Dataset Information

MentaLiST - A fast MLST caller for large MLST schemes.

ABSTRACT: MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing data, MLST methods have evolved towards larger typing schemes, based on a few hundred genes [core genome MLST (cgMLST)] to a few thousand genes [whole genome MLST (wgMLST)]. Such large-scale MLST schemes have been shown to provide a finer resolution and are increasingly used in various contexts such as hospital outbreaks or foodborne pathogen outbreaks. This methodological shift raises new computational challenges, especially given the large size of the schemes involved. Very few available MLST callers are currently capable of dealing with large MLST schemes. We introduce MentaLiST, a new MLST caller, based on a k-mer voting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes. We test it on real and simulated data to show that MentaLiST is faster than any other available MLST caller while providing the same or better accuracy, and is capable of dealing with MLST schemes with up to thousands of genes while requiring limited computational resources. MentaLiST source code and easy installation instructions using a Conda package are available at https://github.com/WGS-TB/MentaLiST.

SUBMITTER: Feijao P

PROVIDER: S-EPMC5857373 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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MentaLiST - A fast MLST caller for large MLST schemes.

Feijao Pedro P Yao Hua-Ting HT Fornika Dan D Gardy Jennifer J Hsiao William W Chauve Cedric C Chindelevitch Leonid L

Microbial genomics 20180110 2

MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing data, MLST methods have evolved towards larger typing schemes, based on a few hundred genes [core genome MLST (cgMLST)] to a few thousand genes [whole genome MLST (wgMLST)]. Such large-scale MLST schemes ...[more]

PMID: 29319471

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Project description:Acinetobacter species assigned to the Acinetobacter calcoaceticus-baumannii (Acb) complex, are Gram-negative bacteria responsible for a large number of human infections. The population structure of Acb has been studied using two 7-gene MLST schemes, introduced by Bartual and coworkers (Oxford scheme) and by Diancourt and coworkers (Pasteur scheme). The schemes have three genes in common but underlie two coexisting nomenclatures of sequence types and clonal complexes, which complicates communication on A. baumannii genotypes. The aim of this study was to compare the characteristics of the two schemes to make a recommendation about their usage. Using genome sequences of 730 strains of the Acb complex, we evaluated the phylogenetic congruence of MLST schemes, the correspondence between sequence types, their discriminative power and genotyping reliability from genomic sequences. In silico ST re-assignments highlighted the presence of a second copy of the Oxford gdhB locus, present in 553/730 genomes that has led to the creation of artefactual profiles and STs. The reliability of the two MLST schemes was tested statistically comparing MLST-based phylogenies to two reference phylogenies (core-genome genes and genome-wide SNPs) using topology-based and likelihood-based tests. Additionally, each MLST gene fragment was evaluated by correlating the pairwise nucleotide distances between each pair of genomes calculated on the core-genome and on each single gene fragment. The Pasteur scheme appears to be less discriminant among closely related isolates, but less affected by homologous recombination and more appropriate for precise strain classification in clonal groups, which within this scheme are more often correctly monophyletic. Statistical tests evaluate the tree deriving from the Oxford scheme as more similar to the reference genome trees. Our results, together with previous work, indicate that the Oxford scheme has important issues: gdhB paralogy, recombination, primers sequences, position of the genes on the genome. While there is no complete agreement in all analyses, when considered as a whole the above results indicate that the Pasteur scheme is more appropriate for population biology and epidemiological studies of A. baumannii and related species and we propose that it should be the scheme of choice during the transition toward, and in parallel with, core genome MLST.

Project description:BackgroundMyocardial T1 mapping shows promise for assessment of cardiomyopathies. Most myocardial T1 mapping techniques, such as modified Look-Locker inversion recovery (MOLLI), generate one T1 map per breath-held acquisition (9-17 heartbeats), which prolongs multislice protocols and may be unsuitable for patients with breath-holding difficulties.PurposeTo develop and characterize novel shortened inversion recovery based T1 mapping schemes of 2-5 heartbeats.Study typeProspective.Population/phantomNumerical simulations, agarose/NiCl2 phantom, 16 healthy volunteers, and 24 patients.Field strength/sequence1.5T/MOLLI.AssessmentAll shortened T1 mapping schemes were characterized and compared with a conventional MOLLI scheme (5-(3)-3) in terms of accuracy, precision, spatial variability, and repeatability.Statistical testsKruskal-Wallis, Wilcoxon rank sum tests, analysis of variance, Student's t-tests, Bland-Altman analysis, and Pearson correlation analysis.ResultsAll shortened schemes provided limited T1 time variations (≤2% for T1 times ≤1200 msec) and limited penalty of precision (by a factor of ~1.4-1.5) when compared with MOLLI in numerical simulations. In phantom, differences between all schemes in terms of accuracy, spatial variability, and repeatability did not reach statistical significance (P > 0.71). In healthy volunteers, there were no statistically significant differences between all schemes in terms of native T1 times and repeatability for myocardium (P = 0.21 and P = 0.87, respectively) and blood (P = 0.79 and P = 0.41, respectively). All shortened schemes led to a limited increase of spatial variability for native myocardial T1 mapping with respect to MOLLI (by a factor of 1.2) (P < 0.0001). In both healthy volunteers and patients, the two-heartbeat scheme and MOLLI led to highly linearly correlated T1 times (correlation coefficients ≥0.83).Data conclusionThe proposed two-heartbeat T1 mapping scheme yields a 5-fold acceleration compared with MOLLI, with highly linearly correlated T1 times, no significant difference of repeatability, and limited spatial variability penalty at 1.5T. This approach may enable myocardial T1 mapping in patients with severe breath-holding difficulties and reduce the examination time of multislice protocols.Level of evidence1 Technical Efficacy Stage: 3 J. Magn. Reson. Imaging 2019;50:641-654.

Dataset Information

MentaLiST - A fast MLST caller for large MLST schemes.

Publications

MentaLiST - A fast MLST caller for large MLST schemes.

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