Advanced Molecular Detection Clips Content (Published on 06/01/2023)
NEWS
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Innovations in Diagnosing Antimicrobial Drug Resistance
Gupte R. Today's Clinical Lab, May 5, 2023. -
Sequencing Study Reveals Oldest Plague Cases in Britain
GenomeWeb, May 30, 2023. -
GA4GH refreshes its strategic plan
Global Alliance for Genomics and Health (GA4GH), May 24, 2023. -
Tally of covid-19 cases after CDC conference climbs to 181
Sun LH. Washington Post, May 26, 2023. -
The COVID-19 virus mutated to outsmart key antibody treatments. Better ones are coming
Service RF. Science, May 24, 2023. -
US will vaccinate birds against avian flu for first time — what researchers think
Kozlov M. Nature, May 26, 2023. -
Canada reports first H5N5 avian flu in a mammal; US reports more H5N1 in animals
Schnirring L. CIDRAP, May 30, 2023. -
Enterovirus Infection - France
WHO, May 31, 2023. -
In China, an Unseen and Dangerous Foe Takes Root: Lethal Fungi
Pasha L. Sixth Tone, May 15, 2023. -
CRISPR-based phage therapy shows promise in first human trial
Dall C. CIDRAP, May 31, 2023.
CONCEPTS / COMMENTS
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The importance of equally accessible genomic surveillance in the age of pandemics.
Safia Zeghbib et al. Biol Futur 2023 5 1-9 -
Why the world needs more transparency on the origins of novel pathogens
Venter M. Nature, May 30, 2023. -
A pan-African pathogen genomics data sharing platform to support disease outbreaks
Christoffels A, et al. Nat Med, May 9, 2023. -
Editorial: Infectious Disease Surveillance Using Artificial Intelligence (AI) and its Role in Epidemic and Pandemic Preparedness.
Dinah V Parums et al. Med Sci Monit 2023 6 e941209 -
Wastewater monitoring can anchor global disease surveillance systems.
Aparna Keshaviah et al. Lancet Glob Health 2023 5 (6) e976-e981 -
Toward Rapid and Accurate Molecular Diagnostics at Home.
Wenpeng Liu et al. Adv Mater 2022 11 (21) e2206525
METHODS / TOOLS
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minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data.
Kian Soon Hoon et al. PeerJ 2023 5 e15339 -
Challenges in prokaryote pangenomics.
Gerry Tonkin-Hill et al. Microb Genom 2023 5 (5) -
Long read genome assemblers struggle with small plasmids.
Jared Johnson et al. Microb Genom 2023 5 (5) -
Management and analysis of high-throughput sequence data for infectious animal diseases.
R J Ellis et al. Rev Sci Tech 2023 5 103-110 -
FAIR in action - a flexible framework to guide FAIRification.
Danielle Welter et al. Sci Data 2023 5 (1) 291 -
PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny.
Alexey Markin et al. Syst Biol 2023 5 -
NCTC3000: a century of bacterial strain collecting leads to a rich genomic data resource.
Jo Dicks et al. Microb Genom 2023 5 (5) -
Unsupervised machine learning framework for discriminating major variants of concern during COVID-19.
Rohitash Chandra et al. PLoS One 2023 5 (5) e0285719 -
Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for more efficient mitigation strategies.
Leonidas Salichos et al. Sci Rep 2023 5 (1) 8470 -
Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations.
Alexander M Kramer et al. Syst Biol 2023 5 -
Genome entropy and network centrality contrast exploration and exploitation in evolution of foodborne pathogens.
Sheryl Le Chang et al. Phys Biol 2023 5 -
Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing.
Ingra M Claro et al. Wellcome Open Res 2023 5 241 -
Predictive analysis for pathogenicity classification of H5Nx avian influenza strains using machine learning techniques.
Akshay Chadha et al. Prev Vet Med 2023 5 105924 -
Multiplexable and Biocomputational Virus Detection by CRISPR-Cas9-Mediated Strand Displacement.
Rosa Márquez-Costa et al. Anal Chem 2023 5 -
Culture-Independent Workflow for Nanopore MinION-Based Sequencing of Influenza A Virus.
Mojnu Miah et al. Microbiol Spectr 2023 5 e0494622 -
A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay.
Lynn M Osikowicz et al. Ticks Tick Borne Dis 2023 5 (5) 102207 -
Genofunc: genome annotation and identification of genome features for automated pipelining analysis of virus whole genome sequences.
Xiaoyu Yu et al. BMC Bioinformatics 2023 5 (1) 218 -
GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach.
Budi Permana et al. BMC Bioinformatics 2023 5 (1) 209 -
A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings.
Louxin Zhang et al. Genome Res 2023 5 -
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance.
Xavier Didelot et al. Virus Evol 2023 5 (1) vead028 -
Epidemiological inference for emerging viruses using segregating sites.
Yeongseon Park et al. Nat Commun 2023 5 (1) 3105
EVOLUTION / ECOLOGY / POPULATIONS
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Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches.
Christina A Ahlstrom et al. Appl Environ Microbiol 2023 5 e0031923 -
The Gonococcal Genetic Island defines distinct sub-populations of Neisseria gonorrhoeae.
Madison A Youngblom et al. Microb Genom 2023 5 (5) -
Within-patient and global evolutionary dynamics of Klebsiella pneumoniae ST17.
Marit A K Hetland et al. Microb Genom 2023 5 (5) -
Yersinia pestis genomes reveal plague in Britain 4000 years ago
Swali P, et al. Nat Commun, May 30, 2023. -
Large genomic deletions delineate Mycobacterium tuberculosis L4 sublineages in South American countries.
Andres Baena et al. PLoS One 2023 5 (5) e0285417 -
Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study.
Francisco José Martínez-Martínez et al. Lancet Glob Health 2023 5 (6) e933-e941 -
Subregional origins of emerging SARS-CoV-2 variants during the second pandemic wave in Côte d'Ivoire.
Etilé A Anoh et al. Virus Genes 2023 3 (3) 370-376 -
Identification of evolutionary trajectories shared across human betacoronaviruses.
Marina Escalera-Zamudio et al. Genome Biol Evol 2023 5 -
Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages.
Kathleen Subramoney et al. Viruses 2023 5 (5) -
SARS-CoV-2 Omicron Specific Mutations Affecting Infectivity, Fusogenicity, and Partial TMPRSS2-Independency.
Romano Strobelt et al. Viruses 2023 5 (5) -
Temporal intra-host variability of mpox virus genomes in multiple body tissues.
Martina Rueca et al. J Med Virol 2023 5 (5) e28791 -
Novel Avian Influenza Virus (H5N1) Clade 2.3.4.4b Reassortants in Migratory Birds, China.
Jing Yang et al. Emerg Infect Dis 2023 5 (6) 1244-1249 -
Novel Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus in Wild Birds, South Korea.
Sun-Hak Lee et al. Emerg Infect Dis 2023 5 (7) -
Mapping the Dynamics of Contemporary PRRSV-2 Evolution and Its Emergence and Spreading Hotspots in the U.S. Using Phylogeography.
Nakarin Pamornchainavakul et al. Pathogens 2023 5 (5) -
The Evolution of Post-Vaccine G8P[4] Group a Rotavirus Strains in Rwanda; Notable Variance at the Neutralization Epitope Sites.
Peter N Mwangi et al. Pathogens 2023 5 (5) -
Spatial genetic structure of 2009 H1N1 pandemic influenza established as a result of interaction with human populations in mainland China.
Seungwon Kim et al. PLoS One 2023 5 (5) e0284716 -
Analysis of the diversity of tick-borne viruses at the border areas in Liaoning Province, China.
Yu Bai et al. Front Microbiol 2023 5 1179156 -
Rapid evolution of A(H5N1) influenza viruses after intercontinental spread to North America.
Ahmed Kandeil et al. Nat Commun 2023 5 (1) 3082 -
Extensive ITR expansion of the 2022 Mpox virus genome through gene duplication and gene loss.
Annika Brinkmann et al. Virus Genes 2023 5 -
Influenza A viruses in gulls in landfills and freshwater habitats in Minnesota, United States.
Elizabeth A Rasmussen et al. Front Genet 2023 5 1172048 -
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany.
Pauline Dianne Santos et al. Virus Evol 2023 5 (1) vead013 -
Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease.
Faith M Anderson et al. PLoS Biol 2023 5 (5) e3001822 -
Genomic variation during culture adaptation of genetically complex Plasmodium falciparum clinical isolates.
Antoine Claessens et al. Microb Genom 2023 5 (5) -
Molecular Screening of Echinococcus spp. and Other Cestodes in Wild Carnivores from Central Italy.
Silvia Crotti et al. Vet Sci 2023 5 (5)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Genome-Based Retrospective Analysis of a Providencia stuartii Outbreak in Rome, Italy: Broad Spectrum IncC Plasmids Spread the NDM Carbapenemase within the Hospital.
Valerio Capitani et al. Antibiotics (Basel) 2023 5 (5) -
Genomic surveillance of multidrug-resistant Klebsiella in Wales reveals persistent spread of Klebsiella pneumoniae ST307 and adaptive evolution of pOXA-48-like plasmids.
Sophia David et al. Microb Genom 2023 5 (5) -
Discovery of a novel sub-lineage of multi-drug resistant Shigella flexneri in Southern California.
Edwin Kamau et al. Int J Infect Dis 2023 3 1-3 -
O-Antigen Diversification Masks Identification of Highly Pathogenic Shiga Toxin-Producing Escherichia coli O104:H4-Like Strains.
Christina Lang et al. Microbiol Spectr 2023 5 e0098723 -
Antimicrobial resistance gene lack in tick-borne pathogenic bacteria.
Márton Papp et al. Sci Rep 2023 5 (1) 8167 -
Markers of epidemiological success of methicillin-resistant Staphylococcus aureus (MRSA) isolates in European populations.
Valérie O Baede et al. Clin Microbiol Infect 2023 5 -
Dissemination of Neisseria gonorrhoeae with decreased susceptibility to extended-spectrum cephalosporins in Southern China, 2021: a genome-wide surveillance from 20 cities.
Yiwen Liao et al. Ann Clin Microbiol Antimicrob 2023 5 (1) 39 -
Characterization of Carbapenemase producing Acinetobacter baumannii Isolates from Danish Patients 2014-2021 - Detection of a New International Clone - IC11.
Frank Hansen et al. Int J Antimicrob Agents 2023 5 106866 -
Isolation and Identification of Multidrug-Resistant Klebsiella pneumoniae Clones from the Hospital Environment.
María Guadalupe Córdova-Espinoza et al. Pathogens 2023 5 (5) -
Carbapenemase-producing Gram-negative bacteria in hospital wastewater, wastewater treatment plants and surface waters in a metropolitan area in Germany, 2020.
Markus Hoffmann et al. Sci Total Environ 2023 5 164179 -
Molecular epidemiology of enterically colonizing Escherichia coli with resistance against third-generation cephalosporins isolated from stool samples of European soldiers with concomitant diarrhea on deployment in Western African Mali.
Katharina Hoffmann et al. Front Microbiol 2023 5 1169829 -
A global survey of Salmonella plasmids and their associations with antimicrobial resistance.
James Robertson et al. Microb Genom 2023 5 (5) -
Evolution, persistence, and host adaption of a gonococcal AMR plasmid that emerged in the pre-antibiotic era.
Wearn-Xin Yee et al. PLoS Genet 2023 5 (5) e1010743 -
The role of plasmids in carbapenem resistant E. coli in Alameda County, California.
Nikolina Walas et al. BMC Microbiol 2023 5 (1) 147 -
Severe Acute Respiratory Syndrome Coronavirus 2 Delta Variant Genomic Variation Associated With Breakthrough Infection in Northern California: A Retrospective Cohort Study.
Jacek Skarbinski et al. J Infect Dis 2023 5 (7) 878-888 -
Evaluation of NS4A, NS4B, NS5 and 3'UTR Genetic Determinants of WNV Lineage 1 Virulence in Birds and Mammals.
Lise Fiacre et al. Viruses 2023 5 (5) -
Prevalence of Transmitted Drug Resistance among HIV-1 Patients in the Aegean Region: Results from the Western part of Turkey.
Ruchan Sertoz et al. Curr HIV Res 2023 5 -
Ex vivo RSA and pfkelch13 targeted-amplicon deep sequencing reveal parasites susceptibility to artemisinin in Senegal, 2017.
Mamadou Samb Yade et al. Malar J 2023 5 (1) 167 -
Identification of Trichomonas vaginalis 5-Nitroimidazole Resistance Targets.
Keonte J Graves et al. Pathogens 2023 5 (5)
DETECTION / DIAGNOSIS
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Detection of Severe Murine Typhus by Nanopore Targeted Sequencing, China.
Panpan Qian et al. Emerg Infect Dis 2023 5 (6) 1275-1277 -
Increased Incidence of Legionellosis after Improved Diagnostic Methods, New Zealand, 2000-2020.
Frances F Graham et al. Emerg Infect Dis 2023 5 (6) 1173-1182 -
Extensively Drug-Resistant Shigella flexneri 2a, California, USA, 2022.
J R Caldera et al. Emerg Infect Dis 2023 5 (7) -
Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat.
Michael S M Brouwer et al. J Antimicrob Chemother 2023 5 -
Highly sensitive detection of antimicrobial resistance genes in hospital wastewater using the multiplex hybrid capture target enrichment.
Hiroaki Baba et al. mSphere 2023 5 e0010023 -
Time required for nanopore whole genome sequencing of Neisseria gonorrhoeae for identification of phylogenetic relationships.
Laura T Phillips et al. J Infect Dis 2023 5 -
Genomic epidemiology of Staphylococcus aureus isolated from bloodstream infections in South America during 2019 supports regional surveillance.
Sabrina Di Gregorio et al. Microb Genom 2023 5 (5) -
Environmental DNA surveillance of biocontamination in a drinking water treatment plant.
Kyu-Young Shim et al. J Hazard Mater 2023 5 131656 -
Surveillance of carbapenem-resistant organisms using next-generation sequencing.
Katelin V Gali et al. Front Public Health 2023 5 1184045 -
No Isolate, No Problem: Using a Novel Insertion Sequence PCR to Link Rats to Human Shigellosis Cases in an Underserved Urban Community.
Gordon Ritchie et al. Microbiol Spectr 2023 5 e0477722 -
Diagnosis of protozoa diarrhoea in Campylobacter patients increases markedly with molecular techniques.
David T S Hayman et al. PLOS Glob Public Health 2023 5 (5) e0001527 -
Detection of Burkholderia pseudomallei with CRISPR-Cas12a based on specific sequence tags.
Jia-Xin Zhang et al. Front Public Health 2023 5 1153352 -
Fast and cost-effective SARS-CoV-2 variant detection using Oxford Nanopore full-length spike gene sequencing.
Cecilia Salazar et al. Microb Genom 2023 5 (5) -
Environmental genomic surveillance of SARS-CoV-2 in wastewater in Rio de Janeiro, Brazil.
Andressa S Gonçalves-Brito et al. J Water Health 2023 5 (5) 653-662 -
Wastewater monitoring for detection of public health markers during the COVID-19 pandemic: Near-source monitoring of schools in England over an academic year.
Francis Hassard et al. PLoS One 2023 5 (5) e0286259 -
Tracking the prevalence and emergence of SARS CoV2 variants of concern using a regional genomic surveillance program.
Ana Jung et al. medRxiv 2023 5 -
RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance.
Stephen R Stockdale et al. Lancet Reg Health Southeast Asia 2023 5 100205 -
First Round of External Quality Assessment Scheme for SARS-CoV-2 Laboratories During the COVID-19 Pandemic in Thailand.
Siriphan Saeng-Aroon et al. Health Secur 2023 5 -
Droplet digital recombinase polymerase amplification for multiplexed detection of human coronavirus.
Ji Wook Choi et al. Lab Chip 2023 4 (10) 2389-2398 -
Enhancing SARS-CoV-2 Surveillance through Regular Genomic Sequencing in Spain: The RELECOV Network.
Sonia Vázquez-Morón et al. Int J Mol Sci 2023 5 (10) -
Mpox virus detection in the wastewater and the number of hospitalized patients in the Poznan metropolitan area, Poland.
Monika Gazecka et al. Int J Infect Dis 2023 5 75-77 -
Metagenomic sequencing, molecular characterization, and Bayesian phylogenetics of imported type 2 vaccine-derived poliovirus, Spain, 2021.
Maria Dolores Fernandez-Garcia et al. Front Cell Infect Microbiol 2023 5 1168355 -
Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa.
Ayodeji E Ogunbayo et al. J Med Virol 2023 5 (5) e28753 -
Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing.
Jonathan L Temte et al. PLOS Glob Public Health 2023 5 (5) e0001422 -
Monitoring viral genomic sequences in transfusion-transmitted viruses.
Daniel Candotti et al. Vox Sang 2023 6
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Multistate, Multiserotype Outbreak of Salmonella Infections Linked to Cashew Brie — United States, 2021
Lewis K, et al. MMWR, May 26, 2023. -
Transmission Dynamics of a Mycobacterium tuberculosis Complex Outbreak in an Indigenous Population in the Colombian Amazon Region.
Francy J Pérez-Llanos et al. Microbiol Spectr 2023 5 e0501322 -
Foodborne Outbreak of Extended Spectrum Beta-lactamase Producing Shigella sonnei Associated with Contaminated Spring Onions in the United Kingdom.
Claire Jenkins et al. J Food Prot 2023 4 (6) 100074 -
Highlighting extended-spectrum beta-lactamase-producing Klebsiella pneumoniae outbreak by routine genomic typing.
F Gravey et al. Heliyon 2023 5 (5) e16131 -
Transmission of Mycobacterium tuberculosis in schools: a molecular epidemiological study using whole-genome sequencing in Guangzhou, China.
Ying Lin et al. Front Public Health 2023 5 1156930 -
Evaluating the role of asymptomatic throat carriage of Streptococcus pyogenes in impetigo transmission in remote Aboriginal communities in Northern Territory, Australia: a retrospective genomic analysis.
Jake A Lacey et al. Lancet Microbe 2023 5 -
Whole-Genome Analysis of Bordetella pertussis MT27 Isolates from School-Associated Outbreaks: Single-Nucleotide Polymorphism Diversity and Threshold of the Outbreak Strains.
Kazunari Kamachi et al. Microbiol Spectr 2023 5 e0406522 -
Using Genomics To Investigate an Outbreak of Vancomycin-Resistant Enterococcus faecium ST78 at a Large Tertiary Hospital in Queensland.
Budi Permana et al. Microbiol Spectr 2023 5 e0420422 -
Genomic epidemiology of SARS-CoV-2 in Russia reveals recurring cross-border transmission throughout 2020.
Alina Matsvay et al. PLoS One 2023 5 (5) e0285664 -
Enterovirus D68 Outbreak in Children, Finland, August-September 2022.
Ville Peltola et al. Emerg Infect Dis 2023 5 (6) 1258-1261 -
Clustered Cases of Waterborne Hepatitis E Virus Infection, France.
Sébastien Lhomme et al. Viruses 2023 5 (5) -
Integrating contact tracing and whole-genome sequencing to track the elimination of dog-mediated rabies: an observational and genomic study.
Kennedy Lushasi et al. Elife 2023 5
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics.
Susan Hromada et al. PLoS Biol 2023 5 (5) e3002100 -
Advances in developing ACE2 derivatives against SARS-CoV-2.
Haoran Zhang et al. Lancet Microbe 2023 3 (5) e369-e378 -
A Web Tool to Estimate Baseline Anti-Spike Monoclonal Antibody Efficacy Based on Regional Genomic Surveillance.
Daniele Focosi et al. Viruses 2023 5 (5) -
Quantification of SARS-CoV-2 spike protein expression from mRNA vaccines using isotope dilution mass spectrometry.
William J H Sutton et al. Vaccine 2023 5 -
Development of a Multi-Epitope Universal mRNA Vaccine Candidate for Monkeypox, Smallpox, and Vaccinia Viruses: Design and In Silico Analyses.
Nino Rcheulishvili et al. Viruses 2023 5 (5)
HOST-MICROBE INTERACTIONS
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Severity Outcomes among Adult Patients with Primary Immunodeficiency and COVID-19 Seen in Emergency Departments, United States, April 2020-August 2021.
Emily Drzymalla et al. J Clin Med 2023 5 (10) -
SARS-CoV-2 Variants Show Different Host Cell Proteome Profiles With Delayed Immune Response Activation in Omicron-Infected Cells.
Melinda Metzler et al. Mol Cell Proteomics 2023 3 (5) 100537 -
GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.
Erola Pairo-Castineira et al. Nature 2023 5 (7962) 764-768
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:Mar 28, 2024
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