Complete genome sequences of slostridium perfringens strain del1 isolated from necrotic enteritis-afflicted chicken farm

Authors: Li, Charles; Yan, Xianghe; Lillehoj, Hyun

Submitted to: Gut Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/20/2017
Publication Date: 2/1/2018
Citation: Li, C.Z., Yan, X., Lillehoj, H.S. 2018. Complete genome sequences of slostridium perfringens strain del1 isolated from necrotic enteritis-afflicted chicken farm. Gut Pathogens. 9:69. https://doi.org/10.1186/s13099-017-0217-6.
DOI: https://doi.org/10.1186/s13099-017-0217-6

Interpretive Summary: The increasing cost in control of infectious diseases and food safety are big challenges that global poultry food industry is meeting. One of top priority diseases in poultry is necrotic enteritis (NE). NE is caused by a kind of intestinal bacteria call Clostridium perfringens (abbreviated as CP) which produces many gut-damage toxins, results in the poultry growth underperformance, and impacts animal welfare and human food safety with estimated economic loss of $6 billions annually in USA. In poultry industry, the increasing incidence of NE disease incidence is also associated with the withdrawal of growth promoting antibiotics as supplement from feed due to government regulation and public concern over appearance of the antibiotic resistant bacteria. Before the effective feed alternative solution to antibiotics is sought, the disease-causing mechanism needs to be elucidated for CP bacteria. The ARS scientists extracted DNA from a very virulent CP bacteria strain Del1 isolated from the intestines of sick chickens infected with necrotic enteritis, sequenced the DNAs from one large chromosome molecule and 4 small DNA molecules called plasmids, and compared their sequences with those of other published CP strains. The sequencing analysis revealed that the bacterial strain Del1 DNA contained numerous genes responsible for toxin and virulence factors, 6 antibiotic resistance and 3 bacterial viruses called bacteriophages (or called as phages in simplicity). These results provide important insight into improved understanding of the disease mechanism of CP in avian necrotic enteritis and novel information on potential targets of toxins and virulence factors that will facilitate the vaccine development to contain CP bacterial infection.

Technical Abstract: Background: Clostridium perfringens (CP) is ubiquitous in the nature. It is a normal inhabitant in the intestinal tracts of animals and human. As the primary etiological agent of gas gangrene, necrosis and bacteremia, CP causes food poisoning, necrotic enteritis (NE), and even death. Recent omics research found increasing incidence of CP as well as most other Clostridium spp., after antibiotic treatment and its virulence is typically linked to highly efficient conjugative transfer of the toxins or plasmids carrying resistance traits. The increasing incidence of NE in poultry is associated with the withdrawal of in-fed antibiotic growth promoters in poultry production due to government regulations. In this report, we sequenced and analyzed the genome of Clostridium perfringens (CP) Del1 strain using the hybrid of PacBio and Illumina Nextera XT technologies. Results: Sequence analysis indicated that CP Strain Del1 comprised a single circular chromosome with a complete 3,559,163 bp genome in size and 4 plasmids: pDel1_1 (82,596 bp), pDel1_2 (69,827 bp), pDel1_3 (49,582 bp), and pDel1_4 (49,728 bp). The genome has 3361 predicted coding DNA sequences (CDS). The chromosome and plasmids harbor numerous genes for pathogenesis and virulence factors, 6 antibiotic and antimicrobial resistance and 3 bacteriophages. The phylogenetic analyses reveal Del1's extensive similarity to Clostridium perfringens CP4 genome and plasmid sequences which have been previously reported. Conclusion: Complete chromosomal genome and plasmid sequences of CP Strain Del1 are revealed in this report. Genome sequencing of the chicken pathogenic isolates from commercial farms could provide valuable insights on the molecular pathogenesis and ecological pressure that drive the emergence of C. perfringens as a gastrointestinal pathogen in food animals and will facilitate the development of logical vaccine against C. perfringens-induced necrotic enteritis in chickens. Keywords: Clostridium perfringens, Genome Sequencing; necrotic enteritis, necrotic enteritis toxin B-like (netB-like)