Establishment of a Publicly Available Core Genome Multilocus Sequence Typing Scheme for Clostridium perfringens.

Mostafa Y Abdel-Glil,Christian Seyboldt,Dag Harmsen,Lothar H Wieler,Jörg Linde,Prasad Thomas,Heinrich Neubauer,Keith A Jolley,Adelumola Oladeinde

doi:10.1128/spectrum.00533-21

Abstract

ABSTRACTClostridium 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 (MLST) scheme for C. perfringens. A total of 1,431 highly conserved core genes (1.34 megabases; 50% of the reference genome genes) were indexed for a core genome-based MLST (cgMLST) scheme for C. perfringens. The scheme was applied to 282 ecologically and geographically diverse genomes, showing that the genotyping results of cgMLST were highly congruent with the core genome-based single-nucleotide-polymorphism typing in terms of resolution and tree topology. In addition, the cgMLST provided a greater discrimination than classical MLST methods for C. perfringens. The usability of the scheme for outbreak analysis was confirmed by reinvestigating published outbreaks of C. perfringens-associated infections in the United States and the United Kingdom. In summary, a publicly available scheme and an allele nomenclature database for genomic typing of C. perfringens have been established and can be used for broad-based and standardized epidemiological studies.IMPORTANCE Global epidemiological surveillance of bacterial pathogens is enhanced by the availability of standard tools and sharing of typing data. The use of whole-genome sequencing has opened the possibility for high-resolution characterization of bacterial strains down to the clonal and subclonal levels. Core genome multilocus sequence typing is a robust system that uses highly conserved core genes for deep genotyping. The method has been successfully and widely used to describe the epidemiology of various bacterial species. Nevertheless, a cgMLST typing scheme for Clostridium perfringens is currently not publicly available. In this study, we (i) developed a cgMLST typing scheme for C. perfringens, (ii) evaluated the performance of the scheme on different sets of C. perfringens genomes from different hosts and geographic regions as well as from different outbreak situations, and, finally, (iii) made this scheme publicly available supported by an allele nomenclature database for global and standard genomic typing.

Highlights

Clostridium perfringens is a spore-forming anaerobic pathogen responsible for a variety of histotoxic and intestinal infections in humans and animals
The core target genes cover 41.2% (1.34 megabases) of the full genome size and were distributed unevenly across the genome, with a higher representation toward one chromosomal replichore (Fig. S3A). This distribution is consistent with previous studies that reported skewed presence of the species core genome [12, 13], possibly reflecting the uneven spread of mobile elements, in C. perfringens genomes with chromosomal cpe [14]
The core genome-based MLST (cgMLST) typing results showed that at least 95% of the cgMLST target genes were present in 273 of the 282 (96%) genomes examined (Table S1a; Fig. S4), with a mean 6 SD of 99.08 6 1.3% of the 1,431 target genes detected per genome for all genomes (Table S1a)

Summary

Introduction

Clostridium perfringens is a spore-forming anaerobic pathogen responsible for a variety of histotoxic and intestinal infections in humans and animals. This study aimed at establishing a publicly available genome-wide multilocus sequence-typing (MLST) scheme for C. perfringens. A publicly available scheme and an allele nomenclature database for genomic typing of C. perfringens have been established and can be used for broad-based and standardized epidemiological studies. IMPORTANCE Global epidemiological surveillance of bacterial pathogens is enhanced by the availability of standard tools and sharing of typing data. C. perfringens produces resistant spores that allow the bacterium to survive in harsh environments and play a central role in the epidemiology of C. perfringens diseases [2] This bacterium produces a wide array of extracellular toxins and enzymes. Owing to the significantly reduced costs of DNA sequencing over time, MLST has been extended to involve many hundreds of genes with the so-called core genome MLST (cgMLST) and whole-genome MLST (wgMLST) providing high resolution for optimal pathogen typing [10]

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Conclusion