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Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Pathogen Genomics and Health Database|AMD Clips|PHGKB
Publication Date: Dec 1, 2022
NEWS

Happy Birthday, Omicron One year after the variant’s discovery, virologists are still scrambling to keep up with Omicron’s rapid evolution.
Zimmer C. New York Times, Nov 26, 2022.

mRNA revolutionized the race for a Covid-19 vaccine. Could cancer be next?
Wosen J. STAT, Nov 21, 2022.

Coronavirus variants are dodging antibody treatments. New lab-made options may help.
Johnson M. Washington Post, Nov 21, 2022.

Experimental flu vaccine, developed using mRNA, seen as potential game changer
Branswell H. STAT, Nov 24, 2022.

UCLA Team Uses Magnets, Microfluidics to Create Handheld Molecular Dx System
Ketchum K. GenomeWeb, Nov 18, 2022.

Mosquito blood meals reveal history of human infections
Mallapaty S. Nature, Nov 25, 2022.

Scientists Revive 48,500-Year-Old ‘Zombie Virus’ Buried in Ice
Wei LD. Bloomberg, Nov 29, 2022.



EVOLUTION / ECOLOGY / POPULATIONS

Genome Sequences of Hemolytic and Nonhemolytic Listeria innocua Strains from Human, Food, and Environmental Sources.
McIntosh Tori et al. Microbiology resource announcements 2022 11 e0072322 Brand

Retrospective molecular investigation of Mayaro and Oropouche viruses at the human-animal interface in West-central Brazil, 2016-2018.
Dias Helver Gonçalves et al. PloS one 2022 11 (11) e0277612 Brand

The first complete genome of the simian malaria parasite Plasmodium brasilianum.
Bajic Marko et al. Scientific reports 2022 11 (1) 19802 Brand


PATHOGENICITY / ANTIMICROBIAL RESISTANCE

Molecular mechanisms of antibiotic resistance revisited.
Darby Elizabeth M et al. Nature reviews. Microbiology 2022 11

An ancestral mycobacterial effector promotes dissemination of infection.
Saelens Joseph W et al. Cell 2022 11 (24) 4507-4525.e18

A Nationwide Plasmidome Surveillance in Thailand Reveals a Limited Variety of New Delhi Metallo-β-Lactamase-Producing Carbapenem-Resistant Enterobacteriaceae Clones and Spreading Plasmids.
Abe Ryuichiro et al. Journal of clinical microbiology 2022 11 e0108022

HIV-1 genetic diversity and transmitted drug resistance to integrase strand transfer inhibitors among recently diagnosed adults in Porto Alegre, South Brazil.
Nunes Cynara Carvalho et al. The Journal of antimicrobial chemotherapy 2022 10 (12) 3510-3514

High Level of Pretreatment and Acquired Human Immunodeficiency Virus Drug Resistance in El Salvador: A Nationally Representative Survey, 2018-2019.
Girón-Callejas Amalia et al. Open forum infectious diseases 2022 11 (11) ofac580 Brand Brand

Dual use of antifungals in medicine and agriculture: How do we help prevent resistance developing in human pathogens?
Verweij Paul E et al. Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy 2022 10 100885 Brand Brand


DETECTION / DIAGNOSIS

Multiplex PCR Assay for Clade Typing of Salmonella enterica Serovar Enteritidis.
Gallichan Sarah et al. Microbiology spectrum 2022 11 e0318222

Culture-Independent Genotyping Improves Surveillance of Neisseria gonorrhoeae, Especially in Oropharyngeal Samples, the Netherlands, 2017 to 2018.
Slaats Michiel H C et al. Pathogens (Basel, Switzerland) 2022 11 (11) Brand

Identification and characterization of mixed infections of Chlamydia trachomatis via high-throughput sequencing.
Zhao Jianhui et al. Frontiers in microbiology 2022 11 1041789

Culture-Independent Detection and Identification of Leptospira Serovars.
Matthias Michael A et al. Microbiology spectrum 2022 11 e0247522

Fecal indicators and antibiotic resistance genes exhibit diurnal trends in the Chattahoochee River: Implications for water quality monitoring.
Nguyen Karena H et al. Frontiers in microbiology 2022 11 1029176 Brand

Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories.
Mögling Ramona et al. Journal of clinical microbiology 2022 11 e0126122

Dynamics of SARS-CoV-2 variants characterized during different COVID-19 waves in Mali.
Koné Amadou et al. IJID Regions (Online) 2022 11

Wastewater genomic surveillance captures early detection of Omicron in Utah
Gupta P, et al. medRxiv, Nov 29, 2022.

Wastewater monitoring in tourist cities as potential sentinel sites for near real-time dynamics of imported SARS-CoV-2 variants.
Sangsanont Jatuwat et al. The Science of the total environment 2022 11 160317

Added Value of Next Generation over Sanger Sequencing in Kenyan Youth with Extensive HIV-1 Drug Resistance.
Novitsky V et al. Microbiology spectrum 2022 11 e0345422

Monitoring monkeypox virus in saliva and air samples in Spain: a cross-sectional study.
Hernaez Bruno et al. The Lancet. Microbe 2022 11


EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

Competitive Transmission of Carbapenem-Resistant Klebsiella pneumoniae in a Newly Opened Intensive Care Unit.
Hu Ya et al. mSystems 2022 11 e0079922

A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings.
Thorpe Harry A et al. Nature microbiology 2022 11 (12) 2054-2067

Global Expansion of SARS-CoV-2 Variants of Concern: Dispersal Patterns and Influence of Air Travel.
Tegally Houriiyah et al. medRxiv : the preprint server for health sciences 2022 12

Tracing the First Days of the SARS-CoV-2 Pandemic in Greece and the Role of the First Imported Group of Travelers.
Bousali Maria et al. Microbiology spectrum 2022 11 e0213422

Lessons learned: use of WGS in real-time investigation of suspected intrahospital SARS-CoV-2 outbreaks.
Berggreen H et al. The Journal of hospital infection 2022 11 81-88


ANTIMICROBIALS / VACCINES / INTERVENTIONS

A multivalent nucleoside-modified mRNA vaccine against all known influenza virus subtypes.
Arevalo Claudia P et al. Science (New York, N.Y.) 2022 11 (6622) 899-904



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.

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