Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Dec 5, 2019

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
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• MIT researchers are building an instrument to study genetics on Mars
  Scoles S. Quartz, Dec 2, 2019.
• Stakeholders Developing Toolkit to Tackle Lack of MDx Outcomes Data in Microbiology
  Johnson M. GenomeWeb, Nov 27, 2019.
• UK Researchers Implement Diagnostics.ai System to Improve Infectious Disease Testing
  Petrone J. GenomeWeb, Dec 4, 2019.
• NanoString-Based Genotype, Phenotype Test Rapidly Detects Antimicrobial Resistance
  Johnson M. GenomeWeb, Nov 26, 2019.
• The US has a new weapon in the fight against antibiotic resistance
  Purdy C. Quartz, Nov 22, 2019.
• Polio Vaccination Causes More Infections than Wild Virus
  Akst J. The Scientist, Nov 25, 2019.
• Malaria parasites fine-tune mutations to resist drugs
  Tilley L, Rosenthal PJ. Nature, Nov 27, 2019.
• Longitudinal Stool Sampling Study Points to Virome Shifts in Children With Islet Autoimmunity
  GenomeWeb, Dec 2, 2019.
• Food for thought about manipulating gut bacteria
  Delzenne NM, Bindels LB. Nature, Dec 4, 2019.

EVENTS / TRAINING / WEB RESOURCES

• December 11 Webinar: Running the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) on your own data
  (webinar) NCBI, Wed Dec 11, 12:00-12:45pm.
• A picture is worth a thousand base pairs: A small but powerful toolset makes sharing genomic data visualizations straightforward
  Nowogrodzki A. Nature, Dec 2, 2019.

CONCEPTS / COMMENTS

• Framing the discussion of microorganisms as a facet of social equity in human health.
  Ishaq Suzanne L et al. PLoS biology 2019 Nov (11) e3000536
• Immunology taught by vaccines.
  Pulendran Bali et al. Science (New York, N.Y.) 2019 Nov (6469) 1074-1075

METHODS / TOOLS

• Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.
  Sevim Volkan et al. Scientific data 2019 Nov (1) 285
• QAlign: Aligning nanopore reads accurately using current-level modeling
  Joshi D, et al. bioRxiv, Dec 3, 2019.
• Phenotypically distinct human sequence is widespread in publicly archived microbial reads: an evaluation of methods for its detection
  Bush SJ, et al. bioRxiv, Nov 27, 2019. 
• A guide to machine learning for bacterial host attribution using genome sequence data.
  Lupolova Nadejda et al. Microbial genomics 2019 Nov
• Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly.
  Kang Joyce B et al. BMC bioinformatics 2019 Dec (Suppl 16) 585
• Phylonium: Fast Estimation of Evolutionary Distances from Large Samples of Similar Genomes.
  Klötzl Fabian et al. Bioinformatics (Oxford, England) 2019 Dec
• Addressing dereplication crisis: Taxonomy-free reduction of massive genome collections using embeddings of protein content
  Viehweger A, et al. bioRxiv, Dec 5, 2019.
• The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales
  Chattaway M, et al. Front Public Health, Nov 21, 2019. 
• VCGIDB: A Database and Web Resource for the Genomic Islands from Vibrio Cholerae .
  Hur YoungJae et al. Pathogens (Basel, Switzerland) 2019 Nov (4)
• Efficient sentinel surveillance strategies for preventing epidemics on networks.
  Colman Ewan et al. PLoS computational biology 2019 Nov (11) e1007517
• EpitoCore: mining conserved epitope vaccine candidates in the core proteome of multiple bacteria strains
  Fiuza TS, et al. bioRxiv, Dec 4, 2019.
• Constructing and Characterizing Bacteriophage Libraries for Phage Therapy of Human Infections.
  Gibson Shelley B et al. Frontiers in microbiology 2019 2537

EVOLUTION / ECOLOGY / POPULATIONS

• Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent.
  Steinig Eike J et al. mBio 2019 Nov (6)
• Changing Molecular Epidemiology of Vibrio cholerae Outbreaks in Shanghai, China.
  Hu Dalong et al. mSystems 2019 Nov (6)
• Comparative genomic analysis and molecular examination of the diversity of enterotoxigenic Escherichia coli isolates from Chile.
  Rasko David A et al. PLoS neglected tropical diseases 2019 Nov (11) e0007828
• Isolation and comparative genomics of Mycobacterium tuberculosis isolates from cattle and their attendants in South India.
  Palaniyandi Kannan et al. Scientific reports 2019 Nov (1) 17892
• Two distinct lineages of chikungunya virus cocirculated in Aruba during the 2014-2015 epidemic.
  Phadungsombat Juthamas et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Nov 104129
• Population Structure and Genetic Diversity among Isolates of Coccidioides posadasii in Venezuela and Surrounding Regions.
  Teixeira Marcus M et al. mBio 2019 Nov (6) 
• What Is Going on With the Genus Dermacentor? Hybridizations, Introgressions, Oh My!
  Goddard Jerome et al. Journal of medical entomology 2019 Nov 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Gut carriage of antimicrobial resistance genes among young children in urban Maputo, Mozambique: Associations with enteric pathogen carriage and environmental risk factors.
  Berendes David et al. PloS one 2019 (11) e0225464
• Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm.
  Eckstrom Korin et al. PloS one 2019 (11) e0219807
• Conservation and global distribution of non-canonical antigens in Enterotoxigenic Escherichia coli.
  Kuhlmann F Matthew et al. PLoS neglected tropical diseases 2019 Nov (11) e0007825
• Unexpected relationships between frequency of antimicrobial resistance, disease phenotype and emm type in group A Streptococcus .
  Sanson Misu A et al. Microbial genomics 2019 Nov (11)
• A mosaic tetracycline resistance gene tet(S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa.
  Lo Stephanie W et al. The Journal of antimicrobial chemotherapy 2019 Dec
• First insights into circulating XDR and pre-XDR Mycobacterium tuberculosis in Southern Brazil.
  Salvato Richard Steiner et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Nov 104127
• Whole blood RNA signatures in leprosy patients identify reversal reactions before clinical onset: a prospective, multicenter study.
  Tió-Coma Maria et al. Scientific reports 2019 Nov (1) 17931
• HIV-1 viral load is elevated in individuals with reverse transcriptase mutation M184V/I during virological failure of first line antiretroviral therapy and is associated with compensatory mutation L74I.
  Gregson J et al. The Journal of infectious diseases 2019 Nov
• Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations.
  Stelzer-Braid Sacha et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2019 Nov 104216

DETECTION / DIAGNOSIS

• Rapid molecular tests for detection of antimicrobial resistance determinants in Gram-negative organisms from positive blood cultures: a systematic review and meta-analysis.
  De Angelis G et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Nov 
• Salmonella Serotyping; Comparison of the Traditional Method to a Microarray-Based Method and an in silico Platform Using Whole Genome Sequencing Data.
  Diep Benjamin et al. Frontiers in microbiology 2019 2554
• Molecular Diagnostic Advances in Transplant Infectious Diseases.
  Young Brittany A et al. Current infectious disease reports 2019 Nov (12) 52
• Evaluation of PCR assays for direct screening of Carbapenemase-Producing Enterobacteriaceae (CPE) from rectal swabs: a diagnostic meta-analysis.
  Saliba Rindala et al. The Journal of hospital infection 2019 Nov 
• Clinical Utility of Advanced Microbiology Testing Tools.
  Miller Melissa B et al. Journal of clinical microbiology 2019 Sep (9) 
• Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination.
  Bhattacharyya Roby P et al. Nature medicine 2019 Nov
• A chip-based potentiometric sensor for a Zika virus diagnostic using 3D surface molecular imprinting.
  Ricotta Vincent et al. The Analyst 2019 Jul (14) 4266-4280
• Clinical and virological findings in patients with Usutu virus infection, northern Italy, 2018.
  Pacenti Monia et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 11 (47)
• Introduction of Cobas Liat Influenza A/B for rapid point-of-care diagnosis of influenza infection in an acute trust.
  Brooke-Pearce Fran et al. Journal of infection prevention 2019 Nov (6) 297-300 
• A Novel Field-Deployable Method for Sequencing and Analyses of Henipavirus Genomes From Complex Samples on the MinION Platform.
  Yinda Claude Kwe et al. The Journal of infectious diseases 2019 Nov
• Multiplex malaria antigen detection by bead-based assay and molecular confirmation by PCR shows no evidence of Pfhrp2 and Pfhrp3 deletion in Haiti.
  Herman Camelia et al. Malaria journal 2019 Nov (1) 380  
• Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics.
  Irinyi Laszlo et al. Medical mycology 2019 Nov

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Transmission dynamics and control of multidrug-resistant Klebsiella pneumoniae in neonates in a developing country.
  Crellen Thomas et al. eLife 2019 Dec
• Phylogenetic Analysis of Human Immunodeficiency Virus from People Who Inject Drugs in Indonesia, Ukraine, and Vietnam: HPTN 074.
  Sivay Mariya V et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Dec
• Analysis of HIV-1 diversity, primary drug resistance and transmission networks in Croatia.
  Oroz Maja et al. Scientific reports 2019 Nov (1) 17307

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• A live-attenuated influenza vaccine (LAIV) elicits enhanced heterologous protection when the internal genes of the vaccine are matched to the challenge virus.
  Smith Andrew et al. Journal of virology 2019 Nov
• Use of molecular HIV surveillance data and predictive modeling to prioritize persons for transmission-reduction interventions.
  Xia Qiang et al. AIDS (London, England) 2019 Dec
• HIV-1 genetic diversity to estimate time of infection and infer adherence to preexposure prophylaxis.
  Council Olivia D et al. AIDS (London, England) 2019 Dec (15) 2299-2307  
• Influenza viruses that require 10 genomic segments as antiviral therapeutics.
  Harding Alfred T et al. PLoS pathogens 2019 Nov (11) e1008098
• Covalent Plasmodium falciparum-selective proteasome inhibitors exhibit a low propensity for generating resistance in vitro and synergize with multiple antimalarial agents.
  Stokes Barbara H et al. PLoS pathogens 2019 06 (6) e1007722

HOST-MICROBE INTERACTIONS

• Plasma lipid profiles discriminate bacterial from viral infection in febrile children.
  Wang Xinzhu et al. Scientific reports 2019 Nov (1) 17714
• Paradoxical clade- and age-specific vaccine effectiveness during the 2018/19 influenza A(H3N2) epidemic in Canada: potential imprint-regulated effect of vaccine (I-REV).
  Skowronski Danuta M et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Nov (46)
• Cigarette smoke exposure induces expression of the pneumococcal erm(B) macrolide resistance gene.
  Matapa Kgashane Given et al. Tobacco induced diseases 2019 82
• Genetic variations in the CXCR5 gene decrease the risk of clinical relapse after discontinuation of nucleos(t)ide analogue therapy in patients with chronic hepatitis B.
  Wu Yin et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Nov 104124
• Association of IL18 genetic polymorphisms with Chagas disease in Latin American populations.
  Strauss Mariana et al. PLoS neglected tropical diseases 2019 Nov (11) e0007859
• Prospective virome analyses in young children at increased genetic risk for type 1 diabetes.
  Vehik Kendra et al. Nature medicine 2019 Dec
• Airway microbiome, host immune response and recurrent wheezing in infants with severe respiratory syncytial virus bronchiolitis.
  Zhang Xiaoyan et al. Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology 2019 Dec
• Stability of the vaginal, oral, and gut microbiota across pregnancy among African American women: the effect of socioeconomic status and antibiotic exposure.
  Dunlop Anne L et al. PeerJ 2019 e8004 
• Effects of sampling strategy and DNA extraction on human skin microbiome investigations.
  Bjerre Rie Dybboe et al. Scientific reports 2019 Nov (1) 17287
• Altered Gut Microbiota and Host Metabolite Profiles in HIV-infected Women.
  Wang Zheng et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Nov

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.