Molecular Diversity of Mycobacterium avium subsp. paratuberculosis in Four Dairy Goat Herds from Thuringia (Germany)

SIMPLE SUMMARY: Paratuberculosis (Johne’s disease) is a chronic granulomatous enteritis that affects domestic and wild ruminants worldwide, mainly dairy and beef cattle, but also small ruminants such as goats and sheep. To gain a better understanding of the disease epidemiology and to develop effective control strategies, it is useful to determine the strain diversity of the causative agent, Mycobacterium avium subsp. paratuberculosis (MAP). The aim of this study was to determine the diversity of MAP isolated from four goat herds affected by paratuberculosis in Thuringia (Germany), as well as the detailed distribution of genotypes among the animals and their environment in one herd (herd 1). A combination of three methods was used to genotype isolates from fecal samples of infected animals, from various intestinal and other tissues of clinically affected animals, and from environmental samples. The six MAP-C genotypes identified could be assigned to five different phylogenetic subgroups. The results suggest individual infection strains within each herd. In herd 1, one predominant strain was found, and two strains occurred sporadically. The genotypes detected were not goat specific. Introduction of MAP into the herd through uncontrolled animal trade or environmental exposure to MAP in barns that were previously used by cattle with unknown paratuberculosis status are suspected as possible sources of infection. ABSTRACT: This study investigated the intra- and inter-herd diversity of Mycobacterium avium subsp. paratuberculosis (MAP) isolates from four goat herds in Thuringia (Germany) that were affected by paratuberculosis for several years. The main focus was on the characterization and distribution of genotypes among animals and the environment of goat herd 1. This study included 196 isolates from the feces of 121 infected goats, various tissues from 13 clinically diseased goats, 29 environmental samples from herd 1, and additionally, 22 isolates of different origin from herds 2 to 4. The isolates, sampled between 2018 and 2022, were genotyped using short-sequence-repeat (SSR) analysis, mycobacterial-interspersed repetitive units–variable-number tandem repeat (MIRU–VNTR) analysis, and a single nucleotide polymorphism (SNP)-based assay for phylogenetic grouping. All the isolates belonged to the MAP-C group. In herd 1, one predominant genotype was determined, while two other genotypes were identified very rarely and only in fecal and environmental samples. One of three further genotypes was found in each of herds 2 to 4. The assignment of genotypes to different phylogenetic clades suggested six different infection strains. The results indicated no epidemiological links between the examined herds. Based on the current MAP genotyping data from Germany, possible sources of infection are MAP-contaminated barns previously used by infected cattle and the purchase of sub-clinically infected goats.