Advanced Molecular Detection Clips Content (Published on 02/09/2023)
NEWS
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Peru confirms H5N1 avian flu in marine mammals, part of southward spread
Schnirring L. CIDRAP, Feb 7, 2023. -
Tracking the bird flu, experts see a familiar threat — and a virus whose course is hard to predict
Branswell H. STAT, Feb 8, 2023. -
An Even Deadlier Pandemic Could Soon Be Here
Tufekci Z. New York Times, Feb 3, 2023. -
No new SARS-CoV-2 strains seen in first 3 weeks after China lifted lockdowns
Van Beusekom M. CIDRAP, Feb 8, 2023. -
COVID drug drives viral mutations — and now some want to halt its use
Callaway E. Nature, Feb 7, 2023. -
Studies spotlight growing threat of drug-resistant Shigella
Dall C. CIDRAP, Feb 6, 2023. -
Studies Link Microbiome Dysfunction, Chronic Fatigue Syndrome
GenomeWeb, Feb 9, 2023.
CONCEPTS / COMMENTS
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How public health authorities can use pathogen genomics in health protection practice: a consensus-building Delphi study conducted in the United Kingdom.
Nicholas Killough et al. Microbial genomics 2023 2 (2)
METHODS / TOOLS
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The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.
Ivan S Gill et al. Microbial genomics 2023 2 (1) -
Leveraging comparative genomics to uncover alien genes in bacterial genomes.
Soham Sengupta et al. Microbial genomics 2023 2 (1) -
Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae.
Ebenezer Foster-Nyarko et al. Microbial genomics 2023 2 (2)
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Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium.
Bas Berbers et al. Microbial genomics 2023 2 (1) -
Split k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospitals and hospitals networks in Berlin, Germany.
Friederike Maechler et al. Microbial genomics 2023 2 (1) -
PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data.
Carmen L Sheppard et al. Microbial genomics 2023 2 (12) -
Optimization of the Illumina COVIDSeq™ protocol for decentralized, cost-effective genomic surveillance.
Rob E Carpenter et al. Practical laboratory medicine 2023 2 e00311 -
The virtual microbiome: A computational framework to evaluate microbiome analyses.
Belén Serrano-Antón et al. PloS one 2023 2 (2) e0280391 -
A novel approach for combining the metagenome, metaresistome, metareplicome and causal inference to determine the microbes and their antibiotic resistance gene repertoire that contribute to dysbiosis.
Vitalii Stebliankin et al. Microbial genomics 2023 2 (12)
EVOLUTION / ECOLOGY / POPULATIONS
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Distribution and origins of Mycobacterium tuberculosis L4 in Southeast Asia.
Philip M Ashton et al. Microbial genomics 2023 2 (2) -
Combining analytical epidemiology and genomic surveillance to identify risk factors associated with the spread of antimicrobial resistance in Salmonella enterica subsp. enterica serovar Heidelberg.
Benjamin M Hetman et al. Microbial genomics 2023 2 (11) -
Large-scale comparative genomics to refine the organization of the global Salmonella enterica population structure.
Chao Chun Liu et al. Microbial genomics 2023 2 (12) -
Laboratory strains of Escherichia coli K-12: things are seldom what they seem.
Douglas F Browning et al. Microbial genomics 2023 2 (2) -
Environmental contamination with highly resistant microorganisms after relocating to a new hospital building with 100% single-occupancy rooms: A prospective observational before-and-after study with a three-year follow-up.
Adriënne S van der Schoor et al. International journal of hygiene and environmental health 2023 1 114106
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Characterization of invasive meningococcal disease case isolates in Atlantic Canada, 2014 to 2020: spatial-temporal variations of clones and predicted meningococcal B vaccine coverage.
Raymond S W Tsang et al. Journal of medical microbiology 2023 2 (12)
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Coordinated evolution at amino acid sites of SARS-CoV-2 spike.
Alexey Dmitrievich Neverov et al. eLife 2023 2 -
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink.
Ashleigh F Porter et al. Virus evolution 2023 2 (1) vead002 -
Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis
Pang Y, et al. Lancet, Feb 8, 2023. -
Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolution in an Immunodeficient Child.
Micheli Filippi et al. The Pediatric infectious disease journal 2023 2 -
Multiplex MinION sequencing suggests enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era.
Mailis Maes et al. Microbial genomics 2023 2 (1) -
Analysis of variola virus molecular evolution suggests an old origin of the virus consistent with historical records.
Diego Forni et al. Microbial genomics 2023 2 (1) -
Epidemiological and genomic analysis of dengue cases in Guangzhou, China, from 2010 to 2019.
Liyun Jiang et al. Scientific reports 2023 2 (1) 2161 -
Genomic Analysis of Early Monkeypox Virus Outbreak Strains, Washington, United States.
Pavitra Roychoudhury et al. Emerging infectious diseases 2023 2 (3) -
Population genetic analysis of Plasmodium knowlesi reveals differential selection and exchange events between Borneo and Peninsular sub-populations.
Anna Turkiewicz et al. Scientific reports 2023 2 (1) 2142
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Whole Genome Sequencing to Predict Antimicrobial Susceptibility Profiles in Neisseria gonorrhoeae.
Claire C Bristow et al. The Journal of infectious diseases 2023 2 -
A bittersweet fate: detection of serotype switching in Pseudomonas aeruginosa.
Mikkel Anbo et al. Microbial genomics 2023 2 (1) -
Emergence of extensively drug-resistant and multidrug-resistant Shigella flexneri serotype 2a associated with sexual transmission among gay, bisexual, and other men who have sex with men, in England: a descriptive epidemiological study.
Katie Thorley et al. The Lancet. Infectious diseases 2023 2 -
Epidemiological and genomic characteristics of global mcr-positive Escherichia coli isolates.
Jiping Shi et al. Frontiers in microbiology 2023 2 1105401 -
Genomic insights of mcr-1 harboring Escherichia coli by geographical region and a One-Health perspective.
William Calero-Cáceres et al. Frontiers in microbiology 2023 2 1032753 -
Genotypic and predicted phenotypic analysis of SARS-COV-2 Omicron subvariants in immunocompromised patients with COVID-19 following tixagevimab-cilgavimab prophylaxis.
Eloy E Ordaya et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2023 2 105382 -
Phenotypic effects of mutations observed in the neuraminidase of human origin H5N1 influenza A viruses.
David Scheibner et al. PLoS pathogens 2023 2 (2) e1011135
DETECTION / DIAGNOSIS
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Development of a simple, rapid, and sensitive molecular diagnostic assay for cholera.
Subhra Chakraborty et al. PLoS neglected tropical diseases 2023 2 (2) e0011113 -
Spike Gene Target Amplification in a Diagnostic Assay as a Marker for Public Health Monitoring of Emerging SARS-CoV-2 Variants - United States, November 2021-January 2023.
Heather M Scobie et al. MMWR. Morbidity and mortality weekly report 2023 2 (5) 125-127
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The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021.
Oliver Eales et al. Microbial genomics 2023 2 (2) -
Wild poliovirus type 3 (WPV3)-shedding event following detection in environmental surveillance of poliovirus essential facilities, the Netherlands, November 2022 to January 2023.
Erwin Duizer et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2023 2 (5) -
Frequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1.
Suraj Balakrishna et al. The Journal of antimicrobial chemotherapy 2023 2 -
Usefulness of dried blood spot samples for monitoring hepatitis C treatment outcome and reinfection among people who inject drugs in a test-and-treat program.
Anna Not et al. Journal of medical virology 2023 2 -
Absence of detectable monkeypox virus DNA in 11,000 English blood donations during the 2022 outbreak.
Chanice Knight et al. Transfusion 2023 2 -
Candida auris admission screening pilot in select units of New York City health care facilities, 2017-2019.
Jemma Rowlands et al. Am J Infect Control 2023 2 (8) 866-870
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Molecular identification and genetic characteristics of Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi in human immunodeficiency virus/acquired immunodeficiency syndrome patients in Shanghai, China.
Yanyan Jiang et al. Parasites & vectors 2023 2 (1) 53
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Genomic reconstruction and directed interventions in a multidrug-resistant Shigellosis outbreak in Seattle, WA, USA: a genomic surveillance study.
Giannoula S Tansarli et al. The Lancet. Infectious diseases 2023 2 -
Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK.
Kate F Cook et al. Frontiers in cellular and infection microbiology 2023 2 1066390
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Investigation of SARS-CoV-2 Transmission in The Tabernacle Choir at Temple Square in the Context of Prevention Protocols, Utah, September-November 2021.
William A Lanier et al. Public Health Rep 2023 2 (3) 416-421
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Surveillance and Analysis of SARS-CoV-2 Variant Importation - China, January-June 2022.
Yenan Feng et al. China CDC weekly 2023 2 (50) 1136-1142 -
Challenges in Harnessing Shared Within-Host Severe Acute Respiratory Syndrome Coronavirus 2 Variation for Transmission Inference.
Katharine S Walter et al. Open forum infectious diseases 2023 2 (2) ofad001
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Vaccine effectiveness estimates from an early-season influenza A(H3N2) epidemic, including unique genetic diversity with reassortment, Canada, 2022/23.
Danuta M Skowronski et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2023 2 (5)
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Early Estimates of Bivalent mRNA Booster Dose Vaccine Effectiveness in Preventing Symptomatic SARS-CoV-2 Infection Attributable to Omicron BA.5- and XBB/XBB.1.5-Related Sublineages Among Immunocompetent Adults - Increasing Community Access to Testing Program, United States, December 2022-January 2023.
Ruth Link-Gelles et al. MMWR. Morbidity and mortality weekly report 2023 2 (5) 119-124
HOST-MICROBE INTERACTIONS
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Pathogen exposure misclassification can bias association signals in GWAS of infectious diseases when using population-based common control subjects.
Dylan Duchen et al. American journal of human genetics 2023 1 (2) 336-348 -
Therapeutic potential of IL6R blockade for the treatment of sepsis and sepsis-related death: A mendelian randomisation study.
Fergus W Hamilton et al. PLoS medicine 2023 1 (1) e1004174 -
Unlocking life-threatening COVID-19 through two types of inborn errors of type I IFNs.
Jean-Laurent Casanova et al. The Journal of clinical investigation 2023 1 (3) -
Multi-‘omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients
Xiong R, et al. Lancet, Feb 8, 2023. -
Role of Microbiota in the Skin Colonization of Candida auris.
Brooke Tharp et al. mSphere 2023 1 e0062322
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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