Whole genome sequencing and analysis of Campylobacter coli YH502 from retail chicken reveals a plasmid-borne type VI secretion system

Authors: GHATAK, SANDEEP - Indian Council Of Agricultural Research (ICAR); He, Yiping; Reed, Sue; Strobaugh Jr, Terence; Irwin, Peter

Submitted to: Genomics Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/5/2017
Publication Date: 2/6/2017
Publication URL: https://handle.nal.usda.gov/10113/5629711
Citation: Ghatak, S., He, Y., Reed, S.A., Strobaugh Jr, T.P., Irwin, P.L. 2017. Whole genome sequencing and analysis of Campylobacter coli YH502 from retail chicken reveals a plasmid-borne type VI secretion system. Genomics Data. 11:128-131.

Interpretive Summary: Campylobacter is one of the most common causes of bacterial foodborne illness in the United States. Within the genus Campylobacter, C. jejuni and C. coli are the two species which cause the most cases of human illness. Both of these pathogens can be frequently found in food, particularly in chicken and other meat products. In this work, we isolated a new C. coli strain from retail chicken and obtained a high quality completed genome sequence by using two different next-generation sequencing technologies. Annotation and bioinformatics analysis of the genome revealed the presence of a number of virulence genes in the strain, indicating a high potential for this organism to cause disease. Further investigation of the genome identified the signatures of beta-lactam and aminoglycoside antibiotic resistance genes. The genetic information found in this work provides insight into this organism's antibiotic resistance and virulence potential, which will aid in understanding the genomic features of this important foodborne pathogen for future control strategies.

Technical Abstract: Campylobacter is a major cause of foodborne illnesses worldwide. Campylobacter infections, commonly caused by ingestion of undercooked poultry and meat products, can lead to gastroenteritis and chronic reactive arthritis in humans. Whole genome sequencing (WGS) is a powerful technology that provides comprehensive genetic information about bacteria and is increasingly being applied to study foodborne pathogens: e.g., evolution, epidemiology/outbreak investigation, and detection. Herein we report the complete genome sequence of Campylobacter coli strain YH502 isolated from retail chicken in the United States. WGS, de novo assembly, and annotation of the genome revealed a chromosome of 1,718,974 bp and a mega-plasmid (pCOS502) of 125,964 bp. GC content of the genome was 31.2% with 1931 coding sequences and 53 non-coding RNAs. Multiple virulence factors including a plasmid-borne type VI secretion system and antimicrobial resistance genes (beta-lactams, fluoroquinolones, and aminoglycoside) were found. The presence of T6SS in a mobile genetic element (plasmid) suggesting plausible horizontal transfer of these virulence genes to other organisms. The C. coli YH502 genome also harbors CRISPR sequences and associated proteins. Phylogenetic analysis based on average nucleotide identity and single nucleotide polymorphisms identified closely related C. coli genomes available in the NCBI database. Taken together, the analyzed genomic data of this potentially virulent strain of C. coli will facilitate further understanding of this important foodborne pathogen most likely leading to better control strategies.