Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Oct 24, 2019

Advanced Molecular Detection Clips Content

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

NEWS

• UK study: Food not likely source of resistant E coli
  Dall C. CIDRAP, Oct 23, 2019.
• New diagnostic tools are essential in the battle against antibiotic resistance
  Stern E. STAT, Oct 24, 2019.
• Triage Test for Tuberculosis Spots Infections Within an Hour
  Williams R. The Scientist, Oct 23, 2019.
• New DRC Ebola cases confirmed as FDA OKs rapid test
  Soucheray S. CIDRAP, Oct 11, 2019.
• NIH and Gates Foundation launch effort to bring genetic cures for HIV, sickle cell disease to world's poor
  Begley S. STAT, Oct 23, 2019.
• Gut microbes help mice overcome their fears by changing brain activity
  Scully RP. New Scientist, Oct 23, 2019.
• The expanding horizons of host-microorganism imaging are clear to see
  Inns PG, Mamou G. Nat Rev Microbiol, Oct 24, 2019.
• Human trial of vaginal microbiome transplantation
  Du Toit A. Nat Rev Microbiol, Oct 18, 2019.
• Your microbiome is what you eat
  York A. Nat Rev Microbiol, Oct 17, 2019.

CONCEPTS / COMMENTS

• Should we be performing metagenomic next-generation sequencing for infectious disease diagnosis in the clinical laboratory?
  Miller Steve et al. Journal of clinical microbiology 2019 Oct
• Turning influenza vaccinology on its head to reveal the stalk.
  Valkenburg Sophie A et al. The Lancet. Infectious diseases 2019 Oct
• Viral quasispecies.
  Domingo Esteban et al. PLoS genetics 2019 Oct (10) e1008271
• Technological challenges and milestones for writing genomes.
  Ostrov Nili et al. Science (New York, N.Y.) 2019 Oct (6463) 310-312
• Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire.
  Koonin Eugene V et al. Nature reviews. Genetics 2019 Oct
• Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.
  Sakowski Eric et al. mSystems 2019 Oct (5)

METHODS / TOOLS

• Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity.
  Maljkovic Berry Irina et al. The Journal of infectious diseases 2019 Oct  
• Third generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing.
  Petersen Lauren M et al. Journal of clinical microbiology 2019 Oct
• dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA.
  Decker Carolyn J et al. Viruses 2019 Oct (10)
• Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix).
  Glenn Travis C et al. PeerJ 2019 e7786 
• HIV-1 genetic diversity to estimate time of infection and infer adherence to pre-exposure prophylaxis.
  Council Olivia D et al. AIDS (London, England) 2019 Oct  
• Inferring putative transmission clusters with Phydelity.
  Han Alvin X et al. Virus evolution 2019 Jul (2) vez039
• The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system.
  Tomic Adriana et al. Scientific data 2019 Oct (1) 214

EVOLUTION / ECOLOGY / POPULATIONS

• Genomic characterization of Haemophilus influenzae: a focus on the capsule locus.
  Potts Caelin C et al. BMC genomics 2019 Oct (1) 733 
• Comparison of Whole-Genome Sequences of Legionella pneumophila in Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016.
  Garner Emily et al. Emerging infectious diseases 2019 Nov (11) 2013-2020
• Limited intra-host diversity and background evolution accompany 40 years of canine parvovirus host adaptation and spread.
  Voorhees Ian E H et al. Journal of virology 2019 Oct
• Genetic and phenotypic characterization of recently discovered enterovirus D type 111.
  Sadeuh-Mba Serge Alain et al. PLoS neglected tropical diseases 2019 Oct (10) e0007797
• Circulation of Chikungunya virus East-Central-South Africa genotype during an outbreak in 2016-17 in Piaui State, Northeast Brazil.
  Cardoso Felipe Daniel et al. Revista do Instituto de Medicina Tropical de Sao Paulo 2019 e57
• Evolutionary, genetic, structural characterization and its functional implications for the influenza A (H1N1) infection outbreak in India from 2009 to 2017.
  Jones Sara et al. Scientific reports 2019 Oct (1) 14690
• Yellow fever virus re-emergence and spread in Southeast Brazil, 2016-2019.
  Giovanetti Marta et al. Journal of virology 2019 Oct
• Simian Foamy Viruses in Central and South America: A New World of Discovery.
  Santos André F et al. Viruses 2019 Oct (10) 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Multiple importations and transmission of colistin-resistant Klebsiella pneumoniae in a hospital in northern India.
  Mathur Purva et al. Infection control and hospital epidemiology 2019 Oct 1-7 
• Whole genome sequencing of Staphylococcus epidermidis bloodstream isolates from a prospective clinical trial reveals that complicated bacteremia is caused by a limited number of closely related sequence types.
  Shelburne Samuel A et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Oct
• Metagenomics: aid to combat antimicrobial resistance in diarrhea.
  De Rituparna et al. Gut pathogens 2019 47 
• Association between antibiotic residues, antibiotic resistant bacteria and antibiotic resistance genes in anthropogenic wastewater - An evaluation of clinical influences.
  Voigt A M et al. Chemosphere 2019 Oct 125032
• Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation.
  Mangas Eugenio L et al. Microbial genomics 2019 Oct
• Genomic differences among carriage and invasive nontypeable pneumococci circulating in South Africa.
  Mohale Thabo et al. Microbial genomics 2019 Oct
• Genomic epidemiology of penicillin-non-susceptible Streptococcus pneumoniae .
  Dewé Tamsin C M et al. Microbial genomics 2019 Oct
• Genome rearrangements induce biofilm formation in Escherichia coli C - an old model organism with a new application in biofilm research.
  Król Jaroslaw E et al. BMC genomics 2019 Oct (1) 767
• Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan.
  Jabbar Abdul et al. Scientific reports 2019 Oct (1) 14996
• Molecular surveillance of antimicrobial resistance and transmission pattern of Mycobacterium leprae in Chinese leprosy patients.
  Chokkakula Santosh et al. Emerging microbes & infections 2019 (1) 1479-1489
• Characterizing early drug resistance-related events using geometric ensembles from HIV protease dynamics.
  Sheik Amamuddy Olivier et al. Scientific reports 2018 12 (1) 17938
• Pan-viral serology implicates enteroviruses in acute flaccid myelitis.
  Schubert Ryan D et al. Nature medicine 2019 Oct 
• Susceptibility to insecticides and resistance mechanisms in three populations of Aedes aegypti from Peru.
  Pinto Jesus et al. Parasites & vectors 2019 Oct (1) 494  

DETECTION / DIAGNOSIS

• Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach.
  Hendriksen Rene S et al. PloS one 2019 (10) e0222531 
• Development and Implementation of Multiplex TaqMan Array Cards for Specimen Testing at Child Health and Mortality Prevention Surveillance Site Laboratories.
  Diaz Maureen H et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Oct (Supplement_4) S311-S321  
• Electrochemical sensors for rapid diagnosis of pathogens in real time.
  Simoska Olja et al. The Analyst 2019 Oct
• Quantitative real-time PCR assay for the rapid identification of the intrinsically multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia .
  Fraser Tamieka A et al. Microbial genomics 2019 Oct
• Rapid and Highly Sensitive DNA Flow Technology Platform to Detect Tick-Borne Bacterial Pathogens in Clinical Samples.
  Jado Isabel et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2019 Oct
• A novel multilocus variable-number tandem repeat analysis for Bordetella parapertussis .
  Kamachi Kazunari et al. Journal of medical microbiology 2019 Oct
• High-Throughput 16S rRNA Sequencing to Assess Potentially Active Bacteria and Foodborne Pathogens: A Case Example in Ready-to-Eat Food.
  Mira Miralles Marina et al. Foods (Basel, Switzerland) 2019 Oct (10)
• Increase in Gonorrhea Incidence Associated With Enhanced Partner Notification Strategy.
  Schleihauf Emily et al. Sexually transmitted diseases 2019 Nov (11) 706-712 
• Evaluation of a Bead-Based Salmonella Molecular Serotyping Method for Salmonella Isolated from Food and Environmental Samples.
  Moore M M et al. Journal of food protection 2019 Oct 1973-1987 
• Comparing the utility of different multilocus sequence typing schemes for identifying outbreak strains of Mycobacterium abscessus subspecies massiliense .
  Cheng Aristine et al. Journal of clinical microbiology 2019 Oct 
• FluChip-8G Insight: HA and NA subtyping of potentially pandemic influenza A viruses in a single assay.
  Toth Evan et al. Influenza and other respiratory viruses 2019 Oct  
• Prevalence of DNA of fourteen human polyomaviruses determined in blood donors.
  Kamminga Sergio et al. Transfusion 2019 Oct
• Geographical Variability Affects CCHFV Detection by RT-PCR: A Tool for In-Silico Evaluation of Molecular Assays.
  Gruber Cesare E M et al. Viruses 2019 10 (10)
• Single-tube, dual channel pentaplexing for the identification of Candida strains associated with human infection.
  Jainlabdin Mohd Hanif et al. Scientific reports 2019 Oct (1) 14692
• Progress in loop-mediated isothermal amplification assay for detection of Schistosoma mansoni DNA: towards a ready-to-use test.
  García-Bernalt Diego J et al. Scientific reports 2019 Oct (1) 14744
• Testing the impact of Whole Genome Amplification on genome comparison using the polyploid flagellated Giardia duodenalis as a model.
  Weisz Filip et al. Experimental parasitology 2019 Oct 107776

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Two carbapenemase-producing Enterobacteriaceae outbreaks detected retrospectively by whole-genome sequencing at an Australian tertiary hospital.
  Marmor Alexandra et al. Infection, disease & health 2019 Oct
• A Cluster of Bacillus cereus Infections in the Neonatal Intensive Care Unit: Epidemiologic and Whole-genome Sequencing Analysis.
  Bar-Meir Maskit et al. The Pediatric infectious disease journal 2019 Nov (11) e301-e306 
• International travel as source of a hospital outbreak with an unusual meticillin-resistant Staphylococcus aureus clonal complex 398, Denmark, 2016.
  Møller Jens Kjølseth et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Oct (42)
• Mass prophylaxis in an outbreak of invasive group A streptococcal disease in a residential aged care facility
  Vasant Bhakti R et al. Communicable diseases intelligence (2018) 2019 May 
• Retrospective investigation of listeriosis outbreaks in small ruminants using different analytical approaches for whole genome sequencing-based typing of Listeria monocytogenes.
  Papic Bojan et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Oct 104047
• Inter-host Transmission of Carbapenemase-Producing Escherichia coli among Humans and Backyard Animals.
  Li Jiyun et al. Environmental health perspectives 2019 Oct (10) 107009
• Isolate-Based Surveillance of Listeria monocytogenes by Whole Genome Sequencing in Austria.
  Cabal Adriana et al. Frontiers in microbiology 2019 2282 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Nanoparticles in the Treatment of Infections Caused by Multidrug-Resistant Organisms.
  Lee Nan-Yao et al. Frontiers in pharmacology 2019 1153
• Methicillin-resistant Staphylococcus aureus (MRSA) in hospitals: latest trends and treatments based on bacteriophages.
  Álvarez Andrea et al. Journal of clinical microbiology 2019 Oct
• Yellow Fever: Integrating Current Knowledge with Technological Innovations to Identify Strategies for Controlling a Re-Emerging Virus.
  Kleinert Robin D V et al. Viruses 2019 Oct (10) 
• Programmable Inhibition and Detection of RNA Viruses Using Cas13.
  Freije Catherine A et al. Molecular cell 2019 Oct
• Genotypic and phenotypic characterization of West Nile virus NS5 methyltransferase mutants.
  Kaiser Jaclyn A et al. Vaccine 2019 Oct 
• Safety and immunogenicity of a multivalent HIV vaccine comprising envelope protein with either DNA or NYVAC vectors (HVTN 096): a phase 1b, double-blind, placebo-controlled trial.
  Pantaleo Giuseppe et al. The lancet. HIV 2019 Oct 

HOST-MICROBE INTERACTIONS

• Individualized recovery of gut microbial strains post antibiotics.
  Koo Hyunmin et al. NPJ biofilms and microbiomes 2019 30
• The effect of antibiotics on the composition of the intestinal microbiota.
  Zimmermann Petra et al. The Journal of infection 2019 Oct 
• Vulnerability of the industrialized microbiota
  Sonnenburg JL, Sonnenburg ED. Science, Oct 25, 2019.
• Universal Newborn Screening for Severe Combined Immunodeficiency (SCID).
  van der Burg Mirjam et al. Frontiers in pediatrics 2019 373 
• Microbe-host interplay in atopic dermatitis and psoriasis.
  Fyhrquist Nanna et al. Nature communications 2019 Oct (1) 4703
• DBP rs16846876 and rs12512631 polymorphisms are associated with progression to AIDS naïve HIV-infected patients: a retrospective study.
  Jiménez-Sousa María Ángeles et al. Journal of biomedical science 2019 Oct (1) 83

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.