Schematic of genomic rearrangements and the IS<i>1311</i> locations in the K10 (Type II) (top), S397 (Type III) (middle) and the Telford (Type I) (bottom) closed reference genomes.

Analysis conducted using MAUVE genome alignment tool: blocks of the same colour indicate homologous genomic regions; lines connect these regions between the different reference strains. Coloured arrows indicate the IS1311 loci; arrows with a grey outline indicate a locus that contains the C-strain specific SNP. The colour of the arrow heads indicates analogous loci, as shown in Table 4.</p

Schematic of the bioinformatic workflow used in this study.

Schematic of the bioinformatic workflow used in this study.</p

Details of closed MAP genome dataset used for verification purposes.

Note, this includes the closed reference genomes in Table 2.</p

SNPs present in IS1311 used to differentiate between subspecies of M. avium and strains of MAP.

SNPs present in IS1311 used to differentiate between subspecies of M. avium and strains of MAP.</p

Excel spreadsheet comprising dataset accession lists from GenBank and the sequence read archive of genomes used in this study.

Excel spreadsheet comprising dataset accession lists from GenBank and the sequence read archive of genomes used in this study.</p

Closed MAP reference genomes used in this study.

Johne’s disease (JD), caused by Mycobacterium avium subspecies paratuberculosis (MAP) is a global burden for livestock producers and has an association with Crohn’s disease in humans. Within MAP there are two major lineages, S/Type I/TypeIII and C/Type II, that vary in phenotype including culturability, host preference and virulence. These lineages have been identified using the IS1311 element, which contains a conserved, single nucleotide polymorphism. IS1311 and the closely related IS1245 element belong to the IS256 family of insertion sequences, are dispersed throughout M. avium taxa but remain poorly characterised. To investigate the distribution and diversity of IS1311 in MAP, 805 MAP genomes were collated from public databases. IS1245 was absent, while IS1311 sequence, copy number and insertion loci were conserved between MAP S lineages and varied within the MAP C lineage. One locus was specific to the S strains, which contained nine IS1311 copies. In contrast, C strains contained either seven or eight IS1311 loci. Most insertion loci were associated with the boundaries of homologous regions that had undergone genome rearrangement between the MAP lineages, suggesting that this sequence may be a driver of recombination. Phylogenomic geographic clustering of MAP subtypes was demonstrated for the first time, at continental scale, and indicated that there may have been recent MAP transmission between Europe and North America, in contrast to Australia where importation of live ruminants is generally prohibited. This investigation confirmed the utility of IS1311 typing in epidemiological studies and resolved anomalies in past studies. The results shed light on potential mechanisms of niche/host adaptation, virulence of MAP and global transmission dynamics.</div

Percentage of MAP genomes (n = 805 genomes) previously identified as Type I, II or III that contain the respective IS<i>1311</i> loci.

The IS1311 loci are numbered in order with respect to the replication origin (oriC) for the relevant reference strain: a) Telford, b) K10 and c) S397. The locus numbers correspond to those described in Table 4, indicating analogous loci in the different strains.</p

Insertion locations of IS1311 within closed reference genomes.

Loci marked with an asterisk (*) contain C223T. Blank rows indicate the absence of an IS1311 locus. Annotations marked by an asterisk (*) were obtained by HMMer searches. The annotation locus tag for the flanking gene is in parentheses. Coloured boxes indicate locus ID as shown in the figures.</p

SNP based phylogeny of the 15 closed genomes using Telford as a reference genome.

Metadata are indicated by coloured blocks. Reported IS1311 type, number of IS1311 sequences present in the genome, number of SNP-containing IS1311 sequences, year of isolation and country of origin are displayed from left to right respectively.</p

Nomenclature of MAP strains, adapted from Mizzi et al. (2021).

Nomenclature of MAP strains, adapted from Mizzi et al. (2021).</p