Advanced Molecular Detection Clips Content (Published on 07/18/2024)
NEWS
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BugSeq Wins BARDA Contract to Develop AI Tools for Metagenomic Pathogen Sequencing
GenomeWeb, Jul 12, 2024. -
Gates Foundation Awards Multiple Omics, Dx Grants in June
GenomeWeb, Jul 8, 2024. -
Meningococcal vaccines shown to be moderately effective against gonorrhea
Dall C. CIDRAP, Jul 9, 2024. -
Fossils of ancient chromosomes found for the first time in 52,000-year-old woolly mammoth skin
Prisco J. CNN, Jul 11, 2024. -
Pneumococcus Evolution, Spread Profiled With Genome Sequences, Mobile Phone Data
Anderson A. GenomeWeb, Jul 3, 2024. -
COVID Lung Proteome Provides Recovery, Convalescence Clues
GenomeWeb, Jul 9, 2024. -
Colorado reports avian flu infections in 5 people who culled sick poultry
Schnirring L. CIDRAP, Jul 15, 2024. -
Seven countries report more polio cases, including wild-type in Afghanistan
Schnirring L. CIDRAP, Jul 12, 2024. -
University of Florida Researchers Using NIH Grant to Develop CRISPR-Based HIV Self-Tests
Cima G. GenomeWeb, Jul 9, 2024. -
Autism Markers Detected in Cross-Kingdom Gut Microbiome Study
Anderson A. GenomeWeb, Jul 8, 2024.
CONCEPTS / COMMENTS
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Building genomic capacity for precision health in Africa.
Alhaji Olono et al. Nat Med 2024 7 -
Slow, difficult and expensive: How the lab supplies market is crippling African science
Mukhwana A, et al. Nat Index, Jul 2, 2024. -
Overcoming colonialism in pathogen genomics.
Senjuti Saha et al. Lancet Digit Health 2024 6 (7) e520-e525 -
Harnessing technology for infectious disease response in conflict zones: Challenges, innovations, and policy implications.
Okechukwu Paul-Chima Ugwu et al. Medicine (Baltimore) 2024 7 (28) e38834 -
Rapid pathogen surveillance: field-ready sequencing solutions.
Kirstyn Brunker et al. Nat Rev Genet 2024 4 -
Anticipating the Next Pandemic.
H Cody Meissner et al. N Engl J Med 2024 7 (3) 196-199 -
Innovative approaches for vaccine trials as a key component of pandemic preparedness - a white paper.
Ullrich Bethe et al. Infection 2024 7 -
Precision public health in the era of genomics and big data.
Megan C Roberts et al. Nat Med 2024 7
METHODS / TOOLS
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An overview of next generation sequencing strategies and genomics tools used for tuberculosis research.
Sushanta Deb et al. J Appl Microbiol 2024 7 -
e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology.
Peiyu Xu et al. bioRxiv 2024 7 -
A gold standard dataset and evaluation of methods for lineage abundance estimation from wastewater.
Jannatul Ferdous Moon et al. Sci Total Environ 2024 7 174515 -
GWarrange: a pre- and post- genome-wide association studies pipeline for detecting phenotype-associated genome rearrangement events.
Yi Ling Tam et al. Microb Genom 2024 7 (7) -
Optimization data for an ARTIC-/Illumina-based whole-genome sequencing protocol and pipeline for SARS-CoV-2 analysis.
Christian Bundschuh et al. Data Brief 2024 7 110607 -
Deepvirusclassifier: a deep learning tool for classifying SARS-CoV-2 based on viral subtypes within the coronaviridae family.
Karolayne S Azevedo et al. BMC Bioinformatics 2024 7 (1) 231 -
H5N1 avian influenza: tracking outbreaks with real-time epidemiological data.
Francesco Branda et al. Lancet Infect Dis 2024 7
EVOLUTION / ECOLOGY / POPULATIONS
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Geographical migration and fitness dynamics of Streptococcus pneumoniae.
Sophie Belman et al. Nature 2024 7 -
Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in Northeast Thailand.
Rathanin Seng et al. Nat Commun 2024 7 (1) 5699 -
Acinetobacter pittii: the emergence of a hospital-acquired pathogen analyzed from the genomic perspective.
Elena Bello-López et al. Front Microbiol 2024 7 1412775 -
Sustained transmission over two decades of a previously unrecognised MPT64 negative Mycobacterium tuberculosis strain in Queensland, Australia: a whole genome sequencing study.
Arnold Bainomugisa et al. Lancet Reg Health West Pac 2024 7 101105 -
Can genomics and meteorology predict outbreaks of legionellosis in urban settings?
Verlaine J Timms et al. Appl Environ Microbiol 2024 7 e0065824 -
Evolution and host-specific adaptation of Pseudomonas aeruginosa.
Aaron Weimann et al. Science 2024 7 (6704) eadi0908 -
Dispersal history of SARS-CoV-2 in Galicia, Spain.
Pilar Gallego-García et al. J Med Virol 2024 6 (7) e29773 -
Dispersal history of SARS-CoV-2 variants Alpha, Delta, and Omicron (BA.1) in Spain.
Pilar Gallego-García et al. medRxiv 2024 7 -
Emergence and fixation of SARS-CoV-2 minority variants in a chronically infected patient receiving therapy in Denmark.
Jannik Fonager et al. APMIS 2024 7 -
Genomic Characterization of Highly Pathogenic Avian Influenza A H5N1 Virus Newly Emerged in Dairy Cattle.
Xiao Hu et al. Emerg Microbes Infect 2024 7 2380421 -
The origin and spread of HIV-1 CRF59_01B epidemic in China: A molecular network and phylogeographic analysis.
Huanchang Yan et al. J Med Virol 2024 7 (7) e29799 -
Persistent Transmission of Circulating Vaccine-Derived Poliovirus - Somalia, January 2017-March 2024.
Amalia Mendes et al. MMWR Morb Mortal Wkly Rep 2024 6 (25) 575-580 -
Human Rotaviruses of Multiple Genotypes Acquire Conserved VP4 Mutations during Serial Passage.
Maximilian H Carter et al. Viruses 2024 6 (6) -
ICTV Virus Taxonomy Profile: Phasmaviridae 2024.
Jens H Kuhn et al. J Gen Virol 2024 7 (7) -
Identifying the strains of dengue circulating in the western province of Sri Lanka during 2019-2022.
Harshi Abeygoonawardena et al. PLOS Glob Public Health 2024 7 (7) e0003150 -
Avian influenza viruses in wild birds in Canada following incursions of highly pathogenic H5N1 virus from Eurasia in 2021-2022.
Jolene A Giacinti et al. mBio 2024 7 e0320323 -
Detection and characterisation of a sixth Candida auris clade in Singapore: a genomic and phenotypic study.
Chayaporn Suphavilai et al. Lancet Microbe 2024 7 -
Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon.
Luis Cabrera-Sosa et al. Sci Rep 2024 7 (1) 16291 -
Plasmodium vivax populations in the western Greater Mekong Subregion evaluated using a genetic barcode.
Yubing Hu et al. PLoS Negl Trop Dis 2024 7 (7) e0012299
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Temporal evolution of bacterial species and their antimicrobial resistance characteristics in wound infections of war-related injuries in Ukraine from 2014 to 2023.
Valentine Kovalchuk et al. J Hosp Infect 2024 7 -
Clonal expansion of Tn1546-like transposon-carrying vancomycin-resistant Enterococcus faecium, a nationwide study in Taiwan, 2004-2018.
Ying-Chi Huang et al. J Glob Antimicrob Resist 2024 7 -
Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study.
Zoe A Dyson et al. Lancet Microbe 2024 7 -
Clinical and genomic features of Mycobacterium avium complex: a multi-national European study.
Nils Wetzstein et al. Genome Med 2024 7 (1) 86 -
Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan.
Tamim Khawaja et al. Nat Commun 2024 6 (1) 5196 -
Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species.
Edson Machado et al. Microb Genom 2024 7 (7) -
Spike deep mutational scanning helps predict success of SARS-CoV-2 clades.
Bernadeta Dadonaite et al. Nature 2024 7 (8021) 617-626 -
Genotypic Analysis of Transmitted and Acquired HIV Drug Resistance in People Living with HIV/AIDS in Surabaya, Indonesia, from 2018 to 2019.
Brian Eka Rachman et al. Acta Med Indones 2024 7 (2) 168-175 -
Two decades of molecular surveillance in Senegal reveal rapid changes in known drug resistance mutations over time.
Yaye D Ndiaye et al. Malar J 2024 7 (1) 205 -
Key gene modules and hub genes associated with pyrethroid and organophosphate resistance in Anopheles mosquitoes: a systems biology approach.
Cynthia Awuor Odhiambo et al. BMC Genomics 2024 7 (1) 665 -
Parallel evolution in mosquito vectors - a duplicated esterase locus is associated with resistance to pirimiphos-methyl in An. gambiae.
Sanjay C Nagi et al. Mol Biol Evol 2024 7
DETECTION / DIAGNOSIS
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Comparison of Bordetella species identification among differing rt-PCR assays in the United States.
Matthew Cole et al. Microbiol Spectr 2024 7 e0078324 -
Development and implementation of a core genome multilocus sequence typing scheme for Yersinia enterocolitica: a tool for surveillance and outbreak detection.
Joao Pires et al. J Clin Microbiol 2024 7 e0004024 -
Molecular methods enhance the detection of pyoderma-related Streptococcus pyogenes and emm-type distribution in children.
Jennifer N Hall et al. J Infect Dis 2024 7 -
National-scale antimicrobial resistance surveillance in wastewater: A comparative analysis of HT qPCR and metagenomic approaches.
Margaret E Knight et al. Water Res 2024 7 121989 -
Highly sensitive wastewater surveillance of SARS-CoV-2 variants by targeted next-generation amplicon sequencing provides early warning of incursion in Victoria, Australia.
James E Merrett et al. Appl Environ Microbiol 2024 7 e0149723 -
Genomic epidemiology of SARS-CoV-2 in Senegal in 2020-2021.
Adjiratou Aissatou Ba et al. J Infect Dev Ctries 2024 7 (6) 851-861 -
South Asia's COVID-19 History and Surveillance: Updated Epidemiological Assessment.
Lori Ann Post et al. JMIR Public Health Surveill 2024 7 -
Central Asian Surveillance Metrics and History of the COVID-19 Pandemic: Longitudinal Analyses.
Alexander Lundberg et al. JMIR Public Health Surveill 2024 7 -
Sub-Saharan Africa Surveillance Metrics and History of the COVID-19 Pandemic: Updated Epidemiological Assessment.
Alexander Lundberg et al. JMIR Public Health Surveill 2024 7 -
SARS-CoV-2 genomic surveillance of migrants arriving to Europe through the Mediterranean routes.
Fabio Tramuto et al. J Glob Health 2024 7 05017 -
KCL TEST: an open-source inspired asymptomatic SARS-CoV-2 surveillance programme in an academic institution.
Joana Reis de Andrade et al. Biol Methods Protoc 2024 7 (1) bpae046 -
Detection and characterization of H5N1 HPAIV in environmental samples from a dairy farm.
Gagandeep Singh et al. Virus Genes 2024 7 -
Next-generation sequencing technology reveals the viruses carried by poultry in the live poultry market of Guangdong, China.
Yang Zhou et al. Vet Microbiol 2024 6 110136 -
Predicting novel mosquito-associated viruses from metatranscriptomic dark matter.
Amanda Araújo Serrão de Andrade et al. NAR Genom Bioinform 2024 7 (3) lqae077 -
Molecular epidemiology of enteroviruses from Guatemalan wastewater isolated from human lung fibroblasts.
Leanna Sayyad et al. PLoS One 2024 7 (7) e0305108 -
A simple and sensitive test for Candida auris colonization, surveillance, and infection control suitable for near patient use.
Sukalyani Banik et al. J Clin Microbiol 2024 6 (7) e0052524 -
Plasmodium vivax genomic surveillance in the Peruvian Amazon with Pv AmpliSeq assay.
Johanna Helena Kattenberg et al. PLoS Negl Trop Dis 2024 7 (7) e0011879 -
Metagenomic next-generation sequencing promotes diagnosis and treatment of Pneumocystis jirovecii pneumonia in non-HIV infected children: a retrospective study.
Zhenyu Zhang et al. BMC Pulm Med 2024 7 (1) 338 -
Loop-Mediated Isothermal Amplification Assay to Detect Invasive Malaria Vector Anopheles stephensi Mosquitoes.
Cristina Rafferty et al. Emerg Infect Dis 2024 7 (9)
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Nosocomial transmission of tet(x3), bla and bla -carrying Acinetobacter baumannii conferring resistance to eravacycline and omadacycline, the Netherlands, March to August 2021.
Ditmer T Talsma et al. Euro Surveill 2024 7 (28) -
Transmission of Brucella canis in a canine kennel following introduction of an infected dog.
Heather Graham et al. Vet Microbiol 2024 7 110183 -
Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing.
Rhys T White et al. Microb Genom 2024 7 (7) -
Continued circulation of mpox: an epidemiological and phylogenetic assessment, European Region, 2023 to 2024.
Aisling M Vaughan et al. Euro Surveill 2024 7 (27) -
Genomic epidemiology and evolution of rhinovirus in western Washington State, 2021-22.
Stephanie Goya et al. J Infect Dis 2024 7 -
Sources of Human Immunodeficiency Virus Infections Among Men Who Have Sex With Men With a Migration Background: A Viral Phylogenetic Case Study in Amsterdam, The Netherlands.
Alexandra Blenkinsop et al. J Infect Dis 2024 7 -
Sustained human outbreak of a new MPXV clade I lineage in eastern Democratic Republic of the Congo.
Emmanuel Hasivirwe Vakaniaki et al. Nat Med 2024 6
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Hepatitis C virus diversity and treatment outcomes in Benin: a prospective cohort study.
Lucrèce Ahovègbé et al. Lancet Microbe 2024 6 (7) 697-706 -
Identification of neutralizing antibodies against monkeypox virus using high-throughput sequencing of A35H3LB cells from patients with convalescent monkeypox.
Ruitian Hou et al. Virus Res 2024 7 199437 -
Fecal microbiota transplantation alters gut phage communities in a clinical trial for obesity.
Michele Zuppi et al. Microbiome 2024 7 (1) 122 -
Diversity and selection analyses identify transmission-blocking antigens as the optimal vaccine candidates in Plasmodium falciparum.
Ilinca I Ciubotariu et al. EBioMedicine 2024 7 105227
HOST-MICROBE INTERACTIONS
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The effect of cesarean delivery on the neonatal gut microbiome in an under-resourced population in the Bronx, NY, USA.
Sandra E Reznik et al. BMC Pediatr 2024 7 (1) 450 -
Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics.
Sophie M Leech et al. Microb Genom 2024 7 (7) -
Multikingdom and functional gut microbiota markers for autism spectrum disorder.
Qi Su et al. Nat Microbiol 2024 7 -
The gut-airway microbiome axis in health and respiratory diseases.
Mustafa Özçam et al. Nat Rev Microbiol 2024 5 (8) 492-506 -
Unravelling the role of gut microbiota in acute pancreatitis: integrating Mendelian randomization with a nested case-control study.
Chang Qu et al. Front Microbiol 2024 7 1401056 -
Detection of Nucleocapsid Antibodies Associated with Primary SARS-CoV-2 Infection in Unvaccinated and Vaccinated Blood Donors.
Eduard Grebe et al. Emerg Infect Dis 2024 7 (8) -
Unveiling ecological/evolutionary insights in HIV viral load dynamics: Allowing random slopes to observe correlational changes to CpG-contents and other molecular and clinical predictors.
Rocío Carrasco-Hernández et al. Epidemics 2024 5 100770 -
Deep mutational scanning reveals functional constraints and antibody-escape potential of Lassa virus glycoprotein complex.
Caleb R Carr et al. Immunity 2024 7 -
Impact of HIV-1 genetic diversity on disease progression: a prospective cohort study in Guangxi.
Xianwu Pang et al. Front Cell Infect Microbiol 2024 7 1415123
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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:Sep 5, 2024