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Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Pathogen Genomics and Health Database|AMD Clips|PHGKB
Publication Date: Dec 8, 2022

METHODS / TOOLS

An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics.
Shen Jiaxian et al. Microbiome 2022 12 (1) 206 Brand

Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.
Zhao Chunyu et al. Current protocols 2022 12 (12) e604

Optimized conditions for Listeria, Salmonella and Escherichia whole genome sequencing using the Illumina iSeq100 platform with point-and-click bioinformatic analysis.
Alvarez Narvaez Sonsiray et al. PloS one 2022 11 (11) e0277659

Interpreting and de-noising genetically engineered barcodes in a DNA virus.
Blois Sylvain et al. PLoS computational biology 2022 11 (11) e1010131

Clinical characteristics of the host DNA-removed metagenomic next-generation sequencing technology for detecting SARS-CoV-2, revealing host local immune signaling and assisting genomic epidemiology.
Zhaoyang Sun et al. Frontiers in immunology 2022 12 1016440

Optimized phylogenetic clustering of HIV-1 sequence data for public health applications.
Chato Connor et al. PLoS computational biology 2022 11 (11) e1010745



PATHOGENICITY / ANTIMICROBIAL RESISTANCE

Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance.
Munk Patrick et al. Nature communications 2022 12 (1) 7251

Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes.
Rothman Jason A et al. Water research 2022 12 119421

Genomic landscape of prominent XDR Acinetobacter clonal complexes from Dhaka, Bangladesh.
Rahman Aura et al. BMC genomics 2022 12 (1) 802

Drug resistance in children and adolescents with HIV in Panama.
Ventosa-Cubillo Judit et al. The Journal of antimicrobial chemotherapy 2022 12

Genomic changes in Kaposi Sarcoma-associated Herpesvirus and their clinical correlates.
Santiago Jan Clement et al. PLoS pathogens 2022 11 (11) e1010524


DETECTION / DIAGNOSIS

Evaluation of molecular typing for national surveillance of invasive clinical Haemophilus influenzae isolates from Denmark.
Slotved Hans-Christian et al. Frontiers in microbiology 2022 12 1030242 Brand

Horizontal Gene Transfer and Loss of Serotype-Specific Genes in Listeria monocytogenes Can Lead to Incorrect Serotype Designations with a Commonly-Employed Molecular Serotyping Scheme.
Brown Phillip et al. Microbiology spectrum 2022 12 e0274522 Brand

Early Warning Surveillance for SARS-CoV-2 Omicron Variants, United Kingdom, November 2021-September 2022.
Foulkes Sarah et al. Emerging infectious diseases 2022 12 (1)

Subgenomic RNA Abundance Relative to Total Viral RNA Among Severe Acute Respiratory Syndrome Coronavirus 2 Variants.
Su Maxwell et al. Open forum infectious diseases 2022 12 (11) ofac619

A comparative analysis exposes an amplification delay distinctive to SARS-CoV-2 Omicron variants of clinical and public health relevance.
Brown K L et al. Emerging microbes & infections 2022 12 1-66

Genomic analysis of SARS-CoV-2 variants of concern circulating in Hawai'i to facilitate public-health policies.
Maison David P et al. PloS one 2022 12 (12) e0278287

Detection and molecular characterization of rabies virus isolates from humans in Cameroon.
Sowe Wobessi Jocelyne N et al. Diagnostic microbiology and infectious disease 2022 11 (1) 115834

Clinical Performance and Trends during the First Two Months of Monkeypox Virus PCR Testing at Two United States Reference Labs.
Lieberman Nicole A P et al. Journal of clinical microbiology 2022 11 e0137122

Multiple traces of monkeypox detected in non-sewered wastewater with sparse sampling from a densely populated metropolitan area in Asia.
Wannigama Dhammika Leshan et al. The Science of the total environment 2022 12 (Pt 1) 159816

A Practical Workflow for the Identification of Aspergillus, Fusarium, Mucorales by MALDI-TOF MS: Database, Medium, and Incubation Optimization.
Barker Kevin R et al. Journal of clinical microbiology 2022 11 e0103222

Surveillance of pfhrp2 and pfhrp3 gene deletions among symptomatic Plasmodium falciparum malaria patients in Central Vietnam.
Thang Ngo Duc et al. Malaria journal 2022 12 (1) 371


EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

Outbreak of Burkholderia stabilis Infections Associated with Contaminated Nonsterile, Multiuse Ultrasound Gel - 10 States, May-September 2021.
Hudson Matthew J et al. MMWR. Morbidity and mortality weekly report 2022 12 (48) 1517-1521 Brand

A geographic cluster of healthcare-associated carbapenemase-producing hypervirulent Klebsiella pneumoniae sequence type 23.
Brennan Caoimhe et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2022 12

Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission.
Goldstein Isaac H et al. PLoS computational biology 2022 12 (12) e1010696

Pattern of SARS-CoV-2 variant B.1.1.519 emergence in Alaska.
Haan Tracie J et al. Scientific reports 2022 11 (1) 20662

Analysis of two choir outbreaks acting in concert to characterize long- range transmission risks through SARS-CoV-2, Berlin, Germany, 2020.
Reichert Felix et al. PloS one 2022 11 (11) e0277699

Occupational Monkeypox Virus Transmission to Healthcare Worker, California, USA, 2022
Alarcon J, et al. Emerg Infect Dis, Jan 5, 2022.

Malaria outbreak in Laos driven by a selective sweep for Plasmodium falciparum kelch13 R539T mutants: a genetic epidemiology analysis.
Wasakul Varanya et al. The Lancet. Infectious diseases 2022 12


ANTIMICROBIALS / VACCINES / INTERVENTIONS

Low neutralization of SARS-CoV-2 Omicron BA.2.75.2, BQ.1.1, and XBB.1 by parental mRNA vaccine or a BA.5-bivalent booster.
Kurhade Chaitanya et al. Nature medicine 2022 12 Brand

Vaccination induces HIV broadly neutralizing antibody precursors in humans.
Leggat David J et al. Science (New York, N.Y.) 2022 12 (6623) eadd6502


HOST-MICROBE INTERACTIONS

SARS-CoV-2 viral load and shedding kinetics.
Puhach Olha et al. Nature reviews. Microbiology 2022 12

Pilot genome-wide association study of antibody response to inactivated SARS-CoV-2 vaccines.
Li Ping et al. Frontiers in immunology 2022 12 1054147

Infectious origin of Alzheimer's disease: Amyloid beta as a component of brain antimicrobial immunity.
Vojtechova Iveta et al. PLoS pathogens 2022 11 (11) e1010929


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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