Seyboldt, C. | bioRxiv Science

bioRxiv2021

Establishment of a publicly available core genome multilocus sequence typing scheme for Clostridium perfringens

Clostridium perfringens is a spore-forming anaerobic pathogen responsible for a variety of histotoxic and intestinal infections in humans and animals. High-resolution genotyping aiming to identify bacteria at strain level has become increasingly important in modern microbiology to understand pathogen transmission pathways and to tackle infection sources. This study aimed at establishing a publicly available genome-wide multilocus sequence-typing scheme for C. perfringens. 1,431 highly conserved core genes (1.34 megabases; 50% of the reference genome genes) were indexed for a core-genome-based MLST scheme for C. perfringens. As an example, we applied the scheme to 87 poultry and 73 non-poultry strains (total=160). The genotyping results of the 160 genomes were congruent in terms of resolution and tree topology between allele-based and single-nucleotide-polymorphism-based core-genome typing. For the analysis of poultry strains of C. perfringens concerning the country of isolation, NetB-toxin gene carriage and clinical disease, we used 60 allelic differences as a clustering threshold. The results showed that poultry strains from a single country formed a cluster (n=17 clusters including 46 strains). Two clusters included six strains from four different countries. These strains were netB-positive, as were seven strains from Denmark and two strains from Finland, possibly indicating common sources of netB-positive strains. In terms of clinical presentation, different clusters of strains were associated with cases of suspected necrotic enteritis. Strains from sick birds grouped with strains from healthy birds or meat samples showing that potentially virulent strains are widespread and that host-related factors contribute significantly to NE. In summary, a publicly available scheme and an allele nomenclature database for genomic typing of C. perfringens has been established and can be used for broad-based and standardised epidemiological studies.

microbiology↗

bioRxiv2019

Global genomic population structure of Clostridioides difficile

Clostridioides difficile is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce EnteroBase, a publicly accessible database (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that the identification of highly related genomes is 89% consistent between cgMLST and single-nucleotide polymorphisms. EnteroBase currently contains 13,515 quality-controlled genomes which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. Hierarchical clustering can be used to identify populations of C. difficile at all epidemiological levels, from recent transmission chains through to pandemic and endemic strains, and is largely compatible with prior ribotyping. Hierarchical clustering thus enables comparisons to earlier surveillance data and will facilitate communication among researchers, clinicians and public-health officials who are combatting disease caused by C. difficile.

microbiology↗