Determination of Genomic Epidemiology of Historical Clostridium perfringens Outbreaks in New York State by Use of Two Web-Based Platforms: National Center for Biotechnology Information Pathogen Detection and FDA GalaxyTrakr

Abstract

Clostridium perfringens is the second-leading cause of bacterial foodborne illness in the United States. The Wadsworth Center (WC) at the New York State Department of Health enumerates infectious dose from primary patient and food samples and until recently, identified C. perfringens to the species level only. We investigated whether whole-genome sequence-based subtyping could benefit epidemiological investigations of this pathogen, as it has with other enteric organisms. We retrospectively sequenced 76 patient and food samples received between May 2010-February 2020, including 52 samples linked epidemiologically to 13 outbreaks and 24 sporadic samples not linked to other samples. Phylogenetic trees were built using two web-based platforms; National Centers for Biotechnology Information Pathogen Detection (NCBI-PD) and GalaxyTrakr (a Galaxy instance supported by the GenomeTrakr initiative). For GalaxyTrakr analyses single nucleotide polymorphism (SNP) matrices and maximum likelihood (ML) trees were generated using 3 different reference genomes. Across the four separate analyses phylogenetic clustering was generally concordant with epidemiologically-identified outbreaks. SNP diversity among phylogenetically-linked samples in an outbreak ranged from 0-20 SNPs, excepting one outbreak ranging from 4-62 SNPs. Importantly, four of the 13 outbreaks harbored one or more samples that were phylogenetic outliers, and for two outbreaks, no samples were closely related. Three specimens were found harboring two distinct genotypes. For samples below CDC enumeration dose threshold, phylogenetic clustering was robust and linked patient and/or food samples. We concluded that WGS phylogenetic clusters are: 1) largely concordant with epidemiologically-defined outbreaks, irrespective of analysis platform or reference genome we employed; 2) have limited pairwise SNP diversity, allowing phylogenetic clusters to be distinguished from sporadic cases; 3) can aid in epidemiological investigations by identifying outlier and polyclonal samples.

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

“…We applied the scheme to published outbreaks strains described by Carey and colleagues ( 16 ) and Kiu and colleagues ( 17 ). The first study ( 16 ) examined 92 strains from 76 patient and food samples by SNP calling and phylogenetic analysis.…”

“…We applied the scheme to published outbreaks strains described by Carey and colleagues ( 16 ) and Kiu and colleagues ( 17 ). The first study ( 16 ) examined 92 strains from 76 patient and food samples by SNP calling and phylogenetic analysis. SNP calling was done by mapping sequencing reads to reference genomes using GalaxyTrakr's pipeline of the Center for Food Safety and Applied Nutrition (CFSAN) ( 18 ) and with NCBI Pathogen Detection, which uses genome assemblies and performs kmer-based clustering followed by 50-SNP single linkage clustering.…”

“…To evaluate the applicability of the C. perfringens cgMLST scheme for outbreak analysis, we reanalyzed published genomic data of C. perfringens strains from foodborne outbreaks in the United States and United Kingdom, as well as outbreaks in care homes in the United Kingdom (Table S1a). The genome sequences from these outbreaks were recently analyzed using SNP approaches ( 16 , 17 ) and made publicly available along with the associated metainformation. In this study, the raw sequencing data were downloaded and de novo processed using FastQC ( 30 ), shovill ( 31 ), FastANI ( 33 ), Quast ( 34 ), and checkM ( 35 ) as mentioned above.…”

GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians

“…By using the validated CFSAN SNP Pipeline in GalaxyTrakr, Wadsworth scientists will be able to provide reliable SNP cluster analyses to support local outbreak investigations. Galax-yTrakr has also served as a valuable tool to complete some retrospective analyses of outbreaks of non-PulseNet organisms, including Clostridium perfringens [18]. The Wadsworth lab has developed their own tools and pipelines, which can be used for local analyses as well as assessing and improving shared resources.…”

Extensive genome analysis identifies novel plasmid families in Clostridium perfringens

“…Targeted genome-wide phylogenetic analysis provides the capacity to understand these host-specific disease relationships, yet existing analysis has largely focused on specific pathogenic strains from one disease host or phenotype [21–25] or has only just recently begun to include rarely sequenced toxinotypes, such as B, C, D and E strains [26–28]. Large-scale genomic studies of C.…”