Two novel toxin variants revealed by whole-genome sequencing of 175 Clostridium botulinum type E strains

Abstract

We sequenced 175 Clostridium botulinum type E strains isolated from food, clinical, and environmental sources from northern Canada and analyzed their botulinum neurotoxin (bont) coding sequences (CDSs). In addition to bont/E1 and bont/E3 variant types, neurotoxin sequence analysis identified two novel BoNT type E variants termed E10 and E11. Strains producing type E10 were found along the eastern coastlines of Hudson Bay and the shores of Ungava Bay, while strains producing type E11 were only found in the Koksoak River region of Nunavik. Strains producing BoNT/E3 were widespread throughout northern Canada, with the exception of the coast of eastern Hudson Bay.

FIG 1

Dendrogram comparing unique full-length bont/E CDSs from the current study to sequences of known bont/E variants (*) using RAxML (1,000 bootstraps). Accession numbers of the bont/E CDSs used for analysis are shown. Two clusters are distinct from bont/E variants E1 to E9 and are termed E10 and E11. The occurrence of each sequence is indicated (parentheses).

FIG 2

CDS alignment depicting the distribution of nucleotide substitutions within bont/E1, bont/E3, and bont/E10 variants. Nucleotide substitutions (|), silent substitutions (×), and codon deletions (△) identified among bont/E variant CDSs indicated on the left (E1, italics; E3, regular font; E10, underlined) compared against reference sequences (E1, accession number X62683; E3, accession number EF028403; and E10, accession number KF861887) are shown.

FIG 3

bont/E CDS alignment depicting the distribution of nucleotide substitutions among variants. The reference sequence used for each of the 11 alignments is indicated (left and Table 3), and horizontal tracks represent the alignment for each variant sequence (right). A scale bar denoting nucleotide position and catalytic light chain (LC), translocation (H_N), and receptor binding (H_C) domains is shown. The vertical lines plotted along the tracks indicate nucleotide substitutions (A, red; C, blue; G, yellow; T, green).

FIG 4

Distribution of BoNT/E C. botulinum. The locations of origin for Canadian BoNT/E C. botulinum characterized in this study (Table 1) are shown. The BoNT/E variant type is indicated (legend, inset). Map source: Natural Resources Canada (http://atlas.gc.ca).