Advanced Molecular Detection Clips Content (Published on 04/06/2023)
NEWS
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UK develops genetic early warning system for future pandemics
McKie R. Guardian, Apr 2, 2023. -
In the War on Bacteria, It’s Time to Call in the Phages
McKenna M. Wired, Apr 2, 2023. -
Antibiotic use breeds 'two-way' resistance in humans and animals
Dall C. CIDRAP, Apr 4, 2023. -
Drug-Resistant Bacteria Tied to Eyedrops Can Spread Person to Person
Jewett C, Jacobs A. New York Times, Apr 3, 2023. -
A critical genetic database is under fire
Economist, Apr 5, 2023. -
COVID-origins data from Wuhan market published: what scientists think
Lewis D, et al. Nature, Apr 5, 2023. -
With new Nature study, scientists continue to debate SARS-CoV-2 origins
Van Beusekom M. CIDRAP, Apr 5, 2023. -
U.S. Study Backs 'Helper' Virus Theory in Kids' Mystery Hepatitis Cases
Hein I. MedPage Today, Mar 31, 2023. -
Often overlooked, a common infection during pregnancy kickstarts a conversation about newborn screening
Chen E. STAT, Apr 5, 2023. -
Real-world data show safety, efficacy of microbiota-based drug for recurrent C diff
Dall C. CIDRAP, Apr 3, 2023.
EVENTS / TRAINING / WEB RESOURCES
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Respiratory Virus and Microbiome Initiative: Parasites and Microbes
Wellcome Sanger Institute (UK).
CONCEPTS / COMMENTS
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Pandemic preparedness strategies must go beyond vaccines
Gupta R, et al. Sci Transl Med, Apr 5, 2023.
METHODS / TOOLS
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VirBot: an RNA viral contig detector for metagenomic data.
Guowei Chen et al. Bioinformatics (Oxford, England) 2023 2 (3) -
genomepy: genes and genomes at your fingertips.
Siebren Frölich et al. Bioinformatics (Oxford, England) 2023 3 (3) -
Search and sequence analysis tools services from EMBL-EBI in 2022.
Fábio Madeira et al. Nucleic acids research 2022 4 (W1) W276-W279 -
Polishing De Novo Nanopore Assemblies of Bacteria and Eukaryotes With FMLRC2.
Q X Charles Mak et al. Molecular biology and evolution 2023 3 (3) -
Defining genomic epidemiology thresholds for common-source bacterial outbreaks: a modelling study.
Audrey Duval et al. The Lancet. Microbe 2023 4 -
A simplified viral RNA extraction method based on magnetic nanoparticles for fast and high-throughput detection of SARS-CoV-2.
Haodong Cui et al. Talanta 2023 3 124479
EVOLUTION / ECOLOGY / POPULATIONS
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Genomic comparison of mecC-carrying methicillin-resistant Staphylococcus aureus from hedgehogs and humans in the Netherlands.
Cindy Dierikx et al. The Journal of antimicrobial chemotherapy 2023 3 -
Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania.
Michaela Zwyer et al. PLoS pathogens 2023 4 (4) e1010893 -
Original and introduced lineages co-driving the persistence of Brucella abortus circulating in West Africa.
Zhiguo Liu et al. Frontiers in public health 2023 4 1106361 -
Molecular characterization and comparative genomic analysis of Acinetobacter baumannii isolated from the community and the hospital: an epidemiological study in Segamat, Malaysia.
Nazmul Hasan Muzahid et al. Microbial genomics 2023 4 (4) -
The evolution of SARS-CoV-2.
Peter V Markov et al. Nature reviews. Microbiology 2023 4 -
The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic.
Jialin Yang et al. Scientific reports 2023 4 (1) 5571 -
Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis.
Sana Naderi et al. eLife 2023 4 -
Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals.
Haogao Gu et al. Nature communications 2023 3 (1) 1793 -
Spatiotemporal Evolution of SARS-CoV-2 Alpha and Delta Variants during Large Nationwide Outbreak of COVID-19, Vietnam, 2021.
Nguyen Thi Tam et al. Emerging infectious diseases 2023 4 (5) -
Evolutionary dynamics of dengue virus in India.
Suraj Jagtap et al. PLoS pathogens 2023 4 (4) e1010862 -
Timing and genotype distribution of symptomatic and asymptomatic sapovirus infections and re-infections in a Nicaraguan birth cohort.
Fredman González et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2022 11 (4) 540.e9-540.e15
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Detection of reassortant influenza B strains from 2004 to 2015 seasons in Barcelona (Catalonia, Spain) by whole genome sequencing.
Cristina Andrés et al. Virus research 2023 4 199089 -
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine.
David E Hufnagel et al. Virus evolution 2023 3 (1) vead015 -
Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains.
Grace Nabakooza et al. Scientific reports 2023 4 (1) 5516 -
Middle East Respiratory Syndrome Coronavirus (MERS-CoV) - a ten-year (2012-2022) global analysis of human and camel infections, genomic sequences, lineages, and geographical origins.
Esam I Azhar et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2023 3
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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First Known Report of mcr-Harboring Enterobacteriaceae in the Dominican Republic.
Angela Perdomo et al. International journal of environmental research and public health 2023 3 (6)
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Streptococcus canis genomic epidemiology reveals the potential for zoonotic transfer.
Davide Pagnossin et al. Microbial genomics 2023 3 (3) -
Evidence of widespread endemic populations of highly multidrug resistant Klebsiella pneumoniae in hospital settings in Hanoi, Vietnam: a prospective cohort study.
My H Pham et al. The Lancet. Microbe 2023 2 (4) e255-e263 -
Deciphering variable resistance to novel carbapenem-based β-lactamase inhibitor combinations in a multi-clonal outbreak caused by Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae resistant to ceftazidime/avibactam.
Vincenzo Di Pilato et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2022 11 (4) 537.e1-537.e8 -
Emerging Invasive Group A Streptococcus M1 Lineage Detected by Allele-Specific PCR, England, 2020.
Xiangyun Zhi et al. Emerging infectious diseases 2023 4 (5) -
Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides difficile.
Kate E Dingle et al. mBio 2023 4 e0024323 -
Adeno-associated virus type 2 in US children with acute severe hepatitis
Servellita V, et al. Nature, Mar 30, 2023.
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Adeno-associated virus 2 infection in children with non-A-E hepatitis.
Antonia Ho et al. Nature 2023 3
DETECTION / DIAGNOSIS
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Application of a core genome sequence typing (cgMLST) pipeline for surveillance of Clostridioides difficile in China.
Yuan Yuan Wang et al. Frontiers in cellular and infection microbiology 2023 3 1109153
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Performance of antigen lateral flow devices in the UK during the alpha, delta, and omicron waves of the SARS-CoV-2 pandemic: a diagnostic and observational study.
David W Eyre et al. The Lancet. Infectious diseases 2023 3 -
A portable thermostatic molecular diagnosis device based on high-efficiency photothermal conversion material for rapid field detection of SARS-CoV-2.
Xinyao Yang et al. Talanta 2023 3 124422 -
Genomic Surveillance for SARS-CoV-2 - China, September 26, 2022 to January 29, 2023.
Shiwen Wang et al. China CDC weekly 2023 4 (7) 143-151 -
Surveillance of SARS-CoV-2 at the Huanan Seafood Market
Liu WJ, et al. Nature, Apr 5, 2023. -
Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels.
Hannah N Kozlowski et al. Analytical chemistry 2023 3 -
Rapid genomic surveillance of SARS-CoV-2 in a dense urban community of Kathmandu Valley using sewage samples.
Rajindra Napit et al. PloS one 2023 3 (3) e0283664 -
Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites.
Sasha V Siegel et al. medRxiv : the preprint server for health sciences 2023 3 -
Identification of two insecticide resistance markers in Ethiopian Anopheles stephensi mosquitoes using a multiplex amplicon sequencing assay.
Holly Acford-Palmer et al. Scientific reports 2023 4 (1) 5612
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation.
Seth Commichaux et al. BMC genomics 2023 4 (1) 165 -
An Outbreak Investigation of Vibrio parahaemolyticus Infections in the United States Linked to Crabmeat Imported from Venezuela: 2018.
Sharon L Seelman et al. Foodborne Pathog Dis 2023 4 (4) 123-131
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Environmental contamination and evaluation of healthcare-associated SARS-CoV-2 transmission risk in temporary isolation wards during the COVID-19 pandemic.
Liang En Wee et al. American journal of infection control 2023 4 (4) 413-419 -
SARS-CoV-2 transmission among health care workers, an outbreak investigation using whole-genome sequencing.
K S Te Paske et al. PloS one 2023 3 (3) e0283292 -
Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020-2022.
Arunachalam Ramaiah et al. Microbial genomics 2023 3 (3) -
Inferring potential non-disclosed men who have sex with men among self-reported heterosexual men with HIV in Southwest China: A genetic network study.
Yi Chen et al. PloS one 2023 3 (3) e0283031 -
HIV acquisition prior to entry into formal sex work: inference from next-generation viral sequencing.
Bronwyn Neufeld et al. AIDS (London, England) 2023 2 (6) 987-992
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Prevalence and Homology of the Pneumococcal Serine-Rich Repeat Protein at the Global Scale.
Javid Aceil et al. Microbiology spectrum 2023 3 e0325222 -
Effect of fecal microbial transplantation on Clostridioides difficile infection: dysbiosis, metabolites and health related quality of life.
Kevin W Garey et al. Open forum infectious diseases 2023 3 (3) ofad113
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SARS-CoV-2 Omicron boosting induces de novo B cell response in humans.
Wafaa B Alsoussi et al. Nature 2023 4 -
Shaping the subway microbiome through probiotic-based sanitation during the COVID-19 emergency: a pre-post case-control study.
Maria D'Accolti et al. Microbiome 2023 3 (1) 64 -
Efficient CRISPR-Cas13d-Based Antiviral Strategy to Combat SARS-CoV-2.
Mouraya Hussein et al. Viruses 2023 3 (3) -
Construction and immunogenicity of an mRNA vaccine against chikungunya virus.
Jingjing Liu et al. Frontiers in immunology 2023 4 1129118
HOST-MICROBE INTERACTIONS
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Recurrent spontaneous Escherichia coli meningitis in an adult: a case report.
Anne V Amulele et al. JAC-antimicrobial resistance 2023 3 (2) dlad029 -
No evidence for a common blood microbiome based on a population study of 9,770 healthy humans.
Cedric C S Tan et al. Nature microbiology 2023 3 -
Genetic predisposition between coronavirus disease 2019 and rheumatic diseases: A 2-sample Mendelian randomization study.
Liuliu Quan et al. International journal of rheumatic diseases 2023 3 (4) 710-717 -
Relating CYP2B6 genotype and efavirenz resistance among post-partum women living with HIV with high viremia in Uganda: a nested cross-sectional study.
Allan Buzibye et al. AIDS research and therapy 2023 4 (1) 20 -
Genetic variations of Plasmodium falciparum circumsporozoite protein and the impact on interactions with human immunoproteins and malaria vaccine efficacy.
Cheikh Cambel Dieng et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2023 2 105418
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.
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