Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jan 9, 2020

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

• A new virus may be the cause of China's mysterious pneumonia outbreak
  Belluz J. Vox, Jan 9, 2020.
• Clinical Investigators Validating Mouth Swab PCR Test for TB
  O'Connor L. GenomeWeb, Jan 7, 2020.
• Stanford Researchers Apply Liquid Biopsy Tools to Molecular Fungal Detection Workflow
  Gilmore J. GenomeWeb, D19.ec 19, 20
• Developers of At-Home Tests Saw Progress in 2019, But Commercialization Challenges Remain
  O'Connor L. 360dx, Jan 2, 2020.
• Rare Shrew-Borne Illness Tied to Fatal Encephalitis
  Walker M. MedPage Today, Jan 7, 2020.
• Kidney Donor's HIV Strain Found in HIV-Positive Recipient
  Walker M. MedPage Today, Jan 8, 2020.
• Against all odds: The inside story of how scientists across three continents produced an Ebola vaccine
  Branswell H. STAT, January 7, 2020.
• New Oral Polio Vaccine to Bypass Key Clinical Trials
  Fortner R. The Scientist, Dec 17, 2019.
• Thirteen tips for engaging with physicists, as told by a biologist
  Kosik K. Nature,

CONCEPTS / COMMENTS

• New data for the tree of life
  York A. Nat Rev Microbiol, Dec 16, 2019.
• Viruses in the Built Environment (VIBE) meeting report.
  Prussin Aaron J et al. Microbiome 2020 Jan (1) 1
• Coinfections by noninteracting pathogens are not independent and require new tests of interaction.
  Hamelin Frédéric M et al. PLoS biology 2019 Dec (12) e3000551
• Personalized public health: An implementation research agenda for the HIV response and beyond.
  Geng Elvin H et al. PLoS medicine 2019 Dec (12) e1003020 

METHODS / TOOLS

• A Conceptual Framework for Abundance Estimation of Genomic Targets in the Presence of Ambiguous Short Sequencing Reads.
  Górczak Katarzyna et al. Journal of computational biology : a journal of computational molecular cell biology 2019 Dec
• Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.
  Waterhouse Robert M et al. BMC biology 2020 Jan (1) 1 
• A Bayesian Multi-Task Approach for Detecting Global Microbiome Associations
  Hatami F. bioRxiv, Jam 9, 2020.

EVOLUTION / ECOLOGY / POPULATIONS

• Distribution of Microbial Communities and Antimicrobial Resistances in Urban Environments and on the ISS Space Station.
  Bezdan Daniela et al. Journal of biomolecular techniques : JBT 2019 Dec (Suppl) S47
• Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens
  Nicholson AC, et al. Int J Syst Evol Microbiol, Jan 2, 2020. 
• Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia.
  Kamau Everlyn et al. BMC genomics 2020 Jan (1) 5
• Origin of the São Paulo Yellow Fever epidemic of 2017-2018 revealed through molecular epidemiological analysis of fatal cases.
  Cunha Marielton Dos Passos et al. Scientific reports 2019 Dec (1) 20418
• Persistence of chikungunya ECSA genotype and local outbreak in an upper medium class neighborhood in Northeast Brazil.
  Goes de Jesus Jaqueline et al. PloS one 2020 (1) e0226098
• Evolution and biological significance of flaviviral elements in the genome of the arboviral vector Aedes albopictus .
  Houé Vincent et al. Emerging microbes & infections 2019 (1) 1265-1279

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Using genomics to understand meticillin- and vancomycin-resistant Staphylococcus aureus infections.
  Giulieri Stefano G et al. Microbial genomics 2020 Jan

DETECTION / DIAGNOSIS

• Diagnostic challenges of central nervous system infection: extensive multiplex panels versus stepwise guided approach.
  Vetter P et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Dec 
• Single cell-based digital PCR detection and association of Shiga toxin-producing Escherichia coli serogroups and major virulence genes.
  Liu Xuming et al. Journal of clinical microbiology 2020 Jan
• Microarray-based detection of resistance and virulence factors in commensal Escherichia coli from livestock and farmers in Egypt.
  Gwida Mayada et al. Veterinary microbiology 2020 Jan 108539
• Rapid Nanopore Whole-Genome Sequencing for Anthrax Emergency Preparedness
  McLaughlin HP, et al. Emerg Infect Dis, Feb 2020.  
• Genomic surveillance enables suitability assessment of Salmonella gene targets used for culture-independent diagnostic testing
  Rockett RJ, et al. bioRxiv, Jan 9, 2020.
• Nested PCR and the TaqMan SNP Genotyping Assay enhanced the sensitivity of drug resistance testing of Mycobacterium leprae using clinical specimens of leprosy patients.
  Chen Xiaohua et al. PLoS neglected tropical diseases 2019 Dec (12) e0007946
• Characterizing viral load burden among HIV-infected women around the time of delivery: Findings from four tertiary obstetric units in Gauteng, South Africa.
  Moyo Faith et al. Journal of acquired immune deficiency syndromes (1999) 2020 Jan 
• Viral load assay performs comparably to early infant diagnosis assay to diagnose infants with HIV in Mozambique: a prospective observational study.
  Vubil Adolfo et al. Journal of the International AIDS Society 2020 Jan (1) e25422
• HCV genotype profile in Brazil of mono-infected and HIV co-infected individuals: A survey representative of an entire country.
  Nutini Mariana Fernanda Rodrigues et al. PloS one 2020 (1) e0227082
• Development of Candida auris Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates.
  de Groot Theun et al. mBio 2020 Jan (1)

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• A retrospective genomic analysis of drug-resistant strains of M. tuberculosis in a high-burden setting, with an emphasis on comparative diagnostics and reactivation and reinfection status.
  Wollenberg Kurt et al. BMC infectious diseases 2020 Jan (1) 17
• Transmitted HIV drug resistance among individuals with newly diagnosed HIV infection: A multicenter observational study.
  Ye Jingrong et al. AIDS (London, England) 2019 Dec

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Phase 1 HIV vaccine trial to evaluate the safety and immunogenicity of HIV subtype C DNA and MF59-adjuvanted subtype C Env protein.
  Hosseinipour Mina C et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jan
• Using the Association Between Antibiotic Susceptibility and Genetic Relatedness to Rescue Old Drugs for Empiric Use
  MacFadden DR, et al. medRxiv, Nov 29, 2019.

HOST-MICROBE INTERACTIONS

• High-resolution mycobiota analysis reveals dynamic intestinal translocation preceding invasive candidiasis.
  Zhai Bing et al. Nature medicine 2020 Jan

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.