Comparison genomics of two closely related isolates of Clostridium perfringens full genome sequences reveals regions of genome plasticity with prevention potential

Abstract

Abstract The spore-forming anaerobic Clostridium perfringens (CP) is the primary etiological agent of necrotic enteritis (NE) disease, one of priority enteric diseases in chickens which is responsible for annual losses of $6 billion in the US poultry industry. Our long term goal is to develop a recombinant vaccine against NE as an antibiotic alternative. Because the design of effective vaccines requires a thorough understanding of the pathogen’s entire genome and their functions, we sequenced the genomes of two closely related Type A CP strains: Del1 and CP15, isolated from NE-afflicted chicken farms. Del1 is very virulent, while CP15 produced very mucoid supernatant in its growth medium culture. PacBio and Illumina sequencing technologies were used to generate accurate de novo and hybrid genome assemblies. In this study, these two assembled full genomes are deposited into NCBI GenBank, annotated and analyzed. Del1 has a circular genome of 3.55 M base pairs (bp) long and four plasmids (82326, 69601, 49550, and 49456 bp) with a total of 3361 predicted open reading frames. CP15 has a genome of 3.34 M bp long and four plasmids (14755, 3843, 3202 and 2421 bp) with a total of 2997 predicted CDS. The sequenced data revealed that Del1 contains a pore-forming toxin netB encoded within one of highly conserved NE-associated loci. In contrast, CP15 did not contain netB gene. Sequenced data also showed that Del1 has a unique ribosomal protection protein which protects ribosomes from the translation inhibition of tetracycline (YP_001967743). These results provide important insight into the pathogenesis of CP in avian NE and novel information on potential targets of toxins and virulence factors that will facilitate the vaccine design.