High Molecular Diversity of Mycobacterium avium subsp. paratuberculosis in Germany Revealed by Multitarget Genotyping

This study investigated the genetic diversity of <i>Mycobacterium avium</i> subsp. <i>paratuberculosis</i> (<i>Map</i>)-the causative agent of paratuberculosis-isolated from different host species in Germany. A total of 500 isolates from 243 cattle herds and 9 other host species originating from 13 federal states were genotyped. A multi-target approach was applied, comprising IS<i>900</i>-RFLP with <i>Bst</i>EII and <i>Pst</i>I digestion; MIRU-VNTR; and SSR1, SSR8, and SSR9 analysis. In total, 93 combined genotypes were identified, 84 in cattle and 21 in non-cattle isolates. Ninety genotypes were assigned to the C-type group, and three genotypes (three from sheep and one from cattle) were assigned to the S-type/subtype III group. Cluster analysis divided genotypes into subgroups similar to those shown for WGS-SNP-based phylogenetic trees. New genotypes were revealed, including INMV262-267 and a specific sequence at locus VNTR7. Five genotypes that were predominant in cattle were also detected in sheep, goats, and deer. The majority of genotypes [61%] were identified only once. Polyclonal infections were observed in individual animals and herds, and various potential <i>Map</i> transmission linkages were uncovered. This high genotype richness of <i>Map</i> reflects the long history of paratuberculosis in Germany and intensive nationwide animal movement and international trading activity.