Table 1.
MAH strains included in the current study [11].
Table 2.
Results of genome assembly using a combination of long and short reads.
Fig 1.
Alignment of chromosome contigs of four MAH strains from Germany.
Identical colours show similar genome blocks, whereas blank spaces indicate the presence of strain-specific genome segments. Red vertical lines in assembly of 17MA0524 denote contig boundaries.
Fig 2.
Inter-strain homology of the two plasmids pMA01 and pMA02 based on comparison of the (A) DNA sequences and (B) the content of COGs.
(A): plasmids of 18MA0850 served as backbone for aligning corresponding plasmids of 17MA0524 (orange), 17MA0531 (yellow) and 18MA0854 (green). The maps further show the GC skew (second inner ring) and predicted coding sequences coloured accorded to COG. In the lower panel (B) the number of CDS per predicted COG of each plasmid is shown.
Fig 3.
Heatmap of an hierarchical cluster analysis based on average nucleotide identity values between the four tapir-associated isolates and foreign strains.
Included were strains that exhibited at least 99.5% ANI to one of the MAH strains of the current study. Blue squares highlight the highest congruence matches.
Fig 4.
Unrooted phylogenetic network, calculated by split decomposition method based on cgSNP alignment of MAH strains of MLST ST9.
The presence of non-linear connections indicates conflicting phylogenetic signals. Strains are coloured according to their place of isolation. The bar indicates base substitution per site.
Table 3.
Numbers of detected cgSNP differences between German isolates before removal of outlier SAMEA5164947 (original), after outlier removal (outlier removed) and after filtering for recombination sites (recombination-adjusted).
Fig 5.
Maximum likelihood trees based on cgSNP alignments of MAH strains of MLST ST9 before (left) and after (right) filtering for recombination sites with Gubbins.
Strains are coloured according to their origin country of isolation. The bars indicate nucleotide substitutions per site, illustrating the drastic reduction in SNP differences despite the fact that the branches appear longer.
Fig 6.
Unrooted neighbour joining tree based on cgMLST allele differences between strains of cgMLST cluster 1 (see S2 Fig).
Strains are coloured according to their place of isolation. The MLST ST, date of isolation and host are given at the right side. The bar indicates allelic differences.
Fig 7.
Pangenome analysis of selected MLST ST9, ST250 and ST196 strains with maximum likelihood tree based on core gene alignment.
The majority of core genes (78.3 kb) is not displayed for better visibility of differing genes. The red square indicates genes unique to MAH strain 17MA0524. A complete visualisation can be found in S4 Fig.
Fig 8.
Number of detected genes which could be assigned to COGs that were unique to either one of the tapir-associated isolates 17MA0524 and 18MA0850 or shared by 17MA0531 and 18MA0854 but missing in the other two investigated strains.
Fig 9.
Maximum likelihood tree based on core gene alignment as given in
Fig 7, with indicators for the presence of plasmid-borne genes detected in pangenome analysis. Blue circles indicate presence of pMA01-borne genes; green circles indicate presence of pMA02-borne genes. Percentages refer to the genes detected on plasmids of 18MA0850 and are indicated by shading.