Advanced Molecular Detection Clips Content (Published on 06/09/2022)
NEWS
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FDA Warns Labs About Illumina Sequencing Instrument Cybersecurity Vulnerability
GenomeWeb, Jun 2, 2022. -
Two new versions of Omicron are gaining ground in the U.S., according to C.D.C. estimates.
Anthes E. New York Times, Jun 8, 2022. -
Princeton-Led Group Develops Cas13 SARS-CoV-2 Assay for Point-of-Care Use
Petrone J. 360dx, May 31, 2022. -
Behind the high-tech COVID-19 tests you probably haven’t heard about
Song V. The Verge, Jun 3, 2022. -
CDC Wastewater Surveillance Shifts to Public Health Labs With Planned Digital PCR Pathogen Panels
Johnson M. GenomeWeb, Jun 3, 2022. -
Wastewater monitoring: how to strengthen and sustain an important public health tool
Keshaviah A, Diamond M. STAT, Jun 9, 2022. -
Nurses' Station Epicenter of One Hospital's COVID Outbreak
Walker M. MedPage Today, Jun 8, 2022. -
Moderna says Omicron-containing booster outperforms current vaccine
Herper M., STAT, Jun 8, 2022. -
Concern grows that human monkeypox outbreak will establish virus in animals outside Africa
Cohen J. Science, Jun 8, 2022. -
‘Testing bottleneck’ for monkeypox puts hope of containment at risk, experts warn
Joseph A, Branswell H. STAT, Jun 7, 2022. -
What the surprising mutations in the monkeypox virus could indicate about the new outbreak
Joseph A. STAT, Jun 2, 2022. -
Genetic data indicate at least two separate monkeypox outbreaks underway, suggesting wider spread
Branswell H. STAT, June 3, 2022. -
Monkeypox Spurs Test Development, Though Scope of Outbreak Remains Unclear
Johnson M. GenomeWeb, Jun 7, 2022.
EVENTS / TRAINING / WEB RESOURCES
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Answering public health questions with testing and sequencing strategies. Learn more with our second COG-Train course ‘From Swab to Server’
(blog post) COG-Train, May 18, 2022. -
outbreak.info: a standardized, open-source database of COVID-19 resources and epidemiology data
(database) Su A, Wu C, Andersen K. Scripps Research Institute, Updated Jun 3, 2022.
CONCEPTS / COMMENTS
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A Tale of Trial and Triumph: Molecular Diagnostics for Severe Acute Respiratory Coronavirus 2 Over the First Two Years of the Coronavirus Disease 2019 Pandemic.
Kanjilal Sanjat et al. Clinics in laboratory medicine 2022 5 (2) xiii-xv -
Immune memory to SARS-CoV-2 Omicron BA.1 breakthrough infections: To change the vaccine or not?
van Zelm Menno C et al. Science immunology 2022 6 eabq5901
METHODS / TOOLS
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Curation of the AMRFinderPlus databases: applications, functionality and impact.
Feldgarden Michael et al. Microbial genomics 2022 6 (6)
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Metagenomic pipeline for identifying co-infections among distinct SARS-CoV-2 variants of concern: study cases from Alpha to Omicron.
Molina-Mora Jose Arturo et al. Scientific reports 2022 6 (1) 9377 -
COVID-19 Variant Surveillance and Social Determinants in Central Massachusetts: Development Study.
Shi Qiming et al. JMIR formative research 2022 6 -
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Gangavarapu K, et al. medRxiv, Jun 7, 2022. -
MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris.
Bagal Ujwal R et al. Methods in molecular biology (Clifton, N.J.) 2022 6 215-228
EVOLUTION / ECOLOGY / POPULATIONS
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Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health.
Alikhan Nabil-Fareed et al. PLoS genetics 2022 6 (6) e1010174
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Complete genome sequences and genomic characterization of five plasmids harbored by environmentally persistent Cronobacter sakazakii strains ST83 H322 and ST64 GK1025B obtained from powdered infant formula manufacturing facilities.
Negrete Flavia J et al. Gut pathogens 2022 6 (1) 23 -
Epidemiologic and Genomic Analysis of the Severe Acute Respiratory Syndrome Coronavirus 2 Epidemic in the Nebraska Region of the United States, March 2020-2021.
Siedlik Jacob A et al. Frontiers in microbiology 2022 6 878342 -
Initial observations about putative APOBEC3 deaminase editing driving short-term evolution of MPXV since 2017
O'Toole A, Rambaut A. Virological, May 30, 2022.
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Antibiotic-resistant organisms establish reservoirs in new hospital built environments and are related to patient blood infection isolates.
Sukhum Kimberley V et al. Communications medicine 2022 6 62 -
The emergence of a multidrug resistant Salmonella Muenchen in Israel is associated with horizontal acquisition of the epidemic pESI plasmid.
Cohen Emiliano et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2022 6 -
Clinical outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) variant and BA.1/BA.1.1 or BA.2 subvariant infection in southern California.
Lewnard Joseph A et al. Nature medicine 2022 6 -
SARS-CoV-2 Omicron variants BA.1 and BA.2 both show similarly reduced disease severity of COVID-19 compared to Delta, Germany, 2021 to 2022.
Sievers Claudia et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2022 6 (22) -
Virological characteristics of the novel SARS-CoV-2 Omicron variants including BA.2.12.1, BA.4 and BA.5
Kimura I, et al. bioRxiv, May 26, 2022. -
Sotrovimab drives SARS-CoV-2 omicron variant evolution in immunocompromised patients.
Destras Grégory et al. The Lancet. Microbe 2022 5 -
Mutational analysis of SARS-CoV-2 variants of concern reveals key tradeoffs between receptor affinity and antibody escape.
Makowski Emily K et al. PLoS computational biology 2022 5 (5) e1010160 -
Detection of recombinant breakpoint in the genome of human enterovirus E11 strain associated with a fatal nosocomial outbreak.
Rueca Martina et al. Virology journal 2022 6 (1) 97
DETECTION / DIAGNOSIS
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Evaluating the potential of third generation metagenomic sequencing for the detection of BRD pathogens and genetic determinants of antimicrobial resistance in chronically ill feedlot cattle.
Freeman Claire N et al. BMC veterinary research 2022 6 (1) 211 -
Europe-wide expansion and eradication of multidrug-resistant Neisseria gonorrhoeae lineages: a genomic surveillance study.
Sánchez-Busó Leonor et al. The Lancet. Microbe 2022 6 (6) e452-e463
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Rapid Detection of Bacterial Pathogens and Antimicrobial Resistance Genes in Clinical Urine Samples With Urinary Tract Infection by Metagenomic Nanopore Sequencing.
Zhang Lei et al. Frontiers in microbiology 2022 6 858777 -
PVBase: A MALDI-TOF MS Database for Fast Identification and Characterization of Potentially Pathogenic Vibrio Species From Multiple Regions of China.
Liu Tingting et al. Frontiers in microbiology 2022 6 872825
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Novel Assays for Molecular Detection of Severe Acute Respiratory Syndrome Coronavirus 2.
Rodino Kyle G et al. Clinics in laboratory medicine 2022 5 (2) 299-307 -
Strategies for Scaling up SARS-CoV-2 Molecular Testing Capacity.
Das Sanchita et al. Clinics in laboratory medicine 2022 5 (2) 261-282 -
Low testing rates limit the ability of genomic surveillance programs to monitor SARS-CoV-2 variants: a mathematical modelling study.
Han Alvin X et al. medRxiv : the preprint server for health sciences 2022 6 -
Variant-driven early warning via unsupervised machine learning analysis of spike protein mutations for COVID-19.
de Hoffer Adele et al. Scientific reports 2022 6 (1) 9275 -
Approaches to Deployment of Molecular Testing for SARS-CoV-2 in Resource-Limited Settings.
Bandawe Gama et al. Clinics in laboratory medicine 2022 5 (2) 283-298 -
Making waves: Wastewater surveillance of SARS-CoV-2 in an endemic future.
Wu Fuqing et al. Water research 2022 5 118535 -
Development of a COVID-19 warning system for neighborhood-scale wastewater-based epidemiology in low incidence situations
Oh C, et al. medRxiv, Jun 8, 2022. -
Wastewater surveillance of SARS-CoV-2 in dormitories as a part of comprehensive university campus COVID-19 monitoring.
Lu Emily et al. Environmental research 2022 6 113580 -
RT-qPCR and ATOPlex sequencing for the sensitive detection of SARS-CoV-2 RNA for wastewater surveillance.
Ahmed Warish et al. Water research 2022 6 118621 -
Improved diagnostic and multiplex RT-qPCR for detecting rubella viral RNA.
Chen Min-Hsin et al. Journal of virological methods 2022 6 114555
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Environmental water surveillance for free-living amoeba in North India.
Krishnamoorthi Sivanantham et al. Indian journal of medical microbiology 2022 6
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Characterisation of Treponema pallidum lineages within the contemporary syphilis outbreak in Australia: a genomic epidemiological analysis.
Taouk Mona L et al. The Lancet. Microbe 2022 6 (6) e417-e426 -
Outbreak of Salmonella Newport linked to imported frozen cooked crayfish in dill brine, Sweden, July to November 2019.
Jansson Mörk Marie et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2022 6 (22)
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Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis
Sherry NL, et al. Lancet Regional Health - Western Pacific, 2022:100446
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Molecular Epidemiology and Genetic Relatedness of Clostridioides difficile Isolates in Pediatric Oncology and Transplant Patients using Whole Genome Sequencing.
Barbar Ruba et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 6 -
Intrahost evolution and forward transmission of a novel SARS-CoV-2 Omicron BA.1 subvariant
Gonzalez-Reiche AS, et al. medRxiv, May 27, 2022. -
Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2.
Huisman Jana S et al. Environmental health perspectives 2022 5 (5) 57011 -
Concordance of SARS-CoV-2 RNA in Aerosols From a Nurses Station and in Nurses and Patients During a Hospital Ward Outbreak.
Stern Rebecca A et al. JAMA network open 2022 6 (6) e2216176 -
One Million and Counting: Estimates of Deaths in the United States from Ancestral SARS-CoV-2 and Variants
Walker J, et al. medRxiv, Jun 2, 2022. -
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Outbreak at a College With High Coronavirus Disease 2019 (COVID-19) Vaccination Coverage-Connecticut, August 2021-September 2021.
Stephen M Bart et al. Clin Infect Dis 2022 6 (Suppl 2) S243-S250
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Monkeypox Outbreak — Nine States, May 2022
Minhaj FS, et al. MMWR, Jun 3, 2022.
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Long COVID after breakthrough SARS-CoV-2 infection.
Al-Aly Ziyad et al. Nature medicine 2022 5
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Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2.
Fang Zhenhao et al. Nature communications 2022 6 (1) 3250
HOST-MICROBE INTERACTIONS
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Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure.
Oelen Roy et al. Nature communications 2022 6 (1) 3267 -
The oral microbiome and breast cancer and non-malignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study.
Wu Zeni et al. International journal of cancer 2022 6 -
How human endogenous retroviruses interact with the microbiota in health and disease.
Dopkins Nicholas et al. Trends in microbiology 2022 6 -
Molecular Assessment of Staphylococcus Aureus Strains in STAT3 Hyper-IgE Syndrome Patients.
Schwierzeck Vera et al. Journal of clinical immunology 2022 6 -
Extended human papillomavirus genotyping to predict progression to high-grade cervical precancer: A prospective cohort study in the southeastern United States.
Bukowski Alexandra et al. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2022 6
indicates that at least one CDC-affiliated author; indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice. Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by Public Health Genomics Branch to provide current awareness of the scientific literature and news. Inclusion in the clips 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 Clips, 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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