Impact of Clostridium botulinum genomic diversity on food safety

Abstract

The deadly botulinum neurotoxin formed by Clostridium botulinum is the causative agent of foodborne botulism. The increasing availability of C. botulinum genome sequences is starting to allow the genomic diversity of C. botulinum Groups I and II and their neurotoxins to be characterised. This information will impact on microbiological food safety through improved surveillance and tracing/tracking during outbreaks, and a better characterisation of C. botulinum Groups I and II, including the risk presented, and new insights into their biology, food chain transmission, and evolution.

Figure 1

Phylogeny of botulinum neurotoxin subtypes. The sources of the sequences are given in supplementary Table 2. The toxin protein sequences were aligned with the Muscle algorithm, and the phylogenetic tree was generated using the Neighbour-Joining method, with the evolutionary distances computed using the JTT matrix-based method and the scale bar shows the number of amino acid substitutions per site. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The analysis involved 41 amino acid sequences. All ambiguous positions were removed for each sequence pair. There were a total of 1409 positions in the final dataset. Alignment and phylogenetic analyses were conducted in MEGA7 [75]. The insets magnify the A, B and E subtypes for visualisation purposes, and do not match the scale bar.

Figure 2

Distribution of botulinum neurotoxin types/subtypes in phylogenetic lineages of 108 Clostridium botulinum Group I isolates (panel a) and 24 Clostridium botulinum Group II isolates (panel b). Trees shown are based on comparison of core single nucleotide polymorphisms identified using parSNP [76], and plotted in the radial format using MEGA7 [75]. The C. botulinum Group I and Group II strains included in this Figure are listed in supplementary Table 3. Strains forming toxin types/subtypes A1, A2, A1(B), B, E and F are indicated in dark blue, green, light blue, red, purple and yellow, respectively. Strains forming toxin types/subtypes A3, Ab, Af, A5(B2′), Ba, Bf, and Bf/a are labelled as ‘others’ in black. Strains identified as ‘NT’ do not contain a botulinum neurotoxin gene.