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Heat-shock protein 70 PCR-RFLP: a universal simple tool for Leishmania species discrimination in the New and Old World

Published online by Cambridge University Press:  05 May 2010

A. M. MONTALVO
Affiliation:
Instituto de Medicina Tropical Pedro Kourí, Departamento de Parasitología, La Habana, Cuba
J. FRAGA
Affiliation:
Instituto de Medicina Tropical Pedro Kourí, Departamento de Parasitología, La Habana, Cuba
L. MONZOTE
Affiliation:
Instituto de Medicina Tropical Pedro Kourí, Departamento de Parasitología, La Habana, Cuba
I. MONTANO
Affiliation:
Instituto de Medicina Tropical Pedro Kourí, Departamento de Parasitología, La Habana, Cuba
S. DE DONCKER
Affiliation:
Institute of Tropical Medicine Antwerp, Antwerp, Belgium
J. C. DUJARDIN
Affiliation:
Institute of Tropical Medicine Antwerp, Antwerp, Belgium Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
G. VAN DER AUWERA*
Affiliation:
Institute of Tropical Medicine Antwerp, Antwerp, Belgium
*
*Corresponding author: Department of Parasitology, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium. Tel: +32 3 2476586. Fax: +32 3 2476359. E-mail: gvdauwera@itg.be
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Summary

Introduction. Species typing in leishmaniasis gains importance in diagnostics, epidemiology, and clinical studies. A restriction fragment length polymorphism (RFLP) assay of PCR amplicons from a partial heat-shock protein 70 gene (hsp70) had been described for the New World, allowing identification of some species. Methods. Based on an initial in silico analysis of 51 hsp70 sequences, most of which we recently determined in the frame of a phylogenetic study, species-specific restriction sites were identified. These were tested by PCR-RFLP on 139 strains from 14 species, thereby documenting both inter- and intra-species variability. Results. Our assay could identify Leishmania infantum, L. donovani, L. tropica, L. aethiopica, L. major, L. lainsoni, L. naiffi, L. braziliensis, L. peruviana, L. guyanensis, and L. panamensis by applying 2 subsequent digests. L. mexicana, L. amazonensis, and L. garnhami did not generate species-specific restriction fragment patterns. Conclusion. Currently no assay is available for global Leishmania species discrimination. We present a universal PCR-RFLP method allowing identification of most medically relevant Old and New World Leishmania species on the basis of a single PCR, obviating the need to perform separate PCRs. The technique is simple to perform and can be implemented in all settings where PCR is available.

Information

Type
Research Article
Copyright
Copyright © Cambridge University Press 2010
Figure 0

Fig. 1. In silico RFLP analysis of hsp70 sequences shown in the dendrogram at the bottom. The GenBank Accession numbers are in parentheses, whereby Accessions starting with XM are derived from a contemporary annotation of full genome sequences and are GenBank specific. The dendrogram is a consensus maximum parsimony tree, whereby the percentages of most parsimonious trees in which each cluster was found is shown at the internodes. As only the topology is represented, branch lengths have no meaning. Species are indicated with lines above the tree, and are abbreviated as follows from left to right: don, Leishmania donovani including L. archibaldi (see Table 1); inf, L. infantum including L. chagasi (see Table 1); aet, L. aethiopica; tro, L. tropica; maj, L. major; ama, L.amazonensis; gar, L. garnhami; mex, L. mexicana; per, L. peruviana; bra, L. braziliensis; nai, L. naiffi; pan, L. panamensis; guy, L. guyanensis; lai, L. lainsoni. The upper part displays the theoretically obtained fragments from digestion with HaeIII, and the different patterns are separated by vertical lines grouping sequences that give identical fragments. The same size marker is depicted on both sides, and the length of each fragment is indicated on the right, as is also the case for the other digests shown below the HaeIII results. Here, digests with different enzymes allowing further separation within the HaeIII defined groups are simulated. Again, only different patterns are depicted, separated by vertical lines grouping the sequences resulting in the same pattern, except for 2 L. amazonensis sequences that differed with HaeIII but were identical with RsaI, and for which the pattern is repeated even though identical to, for instance, L. garnhami. The theoretical RsaI pattern of CUM29 is not given because of a sequence ambiguity in the recognition site distinguishing L. peruviana from L. braziliensis (see Table 2). All strains and isolates included in this figure were also used for wet PCR-RFLP analysis, except those indicated with * following the Accession number in the dendrogram.

Figure 1

Table 1. Strains and isolates analysed in silico or by hsp70 PCR-RFLP

Figure 2

Table 2. SNPs affecting restriction endonuclease recognition sites

Figure 3

Fig. 2. Overview of all PCR-RFLP patterns obtained with the restriction endonucleases indicated. A selection of isolates and strains listed in Table 1 are depicted, all of which, except LEM75, are also included in Fig. 1, using the same species order and abbreviations. The examples shown are representative for each entry in Table 1 according to enzyme and species, except for CUM29 generating a Leishmania peruviana instead of an L. braziliensis pattern (not depicted). L. mexicana M379 shows an isolate-specific pattern for RsaI. The order in which the isolates and strains are shown is identical in the upper and lower panel. The Gene Ruler™ 100 bp DNA Ladder size marker (MM) is depicted on the left hand side for each enzyme, with an indication of fragment sizes.