Advanced Molecular Detection Clips Content (Published on 01/09/2025)
NEWS
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New reports sharpen clinical picture of recent human H5N1 illnesses in US and Canada
Schnirring L. CIDRAP, Dec 31, 2024. -
CDC: H5N1 mutations in severely ill patient could boost spread, but risk remains low
Van Beusekom M. CIDRAP, Dec 27, 2024. -
Why scientists say we are fighting H5N1 bird flu with one hand tied behind our backs
Rust S, Kaplan K. Los Angeles Times, Dec 24, 2024. -
Rapid spread of H5N1 bird flu through California dairy herds suggests unknown paths of transmission
Molteni M. STAT, Dec 20, 2024. -
What will viruses do next? AI is helping scientists predict their evolution
Mallapaty S. Nature, Jan 8, 2024.
CONCEPTS / COMMENTS
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Genomic Surveillance of Foodborne Pathogens: Advances and Obstacles.
Kathleen Gensheimer et al. J Public Health Manag Pract 2025 1
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Wastewater metagenomics in Africa: Opportunities and challenges.
Stephen Kanyerezi et al. PLOS Glob Public Health 2024 12 (12) e0004044 -
Improving the reporting of metagenomic virome-scale data.
Wei-Shan Chang et al. Commun Biol 2024 12 (1) 1687 -
The Growing Phenomenon of 'Frozen' Virus Genome Sequences and Their Likely Origin in Research Facility Escapes.
Steven E Massey et al. Microorganisms 2025 1 (12)
METHODS / TOOLS
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Molecular source attribution.
Elisa Chao et al. PLoS Comput Biol 2022 11 (11) e1010649 -
Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper.
Faye Orcales et al. PLoS Comput Biol 2025 1 (12) e1012579 -
Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection.
Bert Bogaerts et al. BMC Genomics 2025 1 (1) 20 -
Toward optimal disease surveillance with graph-based active learning.
Joseph L-H Tsui et al. Proc Natl Acad Sci U S A 2024 12 (52) e2412424121 -
Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.
Levente Zsichla et al. Viruses 2025 1 (12)
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Linkage-based ortholog refinement in bacterial pangenomes with CLARC.
Indra González Ojeda et al. bioRxiv 2025 1 -
Nanopore Sequencing Allows Recovery of High-Quality Completely Closed Genomes of All Cronobacter Species from Powdered Infant Formula Overnight Enrichments.
Narjol Gonzalez-Escalona et al. Microorganisms 2025 1 (12) -
Targeted sequencing of Enterobacterales bacteria using CRISPR-Cas9 enrichment and Oxford Nanopore Technologies.
Hugh Cottingham et al. mSystems 2025 1 e0141324 -
Reverse Genetics System for Crimean-Congo Hemorrhagic Fever Virus.
Florine Scholte et al. Methods Mol Biol 2024 12 247-256
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The Candida Genome Database: Annotation and Visualization Updates.
Jodi Lew-Smith et al. Genetics 2025 1
EVOLUTION / ECOLOGY / POPULATIONS
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Molecular and niche modeling approaches to identify potential amplifying hosts for an emerging tick-borne pathogen, Rickettsia rickettsii subsp. californica, the causative agent of Pacific Coast tick fever.
Vincent Mai et al. J Med Entomol 2024 12
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Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest.
Jia Wang et al. Microbiol Spectr 2024 12 e0171224 -
Concentration, pathogenic composition, and exposure risks of bioaerosol in large indoor public environments: A comparative study of urban and suburban areas.
Jiasheng Ni et al. Sci Total Environ 2024 11 177790 -
Genomic epidemiology and evolution of Bordetella pertussis under the vaccination pressure of acellular vaccines in Beijing, China, 2020-2023.
Zhen Li et al. Emerg Microbes Infect 2024 12 2447611
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Rapid confirmation of autochthonous origin in suspected cases of melioidosis from French overseas departments in the Caribbean and the Indian Ocean by PCR-high resolution melting (HRM) analysis.
Gasqué Mégane et al. Infect Genet Evol 2024 12 105711 -
Evolution of community-associated MRSA: a 20-year genomic and epidemiological study in Region Örebro County, Sweden.
Jan Kekki et al. Front Microbiol 2025 1 1504860 -
Insights into Treponema pallidum genomics from modern and ancient genomes using a novel mapping strategy.
Marta Pla-Díaz et al. BMC Biol 2025 1 (1) 7 -
Emerging SARS-CoV-2 Variants in Uganda in the Era of COVID-19 Vaccination.
Nicholas Bbosa et al. Viruses 2025 1 (12)
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From Emergence to Evolution: Dynamics of the SARS-CoV-2 Omicron Variant in Florida.
Sobur Ali et al. Pathogens 2025 1 (12) -
Genomic Diversity and Evolution of Identified SARS-CoV-2 Variants in Iraq.
Ahmed A Al-Mankhee et al. Pathogens 2025 1 (12) -
Epidemiology of viral gastroenteritis in children and genetic diversity of rotavirus strains in Kolkata, West Bengal after introduction of rotavirus vaccine.
Ritubrita Saha et al. Vaccine 2024 12 126637
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Genomic analysis of DS-1-like human rotavirus A strains uncovers genetic relatedness of NSP4 gene with animal strains in Manhiça District, Southern Mozambique.
Filomena Manjate et al. Sci Rep 2024 12 (1) 30705
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Genetic diversity of dengue virus circulating in the Philippines (2014-2019) and comparison with dengue vaccine strains.
John Mark Velasco et al. PLoS Negl Trop Dis 2024 12 (12) e0012697
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Evolutionary Relationships of Unclassified Coronaviruses in Canadian Bat Species.
Ayo Yila Simon et al. Viruses 2025 1 (12) -
Genome characterization of a simian foamy virus from a human bitten by an African green monkey.
Anupama Shankar et al. Microbiol Resour Announc 2024 12 e0083224
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Emerging West African Genotype Chikungunya Virus in Mosquito Virome.
Pengpeng Xiao et al. Virulence 2024 12 (1) 2444686 -
Genotypic Clustering of H5N1 Avian Influenza Viruses in North America Evaluated by Ordination Analysis.
Patil Tawidian et al. Viruses 2025 1 (12) -
Intensive transmission in wild, migratory birds drove rapid geographic dissemination and repeated spillovers of H5N1 into agriculture in North America.
Lambodhar Damodaran et al. bioRxiv 2025 1 -
The evolutionary history of Plasmodium falciparum from mitochondrial and apicoplast genomes of China-Myanmar border isolates.
Yini Tian et al. Parasit Vectors 2024 12 (1) 548 -
Canine vector-borne parasites in the Galapagos.
Carla Andreea Culda et al. Parasit Vectors 2024 12 (1) 515 -
Sequencing confirms Anopheles stephensi distribution across southern Yemen.
Yasser A Baheshm et al. Parasit Vectors 2024 12 (1) 507
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Pathogens spread by high-altitude windborne mosquitoes.
R Bamou et al. bioRxiv 2025 1
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Neisseria meningitidis Serogroup Y Sequence Type 1466 and Urogenital Infections.
Sebastiaan J van Hal et al. Emerg Infect Dis 2024 12 (1) 86-93 -
Association between clinical-biological characteristics of Klebsiella pneumoniae and 28-day mortality in patients with bloodstream infection.
Xiaofeng Yu et al. BMC Microbiol 2024 12 (1) 552 -
Comprehensive Analysis of Virulence Genes, Antibiotic Resistance, Biofilm Formation, and Sequence Types in Clinical Isolates of Klebsiella pneumoniae.
Mohsen Nazari et al. Can J Infect Dis Med Microbiol 2024 12 1403019 -
Prevalence of methicillin-resistant Staphylococcus aureus (MRSA) harboring mupirocin and biocide resistance genes in a large health care system.
Rossana Rosa et al. Am J Infect Control 2024 9 (1) 105-109 -
Developing a framework for tracking antimicrobial resistance gene movement in a persistent environmental reservoir.
Amy J Mathers et al. NPJ Antimicrob Resist 2025 1 (1) 50 -
Learning the fitness dynamics of pathogens from phylogenies.
Noémie Lefrancq et al. Nature 2025 1 -
Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii group in Taiwan.
Tran Lam Tu Quyen et al. mSphere 2025 1 e0079324 -
Genetic and Clinical-epidemiologic Profile of hRSV in Pediatric Patients in Southern Brazil: A Four-year Hospital Surveillance Study.
Sonia Mara Raboni et al. Pediatr Infect Dis J 2024 12 -
Genetic and Phenotypic Intra-Clade Variation in Candida auris Isolated from Critically Ill Patients in a New York City Tertiary Care Center.
Marie C Smithgall et al. Clin Chem 2025 1 (1) 185-191 -
Genome sequencing of Plasmodium malariae identifies continental segregation and mutations associated with reduced pyrimethamine susceptibility.
Amy Ibrahim et al. Nat Commun 2024 12 (1) 10779 -
Trichuriasis in Human Patients from Côte d'Ivoire Caused by Novel Trichuris incognita Species with Low Sensitivity to Albendazole/Ivermectin Combination Treatment.
Abhinaya Venkatesan et al. Emerg Infect Dis 2024 12 (1) 104-114
DETECTION / DIAGNOSIS
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Expediting pathogen genomics adoption for enhanced foodborne disease surveillance in Africa.
Aquillah M Kanzi et al. EBioMedicine 2024 12 105500
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Comparison of whole genome sequencing typing tools for the typing of Belgian Legionella pneumophila outbreaks isolates.
Fedoua Echahidi et al. Eur J Clin Microbiol Infect Dis 2024 12
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Prediction of antimicrobial susceptibility of pneumococci based on whole-genome sequencing data: a direct comparison of two genomic tools to conventional antimicrobial susceptibility testing.
Gerardo J Sanchez et al. J Clin Microbiol 2025 1 e0107924 -
Molecular epidemiology of invasive group B Streptococcus in South Africa, 2019-2020.
Buhle Ntozini et al. J Infect Dis 2024 12
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The Application of Digital PCR as a Reference Measurement Procedure to Support the Accuracy of Quality Assurance for Infectious Disease Molecular Diagnostic Testing.
Samreen Falak et al. Clin Chem 2024 12
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Identification of Anthrax as the Cause of a Cluster of Unexplained Deaths, Uganda, 2023: The Role of Metagenomic Next-Generation Sequencing and Postmortem Specimens.
Nicholas Bbosa et al. Am J Trop Med Hyg 2025 1
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Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation.
Aminata Mbaye et al. BMC Infect Dis 2025 1 (1) 3
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Singapore's COVID-19 Genomic Surveillance Programme: Strategies and Insights From a Pandemic Year.
Hao Yi Tan et al. Influenza Other Respir Viruses 2024 12 (12) e70060
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Four Models of Wastewater-Based Monitoring for SARS-CoV-2 Complementing Individual Screening in Jail Settings.
Shanika S Kennedy et al. Am J Public Health 2024 10 (11) 1232-1241
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The molecular epidemiology of respiratory syncytial virus in Ontario, Canada from 2022-2024 using a custom whole genome sequencing assay and analytics package.
Henry Wong et al. J Clin Virol 2024 12 105759
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Epidemiological, molecular, and evolutionary characteristics of G1P[8] rotavirus in China on the eve of RotaTeq application.
Rui Peng et al. Front Cell Infect Microbiol 2024 12 1453862
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Molecular epidemiology of rubella during the pre- and post-elimination eras in the Americas.
Min-Hsin Chen et al. Rev Panam Salud Publica 2024 12 e104
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Advancing poliovirus eradication: lessons learned from piloting direct molecular detection of polioviruses in high-risk and priority geographies.
Paula L Marcet et al. Microbiol Spectr 2024 12 e0227924
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Influenza a Virus Detection at the Human-Swine Interface in US Midwest Swine Farms.
Daniel C A Moraes et al. Viruses 2025 1 (12)
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Performance of whole genome sequencing for respiratory syncytial virus: insights from the first external quality assessment, France, 2024.
Alice Moisan et al. Clin Microbiol Infect 2024 12
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A High Resolution Melting Analysis (HRM) PCR assay for the detection and identification of Old World Leishmania species.
Yusr Saadi-Ben Aoun et al. PLoS Negl Trop Dis 2024 12 (12) e0012762 -
Molecular dissection of laboratory contamination between two schistosome populations.
Kathrin S Jutzeler et al. Parasit Vectors 2024 12 (1) 528
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Outbreak investigations of Salmonella and frozen raw breaded chicken: the mitigation of a significant public health issue in Canada.
Ashley Kerr et al. Epidemiol Infect 2024 12 e180
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National outbreak of Shiga toxin-producing Escherichia coli O145:H28 associated with pre-packed sandwiches, United Kingdom, May-June 2024.
Orlagh Quinn et al. Epidemiol Infect 2024 12 e179
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Burkholderia cenocepacia outbreak linked to taps in a neonatal intensive care unit.
R Purcell et al. Infect Dis Health 2024 12
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Parameters for one health genomic surveillance of Escherichia coli from Australia.
Anne E Watt et al. Nat Commun 2025 1 (1) 17 -
Multiple introductions of NRCS-A Staphylococcus capitis to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey.
Emily A Lees et al. Microb Genom 2025 1 (1) -
Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data.
Brian Lee et al. Nat Commun 2025 1 (1) 441 -
The Impact of Public Health and Social Measures (PHSMs) on SARS-CoV-2 Transmission in the WHO European Region (2020-2022).
Yang Liu et al. Influenza Other Respir Viruses 2024 12 (12) e70036
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SARS-CoV-2 Diversity and Transmission on a University Campus across Two Academic Years during the Pandemic.
Amanda M Casto et al. Clin Chem 2025 1 (1) 192-202 -
Genomic Epidemiology of 2023-2024 Oropouche Outbreak in Iquitos, Peru reveals independent origin from a concurrent outbreak in Brazil.
Maribel Paredes Olortegui et al. medRxiv 2024 12 -
Contribution of HIV transmission bursts to future HIV infections, United States.
Rachael M Billock et al. AIDS 2024 12
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Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation.
Francesco Parino et al. PNAS Nexus 2024 12 (1) pgae561 -
Combining genomics and epidemiology to investigate a zoonotic outbreak of rabies in Romblon Province, Philippines.
Mirava Yuson et al. Nat Commun 2024 12 (1) 10753
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Concurrent Severe Fever with Thrombocytopenia Syndrome Virus Outbreaks on Multiple Fox Farms, China, 2023.
Jian Sun et al. Emerg Microbes Infect 2024 12 2447610 -
Inter-Institutional Dynamics and Impact of Fluconazole-Resistant Candida parapsilosis.
Maya Korem et al. Mycoses 2025 1 (1) e70017
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Developing a universal multi-epitope protein vaccine candidate for enhanced borna virus pandemic preparedness.
Jingjing Zhang et al. Front Immunol 2024 12 1427677 -
Naturally acquired IgG responses to Plasmodium falciparum do not target the conserved termini of the malaria vaccine candidate Merozoite Surface Protein 2.
Julia Zerebinski et al. Front Immunol 2024 12 1501700
HOST-MICROBE INTERACTIONS
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A single mutation in dairy cow-associated H5N1 viruses increases receptor binding breadth.
Marina R Good et al. Nat Commun 2024 12 (1) 10768 -
Virus Evolution in Prolonged Infections of Immunocompromised Individuals.
Zoe Raglow et al. Clin Chem 2025 1 (1) 109-118
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 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.
- Page last reviewed:Feb 1, 2024
- Page last updated:Jan 16, 2025

