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Additional file 3 Table S5. Median values of abiotic river water measurements.

Additional file 1 Fig. S1. Map of study site.

Additional file 2 S1 File. Sapro assay design and validation.

Additional file 2: Table S1. Leptospira quantity data extracted from the articles analyzed in this meta-analysis.

Additional file 4: Table S3. Estimated quantity of Leptospira shed by animals.

Additional file 3: Table S2. Urine volume excreted by animals.

Group I concatenated MLST gene phylogeny. Phylogeny of aligned (MUSCLE [57]) and concatenated MLST genes for Group I genomes inferred with FastTree2 [54]. The MLST profile included aceK, aroE, hsp60, mdh, oppB, recA and rpoB [21]. Taxa labeled ST are 83 sequence types available from PubMLST [77, 78]. Investigation of the concatenated MLST gene phylogeny suggests that diverse BoNT-producing strains have yet to be whole genome sequenced. (PDF 31 kb)

Core genome phylogenies of Group I strains. A) Core genome phylogeny of C. botulinum Group I strains inferred with RAxML [63] using the ASC_GTRGAMMA model on an alignment of 182,200 core genome SNPs produced with NASP [61] using C. sporogenes ATCC 15579 [GenBank:ABKW00000000] as the reference genome. The consistency index is 0.56, and the retention index is 0.91 (computed with the R package phangorn). B) Core genome phylogeny of Group I strains inferred with FastTree2 [54] on a 1780-character core SNP matrix generated with kSNP [59]. The consistency index is 0.64, and the retention index is 0.93. The phylogenies were rooted with the clade that includes C. sporogenes and C. botulinum bont/B serotypes (bottom of Figure). Gray circles indicate bootstrap values over 95 %. While there are small variations in the phylogenies generated with different methods (Fig. 5 and Additional file 4: Figure S1), the overall topology of the Group I tree appears robust. The pairwise overall topological scores computed by Compare2Trees [69] range from 80 to 86 % for the phylogenies presented in Fig. 5 and (Additional file 4: Figure S1). (PDF 59 kb)

Dendrograms clustering Group I and Group II strains by BSR values. A) A dendrogram generated by clustering Group I strains by BSR values with an average linkage method in MeV [76]. B) A dendrogram generated by clustering Group II strains by BSR values with an average linkage method in MeV [76]. (PDF 41 kb)

bont gene phylogeny. A phylogeny inferred with FastTree2 [54] on a nucleotide alignment (MUSCLE [57]) of botulinum neurotoxin genes. Gray circles indicate bootstrap values over 90Â %. The tree was rooted with tetanus toxin gene sequences in FigTree [55]. (PDF 54 kb)

Group I concatenated MLST gene phylogeny. Phylogeny of aligned (MUSCLE [57]) and concatenated MLST genes for Group I genomes inferred with FastTree2 [54]. The MLST profile included aceK, aroE, hsp60, mdh, oppB, recA and rpoB [21]. Taxa labeled ST are 83 sequence types available from PubMLST [77, 78]. Investigation of the concatenated MLST gene phylogeny suggests that diverse BoNT-producing strains have yet to be whole genome sequenced. (PDF 31 kb)

bont gene phylogeny. A phylogeny inferred with FastTree2 [54] on a nucleotide alignment (MUSCLE [57]) of botulinum neurotoxin genes. Gray circles indicate bootstrap values over 90Â %. The tree was rooted with tetanus toxin gene sequences in FigTree [55]. (PDF 54 kb)

Core genome phylogenies of Group II strains. A) Core genome phylogeny of C. botulinum Group II strains inferred with RAxML [63] using the ASC_GTRGAMMA model on an alignment of 200,276 core genome SNPs produced with NASP [61] using C. botulinum strain Alaska E43 [GenBank:CP001078] as the reference. The consistency index is 0.81, and the retention index is 0.90 (computed with the R package phangorn). B) Core genome phylogeny of Group II C. botulinum strains inferred with FastTree2 [54] on a 35,382-character core SNP matrix generated with kSNP [59]. The consistency index is 0.83, and the retention index is 0.90. The phylogenies were rooted with the clade that includes strains Eklund 202F, KAPB-3, Eklund 17B and CDC 66177. Gray circles indicate bootstrap values over 95 %. While there are small variations in the phylogenies generated with different methods (Fig. 6 and Additional file 6: Figure S3), Group II strains are separated into two distinct clades. The pairwise overall topological scores computed by Compare2Trees [69] range from 93 to 100 %. (PDF 35 kb)

Group II concatenated MLST gene phylogeny. Phylogeny of aligned (MUSCLE [57]) and concatenated MLST genes for Group II genomes inferred with FastTree2 [54]. The MLST profile included 16S rRNA genes, atpD, guaA, gyrB, ilvD, lepA, mutL, oppB, pta, pyc, recA, rpoB, trpB and tuf [22]. Taxa labeled C. botulinum are WGS samples. Taxa labeled with single-word name include serotype E strains for which the MLST genes were sequenced by MacDonald and colleagues [22]. (PDF 37 kb)

Dendrograms clustering Group I and Group II strains by BSR values. A) A dendrogram generated by clustering Group I strains by BSR values with an average linkage method in MeV [76]. B) A dendrogram generated by clustering Group II strains by BSR values with an average linkage method in MeV [76]. (PDF 41 kb)

Group II concatenated MLST gene phylogeny. Phylogeny of aligned (MUSCLE [57]) and concatenated MLST genes for Group II genomes inferred with FastTree2 [54]. The MLST profile included 16S rRNA genes, atpD, guaA, gyrB, ilvD, lepA, mutL, oppB, pta, pyc, recA, rpoB, trpB and tuf [22]. Taxa labeled C. botulinum are WGS samples. Taxa labeled with single-word name include serotype E strains for which the MLST genes were sequenced by MacDonald and colleagues [22]. (PDF 37 kb)

Core genome phylogenies of Group I strains. A) Core genome phylogeny of C. botulinum Group I strains inferred with RAxML [63] using the ASC_GTRGAMMA model on an alignment of 182,200 core genome SNPs produced with NASP [61] using C. sporogenes ATCC 15579 [GenBank:ABKW00000000] as the reference genome. The consistency index is 0.56, and the retention index is 0.91 (computed with the R package phangorn). B) Core genome phylogeny of Group I strains inferred with FastTree2 [54] on a 1780-character core SNP matrix generated with kSNP [59]. The consistency index is 0.64, and the retention index is 0.93. The phylogenies were rooted with the clade that includes C. sporogenes and C. botulinum bont/B serotypes (bottom of Figure). Gray circles indicate bootstrap values over 95 %. While there are small variations in the phylogenies generated with different methods (Fig. 5 and Additional file 4: Figure S1), the overall topology of the Group I tree appears robust. The pairwise overall topological scores computed by Compare2Trees [69] range from 80 to 86 % for the phylogenies presented in Fig. 5 and (Additional file 4: Figure S1). (PDF 59 kb)

Core genome phylogenies of Group II strains. A) Core genome phylogeny of C. botulinum Group II strains inferred with RAxML [63] using the ASC_GTRGAMMA model on an alignment of 200,276 core genome SNPs produced with NASP [61] using C. botulinum strain Alaska E43 [GenBank:CP001078] as the reference. The consistency index is 0.81, and the retention index is 0.90 (computed with the R package phangorn). B) Core genome phylogeny of Group II C. botulinum strains inferred with FastTree2 [54] on a 35,382-character core SNP matrix generated with kSNP [59]. The consistency index is 0.83, and the retention index is 0.90. The phylogenies were rooted with the clade that includes strains Eklund 202F, KAPB-3, Eklund 17B and CDC 66177. Gray circles indicate bootstrap values over 95 %. While there are small variations in the phylogenies generated with different methods (Fig. 6 and Additional file 6: Figure S3), Group II strains are separated into two distinct clades. The pairwise overall topological scores computed by Compare2Trees [69] range from 93 to 100 %. (PDF 35 kb)

Table S2. Multi-Locus Sequence Type results obtained from WGS data using SRST2. NF indicates not found and (*) indicates mismatches. (DOC 52Â kb)

Table S2. Multi-Locus Sequence Type results obtained from WGS data using SRST2. NF indicates not found and (*) indicates mismatches. (DOC 52Â kb)

Table S1. Sequencing quality and coverage. Quality breadth is based on the total reference size, 2,780,693 bases, after duplicated regions were removed. In order to pass quality filtering, the loci had to have >10× coverage and a SNP state had to be in >90 % of the reads to be considered. Mean coverage was calculated using a genome size of 2.8 Mb. (DOC 54 kb)

Table S1. Sequencing quality and coverage. Quality breadth is based on the total reference size, 2,780,693 bases, after duplicated regions were removed. In order to pass quality filtering, the loci had to have >10× coverage and a SNP state had to be in >90 % of the reads to be considered. Mean coverage was calculated using a genome size of 2.8 Mb. (DOC 54 kb)