Pathogen Advanced Molecular Detection Database|Archive|PHGKB

CONCEPTS / COMMENTS

Twelve quick tips for software design
Wilson G. PLoS Comput Biol, Feb 24, 2022.

METHODS / TOOLS

Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review.
Duault Hélène et al. Pathogens (Basel, Switzerland) 2022 2 (2)
VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data.
Wagner Darlene D et al. Microbiology spectrum 2022 3 e0256421
Covidex: An ultrafast and accurate tool for SARS-CoV-2 subtyping.
Cacciabue Marco et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2022 3 105261
Assessment of Inter-Laboratory Differences in SARS-CoV-2 Consensus Genome Assemblies between Public Health Laboratories in Australia.
Foster Charles S P et al. Viruses 2022 2 (2)
ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection.
Dezordi Filipe Zimmer et al. Viruses 2022 2 (2)

EVOLUTION / ECOLOGY / POPULATIONS

Molecular Typing of Ukrainian Bacillus anthracis Strains by Combining Whole-Genome Sequencing Techniques.

Brangsch Hanka et al. Microorganisms 2022 2 (2)
WHO Critical Priority Escherichia coli as One Health Challenge for a Post-Pandemic Scenario: Genomic Surveillance and Analysis of Current Trends in Brazil.

Fuga Bruna et al. Microbiology spectrum 2022 3 e0125621
Reoccurring bovine anthrax in Germany on the same pasture after 12 years.

Braun Peter et al. Journal of clinical microbiology 2022 2 jcm0229121
Evolutionary analysis of genomes of SARS-CoV-2-related bat viruses suggests old roots, constant effective population size, and possible increase of fitness

Kurpas MK, et al. bioRxiv, Mar 1, 2022.
Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemi

Nasimiyu C, et al. medRxiv, Feb 28, 2022.
Drivers of adaptive evolution during chronic SARS-CoV-2 infections

Harari S, et al. medRxiv, Feb 28, 2022.
Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology.

Henschel Andreas et al. PloS one 2022 3 (3) e0264682
Surveillance of SARS-CoV-2 in the environment and animal samples of the Huanan Seafood Market

Gao G, et al. Research Square, Feb 25, 2022.
Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E.

Ntumvi Nkom F et al. Virus evolution 2022 3 (1) veab110
Early emergence phase of SARS-CoV-2 Delta variant in Florida

Cella E, et al. medRxiv, Feb 22, 2022.
Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes.

Manuto Laura et al. Viruses 2022 2 (2)
Epidemiology and Genetic Analysis of SARS-CoV-2 in Myanmar during the Community Outbreaks in 2020.

Phyu Wint Wint et al. Viruses 2022 2 (2)
Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect?

Menasria Taha et al. Microorganisms 2022 2 (2)
Molecular Epidemiology of Rotavirus Strains in Symptomatic and Asymptomatic Children in Manhiça District, Southern Mozambique 2008-2019.

Manjate Filomena et al. Viruses 2022 1 (1)
Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti.

Coatsworth H et al. Molecular ecology 2022 3

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

Characterisation of atypical Shiga toxin gene sequences and description of Stx2j, a new subtype.
Gill Alexander et al. Journal of clinical microbiology 2022 2 jcm0222921
Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on bla Transmission.
Dong Huiyue et al. Microbiology spectrum 2022 2 e0215621
Comparative phylogenomics of ESBL-, AmpC- and carbapenemase-producing Klebsiella pneumoniae originating from companion animals and humans.
Garcia-Fierro Raquel et al. The Journal of antimicrobial chemotherapy 2022 2
Epidemiology and Antimicrobial Resistance Profiles of the Nocardia Species in China, 2009 to 2021.
Wang Hao et al. Microbiology spectrum 2022 3 e0156021

DETECTION / DIAGNOSIS

Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool.
Peterson Christy-Lynn et al. Microorganisms 2022 2 (2)
Proteomic Signatures of Antimicrobial Resistance in Yersinia pestis and Francisella tularensis.
Deatherage Kaiser Brooke L et al. Frontiers in medicine 2022 2 821071
Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing.
Marini Simone et al. Briefings in bioinformatics 2022 2
Detection and isolation of SARS-CoV-2 Eta variant from the international travelers and local residents of India.
Yadav Pragya D et al. Journal of medical virology 2022 2
Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant
Ciubotariu I, et al. medRxiv, Feb 28, 2022.
Active surveillance and early detection of community transmission of SARS-CoV-2 Mu variant (B.1.621) in the Brazilian Amazon.
Oliveira Gabriella Sgorlon et al. Journal of medical virology 2022 3
Molecular SARS-CoV-2 surveillance in Bavaria shows no Omicron transmission before the end of November 2021.
Flechsler Jennifer et al. Infection 2022 3
Pathogens that Cause Illness Clinically Indistinguishable from Lassa Fever, Nigeria, 2018.
Ashcroft Jonathan W et al. Emerging infectious diseases 2022 2 (5)

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

Genomic Analysis of Community Transmission Networks for MRSA Among Females Entering a Large Inner-city Jail.
Popovich Kyle J et al. Open forum infectious diseases 2022 2 (3) ofac049
Multistate Outbreak of Melioidosis Associated with Imported Aromatherapy Spray.
Gee Jay E et al. The New England journal of medicine 2022 3 (9) 861-868
SARS-CoV-2 Exposure Investigations Using Genomic Sequencing Among Healthcare Workers and Patients in A Large Academic Center.
Smith Leigh et al. Infection control and hospital epidemiology 2022 3 1-10
Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient.
Sabin Arick P et al. Diagnostic microbiology and infectious disease 2022 3 (1) 115656
Use of Serial Testing to Interrupt a SARS-CoV-2 Outbreak on a Hospital Medical Floor - Minnesota, October-December 2020.
Prabhu Rajesh M et al. Infection control and hospital epidemiology 2022 2 1-16
Probable Animal-to-Human Transmission of SARS-CoV-2 Delta Variant AY.127 Causing a Pet Shop-Related COVID-19 Outbreak in Hong Kong.
Chan Jasper Fuk-Woo et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 3
Autochthonous Outbreak of SARS-CoV-2 Omicron Variant in Booster-Vaccinated (3 Doses) Healthcare Workers in Southern Italy: Just the Tip of the Iceberg?
Loconsole Daniela et al. Vaccines 2022 2 (2)
Transmission of and Infection With COVID-19 Among Vaccinated and Unvaccinated Attendees of an Indoor Wedding Reception in Minnesota.
Wienkes Haley et al. JAMA network open 2022 2 (2) e220536
SARS-CoV-2 B.1.1.529 (Omicron) Variant Transmission Within Households--Four U.S. Jurisdictions, November 2021-February 2022
Baker JM, et al. MMWR, Feb 25, 2022.
Detecting Selection in the HIV-1 Genome during Sexual Transmission Events.
Seifert David et al. Viruses 2022 2 (2)
Increase in Hepatitis A Cases Linked to Imported Strains to Rio de Janeiro, Brazil: A Cross-Sectional Study.
Mello Vinicius M et al. Viruses 2022 2 (2)
Suspected Transmission of Severe Fever with Thrombocytopenia Syndrome Virus from a Cat to a Veterinarian by a Single Contact: A Case Report.
Miyauchi Atsushi et al. Viruses 2022 2 (2)
Using molecular epidemiology to trace the history of the injection-related HIV epidemic in New York City, 1985-2019.
Torian Lucia V et al. AIDS (London, England) 2022 2
Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial - BCPP/ Ya Tsie trial.
Magosi Lerato E et al. eLife 2022 3

ANTIMICROBIALS / VACCINES / INTERVENTIONS

mRNA-1273 and BNT162b2 mRNA vaccines have reduced neutralizing activity against the SARS-CoV-2 omicron variant.
Edara Venkata-Viswanadh et al. Cell reports. Medicine 2022 3 (2) 100529
Covid-19 Vaccine Effectiveness against the Omicron (B.1.1.529) Variant
Andrews N, et al. New Engl J Med, Mar 2, 2022.

HOST-MICROBE INTERACTIONS

Oral Microbiome Is Associated With Incident Hypertension Among Postmenopausal Women.
LaMonte Michael J et al. Journal of the American Heart Association 2022 3 e021930
The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications.
Bai Geng-Hao et al. Viruses 2022 2 (2)
Systematically assessing microbiome-disease associations identifies drivers of inconsistency in metagenomic research.
Tierney Braden T et al. PLoS biology 2022 3 (3) e3001556
Transcriptomic clustering of critically ill COVID-19 patients
Lopez-Martinez C, et al. medRxiv, Mar 2, 2022.

Note: 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.

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Advanced Molecular Detection Clips Content (Published on 03/03/2022)

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