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Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

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

Europe notes increase in NDM-5 E coli, an expanding superbug
Wappes J. CIDRAP, May 12, 2023.

European Move Project Aims to Deploy NGS, Smart Traps to Combat Vector-Borne Diseases
Petrone J. GenomeWeb, May 12, 2023.

Hospital Surveillance Sequencing Helps Link Cases to Nationwide Contaminated Eyedrop Outbreak
Zhang H. GenomeWeb, May 11, 2023.

New Hampshire U.S. News Health New Hampshire lab error incorrectly resulted in salad greens recall
AP, May 12, 2023.

SARS-CoV-2 rewires host chromatin
Du Toit A. Nat Microbiol, Apr 3, 2023.

As COVID-19 Emergency Ends, Bioinformaticians Look Back to Inform Future Pandemic Preparedness
Versel N. GenomeWeb, May 11, 2023.

As Covid Emergency Ends, Surveillance Shifts to the Sewers
Anthes E. New York Times, May 11, 2023.

The Latest COVID Variants Have a Surprising Feature in Common
Zhang S. Atlantic, May 10, 2023.

Brazil detects H5N1 avian flu in wild birds as USDA OKs vaccination for endangered condors
Schnirring L. CIDRAP, May 16, 2023.

Wastewater detections show mpox likely underestimated
Soucheray S. CIDRAP, May 16, 2023.


The Swiss Pathogen Surveillance Platform - towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata.
Aitana Neves et al. Microb Genom 2023 5 (5)

Inferring phylogenies from pandemic-scale genome datasets.
et al. Nat Genet 2023 4 (5) 734-735

ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences.
Rui Yin et al. J Biomed Inform 2023 5 104388

ViralConsensus: A fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data.
Niema Moshiri et al. Bioinformatics 2023 5

MpoxRadar: a worldwide MPXV genomic surveillance dashboard.
Ferdous Nasri et al. Nucleic Acids Res 2023 5

From components to communities: bringing network science to clustering for molecular epidemiology.
Molly Liu et al. Virus Evol 2023 5 (1) vead026


A lung-specific mutational signature enables inference of viral and bacterial respiratory niche.
Christopher Ruis et al. Microb Genom 2023 5 (5)

SARS-CoV-2 variant transition dynamics are associated with vaccination rates, number of co-circulating variants, and convalescent immunity.
Lauren J Beesley et al. EBioMedicine 2023 4 104534

Mumps resurgence in a highly vaccinated population: Insights gained from surveillance in Canada, 2002-2020.
Joanne Hiebert et al. Vaccine 2023 5

The emergence, impact, and evolution of human metapneumovirus variants from 2014 to 2021 in Spain.
Maria Piñana et al. J Infect 2023 5

Ecological interactions of sand flies, hosts, and Leishmania panamensis in an endemic area of cutaneous leishmaniasis in Colombia.
Laura Posada-López et al. PLoS Negl Trop Dis 2023 5 (5) e0011316

Climate change and vector-borne diseases: a multi-omics approach of temperature-induced changes in the mosquito.
Rachel Bellone et al. J Travel Med 2023 5

Multiomics Reveals Symbionts, Pathogens, and Tissue-Specific Microbiome of Blacklegged Ticks (Ixodes scapularis) from a Lyme Disease Hot Spot in Southeastern Ontario, Canada.
Amber R Paulson et al. Microbiol Spectr 2023 5 e0140423


Genomic analysis of 1710 surveillance-based Neisseria gonorrhoeae isolates from the USA in 2019 identifies predominant strain types and chromosomal antimicrobial-resistance determinants.
Jennifer L Reimche et al. Microb Genom 2023 5 (5)

The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage.
Ann E Snaith et al. Microb Genom 2023 5 (5)

The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate.
Farzana T Prity et al. Microb Genom 2023 5 (5)

Plasmid-mediated colistin resistance among human clinical Enterobacterales isolates: national surveillance in the Czech Republic.
Marketa Zelendova et al. Front Microbiol 2023 5 1147846

Rapid cross-border emergence of NDM-5-producing Escherichia coli in the European Union/European Economic Area, 2012 to June 2022.
Marius Linkevicius et al. Euro Surveill 2023 5 (19)

Genome-wide association study of hemolytic uremic syndrome causing Shiga toxin-producing Escherichia coli from Sweden, 1994-2018.
Andreas Matussek et al. Eur J Clin Microbiol Infect Dis 2023 4 (6) 771-779

Global distribution and genomic characteristics of tet(X)-positive Escherichia coli among humans, animals, and the environment.
Yan Li et al. Sci Total Environ 2023 5 164148

Emergence and evolution of drug-resistant Mycobacterium tuberculosis in eastern China: A six-year prospective study.
Luqi Wang et al. Genomics 2023 5 110640

Viral Genetic Determinants of Prolonged Respiratory Syncytial Virus Infection Among Infants in a Healthy Term Birth Cohort.
Dylan Lawless et al. J Infect Dis 2022 11 (10) 1194-1202

Genetic differences of dengue virus 2 in patients with distinct clinical outcome.
Beatriz de Carvalho Marques et al. Braz J Microbiol 2023 5

Recent increase in fluconazole-nonsusceptible Candida parapsilosis in a global surveillance with the expansion of the Erg11 Y132F genotype and a rapid detection method for this alteration.
Cory M Hubler et al. Diagn Microbiol Infect Dis 2023 5 (3) 115957


Molecular detection and genotype analysis of Kudoa septempunctata from food poisoning outbreaks in Korea.
Gyung-Hye Sung et al. Parasites Hosts Dis 2023 5 (1) 15-23

Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis.
Jörg Linde et al. BMC Genomics 2023 5 (1) 258 Brand

Molecular detection of Nocardia: development and application of a real-time PCR assay in sputum and bronchoalveolar lavage fluid samples.
Shuai Wang et al. Eur J Clin Microbiol Infect Dis 2023 5

Viable Norovirus Persistence in Water Microcosms.
Marlee Shaffer et al. Environ Sci Technol Lett 2023 5 (10) 851-855 Brand

Genomic Characterization of Mosquito Isolates of Chikungunya Virus (Outbreak Strains 2022) Using Next-Generation Sequencing.
Amol Nath et al. Vector Borne Zoonotic Dis 2023 5

Looking into sewage: how far can metagenomics help to detect human enteric viruses?
Julien Schaeffer et al. Front Microbiol 2023 5 1161674

Rapid detection of Nipah virus using the one-pot RPA-CRISPR/Cas13a assay.
Jing Miao et al. Virus Res 2023 5 199130

Point-of-Care Testing for Norovirus Typing Using CRISPR/Cas12a Combined with Reverse Transcription Recombinase Polymerase Amplification.
Tanfen Fang et al. Bioconjug Chem 2023 5


Multinational Outbreak of Listeria monocytogenes Infections Linked to Enoki Mushrooms Imported from the Republic of Korea 2016-2020.
Evelyn Pereira et al. J Food Prot 2023 5 100101 Brand Brand

Containment of a Verona Integron-Encoded Metallo-Beta-Lactamase-Producing Pseudomonas aeruginosa Outbreak Associated With an Acute Care Hospital Sink-Tennessee, 2018-2020.
Allison Chan et al. Open Forum Infect Dis 2023 5 (5) ofad194 Brand Brand

Social network and genomic analysis of an OXA-48 carbapenemase-producing Enterobacterales hospital ward outbreak in Ireland, 2018-2019.
Lisa Domegan et al. Infect Prev Pract 2023 5 (2) 100282

Carriage of Neisseria meningitidis among travelers attending the Hajj pilgrimage, circulating serogroups, sequence types and antimicrobial susceptibility: A multinational longitudinal cohort study.
Saber Yezli et al. Travel Med Infect Dis 2023 5 102581

Multistate Outbreak of Salmonella Thompson Infections Linked to Seafood Exposure - United States, 2021.
Ann Q Shen et al. MMWR Morb Mortal Wkly Rep 2023 5 (19) 513-516 Brand Brand

Outbreak report of SARS-CoV-2 infection by airborne transmission: Epidemiologic and molecular evidence.
María-Cristina Navas et al. Biomedica 2023 5 (1) 121-130


Development of a novel minigenome and recombinant VSV expressing Seoul hantavirus glycoprotein-based assays to identify anti-hantavirus therapeutics.
Punya Shrivastava-Ranjan et al. Antiviral Res 2023 5 105619 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 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.