Results 1 to 10 of about 3,479,520 (326)

Evolution of the orthopoxvirus core genome. [PDF]

Virus Res, 2023
Orthopoxviruses comprise several relevant pathogens, including the causative agent of smallpox and monkeypox virus. Analysis of orthopoxvirus genome evolution mainly focused on gene gains/losses. We instead analyzed core genes, which are conserved in all orthopoxviruses.
Molteni C, Forni D, Cagliani R, Mozzi A, Clerici M, Sironi M.   +5 more
europepmc   +6 more sources

Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST. [PDF]

Microb Genom, 2023
Core genome multilocus sequence typing (cgMLST) has gained in popularity for bacterial typing since whole-genome sequencing (WGS) has become affordable.
Biguenet A, Bordy A, Atchon A, Hocquet D, Valot B.   +4 more
europepmc   +2 more sources

Parsnp 2.0: scalable core-genome alignment for massive microbial datasets. [PDF]

Bioinformatics
Motivation Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, the process of identifying nucleotides across multiple genomes which share a common ancestor, is used as the
Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ.   +5 more
europepmc   +3 more sources

Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. [PDF]

Cell Rep, 2023
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown.
Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy AE, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett KD, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J.   +38 more
europepmc   +2 more sources

An evolutionary view of the Fusarium core genome. [PDF]

BMC Genomics
Fusarium , a member of the Ascomycota fungi, encompasses several pathogenic species significant to plants and animals. Some phytopathogenic species have received special attention due to their negative economic impact on the agricultural industry around ...
Gomez-Chavarria DA, Rua-Giraldo AL, Alzate JF.   +2 more
europepmc   +2 more sources

Core Genome Multilocus Sequence Typing Scheme for Improved Characterization and Epidemiological Surveillance of Pathogenic Brucella. [PDF]

J Clin Microbiol, 2022
Brucellosis poses a significant burden to human and animal health worldwide. Robust and harmonized molecular epidemiological approaches and population studies that include routine disease screening are needed to efficiently track the origin and spread of
Abdel-Glil MY, Thomas P, Brandt C, Melzer F, Subbaiyan A, Chaudhuri P, Harmsen D, Jolley KA, Janowicz A, Garofolo G, Neubauer H, Pletz MW.   +11 more
europepmc   +2 more sources

mOTUpan: a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation. [PDF]

NAR Genom Bioinform, 2022
Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome assembled genomes (MAGs) or single-cell assembled genomes (SAGs).
Buck M, Mehrshad M, Bertilsson S.
europepmc   +2 more sources

Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF [PDF]

mSystems, 2018
The robust ability of Enterococcus faecalis to survive outside the host and to spread via oral-fecal transmission and its high degree of intrinsic and acquired antimicrobial resistance all complicate the treatment of hospital-acquired enterococcal ...
Jennifer L. Dale, Kenneth B. Beckman, Julia L. E. Willett, Jennifer L. Nilson, Nagendra P. Palani, Joshua A. Baller, Adam Hauge, Daryl M. Gohl, Raymond Erickson, Dawn A. Manias, Michael J. Sadowsky, Gary M. Dunny   +11 more
openalex   +2 more sources

Whole Genome and Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analyses of Listeria monocytogenes Isolates Associated with an Outbreak Linked to Cheese, United States, 2013 [PDF]

Applied and Environmental Microbiology, 2017
Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative ...
Yi Chen, Yan Luo, Heather A. Carleton, Ruth Timme, David Melka, Tim Muruvanda, Charles Wang, George Kastanis, Lee S. Katz, Lauren Turner, Angela Fritzinger, Terence Moore, Robert Stones, Joseph Blankenship, Monique Salter, Mickey E. Parish, Thomas S. Hammack, Peter S. Evans, Cheryl L. Tarr, Marc W. Allard, Errol Strain, Eric W. Brown   +21 more
openalex   +2 more sources

Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing

PLoS ONE, 2017
Staphylococcus aureus is a leading cause of bacteremia in hospitalized patients. Whether or not S. aureus bacteremia (SAB) is associated with clonality, implicating potential nosocomial transmission, has not, however, been investigated.
Kyung Hwa Park, Kerryl E. Greenwood‐Quaintance, James R. Uhl, Scott A. Cunningham, Nicholas Chia, Patricio Jeraldo, Priya Sampathkumar, Heidi Nelson, Robin Patel   +8 more
openalex   +3 more sources