Advanced Molecular Detection Clips Content (Published on 11/03/2022)
NEWS
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COVID ‘variant soup’ is making winter surges hard to predict
Callaway E. Nature, Oct 28, 2022. -
Fair Warning: “Swientists” hunt for influenza virus at hog shows, hoping to cut off the next pandemic at the pen
Cohen J. Science, Oct 27, 2022. -
More Evidence of Monkeypox Spread Before Symptoms Appear
Kneisei K. MedPage Today, Nov 2, 2022.
CONCEPTS / COMMENTS
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Building a Resilient Scientific Network for COVID-19 and Beyond.
Babady N Esther et al. mBio 2022 9 (5) e0222322 -
Ethics and governance challenges related to genomic data sharing in southern Africa: the case of SARS-CoV-2.
Moodley Keymanthri et al. The Lancet. Global health 2022 10 -
Combining pathogen and host metagenomics for a better sepsis diagnostic
Gant V, Singer M. Nat Microbiol, Oct 26, 2022.
METHODS / TOOLS
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Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts.
Smith Byron J et al. Frontiers in bioinformatics 2022 10 867386 -
RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis.
Lucaci Alexander G et al. PloS one 2022 11 (11) e0275623 -
CO-CONNECT: A hybrid architecture to facilitate rapid discovery and access to UK wide data in the response to the COVID-19 pandemic.
Jefferson Emily et al. Journal of medical Internet research 2022 11 -
Ampliseq for Illumina Technology Enables Detailed Molecular Epidemiology of Rabies Lyssaviruses from Infected Formalin-Fixed Paraffin-Embedded Tissues.
Nadin-Davis Susan Angela et al. Viruses 2022 10 (10)
EVOLUTION / ECOLOGY / POPULATIONS
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Clinical and genomic characterization of hypervirulent Klebsiella pneumoniae (hvKp) infections via passive surveillance in Southern California, 2020-2022
Kamau E, et al. Front Microbiol. 2022 Oct 14;13:1001169. -
Comparative analysis of Vibrio cholerae isolates from Ghana reveals variations in genome architecture and adaptation of outbreak and environmental strains.
Adade Nana Eghele et al. Frontiers in microbiology 2022 10 998182 -
Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States.
Cardenas-Alvarez Maria X et al. Microbiology spectrum 2022 10 e0157922 -
Phylodynamic signatures in the emergence of community-associated MRSA.
Steinig Eike et al. Proceedings of the National Academy of Sciences of the United States of America 2022 11 (45) e2204993119 -
Temporal dynamics of SARS-CoV-2 genome mutations that occurred in vivo on an aircraft.
He Yaqing et al. Biosafety and health 2022 11 -
Evolutionary Pattern Comparisons of the SARS-CoV-2 Delta Variant in Countries/Regions with High and Low Vaccine Coverage.
Zhang Jiahao et al. Viruses 2022 10 (10) -
Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses.
Colmant Agathe M G et al. Frontiers in microbiology 2022 10 997058 -
Genomic Epidemiology Reveals the Circulation of the Chikungunya Virus East/Central/South African Lineage in Tocantins State, North Brazil.
Souza Ueric José Borges de et al. Viruses 2022 10 (10) -
Genomics and metagenomics of Madurella mycetomatis, a causative agent of black grain mycetoma in Sudan.
Litvintseva Anastasia P et al. PLoS neglected tropical diseases 2022 11 (11) e0010787
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Microbiome profiling and characterization of virulent and vancomycin-resistant Enterococcus faecium from treated and untreated wastewater, beach water and clinical sources.
Dželalija Mia et al. The Science of the total environment 2022 10 159720 -
Epidemiological links and antimicrobial resistance of clinical Salmonella enterica ST198 isolates: a nationwide microbial population genomic study in Switzerland.
Biggel Michael et al. Microbial genomics 2022 10 (10) -
Prevalence and genetic basis of first-line drug resistance of Mycobacterium tuberculosis in Ca Mau, Vietnam.
Callum Jack et al. ERJ open research 2022 10 (4) -
Occurrence and Molecular Characterization of Multidrug-Resistant Vegetable-Borne Listeria monocytogenes Isolates.
Ntshanka Zizipho et al. Antibiotics (Basel, Switzerland) 2022 10 (10) -
Molecular Epidemiology of Neonatal-Associated Staphylococcus haemolyticus Reveals Endemic Outbreak.
Westberg Ronja et al. Microbiology spectrum 2022 10 e0245222 -
Clinical and genomic analysis of virulence-related genes in bloodstream infections caused by Acinetobacter baumannii.
Bai Bing et al. Virulence 2022 10 (1) 1920-1927
DETECTION / DIAGNOSIS
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The Comparison of Metagenomic Next-Generation Sequencing with Conventional Microbiological Tests for Identification of Pathogens and Antibiotic Resistance Genes in Infectious Diseases.
Lu Hongzhi et al. Infection and drug resistance 2022 10 6115-6128 -
Highly Sensitive Detection of Isoniazid Heteroresistance in Mycobacterium Tuberculosis by Droplet Digital PCR
Zheng Y, et al. Infect Drug Resist, Oct 28, 2022. -
Rapid Identification of Drug Resistance and Phylogeny in M. tuberculosis, Directly from Sputum Samples.
Barbosa-Amezcua Martín et al. Microbiology spectrum 2022 9 (5) e0125222 -
Evaluation of the use of CRISPR loci for discrimination of Salmonella enterica subsp. enterica serovar Enteritidis strains recovered in Canada and comparison with other subtyping methods.
Nadin-Davis Susan et al. AIMS microbiology 2022 11 (3) 300-317 -
Tracing the origin of SARS-CoV-2 Omicron-like Spike sequences detected in wastewater
Shafer MM, et al. medRxiv, Oct 31, 2022. -
Separating Signal from Noise in Wastewater Data: An Algorithm to Identify Community-Level COVID-19 Surges
Keshaviah A, et al. medRxiv, Oct 27, 2022. -
Identifying trends in SARS-CoV-2 RNA in wastewater to infer changing COVID-19 incidence: Effect of sampling frequency
Chan EM, et al. medRxiv, Oct 30, 2022. -
Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants.
Cuypers Lize et al. Viruses 2022 10 (10) -
Comparative HIV-1 Phylogenies Characterized by PR/RT, Pol and Near-Full-Length Genome Sequences.
Topcu Cicek et al. Viruses 2022 10 (10) -
A collaborative approach to improve representation in viral genomic surveillance.
Kim Paul Y et al. bioRxiv : the preprint server for biology 2022 10 -
Wastewater Testing and Detection of Poliovirus Type 2 Genetically Linked to Virus Isolated from a Paralytic Polio Case — New York, March 9–October 11, 2022
Ryerson AB, et al. MMWR, Oct 28, 2022.
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Cluster of Burkholderia cepacia Complex Infections Associated With Extracorporeal Membrane Oxygenation Water Heater Devices.
Rhee Chanu et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 3 (9) 1610-1617
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Spatial scale of tuberculosis transmission in Lima, Peru.
Huang Chuan-Chin et al. Proceedings of the National Academy of Sciences of the United States of America 2022 11 (45) e2207022119 -
The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya
Githinji G, et al. medRxiv, Oct 27, 2022. -
Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border.
Douglas Jordan et al. Nature communications 2022 10 (1) 6484
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Population-based screening in a municipality after a primary school outbreak of the SARS-CoV-2 Alpha variant, the Netherlands, December 2020-February 2021.
van Beek Janko et al. PloS one 2022 10 (10) e0276696 -
Comparative hospitalization risk for SARS-CoV-2 Omicron and Delta variant infections, by variant predominance periods and patient-level sequencing results, New York City, August 2021-January 2022.
Sharon K Greene et al. Influenza Other Respir Viruses 2022 11 (1) e13062
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One health genomic surveillance and response to a university-based outbreak of the SARS-CoV-2 Delta AY.25 lineage, Arizona, 2021.
Hayley D Yaglom et al. PLoS One 2022 10 (10) e0272830
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SARS-CoV-2 Transmission from Human to Pet and Suspected Transmission from Pet to Human, Thailand.
Piewbang Chutchai et al. Journal of clinical microbiology 2022 10 e0105822 -
Whole genome sequencing and molecular epidemiology of the 2021 African swine fever virus outbreak in the Dominican Republic.
Lakin Steven M et al. Transboundary and emerging diseases 2022 10 -
HIV transmission among acutely infected participants of a Dutch cohort study 2015-2021 is not associated with large, clustered outbreaks.
Prins Henrieke A B et al. AIDS (London, England) 2022 10
HOST-MICROBE INTERACTIONS
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Respiratory syncytial virus: host genetic susceptibility and factors associated with disease severity in a cohort of pediatric patients.
I G Giamberardino Heloisa et al. Journal of tropical pediatrics 2022 11 (6)
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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- Page last updated:Jan 16, 2025