core genome
The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers
... the core ge- nome phylogeny ...The core genome of each primary clade was aligned against all surveyed genomes (n ⫽ 1,130) to identify species- or clade-specific mark- ...of genome assembly ...
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Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome Wide Typing of Clostridium difficile
... A core genome gene was considered a “good target” only if all of the above-listed criteria were met, in which case the complete sequence was analyzed in comparison to the reference ...
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Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole Genome Sequence Based Typing of Listeria monocytogenes
... RefSeq genome sequences of ...42 genome sequences, including ...for core genome gene definition were fed into the MLST ⫹ target definer and resulted in 1,701 genes out of 2,867 genes of strain ...
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Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing
... of core and noncore genes in the LT2 ...of core genome size. The graph shows the descending trend of the core genome size of ...of core genes among different ...
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Hash Based Core Genome Multilocus Sequence Typing for Clostridium difficile
... to core genome multilocus sequence typing (cgMLST) in which alleles at each gene are reproducibly converted to a unique hash, or short string of letters ...a genome to 100,000 others took ⬍ 1 min ...
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Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade
... HTCC9565 genome is estimated to be from ⬍1 to ...HIMB114 genome is more difficult to estimate, a second recently sequenced subclade IIIa genome is complete at ...(mean genome size of 1.337 ⫾ ...
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A Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalis
... Whole- genome sequencing (WGS) enables unraveling of epidemiological linkages and puta- tive transmission events between humans, animals, and ...food. Core genome multilo- cus sequence typing ...
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Defining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus
... with core genome MLST (cgMLST) analysis as one of the most straightforward ways to explore complex genomic data in an epidemiological con- ...the genome of strain RIMD 2210633 as a reference (with a ...
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Importance of Core Genome Functions for an Extreme Antibiotic Resistance Trait
... Tobramycin-sensitive mutants of A. baumannii AB5075. We initially asked if there were functions other than the known modifying and efflux functions that contribute to the high-level tobramycin resistance of AB5075. To ...
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Using Core Genome Alignments To Assign Bacterial Species
... a core genome alignment from a larger subset of genomes, its use is limited to intraspecies comparisons (45), making it currently unamenable to this ...a core genome alignment from every ...
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Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome
... the genome assemblies were of good quality and therefore did not distort the outputs by applying a stringent quality control (QC) ...legitimate core genes being wrongly defined as accessory genes in our ...
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Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum
... study, core genome SNP typing and cgMLST performed equally in typing our samples and their results were similar, evidencing the validity of cgMLST to be used for ...over core genome SNP typing ...
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Core Genome Multilocus Sequence Typing Scheme for High Resolution Typing of Enterococcus faecium
... of genome-wide variation, thereby providing the optimal resolution to infer phy- logenetic relatedness, thus identifying possible, probable, or un- likely cases of epidemiological linkage of ...a ...
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Pathogenicity Locus, Core Genome, and Accessory Gene Contributions to Clostridium difficile Virulence
... similar core genome sequences were found to cause a range of disease severity in the host, suggesting that in vivo pathology is, at least in part, attributable to differences in noncore, accessory gene ...
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The applied development of a tiered multilocus sequence typing (MLST) scheme for Dichelobacter nodosus
... whole genome sequencing is scalable to incorporate core genome typing and whole genome typing, which provides some “future proofing” of the technique (Jolley and Maiden, ...
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Distinct Biological Potential of Streptococcus gordonii and Streptococcus sanguinis Revealed by Comparative Genome Analysis
... using core-genome Single Nucleotide Polymorphism (SNP) data, providing a more robust tree compared to the single gene ...the core-genome SNP-based tree ...the core-genome ...
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A genomic overview of the population structure of Salmonella
... accessory genome is extremely volatile due to the repeated acquisition and loss of mobile, selfish DNA within individual strains ...in core restriction sites. According to core genome SNPs, ...
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Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with infectious bovine keratoconjunctivitis versus the deep nasopharynx of asymptomatic cattle
... draft genome sequence of the type strain (ATCC BAA-1259) [6] was included in EDGAR calculations, with its existing annotation, along with the sequences generated in this ...other genome and the singleton ...
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A Novel Protective Vaccine Antigen from the Core Escherichia coli Genome
... A smaller subset of 3,042 genes present in more than 99% of strains in EcoDS was also defined. These genes were used to trace novel vaccinology strategies. In order to identify potential surface-exposed and secreted ...
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Whole genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals
... Figure 1. Phylogeography, recombination map and antibiotic resistance distribution of S. haemolyticus. Left panel: a maximum likelihood tree constructed from substitutions in the core genome of S. ...
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