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Advanced Molecular Detection Clips Database|AMD Clips|Public Health Genomics and Precision Health Knowledge Base (PHGKB) PHGKB Horizon Scan > Advanced Molecular Detection Clips


Update Date: Feb 22, 2024


WEB RESOURCES / TRAINING

Turning sequencing into surveillance: Who, where, what, when, and why of samples
(blog post) Allen K. Applied and Genomic Epidemiology in Public Health, Feb 19, 2024.



CONCEPTS / COMMENTS

Genomics for Emerging Pathogen Identification and Monitoring: Prospects and Obstacles
Vashisht V, et al. BioMedInformatics. 2023;3(4):1145-1177.

Large language models for science and medicine.
Amalio Telenti et al. Eur J Clin Invest 2024 2 e14183

Project NexGen: Developing the Next Generation of COVID-19 Vaccines and Therapeutics to Respond to the Present and Prepare for the Future.
Kimberly A Hofmeyer et al. Clin Infect Dis 2024 2


METHODS / TOOLS

PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli.
Julian A Paganini et al. Microb Genom 2024 2 (2)

The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.
Ryan Cook et al. Microb Genom 2024 2 (2)

HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data.
Budi Permana et al. Microb Genom 2024 2 (2)

A novel synthetic nucleic acid mixture for quantification of microbes by mNGS.
Hailing Wanghu et al. Microb Genom 2024 2 (2)

Nanopore adaptive sampling effectively enriches bacterial plasmids.
Jens-Uwe Ulrich et al. mSystems 2024 2 e0094523

Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression.
Leo A Featherstone et al. Syst Biol 2024 2

Extracting, filtering and simulating cellular barcodes using CellBarcode tools.
Wenjie Sun et al. Nat Comput Sci 2024 2

ARGprofiler-a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets.
Hannah-Marie Martiny et al. Bioinformatics 2024 2

ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data.
Xiaokai Wang et al. Microb Genom 2024 2 (2)

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.
Nadim Rahman et al. Microb Genom 2024 2 (2) Brand

ViTAL: Vision TrAnsformer based low coverage SARS-CoV-2 lineage assignment.
Zuher Jahshan et al. Bioinformatics 2024 2

Inferring HIV transmission patterns from viral deep-sequence data via latent typed point processes.
Fan Bu et al. Biometrics 2024 2 (1)


EVOLUTION / ECOLOGY / POPULATIONS

Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment.
Poorvi Saini et al. mBio 2024 2 e0354523

The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies.
Samuel Lipworth et al. Nat Commun 2024 2 (1) 1612

Prevalence of persistent SARS-CoV-2 in a large community surveillance study.
Mahan Ghafari et al. Nature 2024 2

Whole Genome Sequencing of DENV-2 isolated from Aedes aegypti mosquitoes in Esmeraldas, Ecuador. Genomic epidemiology of genotype III Southern Asian-American in the country.
Andrés Carrazco-Montalvo et al. bioRxiv 2024 2

The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time.
Aniqa Shahid et al. J Virol 2024 1 (2) e0165523

Contemporary and historical human migration patterns shape hepatitis B virus diversity.
Barney I Potter et al. Virus Evol 2024 2 (1) veae009

Geographic characteristics of HTLV-1 molecular subgroups and genetic substitutions in East Asia: Insights from complete genome sequencing of HTLV-1 strains isolated in Taiwan and Japan.
Satoshi Nozuma et al. PLoS Negl Trop Dis 2024 2 (2) e0011928

Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries.
Abebe A Fola et al. medRxiv 2024 2



DETECTION / DIAGNOSIS

Multicenter evaluation of BioCode GPP for syndromic molecular detection of gastrointestinal pathogens from stool specimens.
Colleen Knoth et al. J Clin Microbiol 2024 2 e0154523 Brand Brand

Simultaneous identification of DNA and RNA pathogens using metagenomic sequencing in cases of severe acute respiratory infection.
Nana Xie et al. J Med Virol 2024 2 (2) e29406

Comparative evaluation of the detection rate, workflow and associated costs of a multiplex PCR panel versus conventional methods in diagnosis of infectious gastroenteritis.
J Ambrosius-Eichner et al. J Med Microbiol 2024 2 (2) Brand

Systematic SARS-CoV-2 S-gene sequencing in wastewater samples enables early lineage detection and uncovers rare mutations in Portugal.
Ana C Reis et al. Sci Total Environ 2024 2 170961 Brand

Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria.
Jeremy V Camp et al. Front Mol Biosci 2024 2 1327699 Brand

Non-SARS-CoV-2 respiratory viral detection and whole genome sequencing from COVID-19 rapid antigen test devices: a laboratory evaluation study.
Michael A Moso et al. Lancet Microbe 2024 2

BA.2.86 variant emergence and spread dynamics through wastewater monitoring in Paris, France.
Sébastien Wurtzer et al. Sci Total Environ 2024 1 170355 Brand

Validation of the VirCapSeq-VERT system for differential diagnosis, detection, and surveillance of viral infections.
Vishal Kapoor et al. J Clin Microbiol 2023 12 (1) e0061223

Rapid detection of high consequence and emerging viral pathogens in pigs.
Alison C Neujahr et al. Front Vet Sci 2024 2 1341783

Validation of dried blood spots for capturing hepatitis C virus diversity for genomic surveillance.
Damien C Tully et al. J Viral Hepat 2024 2

Reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV) by SARS-CoV-2 in non-hospitalised HIV-infected patients.
Humaira Lambarey et al. EBioMedicine 2024 2 104986

Development of a novel mycobiome diagnostic for fungal infection.
Danielle Weaver et al. BMC Microbiol 2024 2 (1) 63

Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing.
Mariateresa de Cesare et al. Nat Commun 2024 2 (1) 1413

Enhancing Trypanosomatids Identification and Genotyping with Oxford Nanopore Sequencing: Development and Validation of an 18S rRNAs Amplicon-Based Method.
Lissa Cruz-Saavedra et al. J Mol Diagn 2024 2


EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

Coupled models of genomic surveillance and evolving pandemics with applications for timely public health interventions.
Baltazar Espinoza et al. Proc Natl Acad Sci U S A 2023 11 (48) e2305227120

Notes from the Field: Rapidly Linking an Outbreak of Salmonella Typhimurium Infections to Domestically Grown Cantaloupes Through Early Collaboration - United States, 2022.
Colin Schwensohn et al. MMWR Morb Mortal Wkly Rep 2024 2 (5) 114-115 Brand Brand

Health Department: Indiana | Iowa

Real-Time Genomic Epidemiologic Investigation of a Multispecies Plasmid-Associated Hospital Outbreak of NDM-5-Producing Enterobacterales Infections.
Nathan J Raabe et al. Int J Infect Dis 2024 2 Brand

Transmission of drug-resistant Mycobacterium tuberculosis isolates between Finnish- and foreign-born cases, 2014-2021: A molecular epidemiological study.
Jiahui Zhu et al. Tuberculosis (Edinb) 2024 2 102492

Sexual transmission of urogenital bacteria: whole metagenome sequencing evidence from a sexual network study.
Kayla A Carter et al. mSphere 2024 2 e0003024

Detecting, mapping, and suppressing the spread of a decade-long Pseudomonas aeruginosa nosocomial outbreak with genomics
Stribling W, et al. eLife, Feb 13, 2024. Brand

Transmission dynamics of drug-resistant tuberculosis in Ningbo, China: an epidemiological and genomic analysis.
Yang Che et al. Front Cell Infect Microbiol 2024 2 1327477

Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 in a County Jail.
Timileyin Adediran et al. Open Forum Infect Dis 2024 2 (2) ofad675

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Household Transmission during the Omicron Era in Massachusetts: A Prospective, Case-Ascertained Study using Genomic Epidemiology.
Jaspreet Banga et al. medRxiv 2024 2

Hepatitis E outbreak in the health district of Bocaranga-Koui, Central African Republic, 2018-2019.
Marina Prisca de Marguerite Nombot-Yazenguet et al. BMC Infect Dis 2024 2 (1) 215


ANTIMICROBIALS / VACCINES / INTERVENTIONS

Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted.
Delphine Diana Acar et al. EBioMedicine 2024 1 104960

Nanobody engineering for SARS-CoV-2 neutralization and detection.
Liina Hannula et al. Microbiol Spectr 2024 2 e0419922

AGA Clinical Practice Guideline on Fecal Microbiota–Based Therapies for Select Gastrointestinal Diseases
Peery AF, et al. Gastroenterology, 2024:166(3):409-434. Brand



Note: Brand indicates that at least one CDC-affiliated author; Brand indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice.

About AMD Clips

Clips are selected from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in infectious disease public health surveillance, investigation, and development of new diagnostics and interventions. The collection is not comprehensive but aims to capture highlights, while surveying a wide range of topics.

Note:

  • Brand indicates that at least one CDC-affiliated author.
  • Brand indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice.
  • Health Department: identifies articles having authors affiliated with U.S. public health departments, either at the indicated state or its sub-jurisdictions (city, county); health departments in U.S. territories are labeled Other.

Disclaimer: Articles listed in the Public Health Knowledge Base are selected by the CDC Office of Public Health Genomics to provide current awareness of the literature and news. Inclusion in the update 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 update, 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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