Open AccessMolecular Typing of Mycobacterium bovis Strains Isolated in Italy from 2000 to 2006 and Evaluation of Variable-Number Tandem Repeats for Geographically Optimized Genotyping
Author(s) -
Maria Beatrice Boniotti,
Maria Goria,
Daniela Loda,
Annalisa Garrone,
Alessandro Benedetto,
Alessandra Mondo,
Ernesto Tisato,
Mariagrazia Zai,
Simona Zoppi,
Alessandro Dondo,
Silvia Tagliabue,
Stefano Bonora,
G. Zanardi,
Maria Lodovica Pacciarini
Publication year - 2009
Publication title -
journal of clinical microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.349
H-Index - 255
eISSN - 1070-633X
pISSN - 0095-1137
DOI - 10.1128/jcm.01192-08
Subject(s) - genotyping , tandem repeat , biology , typing , genotype , variable number tandem repeat , genetics , molecular epidemiology , mycobacterium bovis , genetic diversity , microsatellite , allele , mycobacterium tuberculosis , tuberculosis , medicine , population , genome , gene , environmental health , pathology
Spoligotyping and exact tandem repeat (ETR) analysis ofMycobacterium bovis andM. caprae isolated strains has been routinely carried out in Italy since 2000 to obtain a database of genetic profiles and support traditional epidemiological investigations. In this study, we characterized 1,503M. bovis and 57M. caprae isolates obtained from 2000 to 2006 in 747 cattle herds mainly located in northern Italy. We identified 81 spoligotypes and 113 ETR profiles, while the combination of spoligotyping/ETR analysis differentiated 228 genotypes, with genotypic diversity indices of 0.70 (spoligotyping), 0.94 (ETR-A to -E typing), and 0.97 (spoligotyping/ETR-A to -E typing), respectively. Despite the high degree of resolution obtained, the spoligotyping/ETR methods were not discriminative enough in the case of genotypes characterized by the combination of SB0120, the predominant spoligotype in Italy, with the most common ETR profiles. To obtain a more informative subset of typing loci, 24 mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) markers were evaluated by analyzing a panel of 100 epidemiologically unrelated SB0120 isolates. The panel was differentiated into 89 profiles with an overall genotypic diversity of 0.987 that could be also achieved by using a minimal group of 13 loci: ETR-A, -B, and -E; MIRU 26 and 40; and VNTR 2163a, 2163b, 3155, 1612, 4052, 1895, 3232, and 3336. The allelic diversity index and the stability of single loci was evaluated to provide the most discriminative genotyping method for locally prevalent strains.