title: Whole genome sequencing and analysis ofCampylobacter coliYH502 from retail chicken reveals a plasmid-borne type VI secretion system.
abstract: Campylobacteris a major cause of foodborne illnesses worldwide.Campylobacterinfections, 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 ofCampylobacter colistrain YH502 isolated from retail chicken in the United States. WGS,de novoassembly, 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) suggests plausible horizontal transfer of these virulence genes to other organisms. TheC. coliYH502 genome also harbors CRISPR sequences and associated proteins. Phylogenetic analysis based on average nucleotide identity and single nucleotide polymorphisms identified closely relatedC. coligenomes available in the NCBI database. Taken together, the analyzed genomic data of this potentially virulent strain ofC. coliwill facilitate further understanding of this important foodborne pathogen most likely leading to better control strategies. The chromosome and plasmid sequences ofC. coliYH502 have been deposited in GenBank under the accession numbers CP018900.1 and CP018901.1, respectively.
authors.affiliation: Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya 793103, India.
authors.forename: Sandeep
authors.initials: S
authors.lastname: Ghatak
authors.affiliation: Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA.
authors.forename: Yiping
authors.initials: Y
authors.lastname: He
authors.affiliation: Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA.
authors.forename: Sue
authors.initials: S
authors.lastname: Reed
authors.affiliation: Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA.
authors.forename: Terence
authors.initials: T
authors.lastname: Strobaugh
authors.affiliation: Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Irwin
keywords: Campylobacter coli (C. coli); Plasmid; Type VI secretion system (T6SS); Whole genomes sequencing (WGS)