Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jul 2, 2020

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

• Study shows antibiotic resistance genes persist in E. coli through 'genetic capitalism'
  UNC, Phys.Org, Jun 29, 2020.
• Swine flu strain with human pandemic potential increasingly found in pigs in China
  Cohen J. Science, Jun 29, 2020.
• Labs Launching SARS-CoV-2 Testing Programs Aimed at Colleges and Universities
  Bonislawski A. 360dx, Jun 26, 2020.
• This coronavirus mutation has taken over the world. Scientists are trying to understand why.
  Kaplan S, Aschenbach J. Washington Post, Jun 29, 2020.
• ?ooled testing for COVID-19 holds promise and pitfalls
  Perrone M. AP / Los Angeles Times, Jun 30, 2020.
• Single-Cell COVID-19 Study Suggests Chemokine Receptor Inhibition Could Quell Immune Hyperactivation
  GenomeWeb, Jun 26, 2020.
• A race to determine what drives COVID-19 severity
  Koutsakos M,Kedzierska K. Nature, Jun 29, 2020.
• New journal will vet Covid-19 preprints, calling out misinformation and highlighting credible research
  Begley S. STAT, Jun 29, 2020.
• NIH study shows genomic variation causing common autoinflammatory disease may increase resilience to bubonic plague
  (news release) NIH, Jun 29, 2020.

EVENTS / TRAINING / WEB RESOURCES

• A Guide for Decision Makers using Data to Understand the Extent and Spread of COVID-19
  (report) NASEM, Jun 2020.

CONCEPTS / COMMENTS

• What Is Metagenomics Teaching Us, and What Is Missed?
  New Felicia N et al. Annual review of microbiology 2020 Jun
• The past, present and future of ancient bacterial DNA.
  Arning Nicolas et al. Microbial genomics 2020 Jun
• Editorial overview: Frontiers in microbiome studies: viewing vast vistas with roadmap in hand.
  Guillemin Karen et al. Current opinion in microbiology 2019 08 iii-iv

METHODS / TOOLS

• Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data.
  Stohr Joep J J M et al. Microbial genomics 2020 Jun
• DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy.
  Xie Ruopeng et al. Briefings in bioinformatics 2020 Jun
• Matrix-assisted laser desorption/ionization time-of-flight MS for the accurate identification of Burkholderia cepacia complex and Burkholderia gladioli in the clinical microbiology laboratory.
  Wong Kendrew S K et al. Journal of medical microbiology 2020 Jun 
• High-Throughput Stool Metaproteomics: Method and Application to Human Specimens.
  Gonzalez Carlos G et al. mSystems 2020 Jun (3)
• A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples
  Ramos-Mandujano G, et al. medRxiv, Jun 29, 2020.
• Global molecular diversity of RSV - the "INFORM RSV" study.
  Langedijk Annefleur C et al. BMC infectious diseases 2020 Jun (1) 450
• Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing.
  Zecha Jana et al. Molecular & cellular proteomics : MCP 2020 Jun
• periscope: sub-genomic RNA identification in SARS-CoV-2 ARTIC Network Nanopore Sequencing Data
  Parker MD, et al. bioRxiv, Jul 1, 2020.
• Data stream dataset of SARS-CoV-2 genome.
  Barbosa Raquel de M et al. Data in brief 2020 Aug 105829
• Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples
  Xiao M, et al. Genome Med, Jun 30, 2020.

EVOLUTION / ECOLOGY / POPULATIONS

• Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies.
  Collis Rose M et al. PloS one 2020 (6) e0235066
• Coding potential and sequence conservation of SARS-CoV-2 and related animal viruses.
  Cagliani Rachele et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 09 104353
• Distinct genetic spectrums and evolution patterns of SARS-CoV-2.
  Liu Sheng et al. medRxiv : the preprint server for health sciences 2020 Jun
• Comparative genomics provides an operational classification system and reveals early emergence and biased spatio-temporal distribution of SARS-CoV-2
  Chiara M, et al. bioRxiv, Jun 28, 2020.
• A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species
  Tengs T, et al. bioRxiv, Jun 28, 2020.
• Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2
  Wang D, et al. bioRxiv, Jun 26, 2020.
• The establishment of reference sequence for SARS-CoV-2 and variation analysis.
  Wang Changtai et al. Journal of medical virology 2020 06 (6) 667-674
• Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2.
  Li Xingguang et al. Journal of medical virology 2020 06 (6) 602-611
• No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2
  van Dorp L, et al. bioRxiv, Jun 30, 2020.
• Genetic diversity and phylogenetic analysis of Crimean-Congo Hemorrhagic Fever viruses circulating in Pakistan during 2019.
  Umair Massab et al. PLoS neglected tropical diseases 2020 Jun (6) e0008238
• Genomic surveillance of the Chikungunya Virus (CHIKV) in Northeast Brazil after the first outbreak in 2014.
  Rodrigues Ayslany Melo et al. Revista da Sociedade Brasileira de Medicina Tropical 2020 e20190583
• Whole-genome sequencing reveals origin and evolution of influenza A(H1N1)pdm09 viruses in Lincang, China, from 2014 to 2018.
  Zhao Xiao-Nan et al. PloS one 2020 (6) e0234869

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Emergence of vancomycin- and teicoplanin-resistant Enterococcus faecium via vanD5-harbouring large genomic island.
  Sato Toyotaka et al. The Journal of antimicrobial chemotherapy 2020 Jun
• Comparative genomics and antimicrobial resistance profiling of Elizabethkingia isolates reveals nosocomial transmission and in vitro susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole.
  Burnard Delaney et al. Journal of clinical microbiology 2020 Jun
• Loss of phenotypic inheritance associated with ydcI mutation leads to increased frequency of small, slow persisters in Escherichia coli .
  Hingley-Wilson Suzanne M et al. Proceedings of the National Academy of Sciences of the United States of America 2020 02 (8) 4152-4157
• Phenotypic and Genomic Characterization of Virulence Heterogeneity in Multidrug-Resistant ST11 Klebsiella pneumoniae During Inter-Host Transmission and Evolution.
  Liu Chao et al. Infection and drug resistance 2020 1713-1721
• Genome sequencing of Mycobacterium tuberculosis clinical isolates revealed isoniazid resistance mechanisms undetected by conventional molecular methods.
  Laurent Sacha et al. International journal of antimicrobial agents 2020 Jun 106068
• Understanding the Emergence of Multidrug-Resistant Candida : Using Whole-Genome Sequencing to Describe the Population Structure of Candida haemulonii Species Complex.
  Gade Lalitha et al. Frontiers in genetics 2020 554 

DETECTION / DIAGNOSIS

• Genomic surveillance enables suitability assessment of Salmonella gene targets used for culture-independent diagnostic testing.
  Rockett Rebecca J et al. Journal of clinical microbiology 2020 Jun 
• Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants.
  Hicks Allison L et al. eLife 2020 Jun
• Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study.
  Levade Inès et al. The Journal of infectious diseases 2020 Jul
• Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2
  Wylezich C, et al. bioRxiv, Jul 1, 2020.
• Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay
  Buck MD, et al. medRxiv, Jul 1, 2020.
• Ultra-sensitive and high-throughput CRISPR-p owered COVID-19 diagnosis.
  Huang Zhen et al. Biosensors & bioelectronics 2020 Sep 112316
• Molecular detection of SARS-CoV-2 in formalin-fixed, paraffin-embedded specimens.
  Liu Jun et al. JCI insight 2020 06 (12)
• Rapid Direct Nucleic Acid Amplification Test without RNA Extraction for SARS-CoV-2 Using a Portable PCR Thermocycler.
  Wee Soon Keong et al. Genes 2020 06 (6)
• Test sensitivity is secondary to frequency and turnaround time for COVID-19 surveillance
  Larremore DB, et al. medRxiv, Jun 27, 2020.
• A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes
  Rodriguez-Manzano et al., medRxiv, Jun 30, 2020.
• Sentinel Coronavirus Environmental Monitoring Can Contribute to Detecting Asymptomatic SARS-CoV-2 Virus Spreaders and Can Verify Effectiveness of Workplace COVID-19 Controls
  Marshall D, et al. medRxiv, Jun 29, 2020.
• Identification of SARS-CoV-2 RNA in Healthcare Heating, Ventilation, and Air Conditioning Units
  Horve PF, et al. medRxiv, Jun 28, 2020.
• SARS-CoV-2 has been circulating in northern Italy since December 2019: evidence from environmental monitoring
  La Rosa G, et al. medRxiv, Jun 26, 2020.
• Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR
  Mello CJ, et al. medRxiv, Jun 26, 2020.
• Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection.
  Ben-Ami Roni et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Jun
• Molecular, serological, and biochemical diagnosis and monitoring of COVID-19: IFCC taskforce evaluation of the latest evidence.
  Bohn Mary Kathryn et al. Clinical chemistry and laboratory medicine 2020 06 (7) 1037-1052 
• Analytical evaluation of the microarray-based FluChip-8G Influenza A+B Assay.
  Taylor Amber W et al. Journal of virological methods 2019 11 113686 
• Genome-wide mapping using new AFLP markers to explore intraspecific variation among pathogenic Sporothrix species.
  de Carvalho Jamile Ambrósio et al. PLoS neglected tropical diseases 2020 Jul (7) e0008330

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• A Large Scale Waterborne Campylobacteriosis Outbreak, Havelock North, New Zealand.
  Gilpin Brent J et al. The Journal of infection 2020 Jun 
• Betacoronavirus Genomes: How Genomic Information has been Used to Deal with Past Outbreaks and the COVID-19 Pandemic.
  Llanes Alejandro et al. International journal of molecular sciences 2020 Jun (12) 
• Unsupervised cluster analysis of SARS-CoV-2 genomes indicates that recent (June 2020) cases in Beijing are from a genetic subgroup that consists of mostly European and South(east) Asian samples, of which the latter are the most recent
  Hahn G, et al. bioRxiv, Jun 30, 2020.
• Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region
  Maurano MT, et al. medRxiv, Jun 25, 2020.
• Genomic epidemiology of SARS-CoV-2 in Colombia
  Laiton-Donato K, et al. medRxiv, Jun 29, 2020.
• SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020.
  Oreshkova Nadia et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 06 (23) 
• Large SARS-CoV-2 Outbreak Caused by Asymptomatic Traveler, China
  Liu J, et al. Emerg Infect Dis, Jun 30, 2020.
• Nosocomial outbreak of the Middle East Respiratory Syndrome coronavirus: A phylogenetic, epidemiological, clinical and infection control analysis.
  Barry Mazin et al. Travel medicine and infectious disease 2020 Jun 101807 
• A geographic hotspot and emerging transmission cluster of the HIV-1 epidemic among older adults in a rural area of eastern China.
  Jiang Jun et al. AIDS research and human retroviruses 2020 Jun
• Outbreak of hepatitis A virus infection in Taiwan, June 2015 to September 2017.
  Chen Wan-Chin et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Apr (14) 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Advanced bioinformatics rapidly identifies existing therapeutics for patients with coronavirus disease-2019 (COVID-19).
  Kim Jason et al. Journal of translational medicine 2020 Jun (1) 257
• Immune modulation in COVID-19: Strategic considerations for personalized therapeutic intervention.
  Hall Mark W et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jul
• Metagenomic Characterization of Gut Microbiota of Carriers of Extended-Spectrum Beta-Lactamase or Carbapenemase-Producing Enterobacteriaceae Following Treatment with Oral Antibiotics and Fecal Microbiota Transplantation: Results from a Multicenter Randomized Trial.
  Leo Stefano et al. Microorganisms 2020 Jun (6)

HOST-MICROBE INTERACTIONS

• Polymorphisms in the ACE2 Locus Associate with Severity of COVID-19 Infection
  Wooster C, et al. medRxiv, Jun 22, 2020.
• Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge.
  Zuo Tao et al. Gastroenterology 2020 Jun
• Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal Tract.
  Lee Jaewon J et al. Genes 2020 06 (6)
• Deciphering the Role of Host Genetics in Susceptibility to Severe COVID-19
  Carter-Timofte M, et al. Front Immunol, Jun 30, 2020.
• Study protocol for the ABERRANT study: antibiotic-induced disruption of the maternal and infant microbiome and adverse health outcomes - a prospective cohort study among children born at term.
  Volery Maryse et al. BMJ open 2020 Jun (6) e036275

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.