Complete genomic sequence and analysis of β2 toxin gene mapping of Clostridium perfringens JXJA17 isolated from piglets in China

Abstract

Clostridium perfringens (Cp) is a ubiquitous opportunistic pathogen of humans and animals in the natural environment and animal intestines. The pathogenicity of Cp depends on the production of toxins encoded by genes on the chromosomes or plasmids. In contemporary literature, there is no clear consensus about the pathogenicity of CpA β2 toxin. To analyze the homology of the genome of piglet source CpA and its β2 toxin, we sequenced the whole genome of strain JXJA17 isolated from diarrhea piglets using the Illumina Miseq and Pacbio Sequel platforms. The genome was composed of a circular chromosome with 3,324,072 bp (G + C content: 28.51%) and nine plasmids. Genome and 16S rDNA homology analysis revealed a close relation of the JXJA17 strain with the JGS1495, Cp-06, Cp-16, and FORC_003 strains. These strains were isolated from different samples and belonged to different toxin-types. JXJA17 strain was found to carry two toxin genes (plc and cpb2). In contrast to other Cp strains, the cpb2 of JXJA17 was located on a large plasmid (58 kb) with no co-localization of other toxin genes or antibiotic resistance genes. Analysis of JXJA17 genome homology and its cpb2 would facilitate our further study the relationship between β2 toxin and piglet diarrhea.

Figure 1

Circular map of the Clostridium perfringens JXJA17 strain chromosome. Summary of gene annotation and GC skew analysis of the genome of the JXJA17 strain. Circles (from inner to outer): circle 1 represents the scale; circle 2 shows the GC skew; circle 3 shows the GC content; circles 4 and 7 show the COG of each coding sequences (CDSs); and circles 5 and 6 show the positions of CDS. The genome atlas was drawn using CGView 1.0 (http://stothard.afns.ualberta.ca/cgview_server/).

Figure 2

Phylogenetic tree depicting the relationship between JXJA17 and 205 reference Cp strains, constructed based on the genomic BLAST in NCBI (https://www.ncbi.nlm.nih.gov/genome/tree/158).

Figure 3

Comparative alignment of the sequenced C. perfringens plasmids carrying the cpb2. Arrows represent ORFs, and are colored as follows: red arrows—cpb2; yellow arrows—cpe; fuchsia arrows—etx; dark blue arrows—Pcp conjugation locus; green arrows—Tcp conjugation locus; gray arrows—antibiotic resistance; light blue arrows—insertion sequence. ORFs open reading frames.

Figure 4

Collinearity analyses of plasmids JXJA17_p1, pFORC3, pJFP55G, pJFP838D, pJIR3844, pCpb2-CP1, pCP8533etx, pCP13, and pCPF5603. Results aligned by using Mauve 2.4.0. (http://darlinglab.org/mauve).