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Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Pathogen Genomics and Health Database|AMD Clips|PHGKB
Publication Date: Mar 16, 2023

Safety by design: Biosafety and biosecurity in the age of synthetic genomics.
Stefan A Hoffmann et al. iScience 2023 3 (3) 106165

Data pipelines in a public health emergency: The human in the machine.
Katy A M Gaythorpe et al. Epidemics 2023 3 100676

Sewage surveillance of antibiotic resistance holds both opportunities and challenges
Larsson DGJ, et al. Nat Rev Microbiol. 2023; 21:213–214.

A National Hepatitis C Elimination Program in the United States: A Historic Opportunity.
Rachael L Fleurence et al. JAMA 2023 3

Identifying animal viruses in humans
Warren CJ, Sawyer SL. Science, Mar 9, 2023.

Aerosolize this: Generation, collection, and analysis of aerosolized virus in laboratory settings.
Jessica A Belser et al. PLoS pathogens 2023 3 (3) e1011178 Brand

Toward a global virus genomic surveillance network.
Verity Hill et al. Cell host & microbe 2023 3


Palidis: fast discovery of novel insertion sequences.
Victoria R Carr et al. Microbial genomics 2023 3 (3)

Benchmarking machine learning robustness in Covid-19 genome sequence classification.
Sarwan Ali et al. Scientific reports 2023 3 (1) 4154


Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli.
Tracy H Hazen et al. Nature communications 2023 3 (1) 1400

Different Roles of Wild Boars and Livestock in Salmonella Transmission to Humans in Italy.
Luca Bolzoni et al. EcoHealth 2023 3

SARS-CoV-2 Exposure in Norway Rats (Rattus norvegicus) from New York City.
Yang Wang et al. mBio 2023 3 e0362122

Emergence and Persistent Dominance of SARS-CoV-2 Omicron BA.2.3.7 Variant, Taiwan.
Pei-Lan Shao et al. Emerging infectious diseases 2023 3 (4)

SARS-CoV-2 Omicron Replacement of Delta as Predominant Variant, Puerto Rico.
Gilberto A Santiago et al. Emerging infectious diseases 2023 3 (4)

Geographical origin of Plasmodium vivax in the Hainan Island, China: insights from mitochondrial genome.
Yuchun Li et al. Malaria journal 2023 3 (1) 84

Genomic analysis of Leishmania turanica strains from different regions of Central Asia.
Tatiana S Novozhilova et al. PLoS neglected tropical diseases 2023 3 (3) e0011145


Molecular surveillance reveals the emergence and dissemination of NDM-5-producing Escherichia coli high-risk clones in Germany, 2013 to 2019.
Jörg B Hans et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2023 3 (10)

Carbapenem-Resistant and ESBL-Producing Enterobacterales Emerging in Central Texas.
Jennifer K Parker et al. Infection and drug resistance 2023 3 1249-1261

The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China.
Qi Jiang et al. Microbiology spectrum 2023 3 e0399122

Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study.
Nazreen F Hadjirin et al. Microbial genomics 2023 3 (3)

Extended-Spectrum β-Lactamase Genes Traverse the Escherichia coli Populations of Intensive Care Unit Patients, Staff, and Environment.
Robert A Moran et al. Microbiology spectrum 2023 3 e0507422

Analysis of Corynebacterium silvaticum genomes from Portugal reveals a single cluster and a clade suggested to produce diphtheria toxin.
Marcus Vinicius Canario Viana et al. PeerJ 2023 3 e14895

The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection.
Hannah Goldswain et al. Genome biology 2023 3 (1) 47

Early computational detection of potential high-risk SARS-CoV-2 variants.
Karim Beguir et al. Computers in biology and medicine 2023 2 106618

Mpox respiratory transmission: the state of the evidence.
Amy Beeson et al. The Lancet. Microbe 2023 3 Brand

Molecular Markers of Sulfadoxine-Pyrimethamine Resistance in Samples from Children with Uncomplicated Plasmodium falciparum at Three Sites in Angola in 2019.
Stefano R Rosillo et al. Antimicrobial agents and chemotherapy 2023 3 e0160122 Brand


Single-cell pathogen diagnostics for combating antibiotic resistance
Li H, et al. Nat Rev Methods Primers, Feb 2, 2023.

Comparative Evaluation of Current Biochemical-, Sequencing-, and Proteomic-Based Identification Methods for the Streptococcus bovis Group.
Nicole E Putnam et al. Journal of clinical microbiology 2023 3 e0171222

Core genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing.
Linda Grillova et al. BMC infectious diseases 2023 3 (1) 157

Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort study.
Paul K Drain et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2023 3 105420

Sub genomic analysis of SARS-CoV-2 using short read amplicon-based sequencing.
Lian Chye Winston Koh et al. Frontiers in genetics 2023 3 1086865

Retrospective Screening of Clinical Samples for Monkeypox Virus DNA, California, USA, 2022.
Caitlin A Contag et al. Emerging infectious diseases 2023 3 (4)

Adeno-Associated Virus 2 and Human Adenovirus F41 in Wastewater during Outbreak of Severe Acute Hepatitis in Children, Ireland
Martin NA, et al. Emerg Infect Dis, Mar 15, 2023.

Toward waterborne protozoa detection using sensing technologies.
Sara Nemati et al. Frontiers in microbiology 2023 3 1118164

Molecular Surveillance of Malaria Using the PF AmpliSeq Custom Assay for Plasmodium falciparum Parasites from Dried Blood Spot DNA Isolates from Peru.
Johanna Helena Kattenberg et al. Bio-protocol 2023 3 (5) e4621


Forecasting the trajectory of the COVID-19 pandemic into 2023 under plausible variant and intervention scenarios: a global modelling study
Reiner R, et al. medRxiv, Mar 8, 2023.

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.
S Cotton et al. The Journal of hospital infection 2023 3 Brand

Coronavirus disease 2019 (COVID-19) outbreak on an in-patient medical unit associated with unrecognized exposures in common areas-Epidemiological and whole-genome sequencing investigation.
Dylan C Kain et al. Infection control and hospital epidemiology 2023 3 1-5 Brand

Public Health Response to Clusters of Rapid HIV Transmission Among Hispanic or Latino Gay, Bisexual, and Other Men Who Have Sex with Men - Metropolitan Atlanta, Georgia, 2021-2022.
Carlos Saldana et al. MMWR. Morbidity and mortality weekly report 2023 3 (10) 261-264 Brand

Phylodynamics and migration data help describe HIV transmission dynamics in internally displaced people who inject drugs in Ukraine.
Ganna Kovalenko et al. PNAS nexus 2023 3 (3) pgad008


Vaccine-derived poliovirus serotype 2 outbreaks and response in the Democratic Republic of the Congo, 2017-2021.
Mary M Alleman et al. Vaccine 2023 3 Brand Brand


MUC5AC genetic variation is associated with tuberculous meningitis CSF cytokine responses and mortality.
Michelle C Sabo et al. The Journal of infectious diseases 2023 2

An APOBEC3 Mutational Signature in the Genomes of Human-Infecting Orthopoxviruses.
Diego Forni et al. mSphere 2023 3 e0006223

Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites.
Debby Bogaert et al. Cell host & microbe 2023 3 (3) 447-460.e6

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 Weekly AMD Clips

Clips are selected weekly 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. CDC-authored articles are flagged. Items marked I&E address aspects of implementation or evaluation in clinical or public health practice.

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.