MLSTest: Novel software for multi-locus sequence data analysis in eukaryotic organisms

Tomasini, Nicolás; Lauthier, Juan José; Llewellyn, Martin S.; Diosque, Patricio

doi:10.1016/j.meegid.2013.08.029

Cited by 62 publications

(53 citation statements)

References 48 publications

(59 reference statements)

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“…Here we decided to implement the average states methodology to derive genetic distances and phylogenies. Both approaches can be found in the software MLSTest [52] producing results that enable resolution at the DTU level and an associated DP of 1 for the panel tested. A significant advantage of MLST based analysis over sequential PCR based gels is that once generated, sequences can be applied to a range of complementary downstream analyses.…”

Section: Discussionmentioning

confidence: 99%

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Optimized Multilocus Sequence Typing (MLST) Scheme for Trypanosoma cruzi

et al. 2014

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Trypanosoma cruzi, the aetiological agent of Chagas disease possess extensive genetic diversity. This has led to the development of a plethora of molecular typing methods for the identification of both the known major genetic lineages and for more fine scale characterization of different multilocus genotypes within these major lineages. Whole genome sequencing applied to large sample sizes is not currently viable and multilocus enzyme electrophoresis, the previous gold standard for T. cruzi typing, is laborious and time consuming. In the present work, we present an optimized Multilocus Sequence Typing (MLST) scheme, based on the combined analysis of two recently proposed MLST approaches. Here, thirteen concatenated gene fragments were applied to a panel of T. cruzi reference strains encompassing all known genetic lineages. Concatenation of 13 fragments allowed assignment of all strains to the predicted Discrete Typing Units (DTUs), or near-clades, with the exception of one strain that was an outlier for TcV, due to apparent loss of heterozygosity in one fragment. Monophyly for all DTUs, along with robust bootstrap support, was restored when this fragment was subsequently excluded from the analysis. All possible combinations of loci were assessed against predefined criteria with the objective of selecting the most appropriate combination of between two and twelve fragments, for an optimized MLST scheme. The optimum combination consisted of 7 loci and discriminated between all reference strains in the panel, with the majority supported by robust bootstrap values. Additionally, a reduced panel of just 4 gene fragments displayed high bootstrap values for DTU assignment and discriminated 21 out of 25 genotypes. We propose that the seven-fragment MLST scheme could be used as a gold standard for T. cruzi typing, against which other typing approaches, particularly single locus approaches or systematic PCR assays based on amplicon size, could be compared.

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Section: Discussionmentioning

confidence: 99%

“…MLST data were analysed with MLSTest software (http://ipe.unsa.edu.ar/software) [52] with the objective of identifying the most resolutive and minimum number of targets for unequivocal DTU assignment and potential fine scale characterisation. MLSTest contains a suite of MLST data specific analytical tools.…”

Section: Methodsmentioning

confidence: 99%

Optimized Multilocus Sequence Typing (MLST) Scheme for Trypanosoma cruzi

et al. 2014

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“…The MLSTest 1.0 software was used for building a dendrogram from the consensus sequences using the neighbor joining method with 1000 bootstrap repetitions (Tomasini et al, 2013).…”

Section: Pcr Detection Direct Sequencing and Analysis Of The Leishmmentioning

confidence: 99%

Genetic and clinical characterization of canine leishmaniasis caused by Leishmania (Leishmania) infantum in northeastern Argentina

Barroso

Nevot²,

Hoyos

et al. 2015

Acta Tropica

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“…The cyt b sequences obtained were assembled and edited by Genetyx Mac 11.0.0 (Software Development Co. Ltd., Japan). Data were processed to generate a neighbor-joining tree with 1,000 bootstrap replications using the MLSTest v1.0 software, 18 leading to species/genotype identification. Data from field samples were compared with the Argentinean and World Health Organization (WHO) reference strains of the genus Leishmania reported previously.…”

Section: Methodsmentioning

confidence: 99%

Visceral Leishmaniasis Caused by Leishmania infantum in Salta, Argentina: Possible Reservoirs and Vectors

Barroso¹,

Marco²,

Locatelli³

et al. 2015

The American Society of Tropical Medicine and Hygiene

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Abstract. Cases of human visceral leishmaniasis (HVL) were not recorded until recently in the Chaco region of northwestern Argentina. Dogs were surveyed at the sites of infection of two HVL index cases in the Chaco region of Salta province. Canine cases (CanL) were diagnosed by two parasitological methods, two molecular methods targeting mini-and maxicircle DNA, and immunochromatographic dipstick. Among 77 dogs studied, 10 (13%) were found infected with Leishmania spp. In seven dogs and two humans, the infecting species was typed as Leishmania (Leishmania) infantum. The same genotype was detected in the human and two of the CanL. Although several diagnostic methods displayed weak or moderate agreement, the concordance values for serology versus maxicircle PCR were very good (Kappa index = 0.84). Sandflies captured in the area were identified as Lutzomyia migonei and Lu. cortelezzii/Lu. sallesi (cortelezzii complex). The focal appearance of leishmaniasis in dogs and humans in a sylvatic region and its relatively low prevalence of infection suggests that L. (L.) infantum transmission to dogs and humans may, in this region, stem from sylvatic reservoirs.

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MLSTest: Novel software for multi-locus sequence data analysis in eukaryotic organisms

Cited by 62 publications

References 48 publications

Optimized Multilocus Sequence Typing (MLST) Scheme for Trypanosoma cruzi

Optimized Multilocus Sequence Typing (MLST) Scheme for Trypanosoma cruzi

Genetic and clinical characterization of canine leishmaniasis caused by Leishmania (Leishmania) infantum in northeastern Argentina

Visceral Leishmaniasis Caused by Leishmania infantum in Salta, Argentina: Possible Reservoirs and Vectors

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