A simple strain typing assay for Trypanosoma cruzi: Discrimination of major evolutionary lineages from a single amplification product

PLoS Neglected Tropical Diseases

Volumn 6, Issue 7, 2012, Pages

  Cosentino, Raul O ^a   Agüero, Fernán ^a  

^a INSTITUTO DE INVESTIGACIONES BIOTECNOLÓGICAS   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

C 5 STEROL DESATURASE; OXYGENASE; UNCLASSIFIED DRUG; PROTOZOAL DNA; RESTRICTION ENDONUCLEASE;

ALLELE; ARTICLE; DNA SEQUENCE; GENE; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARASITE IDENTIFICATION; POLYMERASE CHAIN REACTION; POLYMORPHIC LOCUS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RESTRICTION MAPPING; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; TCMK GENE; TCSC5D GENE; TRYPANOSOMA CRUZI; CHAGAS DISEASE; CHEMISTRY; CLASSIFICATION; DNA FINGERPRINTING; ECONOMICS; EVALUATION; GENETICS; HUMAN; MASS SCREENING; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PARASITOLOGY;

CHAGAS DISEASE; DNA FINGERPRINTING; DNA RESTRICTION ENZYMES; DNA, PROTOZOAN; HUMANS; MASS SCREENING; MOLECULAR SEQUENCE DATA; PARASITOLOGY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; TRYPANOSOMA CRUZI;

EID: 84864622808     PISSN: 19352727     EISSN: 19352735     Source Type: Journal    
DOI: 10.1371/journal.pntd.0001777     Document Type: Article

References (45)

1. Rassi A, Rassi A, Marin Neto JA, ((2010)) Chagas disease. Lancet 375:: 1388--1402.
2. Dvorak JA, ((1984)) The natural heterogeneity of Trypanosoma cruzi: biological and medical implications. J Cell Biochem 24:: 357--371.
3. Tibayrenc M, Ayala FJ, ((1998)) Isozyme variability in Trypanosoma cruzi, the agent of Chagas' disease: Genetical, taxomonical, and epidemiological significance. Evolution 42:: 277--292.
4. Tibayrenc M, Ward P, Moya A, Ayala FJ, ((1986)) Natural populations of Trypanosoma cruzi, the agent of Chagas disease, have a complex multiclonal structure. Proc Natl Acad Sci U S A 83:: 115--119.
5. Tibayrenc M, Ayala FJ, ((2002)) The clonal theory of parasitic protozoa: 12 years on. Trends Parasitol 18:: 405--410.
6. Miles MA, Souza A, Povoa M, Shaw JJ, Lainson R, et al. ((1978)) Isozymic heterogeneity of Trypanosoma cruzi in the first autochthonous patients with Chagas' disease in Amazonian Brazil. Nature 272:: 819--821.
7. Souto RP, Fernandes O, Macedo AM, Campbell DA, Zingales B, ((1996)) DNA markers define two major phylogenetic lineages of Trypanosoma cruzi. Mol Biochem Parasitol 83:: 141--152.
8. Robello C, Gamarro F, Castanys S, Alvarez Valin F, ((2000)) Evolutionary relationships in Trypanosoma cruzi: molecular phylogenetics supports the existence of a new major lineage of strains. Gene 246:: 331--338.
9. de Freitas JM, Pinto LA, Pimenta JR, Bastos Rodrigues L, Gonçalves VF, et al. ((2006)) Ancestral genomes, sex, and the population structure of Trypanosoma cruzi. PLoS Pathog 2:: e24.
10. Barnabé C, Brisse S, Tibayrenc M, ((2000)) Population structure and genetic typing of Trypanosoma cruzi, the agent of Chagas disease: a multilocus enzyme electrophoresis approach. Parasitology 120 (Pt 5): 513--526.
11. Brisse S, Barnabé C, Tibayrenc M, ((2000)) Identification of six Trypanosoma cruzi phylogenetic lineages by random amplified polymorphic DNA and multilocus enzyme electrophoresis. Int J Parasitol 30:: 35--44.
12. Brisse S, Verhoef J, Tibayrenc M, ((2001)) Characterisation of large and small subunit rRNA and mini-exon genes further supports the distinction of six Trypanosoma cruzi lineages. Int J Parasitol 31:: 1218--1226.
13. Zingales B, Andrade SG, Briones MRS, Campbell DA, Chiari E, et al. ((2009)) A new consensus for Trypanosoma cruzi intraspecific nomenclature: second revision meeting recommends TcI to TcVI. Mem Inst Oswaldo Cruz 104:: 1051--1054.
14. Zingales B, Miles MA, Campbell DA, Tibayrenc M, Macedo AM, et al. ((2012)) The revised Trypanosoma cruzi subspecific nomenclature: rationale, epidemiological relevance and research applications. Infect Genet Evol 12:: 240--253.
15. Marcili A, Lima L, Cavazzana M, Junqueira ACV, Veludo HH, et al. ((2009)) A new genotype of Trypanosoma cruzi associated with bats evidenced by phylogenetic analyses using SSU rDNA, cytochrome b and Histone H2B genes and genotyping based on ITS1 rDNA. Parasitology 136:: 641--655.
16. Yeo M, Mauricio IL, Messenger LA, Lewis MD, Llewellyn MS, et al. ((2011)) Multilocus sequence typing (MLST) for lineage assignment and high resolution diversity studies in Trypanosoma cruzi. PLoS Negl Trop Dis 5:: e1049.
17. Flores López CA, Machado CA, ((2011)) Analyses of 32 loci clarify phylogenetic relationships among Trypanosoma cruzi lineages and support a single hybridization prior to human contact. PLoS Negl Trop Dis 5:: e1272.
18. Machado CA, Ayala FJ, ((2001)) Nucleotide sequences provide evidence of genetic exchange among distantly related lineages of Trypanosoma cruzi. Proc Natl Acad Sci U S A 98:: 7396--7401.
19. Westenberger SJ, Barnabé C, Campbell DA, Sturm NR, ((2005)) Two hybridization events define the population structure of Trypanosoma cruzi. Genetics 171:: 527--543.
20. Andrade V, Brodskyn C, Andrade SG, ((1983)) Correlation between isoenzyme patterns and biological behaviour of different strains of Trypanosoma cruzi. Trans R Soc Trop Med Hyg 77:: 796--799.
21. Revollo S, Oury B, Laurent JP, Barnabé C, Quesney V, et al. ((1998)) Trypanosoma cruzi: impact of clonal evolution of the parasite on its biological and medical properties. Exp Parasitol 89:: 30--39.
22. Miles MA, Cedillos RA, Póvoa MM, de Souza AA, Prata A, et al. ((1981)) Do radically dissimilar Trypanosoma cruzi strains (zymodemes) cause Venezuelan and Brazilian forms of Chagas' disease? Lancet 1:: 1338--1340.
23. Macedo AM, Pena SD, ((1998)) Genetic Variability of Trypanosoma cruzi:Implications for the Pathogenesis of Chagas Disease. Parasitol Today 14:: 119--124.
24. Andrade LO, Machado CR, Chiari E, Pena SD, Macedo AM, ((1999)) Differential tissue distribution of diverse clones of Trypanosoma cruzi in infected mice. Mol Biochem Parasitol 100:: 163--172.
25. Vago AR, Andrade LO, Leite AA, d'Avila Reis D, Macedo AM, et al. ((2000)) Genetic characterization of Trypanosoma cruzi directly from tissues of patients with chronic Chagas disease: differential distribution of genetic types into diverse organs. Am J Pathol 156:: 1805--1809.
26. Lewis MD, Ma J, Yeo M, Carrasco HJ, Llewellyn MS, et al. ((2009)) Genotyping of Trypanosoma cruzi: systematic selection of assays allowing rapid and accurate discrimination of all known lineages. Am J Trop Med Hyg 81:: 1041--1049.
27. Aliaga C, Brenière SF, Barnabé C, ((2011)) Further interest of miniexon multiplex PCR for a rapid typing of Trypanosoma cruzi DTU groups. Infect Genet Evol 11:: 1155--1158.
28. Tibayrenc M, Neubauer K, Barnabé C, Guerrini F, Skarecky D, et al. ((1993)) Genetic characterization of six parasitic protozoa: parity between random-primer DNA typing and multilocus enzyme electrophoresis. Proc Natl Acad Sci U S A 90:: 1335--1339.
29. Lauthier JL, Tomasini N, Barnabé C, Monje Rumi MM, Alberti D'Amato AM, et al. ((2012)) Candidate targets for Multilocus Sequence Typing of Trypanosoma cruzi: Validation using parasite stocks from the Chaco Region and a set of reference strains. Infect Genet Evol 12:: 350--358.
30. Lima L, da Silva FM, Neves L, Attias M, Takata CSA, et al. ((2012)) Evolutionary Insights from Bat Trypanosomes: Morphological, Developmental and Phylogenetic Evidence of a New Species, Trypanosoma (Schizotrypanum) erneyi sp. nov., in African Bats Closely Related to Trypanosoma (Schizotrypanum) cruzi and Allied Species. Protist in press.
31. Ewing B, Hillier L, Wendl MC, Green P, ((1998)) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:: 175--185.
32. Ewing B, Green P, ((1998)) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:: 186--194.
33. Nickerson DA, Tobe VO, Taylor SL, ((1997)) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using uorescence-based resequencing. Nucleic Acids Res 25:: 2745--2751.
34. Gordon D, ((2003)) Viewing and editing assembled sequences using Consed. Curr Protoc Bioinformatics Chapter 11:: Unit11.2.
35. Ackermann AA, Carmona SJ, Agüero F, ((2009)) TcSNP: a database of genetic variation in Trypanosoma cruzi. Nucleic Acids Res 37:: D544--D549.
36. Weatherly BD, Boehlke C, Tarleton RL, ((2009)) Chromosome level assembly of the hybrid Trypanosoma cruzi genome. BMC Genomics 10:: 255.
37. Ngamphiw C, Kulawonganunchai K, Assawamakin A, Jenwitheesuk E, Tongsima S, ((2008)) VarDetect: a nucleotide sequence variation exploratory tool. BMC Bioinformatics 9 Suppl 12:: S9.
38. Jensen MA, Straus N, ((1993)) Effect of PCR conditions on the formation of heteroduplex and single-stranded DNA products in the amplification of bacterial ribosomal DNA spacer regions. PCR Methods Appl 3:: 186--194.
39. Wang GC, Wang Y, ((1996)) The frequency of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from different bacterial species. Microbiology 142 (Pt 5): 1107--1114.
40. Thompson JR, Marcelino LA, Polz MF, ((2002)) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res 30:: 2083--2088.
41. Rozas M, De Doncker S, Adaui V, Coronado X, Barnabé C, et al. ((2007)) Multilocus polymerase chain reaction restriction fragment-length polymorphism genotyping of Trypanosoma cruzi (Chagas disease): taxonomic and clinical applications. J Infect Dis 195:: 1381--1388.
42. Morel C, Chiari E, Camargo EP, Mattei DM, Romanha AJ, et al. ((1980)) Strains and clones of Trypanosoma cruzi can be characterized by pattern of restriction endonuclease products of kinetoplast DNA minicircles. Proc Natl Acad Sci U S A 77:: 6810--6814.
43. Burgos JM, Altcheh J, Bisio M, Duffy T, Valadares HMS, et al. ((2007)) Direct molecular profiling of minicircle signatures and lineages of Trypanosoma cruzi bloodstream populations causing congenital Chagas disease. Int J Parasitol 37:: 1319--1327.
44. Alchaar D'Avila D, Macedo AM, Silva Valadares HM, Dias Gontijo E, de Castro AM, et al. ((2009)) Probing population dynamics of Trypanosoma cruzi during progression of the chronic phase in chagasic patients. J Clin Microbiol 47:: 1718--1725.
45. Urban I, Santurio LB, Chidichimo A, Yu H, Chen X, et al. ((2011)) Molecular diversity of the Trypanosoma cruzi TcSMUG family of mucin genes and proteins. Biochem J 438:: 303--313.