Advanced Molecular Detection Clips Content (Published on 10/27/2022)
NEWS
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NIST Analysis Discovers Sample Processing Bias in Metagenomic Wastewater Surveillance
Zhang H. GenomeWeb, Oct 19, 2022. -
Chan Zuckerberg Initiative, Gates Foundation Award $2M for Metagenomic Pathogen Research
GenomeWeb, Oct 24, 2022. -
Which COVID studies pose a biohazard? Lack of clarity hampers research
Callaway E, Kozlov M. Nature, Oct 21, 2022. -
Omicron keeps finding new evolutionary tricks to outsmart our immunity
Stein R. NPR, Oct 25, 2022. -
FDA’s vaccines chief sees possibility of more Covid boosters — sooner than he’d like
Branswell H. STAT, Oct 21, 2022. -
WHO: Ugandan Ebola outbreak ‘rapidly evolving’ after 1 month
Muhumuza R, Larson K. AP, Oct 20, 2022. -
Merck locates frozen batch of undisclosed Ebola vaccine, will donate for testing in Uganda’s outbreak
Cohen J. Science, Oct 23, 2022. -
Administration eyes national hepatitis C treatment plan
Raman S. Roll Call, Oct 25, 2022. -
Immune system-evading hybrid virus observed for first time
Geddes L. Guardian, Oct 24, 2022.
POLICY
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Data-enabled responses to pandemics: policy lessons from COVID-19.
Dhami Sangeeta et al. Nature medicine 2022 10
CONCEPTS / COMMENTS
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The potential of genomics for infectious disease forecasting.
Stockdale Jessica E et al. Nature microbiology 2022 10
METHODS / TOOLS
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SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework.
Skums Pavel et al. Cell systems 2022 10 (10) 844-856.e4
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The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.
Walker Kimberly et al. F1000Research 2022 10 530 -
Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications.
Govender Kumeren N et al. Microbial genomics 2022 10 (10) -
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.
Alcock Brian P et al. Nucleic acids research 2022 10 -
Guiding the design of SARS-CoV-2 genomic surveillance by estimating the resolution of outbreak detection.
Suster Carl J E et al. Frontiers in public health 2022 10 1004201 -
MixviR: an R Package for Exploring Variation Associated with Genomic Sequence Data from Environmental SARS-CoV-2 and Other Mixed Microbial Samples.
Sovic Michael G et al. Applied and environmental microbiology 2022 10 e0087422 -
Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus.
Nicholas F G Chen et al. medRxiv 2022 10
EVOLUTION / ECOLOGY / POPULATIONS
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One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia.
White Rhys T et al. Microbial genomics 2022 10 (10) -
Genomic Epidemiology of Vibrio cholerae O139, Zhejiang Province, China, 1994–2018
Luo Y, et al. Emerg Infect Dis, Oct 13, 2022. -
The Threat of Potentially Pathogenic Bacteria in the Feces of Bats.
Huang Yuyuan et al. Microbiology spectrum 2022 10 e0180222 -
Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron
van Dorp C, et al. Virus Evol, Oct 7, 2022. -
Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease.
Iša Pavel et al. BMC infectious diseases 2022 10 (1) 792 -
Multiple lineages of monkeypox virus detected in the United States, 2021-2022.
Crystal M Gigante et al. Science 2022 10 (6619) 560-565
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Evolutionary dynamics of the clade 2.3.4.4B H5N8 high pathogenicity avian influenza outbreaks in coastal seabirds and other species in southern Africa from 2017-2019.
Peyrot Belinda M et al. Transboundary and emerging diseases 2022 10 -
Iceland as Stepping Stone for Spread of Highly Pathogenic Avian Influenza Virus between Europe and North America.
Günther Anne et al. Emerging infectious diseases 2022 10 (12)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Molecular characteristics of global β-lactamase-producing Enterobacter cloacae by genomic analysis.
Hu Jincao et al. BMC microbiology 2022 10 (1) 255 -
Transmission of ST45 and ST2407 extended-spectrum β-lactamase-producing Klebsiella pneumoniae in neonatal intensive care units, associated with contaminated environments.
Shi Qiucheng et al. Journal of global antimicrobial resistance 2022 10 -
Emergence of a Superplasmid Coharboring Hypervirulence and Multidrug Resistance Genes in Klebsiella pneumoniae Poses New Challenges to Public Health.
Jia Xinmiao et al. Microbiology spectrum 2022 10 e0263422 -
Whole-genome sequencing of presumptive MDR-TB isolates from a tertiary healthcare setting in Mumbai.
Zade Amrutraj et al. Journal of global antimicrobial resistance 2022 10 -
Klebsiella pneumoniae ST147: and then there were three carbapenemases.
Mataseje L F et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2022 10 -
Polyclonal Dissemination of OXA-232 Carbapenemase-Producing Klebsiella pneumoniae, France, 2013-2021.
Emeraud Cecile et al. Emerging infectious diseases 2022 10 (11) 2304-2307 -
Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial.
Choudhary Manish C et al. Nature microbiology 2022 10 -
Comparison of Rhinovirus A-, B-, and C-Associated Respiratory Tract Illness Severity Based on the 5'-Untranslated Region Among Children Younger Than 5 Years.
Sayama Akiko et al. Open forum infectious diseases 2022 10 (10) ofac387 -
Unassigned Complex Unique Recombinant Forms Related to CRF36_cpx in Children Identified in an HIV-1 Outbreak in Pakistan.
Abidi Syed Hani et al. AIDS research and human retroviruses 2022 7 (10) 806-811 -
Molecular identification, antifungal susceptibility, and resistance mechanisms of pathogenic yeasts from the China antifungal resistance surveillance trial (CARST-fungi) study.
Wang Qiqi et al. Frontiers in microbiology 2022 10 1006375
DETECTION / DIAGNOSIS
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Comparative Analysis of the Molecular Characteristics of Group B Streptococcus Isolates Collected from Pregnant Korean Women Using Whole-genome Sequencing.
Lee Yangsoon et al. Annals of laboratory medicine 2022 10 (2) 180-186 -
Performance Comparison Between Fourier-Transform Infrared Spectroscopy-based IR Biotyper and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for Strain Diversity.
Jun Son Young et al. Annals of laboratory medicine 2022 10 (2) 174-179 -
Leptospira enrichment culture followed by ONT metagenomic sequencing allows better detection of Leptospira presence and diversity in water and soil samples.
Gorman Myranda et al. PLoS neglected tropical diseases 2022 10 (10) e0010589 -
Large-Scale Evaluation of a Rapid Fully Automated Analysis Platform to Detect and Refute Outbreaks Based on MRSA Genome Comparisons.
Raven Kathy E et al. mSphere 2022 10 e0028322
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SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing.
Mannsverk Steinar et al. Virology journal 2022 10 (1) 164 -
Detection of human adenovirus F41 in wastewater and its relationship to clinical cases of acute hepatitis of unknown aetiology.
Reyne Marina I et al. The Science of the total environment 2022 10 (Pt 2) 159579 -
Molecular Detection of Haplorchis pumilio Eggs in Schoolchildren, Kome Island, Lake Victoria, Tanzania
Shin H, et al. Emerg Infect Dis, Nov 2022. -
MALDI-TOF MS: An effective tool for a global surveillance of dengue vector species.
Rakotonirina Antsa et al. PloS one 2022 10 (10) e0276488
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Viral whole-genome sequencing to assess impact of universal masking on SARS-CoV-2 transmission among pediatric healthcare workers.
Kociolek Larry K et al. Infection control and hospital epidemiology 2021 10 (10) 1408-1412
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Fungal Endophthalmitis Outbreak after Cataract Surgery, South Korea, 2020
Yoon SJ, et al. Emerg Infect Dis, Nov 2022.
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Meningococcal disease in North America: Updates from the Global Meningococcal Initiative.
Edwin J Asturias et al. J Infect 2022 10 (6) 611-622
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A research and development (R&D) roadmap for broadly protective coronavirus vaccines: Setting a path to address coronavirus threats.
Moore Kristine A et al. Vaccine 2022 9 (42) 6001-6003 -
Protection against Omicron from Vaccination and Previous Infection in a Prison System.
Chin Elizabeth T et al. The New England journal of medicine 2022 10 -
Effectiveness of COVID-19 mRNA Vaccines Against COVID-19-Associated Hospitalizations Among Immunocompromised Adults During SARS-CoV-2 Omicron Predominance - VISION Network, 10 States, December 2021-August 2022.
Britton Amadea et al. MMWR. Morbidity and mortality weekly report 2022 10 (42) 1335-1342
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Effectiveness of Monovalent mRNA Vaccines Against COVID-19-Associated Hospitalization Among Immunocompetent Adults During BA.1/BA.2 and BA.4/BA.5 Predominant Periods of SARS-CoV-2 Omicron Variant in the United States - IVY Network, 18 States, December 26, 2021-August 31, 2022.
Surie Diya et al. MMWR. Morbidity and mortality weekly report 2022 10 (42) 1327-1334
HOST-MICROBE INTERACTIONS
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The potential of tailoring the gut microbiome to prevent and treat cardiometabolic disease.
Chakaroun Rima Mohsen et al. Nature reviews. Cardiology 2022 10 -
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults.
Kalantar Katrina L et al. Nature microbiology 2022 10 -
Imprinted antibody responses against SARS-CoV-2 Omicron sublineages.
Park Young-Jun et al. Science (New York, N.Y.) 2022 10 eadc9127 -
Coronavirus Host Genomics Study: South Africa (COVIGen-SA).
May Andrew K et al. Global health, epidemiology and genomics 2022 10 7405349 -
Robust Machine Learning predicts COVID-19 Disease Severity based on Single-cell RNA-seq from multiple hospitals
Lemsara A, et al. medRxiv, Oct 22, 2022. -
Genome-wide association studies of COVID-19: Connecting the dots.
Ferreira Leonardo C et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2022 10 105379 -
A machine learning approach utilizing DNA methylation as an accurate classifier of COVID-19 disease severity.
Bowler Scott et al. Scientific reports 2022 10 (1) 17480 -
An explainable model of host genetic interactions linked to COVID-19 severity
Onoja A, et al. Commun Biol, Oct 26, 2022. -
Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis.
Kelly Jenna N et al. Frontiers in immunology 2022 10 978824
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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