricto, Southeastern United States.
  Lockhart Shawn R et al. Emerging infectious diseases 2018 Nov (11) 2095-2097
• Identification of free-living amoebae isolated from tap water in Istanbul, Turkey.
  Üstüntürk-Onan Miray et al. Experimental parasitology 2018 Oct 34-37
• Plant-feeding phlebotomine sand flies, vectors of leishmaniasis, prefer Cannabis sativa .
  Abbasi Ibrahim et al. Proceedings of the National Academy of Sciences of the United States of America 2018 Oct

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Phylogenomic analysis of extraintestinal pathogenic Escherichia coli ST1193, an emerging multidrug-resistant clonal group.
  Johnson Timothy J et al. Antimicrobial agents and chemotherapy 2018 Oct
• Determination of virulence and fitness genes associated with the pheU , pheV and selC integration sites of LEE-negative food-borne Shiga toxin-producing Escherichia coli strains.
  Saile Nadja et al. Gut pathogens 2018 43
• Increasing prevalence of Neisseria gonorrhoeae with decreased susceptibility to ceftriaxone and resistance to azithromycin in Hangzhou, China (2015-17).
  Yan Jing et al. The Journal of antimicrobial chemotherapy 2018 Oct
• Phenotypic Variation in the Group A Streptococcus Due to Natural Mutation of the Accessory Protein-Encoding Gene rocA .
  Sarkar Poulomee et al. mSphere 2018 Oct (5)
• Antimicrobial Resistance in Neisseria gonorrhoeae: Proceedings of the STAR Sexually Transmitted Infection-Clinical Trial Group Programmatic Meeting.
  Cristillo Anthony D et al. Sexually transmitted diseases 2018 Oct  
• Heteroresistance to the model antimicrobial peptide polymyxin B in the emerging Neisseria meningitidis linage11.2 urethritis clade: mutations in the pilMNOPQ operon.
  Tzeng Yih-Ling et al. Molecular microbiology 2018 Oct
• Transcriptome Analysis of Neisseria gonorrhoeae during Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants between Men and Women.
  Nudel Kathleen et al. mSphere 2018 08 (3) 
• Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia.
  Merker Matthias et al. eLife 2018 10
• New epidemic cluster of pre-extensively drug resistant isolates of Mycobacterium tuberculosis Ural family emerging in Eastern Europe.
  Sinkov Viacheslav et al. BMC genomics 2018 Oct (1) 762
• Genetic characterization of the first detected human case of avian influenza A (H5N6) in Anhui Province, East China.
  He Jun et al. Scientific reports 2018 Oct (1) 15282
• Naturally-occurring single mutations in Ebola observably impact infectivity.
  Wong Gary et al. Journal of virology 2018 Oct
• Molecular Surveillance of Plasmodium falciparum Drug Resistance Markers in Clinical Samples from Botswana.
  Tawe Leabaneng et al. The American journal of tropical medicine and hygiene 2018 Oct

DETECTION / DIAGNOSIS

• Linezolid and Vancomycin-Resistant Enterococcus faecium in Solid Organ Transplant Recipients: Infection Control and Antimicrobial Stewardship Using Whole Genome Sequencing.
  Abbo Lilian et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Oct 
• Integration of sample preparation and analysis into an optofluidic chip for multi-target disease detection.
  Meena Gopikrishnan G et al. Lab on a chip 2018 Oct
• Applying Rapid Whole Genome Sequencing to Predict Phenotypic Antimicrobial Susceptibility Testing Results Among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates.
  Tamma Pranita D et al. Antimicrobial agents and chemotherapy 2018 Oct
• High Relative Frequency of Enteroaggregative Escherichia coli among Patients with Reportable Enteric Pathogens, Minnesota, 2016-2017.
  Beczkiewicz Aaron et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Oct
• Notes from the Field: Intestinal Colonization and Possible Iatrogenic Botulism in Mouse Bioassay-Negative Serum Specimens - Los Angeles County, California, November 2017.
  Halai Umme-Aiman et al. MMWR. Morbidity and mortality weekly report 2018 Nov (43) 1221-1222  
• Outbreak of multidrug-resistant tuberculosis in South Africa undetected by WHO-endorsed commercial tests: an observational study.
  Makhado Ndivhuho A et al. The Lancet. Infectious diseases 2018 Oct
• Assessment of Validity of a Blood-Based 3-Gene Signature Score for Progression and Diagnosis of Tuberculosis, Disease Severity, and Treatment Response 
  Warsinske HC, et al. JAMA Network Open, Oct 26, 2018.
• The Evolution of Genotyping Strategies To Detect, Analyze, and Control Transmission of Tuberculosis.
  García De Viedma Darío et al. Microbiology spectrum 2018 Oct (5)
• Assessment of enteroviruses from sewage water and clinical samples during eradication phase of polio in North India.
  Tiwari Sarika et al. Virology journal 2018 Oct (1) 157
• Surveillance and Diagnosis of West Nile Virus in the Face of Flavivirus Cross-Reactivity.
  Lustig Yaniv et al. Frontiers in microbiology 2018 2421
• Valve-enabled Sample Preparation and RNA Amplification in a Coffee Mug for Zika Virus Detection.
  Jiang Xiao et al. Angewandte Chemie (International ed. in English) 2018 Oct
• Validation of a High-throughput, Multiplex, Real-time Qualitative Polymerase Chain Reaction Assay for the Detection of Sabin Oral Polio Vaccine in Environmental Samples.
  Altamirano Jonathan et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Oct (suppl_1) S98-S102
• West Nile virus associated with equid encephalitis in Brazil, 2018.
  Silva Aila Solimar Gonçalves et al. Transboundary and emerging diseases 2018 Oct 
• Host Gene Expression in Nose and Blood for the Diagnosis of Viral Respiratory Infection.
  Yu Jinsheng et al. The Journal of infectious diseases 2018 Oct
• Five-year China Hospital Invasive Fungal Surveillance Net (CHIF-NET) study of invasive fungal infections caused by noncandidal yeasts: species distribution and azole susceptibility.
  Xiao Meng et al. Infection and drug resistance 2018 1659-1667 
• High proportions of pfhrp2 gene deletion and performance of HRP2-based rapid diagnostic test in Plasmodium falciparum field isolates of Odisha.
  Pati Pallabi et al. Malaria journal 2018 Oct (1) 394 
• Identification of potential whole blood MicroRNA biomarkers for the blood stage of adult imported falciparum malaria through integrated mRNA and miRNA expression profiling.
  Li Jing-Jing et al. Biochemical and biophysical research communications 2018 Oct
• Molecular detection and genotyping of pathogenic protozoan parasites in raw and treated water samples from southwest Colombia.
  Sánchez Claudia et al. Parasites & vectors 2018 Oct (1) 563 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Outbreak of Burkholderia cepacia complex infections associated with contaminated octenidine mouthwash solution, Germany, August to September 2018.
  Becker Sören L et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Oct (42)
• A genomic infection control study for Staphylococcus aureus in two Ghanaian hospitals.
  Donkor Eric S et al. Infection and drug resistance 2018 1757-1765
• Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis.
  Whaley Melissa J et al. Scientific reports 2018 Oct (1) 15803 
• Outbreak of Neisseria meningitidis serogroup C outside the meningitis belt-Liberia, 2017: an epidemiological and laboratory investigation.
  Bozio Catherine H et al. The Lancet. Infectious diseases 2018 Oct 
• First use of whole-genome sequencing to investigate a cluster of Yersinia enterocolitica, Liverpool, United Kingdom, 2017.
  Inns Thomas et al. Journal of medical microbiology 2018 Oct 
• Suspected transmission and subsequent spread of MRSA from farmer to dairy cows.
  Unnerstad Helle Ericsson et al. Veterinary microbiology 2018 Nov 114-119
• Quasispecies Diversity Is a Major Risk Factor for Vertical Hepatitis C Virus Transmission.
  Larouche Ariane et al. The Journal of infectious diseases 2018 Oct
• Public health investigation and response to a hepatitis A outbreak from imported scallops consumed raw-Hawaii, 2016.
  Viray M A et al. Epidemiology and infection 2018 Oct 1-8  
• Hepatitis A outbreak linked to imported frozen strawberries by sequencing, Sweden and Austria, June to September 2018.
  Enkirch Theresa et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Oct (41) 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation.
  Staley Christopher et al. Microbiome 2018 Sep (1) 166 
• Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin
  Laursen NS, et al. Science, Nov 2, 2018.

HOST-MICROBE INTERACTIONS

• Microbiome dataset from the upper respiratory tract of patients living with HIV, HIV/TB and TB from Myanmar.
  Htun Kyaw Soe et al. Data in brief 2018 Dec 354-357
• Temporal development of the gut microbiome in early childhood from the TEDDY study.
  Stewart Christopher J et al. Nature 2018 Oct (7728) 583-588
• Precision identification of diverse bloodstream pathogens in the gut microbiome.
  Tamburini Fiona B et al. Nature medicine 2018 Oct
• Yersinia pseudotuberculosis exploits CD209 receptors for promoting host dissemination and infection.
  He Ying-Xia et al. Infection and immunity 2018 Oct
• Frequency and Geographic Distribution of CARD9 Mutations in Patients With Severe Fungal Infections.
  Vaezi Afsane et al. Frontiers in microbiology 2018 2434

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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