Advanced Molecular Detection Clips Content (Published on 03/30/2023)
NEWS
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New clues to pandemic's origin surface, causing uproar.
Jon Cohen et al. Science (New York, N.Y.) 2023 3 (6638) 1175-1176 -
COVID-origins report sparks debate over major genome hub GISAID
Mallapaty S. Nature, Mar 29, 2023. -
Cases of Marburg going unreported in Equatorial Guinea, WHO says
Branswell H. STAT, Mar 29, 2023. -
Gut bacteria in babies may predict type 1 diabetes in later life, study finds
McKie R. Guardian, Mar 26, 2023. -
White House Report Outlines Goals to Advance Genomic Research, Precision Therapy Development
GenomeWeb, Mar 24, 2023.
METHODS / TOOLS
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Inferring the heritability of bacterial traits in the era of machine learning.
T Tien Mai et al. Bioinformatics advances 2023 3 (1) vbad027 -
Reference-free phylogeny from sequencing data.
Petr Ryšavý et al. BioData mining 2023 3 (1) 13 -
Real-Time Nanopore Q20+ Sequencing Enables Extremely Fast and Accurate Core Genome MLST Typing and Democratizes Access to High-Resolution Bacterial Pathogen Surveillance.
Gabriel E Wagner et al. Journal of clinical microbiology 2023 3 e0163122 -
Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens.
Zachary R Stromberg et al. PLOS global public health 2023 3 (2) e0000207 -
The impact of sampling bias on viral phylogeographic reconstruction.
Pengyu Liu et al. PLOS global public health 2023 3 (9) e0000577 -
The K-mer antibiotic resistance gene variant analyzer (KARGVA).
Simone Marini et al. Frontiers in microbiology 2023 3 1060891 -
Genomics-informed outbreak investigations of SARS-CoV-2 using civet.
Áine O'Toole et al. PLOS global public health 2023 3 (12) e0000704 -
Implementation and Evaluation of the Clear Dx Platform for Sequencing SARS-CoV-2 Genomes in a Public Health Laboratory.
Arunachalam Ramaiah et al. Microbiology spectrum 2023 3 e0495722 -
A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses.
William T Harvey et al. PLoS computational biology 2023 3 (3) e1010885
EVOLUTION / ECOLOGY / POPULATIONS
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The genomic epidemiology of Escherichia albertii infecting humans and birds in Great Britain.
Rebecca J Bengtsson et al. Nature communications 2023 3 (1) 1707 -
The changing epidemiology of Neisseria gonorrhoeae genogroups and antimicrobial resistance in Queensland, Australia, 2010-15: a case series analysis of unique Neisseria gonorrhoeae isolates.
Lisa McHugh et al. Sexual health 2023 3 -
Holobiont Urbanism: sampling urban beehives reveals cities' metagenomes.
Elizabeth Hénaff et al. Environmental microbiome 2023 3 (1) 23 -
Genomic Characterization of Staphylococcus aureus in Wildlife.
Carmen Martínez-Seijas et al. Animals : an open access journal from MDPI 2023 3 (6) -
Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022.
Abay Sisay et al. Genes 2023 3 (3) -
SARS-CoV-2 Molecular Evolutionary Dynamics in the Greater Accra Region, Ghana.
Bright Adu et al. Emerging infectious diseases 2023 3 (4) 862-865 -
Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique.
Nalia Ismael et al. PLOS global public health 2023 3 (3) e0001593 -
H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks.
L Carnegie et al. Virus evolution 2023 3 (1) vead014 -
Molecular Tracking of the Origin of Vesicular Stomatitis Outbreaks in 2004 and 2018, Ecuador.
David Vasco-Julio et al. Veterinary sciences 2023 3 (3) -
Changing molecular epidemiology of Hepatitis A virus in Santiago, Chile from 2010 to 2021.
Jorge Levican et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2023 3 105428 -
Vector mapping and bloodmeal metabarcoding demonstrate risk of urban Chagas disease transmission in Caracas, Venezuela.
Maikell Segovia et al. PLoS neglected tropical diseases 2023 3 (3) e0010613
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Phylogenomic investigation of an outbreak of fluoroquinolone-resistant Salmonella enterica subsp. enterica serovar Paratyphi A in Phnom Penh, Cambodia.
Rutaiwan Dusadeepong et al. Microbial genomics 2023 3 (3) -
The COVID-19 Pandemic Sparked Off a Large-Scale Outbreak of Carbapenem-Resistant Acinetobacter baumannii from the Endemic Strains at an Italian Hospital.
Greta Petazzoni et al. Microbiology spectrum 2023 3 e0450522
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Allelic diversity uncovers protein domains contributing to the emergence of antimicrobial resistance.
Trudy-Ann Grant et al. PLoS genetics 2023 3 (3) e1010490 -
Travel-associated lineages and unique endemic antimicrobial-susceptible lineages of Neisseria gonorrhoeae predominate in Western Australia.
Barakat A Al Suwayyid et al. Microbial genomics 2023 3 (3) -
Perspective on the origin, resistance, and spread of the emerging human fungal pathogen Candida auris.
Cheshta Sharma et al. PLoS pathogens 2023 3 (3) e1011190
DETECTION / DIAGNOSIS
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MGIT-seq for the Identification of Nontuberculous Mycobacteria and Drug Resistance: a Prospective Study.
Kiyoharu Fukushima et al. Journal of clinical microbiology 2023 3 e0162622 -
Nanopore-based enrichment of antimicrobial resistance genes - a case-based study.
Adrian Viehweger et al. GigaByte (Hong Kong, China) 2023 3 gigabyte75 -
Emergence of Ehrlichiosis by a new tick-borne Ehrlichia species in China.
Miao Lu et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2023 3 -
Powassan Virus Infection Detected by Metagenomic Next-Generation Sequencing, Ohio, USA.
Marjorie Farrington et al. Emerging infectious diseases 2023 3 (4) 838-841
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Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods.
Julie A Shay et al. Environmental microbiome 2023 3 (1) 25 -
Combined Use of RT-qPCR and NGS for Identification and Surveillance of SARS-CoV-2 Variants of Concern in Residual Clinical Laboratory Samples in Miami-Dade County, Florida.
Yamina L Carattini et al. Viruses 2023 3 (3) -
Non-systematic reporting biases of the SARS-CoV-2 variant Mu could impact our understanding of the epidemiological dynamics of emerging variants.
Mary E Petrone et al. Genome biology and evolution 2023 3 -
Scalable RT-LAMP-based SARS-CoV-2 testing for infection surveillance with applications in pandemic preparedness.
Dan Lou et al. EMBO reports 2023 3 e57162 -
Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings.
Nikita S D Sahadeo et al. PLOS global public health 2023 3 (2) e0001455
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Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods.
Andrew W Bartlow et al. PLOS global public health 2023 3 (7) e0000811
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Adeno-Associated Virus 2 and Human Adenovirus F41 in Wastewater during Outbreak of Severe Acute Hepatitis in Children, Ireland.
Niamh A Martin et al. Emerging infectious diseases 2023 3 (4) 751-760 -
Pan-Yellow Fever Virus Detection and Lineage Assignment by Real-Time RT-PCR and Amplicon Sequencing.
Giovanni Faggioni et al. Journal of virological methods 2023 3 114717 -
Standardized evaluation of Zika nucleic acid tests used in clinical settings and blood screening.
Mars Stone et al. PLoS neglected tropical diseases 2023 3 (3) e0011157 -
High-Throughput Microsatellite Markers Development for Genetic Characterization of Emerging Sporothrix Species.
Luiza Chaves de Miranda Leonhardt Losada et al. Journal of fungi (Basel, Switzerland) 2023 3 (3) -
Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies.
Olivia A Pilling et al. PLoS pathogens 2023 3 (3) e1011230 -
MALDI-TOF: A new tool for the identification of Schistosoma cercariae and detection of hybrids.
Antoine Huguenin et al. PLoS neglected tropical diseases 2023 3 (3) e0010577
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Tuberculosis Outbreak in a State Prison System - Washington, 2021-2022.
Randy M Stalter et al. MMWR. Morbidity and mortality weekly report 2023 3 (12) 309-312
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A One Health approach revealed the long-term role of Mycobacterium caprae as the hidden cause of human tuberculosis in a region of Spain, 2003 to 2022.
Miguel Martínez-Lirola et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2023 3 (12) -
Sensitivity of National Healthcare Safety Network definitions to capture healthcare-associated transmission identified by whole-genome sequencing surveillance.
Alexander J Sundermann et al. Infection control and hospital epidemiology 2023 3 1-3
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Top-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas.
Zulema Udaondo et al. Microbiology spectrum 2023 3 e0490122 -
Combining viral genomics and clinical data to assess risk factors for severe COVID-19 (mortality, ICU admission, or intubation) amongst hospital patients in a large acute UK NHS hospital Trust.
Max Foxley-Marrable et al. PloS one 2023 3 (3) e0283447 -
Patient and ward related risk factors in a multi-ward nosocomial outbreak of COVID-19: Outbreak investigation and matched case-control study.
Jenine Leal et al. Antimicrobial resistance and infection control 2023 3 (1) 21 -
Investigation of an outbreak of COVID-19 among U.S. military personnel and beneficiaries stationed in the Republic of Korea, June-July 2021.
Shilpa Hakre et al. PLOS global public health 2023 3 (5) e0000236 -
On-demand, hospital-based, severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic epidemiology to support nosocomial outbreak investigations: A prospective molecular epidemiology study.
Patrick Benoit et al. Antimicrobial stewardship & healthcare epidemiology : ASHE 2023 3 (1) e45 -
Population-based SARS-CoV-2 whole genome sequencing and contact tracing during the COVID-19 pandemic in Switzerland.
Nanina Anderegg et al. The Journal of infectious diseases 2023 3 -
Spatial analysis of genetic clusters and epidemiologic factors related to wild poliovirus type 1 persistence in Afghanistan and Pakistan.
Amalia Mendes et al. PLOS global public health 2023 3 (6) e0000251
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One Health responses to prevent the occurrence of rabies due to attacks by a rabid stray dog.
Yuehong Wei et al. Veterinary medicine and science 2022 10 (2) 618-624
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The role of high-risk geographies in the perpetuation of the HIV epidemic in rural South Africa: A spatial molecular epidemiology study.
Diego F Cuadros et al. PLOS global public health 2023 3 (2) e0000105 -
A pseudo-outbreak of Cyberlindnera fabianii funguria: Implication from whole genome sequencing assay.
Xin Fan et al. Frontiers in cellular and infection microbiology 2023 3 1130645
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Fatal Human Rabies Infection with Suspected Host-mediated Failure of Post-Exposure Prophylaxis Following a Recognized Zoonotic Exposure-Minnesota, 2021.
Stacy M Holzbauer et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2023 3
HOST-MICROBE INTERACTIONS
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The forecasting power of the microbiome.
Sara Correa-Garcia et al. Trends in microbiology 2022 12 -
Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition.
Kayla A Carter et al. mSystems 2023 3 e0100322 -
New perspectives into the vaginal microbiome with systems biology.
Christina Y Lee et al. Trends in microbiology 2022 10 (4) 356-368 -
Environment pollutants exposure affects the endogenous activation of within-host Mycobacterium tuberculosis.
Bilin Tao et al. Environmental research 2023 3 115695 -
Allele-dependent interaction of LRRK2 and NOD2 in leprosy.
Monica Dallmann-Sauer et al. PLoS pathogens 2023 3 (3) e1011260 -
Association of Glucose-6-Phosphate Dehydrogenase Deficiency With Outcomes in US Veterans With COVID-19.
Sarah H Elsea et al. JAMA network open 2023 3 (3) e235626 -
COVID-19 and the Genetics of Inflammation.
Yasmeen Choudhri et al. Critical care medicine 2023 3 -
Helicobacter pylori, Homologous-Recombination Genes, and Gastric Cancer.
Yoshiaki Usui et al. The New England journal of medicine 2023 3 (13) 1181-1190 -
Evidence for virus-mediated oncogenesis in bladder cancers arising in solid organ transplant recipients.
Gabriel J Starrett et al. eLife 2023 3
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 the CDC Office of Genomics and Precision Public Health 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.
- Page last reviewed:Feb 1, 2023
- Page last updated:Sep 21, 2023
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