Results 71 to 80 of about 5,264 (155)

Development of cgMLST schemes for Klebsiella oxytoca and Klebsiella planticola species complexes

, 2023
Core genome multi-locus sequence typing (cgMLST) provides a high level of resolution typing among bacterial populations. Two novel cgMLST schemes have been implemented for Klebsiella oxytoca and Klebsiella (Raoultella) planticola species complexes (KoSC ...
Frédérique Pasquali, Carla Rodrigues, Gerardo Manfreda, Federica Palma, Lucia Gambi, Cecilia Crippa, Alex Lucchi, Sylvain Brisse, Alessandra De Cesare   +8 more
core   +1 more source

Additional file 2 of In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes

, 2022
Additional file 2 Standardized matrices of the cgMLST workflows BIGSdb (n = 423), INNUENDO (n = 339), GENPAT (n = 423), SeqSphere (n = 423), BioNumericsAB (n = 423), BioNumericsAF (n = 423) and MentaLiST (n = 423) applied to downsampled paired-end reads ...
Federica Palma (12312736), Marina Torresi (12312748), Anna Janowicz (12312739), Cesare Cammà (11627980), Alexis Criscuolo (12312754), Giuliano Garofolo (12312751), Adriano Di Pasquale (11627965), Alexandra Moura (12312742), Iolanda Mangone (11627971), Alexandra Chiaverini (12312745), Nicolas Radomski (11627968), Sylvain Brisse (9701061)   +11 more
core   +1 more source

L. anisa cgMLST 3140 targets ref-seqs.fasta

, 2018
cgMLST scheme was constructed using the genomes of three L. anisa strains downloaded from NCBI (RefSeq: NZ_CANP00000000.1; RefSeq: NZ_NBTX00000000.1; RefSeq: NZ_LNXS00000000.1), using Ridom SeqSphere+ cgMLST Target Definer with the following parameters ...
Giuseppe Fleres (5261831)
core   +1 more source

Accurate and reproducible whole-genome genotyping for bacterial genomic surveillance with Nanopore sequencing data

Journal of Clinical Microbiology
Despite recent advances in error rate reduction, until recently, Oxford Nanopore Technologies (ONT) sequences lacked the accuracy required for fine-scale bacterial genomic analysis.
K. Prior, K. Becker, C. Brandt, A. Cabal Rosel, J. Dabernig-Heinz, C. Kohler, M. Lohde, W. Ruppitsch, F. Schuler, G. E. Wagner, A. Mellmann   +10 more
doaj   +1 more source

A core genome MLST scheme for Borrelia burgdorferi sensu lato improves insights into the evolutionary history of the species complex

Cell Reports: Methods
Summary: Multi-locus sequence typing (MLST) based on eight genes has become the method of choice for Borrelia typing and is extensively used for population studies.
Sabrina Hepner, Keith A. Jolley, Santiago Castillo-Ramirez, Evangelos Mourkas, Alexandra Dangel, Andreas Wieser, Johannes Hübner, Andreas Sing, Volker Fingerle, Gabriele Margos   +9 more
doaj   +1 more source

Comparison of indistinguishable or closely related isolates based on cgMLST.

, 2019
Comparison of indistinguishable or closely related isolates based on cgMLST.
Paula Mölling, Faisal Ahmad Khan, Jana Jass (677208), Bo Söderquist, Faisal Ahmad Khan (7832540), Anna Fagerström (3594854), Anna Fagerström, Paula Mölling (471622), Martin Sundqvist (367060), Bo Söderquist (466146), Martin Sundqvist, Jana Jass   +11 more
core   +1 more source

Distribution of COG functional classes for the loci of (A) Lm-cgMLST (1701 loci) and (B) LmScheme_370.

, 2021
Distribution of COG functional classes for the loci of (A) Lm-cgMLST (1701 loci) and (B) LmScheme_370.
Yen-Yi Liu (183718), Chih-Chieh Chen (20257)   +1 more
core   +1 more source

MiST: rapid, accurate and flexible (core-genome) multi-locus sequence typing (MLST) allele calling from draft genomes

BMC Genomics
Background Multi-locus sequence typing (MLST) is a typing method to differentiate bacteria based on the sequence of several housekeeping genes. Identifiers are assigned to unique allele sequences for each locus in the scheme, and the combination of these
Bert Bogaerts, Nancy H. C. Roosens, Kevin Vanneste   +2 more
doaj   +1 more source

A high level of concordance observed between cgMLST cluster and serovar.

, 2016
The concordance was based on the proportion of genomes in a cgMLST cluster that belonged to the predominant predicted serovar in the group. The cgMLST clusters were defined at a similarity threshold of 85%; only clusters with four or more members are ...
Erika J. Lingohr (729155), Victor P. J. Gannon (162481), Catherine E. Yoshida (847368), Peter Kruczkiewicz (847369), Chad R. Laing (162463), Eduardo N. Taboada (380256), John H. E. Nash (262290)   +6 more
core   +1 more source

Supplementary Figure 2. Phylogenetic trees inferred from cgMLST and SNP data.

, 2017
Supplementary Figure 2. Phylogenetic trees inferred from cgMLST and SNP data. The cgMLST tree (left) is identical to the one in Figure 1 (without the mutS isolate CSID 3015183688).
Amandine PERRIN (3694132)
core   +1 more source