New Insights into the Genetic Diversity of Clostridium botulinum Group III through Extensive Genome Exploration.

Cédric Woudstra,Rozenn Souillard,Isabelle Mermoud,Patrick Fach,Caroline Le Maréchal,Marie-Hélène Bayon-Auboyer,Denise Desoutter

doi:10.3389/fmicb.2016.00757

Abstract

Animal botulism is caused by group III Clostridium botulinum strains producing type C and D toxins, or their chimeric forms C/D and D/C. Animal botulism is considered an emerging disease in Europe, notably in poultry production. Before our study, 14 genomes from different countries were available in the public database, but none were from France. In order to investigate the genetic relationship of French strains with different geographical areas and find new potential typing targets, 17 strains of C. botulinum group III were sequenced (16 from France and one from New Caledonia). Fourteen were type C/D strains isolated from chickens, ducks, guinea fowl and turkeys and three were type D/C strains isolated from cattle. The New Caledonian strain was a type D/C strain. Whole genome sequence analysis showed the French strains to be closely related to European strains from C. botulinum group III lineages Ia and Ib. The investigation of CRISPR sequences as genetic targets for differentiating strains in group III proved to be irrelevant for type C/D due to a deficient CRISPR/Cas mechanism, but not for type D/C. Conversely, the extrachromosomal elements of type C/D strains could be used to generate a genetic ID card. The highest level of discrimination was achieved with SNP core phylogeny, which allowed differentiation up to strain level and provide the most relevant information for genetic epidemiology studies and discrimination.

Highlights

Clostridium botulinum is the aetiological agent of botulism, a deadly paralytic disease that can affect both humans and animals
We previously showed that animal botulism in Europe is mainly due to mosaic type C/D in avian species, and type D/C in cattle (Woudstra et al, 2012)
GC content, and the number of coding sequences were concordant with reference strains C. botulinum type C/D BKT015925 (Skarin et al, 2011)

Summary

Introduction

Clostridium botulinum is the aetiological agent of botulism, a deadly paralytic disease that can affect both humans and animals. The development of new methods for the rapid molecular detection (Woudstra et al, 2012) and characterization (Anza et al, 2014; Woudstra et al, 2015a) of strains involved in outbreaks have so far revealed marked genetic similarity This supports the hypothesis that one clade of closely related strains responsible for animal botulism dominates in Europe. This assumption is based on information gathered on strains isolated from outbreaks and typed using methods such as PFGE or flagellin gene detection by real-time PCR (Anza et al, 2014; Woudstra et al, 2015a). The level of discrimination provided by these techniques may be insufficient to differentiate closely related genetic strains

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