Advanced Molecular Detection Clips Content (Published on 12/14/2023)
NEWS
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CDC Urges Clinicians to Be Aware of Potential Clade I Mpox Cases From DRC
Kahn K. MedPage Today, Dec 8, 2023. -
Why has swine flu emerged in a person in the UK — and what’s next?
Sanderson K. Nature, Nov 29, 2023. -
Self-copying RNA vaccine wins first full approval: what’s next?
Dolgin E. Nature, Dec 6, 2023. -
Is the flu shot market a slam dunk for mRNA vaccines? Experts aren’t so sure
Branswell H. STAT, Dec 5, 2023.
EVENTS / TRAINING / WEB RESOURCES
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Applied and Genomic Epidemiology in Public Health
(blog) Allen K. Substack.com
CONCEPTS / COMMENTS
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Whole-genome sequencing surveillance: Growing evidence for a future potential practice standard of infection prevention.
Alexander J Sundermann et al. Infect Control Hosp Epidemiol 2023 12 1-2 -
Editorial: Wastewater-based epidemiological surveillance of respiratory pathogens.
David Champredon et al. Front Public Health 2023 12 1328452 -
Uncovering the Holocene roots of contemporary disease-scapes: bringing archaeology into One Health.
Kristen M Rayfield et al. Proc Biol Sci 2023 12 (2012) 20230525 -
Developing One Health surveillance systems.
et al. One Health 2023 11 100617 -
Vulnerability of pangolin SARS-CoV-2 lineage assignment to adversarial attack.
Amiel Meiseles et al. Artif Intell Med 2023 12 102722 -
Weaponized genomics: potential threats to international and human security.
Subhayan Chattopadhyay et al. Nat Rev Genet 2023 11 -
Scaling up robust immunopeptidomics technologies for a global T cell surveillance digital network.
Saketh Kapoor et al. J Exp Med 2023 11 (1) -
Ten simple rules for managing laboratory information.
Casey-Tyler Berezin et al. PLoS Comput Biol 2023 12 (12) e1011652
METHODS / TOOLS
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A search-based geographic metadata curation pipeline to refine sequencing institution information and support public health.
Kun Zhao et al. Front Public Health 2023 11 1254976 -
Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications.
Ruth E Timme et al. Microb Genom 2023 12 (12) -
Hostile: accurate decontamination of microbial host sequences.
Bede Constantinides et al. Bioinformatics 2023 12 -
Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis.
Alix Vincent Thorn et al. Microbiol Spectr 2023 12 e0241323 -
primerJinn: a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and performing in silico PCR.
Jason D Limberis et al. BMC Bioinformatics 2023 12 (1) 468 -
Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance.
Sara E Zufan et al. Microb Genom 2023 11 (11) -
Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency.
Eslam Abousamra et al. medRxiv 2023 12 -
Targeted amplification-based whole genome sequencing of Monkeypox virus in clinical specimens.
S Isabel et al. Microbiol Spectr 2023 12 e0297923 -
Effectiveness of Self-Collected, Ambient Temperature-Preserved Nasal Swabs Compared to Samples Collected by Trained Staff for Genotyping of Respiratory Viruses by Shotgun RNA Sequencing: Comparative Study.
Raymond Soto et al. JMIR Form Res 2023 11 e32848 -
HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations.
Roxana Cintron et al. Viruses 2023 11 (11) -
Selective whole-genome sequencing of Plasmodium parasites directly from blood samples by nanopore adaptive sampling.
Katlijn De Meulenaere et al. mBio 2023 12 e0196723 -
Whole genome enrichment approach for genomic surveillance of Toxoplasma gondii.
Balaji Sundararaman et al. Food Microbiol 2023 12 104403
EVOLUTION / ECOLOGY / POPULATIONS
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A novel invasive Streptococcus pyogenes variant sublineage derived through recombinational replacement of the emm12 genomic region.
Yvette Unoarumhi et al. Sci Rep 2023 12 (1) 21510 -
Genomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993-2019.
Ashley N Williams et al. Microb Genom 2023 11 (11) -
Ecological and clinical evidence of the establishment of West Nile virus in a large urban area in Europe, Berlin, Germany, 2021 to 2022.
Claudia Ruscher et al. Euro Surveill 2023 12 (48) -
Emergence of Dengue Virus Serotype 2 Cosmopolitan Genotype, Colombia.
David Martínez et al. Emerg Infect Dis 2023 12 (1) -
Lassa Virus in Novel Hosts: Insights into the Epidemiology of Lassa Virus Infections in Southern Nigeria.
Anise Nkenjop Happi et al. Emerg Microbes Infect 2023 12 2294859 -
Emergence of Novel Norovirus GII.4 Variant.
Preeti Chhabra et al. Emerg Infect Dis 2023 12 (1) -
Surveillance and Genetic Analysis of Jamestown Canyon Virus in New York State: 2001-2022.
Kiet A Ngo et al. Am J Trop Med Hyg 2023 11 (6) 1329-1332 -
Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal.
Stephen F Schaffner et al. Nat Commun 2023 11 (1) 7268
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Tigecycline-resistant Klebsiella pneumoniae strains from sewage in Norway carry heavy-metal resistance genes encoding conjugative plasmids.
Vera Radisic et al. J Glob Antimicrob Resist 2023 11 -
Comparison of carbapenem-susceptible and carbapenem-resistant Enterobacterales at nine sites in the USA, 2013-2016: a resource for antimicrobial resistance investigators.
Joseph D Lutgring et al. Microb Genom 2023 11 (11) -
Genomic analysis of azithromycin-resistant Salmonella from food animals at slaughter and processing, and retail meats, 2011-2021, United States.
Beilei Ge et al. Microbiol Spectr 2023 11 e0348523 -
Genomic and Phenotypic Characterization of Shiga Toxin-Producing Escherichia albertii Strains Isolated from Wild Birds in a Major Agricultural Region in California.
Michelle Qiu Carter et al. Microorganisms 2023 11 (11) -
Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258.
Alejandro Piña-Iturbe et al. Microb Genom 2023 12 (12) -
Bedaquiline resistance in patients with drug-resistant tuberculosis in Cape Town, South Africa: a retrospective longitudinal cohort study.
Brigitta Derendinger et al. Lancet Microbe 2023 11 -
Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era.
Salvador Castañeda-Barba et al. Nat Rev Microbiol 2023 7 (1) 18-32 -
Virologic non-suppression and HIV drug resistance among people who inject drugs and their sexual and injecting partners in Kenya.
Bhavna H Chohan et al. AIDS Res Hum Retroviruses 2023 12 -
Distribution of Plasmodium falciparum K13 gene polymorphisms across transmission settings in Ghana.
Cheikh Cambel Dieng et al. BMC Infect Dis 2023 11 (1) 801
DETECTION / DIAGNOSIS
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Exploiting genomics for antimicrobial resistance surveillance at One Health interfaces.
Dishon M Muloi et al. Lancet Microbe 2023 11 -
Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group.
Kate S Baker et al. Lancet Microbe 2023 11 -
Innovations in genomic antimicrobial resistance surveillance.
Nicole E Wheeler et al. Lancet Microbe 2023 11 -
Genomics for public health and international surveillance of antimicrobial resistance.
Kate S Baker et al. Lancet Microbe 2023 11 -
Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities.
Elita Jauneikaite et al. Lancet Microbe 2023 11 -
Implementation of national whole-genome sequencing of Mycobacterium tuberculosis, National Public Health Laboratory, Singapore, 2019-2022.
Ansel Yi Herh Lim et al. Microb Genom 2023 11 (11) -
Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing.
Giovanni Ghielmetti et al. Front Microbiol 2023 12 1307440 -
A precision overview of genomic resistance screening in Ecuadorian isolates of Mycobacterium tuberculosis using web-based bioinformatics tools.
Gabriel Morey-León et al. PLoS One 2023 12 (12) e0294670 -
Genomic surveillance of antimicrobial-resistant Escherichia coli in fecal sludge and sewage in Uganda.
Ryota Gomi et al. Water Res 2023 11 120830 -
VarLOCK: sequencing-independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance.
Xinsheng Nan et al. Sci Rep 2023 11 (1) 20832 -
A bead-based multiplex assay covering all coronaviruses pathogenic for humans for sensitive and specific surveillance of SARS-CoV-2 humoral immunity.
Daniel Stern et al. Sci Rep 2023 12 (1) 21846 -
Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems.
Kayla G Barnes et al. Nat Commun 2023 11 (1) 7883 -
Targeted amplification and genetic sequencing of the severe acute respiratory syndrome coronavirus 2 surface glycoprotein.
Matthew W Keller et al. Microbiol Spectr 2023 12 e0298223 -
Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North-South collaboration.
Waqasuddin Khan et al. BMJ Glob Health 2023 11 (11) -
Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings.
Nicholas R Minor et al. Sci Rep 2023 12 (1) 21398 -
Preparing for mpox resurgence: Surveillance lessons from outbreaks in Toronto, Canada.
Herveen Sachdeva et al. J Infect Dis 2023 11 -
Multi-locus sequencing typing reveals geographically related intraspecies variability of Sporothrix brasiliensis.
Vanessa Brito de Souza Rabello et al. Fungal Genet Biol 2023 12 103845 -
Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana.
Sophia T Girgis et al. Nat Microbiol 2023 11 (12) 2365-2377 -
Evaluation of Vector-Enabled Xenosurveillance in Rural Guatemala.
Rebekah J McMinn et al. Am J Trop Med Hyg 2023 11 (6) 1303-1310 -
First detection of Anopheles stephensi in Ghana using molecular surveillance.
Yaw A Afrane et al. bioRxiv 2023 12
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Notes from the Field: A Cluster of Multi-Strain Invasive Pneumococcal Disease Among Persons Experiencing Homelessness and Use of Pneumococcal Conjugate Vaccine - El Paso County, Colorado, 2022.
Jessica Callaway et al. MMWR Morb Mortal Wkly Rep 2023 11 (46) 1277-1278 -
Tuberculosis in Ukrainian War Refugees and Migrants in the Czech Republic and Slovakia: A Molecular Epidemiological Study.
Matúš Dohál et al. J Epidemiol Glob Health 2023 12 -
Approaches and challenges to inferring the geographical source of infectious disease outbreaks using genomic data.
Zhiyuan Chen et al. Lancet Microbe 2023 12 -
Antimicrobial resistance in multistate outbreaks of nontyphoidal Salmonella infections linked to animal contact-United States, 2015-2018.
Erin Frey et al. J Clin Microbiol 2023 12 e0098123 -
Transmitted drug resistance to antiretroviral drugs in Spain during the period 2019-2021.
Laura Viñuela et al. J Med Virol 2023 12 (12) e29287 -
The molecular epidemiology of HIV-1 in Sweden 1996 to 2022, and the influence of migration from Ukraine.
Anna Weibull Wärnberg et al. Euro Surveill 2023 12 (48) -
Unveiling invisible farm-to-farm PRRSV-2 transmission links and routes through transmission tree and network analysis.
Nakarin Pamornchainavakul et al. Evol Appl 2023 11 (10) 1721-1734 -
Clade I-Associated Mpox Cases Associated with Sexual Contact, the Democratic Republic of the Congo.
Emile M Kibungu et al. Emerg Infect Dis 2023 11 (1) -
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda.
Mélodie Monod et al. Nat Microbiol 2023 12 -
Pretreatment HIV Drug Resistance and the Molecular Transmission Network Among HIV-Positive Individuals in China in 2022: Multicenter Observational Study.
Hongli Chen et al. JMIR Public Health Surveill 2023 11 e50894 -
Epidemiology of giardiasis and assemblages A and B and effects on diarrhea and growth trajectories during the first 8 years of life: Analysis of a birth cohort in a rural district in tropical Ecuador.
Tannya Sandoval-Ramírez et al. PLoS Negl Trop Dis 2023 11 (11) e0011777
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Genome-based prediction of cross-protective, HLA-DR-presented epitopes as putative vaccine antigens for multiple Bordetella species.
Muktha S Natrajan et al. Microbiol Spectr 2023 12 e0352723 -
SARS-CoV-2 Epidemiology and COVID-19 mRNA Vaccine Effectiveness Among Infants and Children Aged 6 Months-4 Years - New Vaccine Surveillance Network, United States, July 2022-September 2023.
Ayzsa Tannis et al. MMWR Morb Mortal Wkly Rep 2023 11 (48) 1300-1306 -
Effectiveness of the Original Monovalent Coronavirus Disease 2019 Vaccines in Preventing Emergency Department or Urgent Care Encounters and Hospitalizations Among Adults With Disabilities: VISION Network, June 2021-September 2022.
Palak Patel et al. Open Forum Infect Dis 2023 11 (11) ofad474 -
Symptoms, viral loads, and rebound among COVID-19 outpatients treated with nirmatrelvir/ritonavir compared to propensity score matched untreated individuals.
Sarah E Smith-Jeffcoat et al. Clin Infect Dis 2023 11 -
Effectiveness of a bivalent mRNA vaccine dose against symptomatic SARS-CoV-2 infection among U.S. Healthcare personnel, September 2022-May 2023.
Ian D Plumb et al. Vaccine 2023 11 -
Standard-dose versus MF59-adjuvanted, high-dose or recombinant-hemagglutinin influenza vaccine immunogenicity in older adults: comparison of A(H3N2) antibody response by prior season's vaccine status.
Shuyi Zhong et al. J Infect Dis 2023 11 -
Efficacy and Safety of an mRNA-Based RSV PreF Vaccine in Older Adults.
Eleanor Wilson et al. N Engl J Med 2023 12 (24) 2233-2244
HOST-MICROBE INTERACTIONS
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Pre-existing cross-reactive neutralizing activity against SARS-CoV-2 and seasonal coronaviruses prior to the COVID-19 pandemic (2014-2019) with limited immunity against recent emerging SARS-CoV-2 variants, Vietnam.
Thi Thanh Ngan Nguyen et al. Int J Infect Dis 2023 11 -
Monogenic etiologies of persistent human papillomavirus infections: a comprehensive systematic review.
Sajjad Biglari et al. Genet Med 2023 11 101028
Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by Public Health Genomics Branch 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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- Page last updated:May 2, 2024
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