Complete Genome Sequence of Campylobacter coli Strain P4581, a Hybrid Carrying Campylobacter jejuni Genomic Content, Isolated from Rhesus Monkey, Macaca mulatta

ABSTRACT

Campylobacter coli is a leading bacterial cause of human gastroenteritis. We reported the circularized 1.8-Mbp complete genome of MLST type 1055 C. coli strain P4581 isolated from a rhesus monkey, Macaca mulatta, hybridizing Illumina short- and Nanopore long-reads.

ANNOUNCEMENT

Campylobacter coli and C. jejuni are two major pathogens causing gastroenteritis in humans and other animals. Horizontal gene transfer among C. coli and C. jejuni is an evolutionary force for generating large numbers of the new genomic types, “hybrids.” with novel genes or genetic elements (1, 2). Recent evolutionary studies of the Campylobacter population revealed that some C. coli carries more than 10% of C. jejuni reference genomic contents. These C. coli strains containing C. jenuni genomic contents were designated “Hybrid (with >10%)” or “Half hybrid (with <10%)”. Some of these hybrid C. coli strains display ambiguous diagnostic results (3). Though overwhelming genome data of Campylobacter isolates from humans and poultry are currently available, those from nonhuman primates are rare.

Rhesus monkey fecal samples, collected from a nonhuman primate colony at a research center in Arkansas, were screened for Campylobacter species as part of routine surveillance by culturing on Campylobacter Selective media (Remel, San Diego, CA) at 42°C for 4 days under microaerobic conditions (5% O₂, 10% CO₂, and 85% N₂). A typical curved Gram-negative rod-shaped isolate was identified as C. coli using a matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) Biotyper (Bruker, Billerica, MA).

Genomic DNA was isolated from an overnight culture under microaerobic conditions as described earlier using the Blood & Tissue kit (Qiagen, Redwood City, CA), and the quality and quantity of DNA were determined using a NanoDrop spectrophotometer and Qubit fluorometer (Fisher, Waltham, MA). The same genomic DNA was used for Illumina and Nanopore sequencing with no shearing. Following the manufacturer’s protocols, for short reads, a genomic library was constructed using a Nextera XT Library Prep kit and sequenced using a MiSeq v2 Reagent kit in the 250 bp paired-end mode on MiSeq (Illumina, San Diego, CA). Long read sequencing was performed using a NEBNext Companion Module E7180 (New England BioLabs, Ipswich, MA), the ligation sequencing kit SQK-LAK109, and a flow cell FLO-MIN107 on Nanopore MinIon (Oxford Nanopore, Oxford, UK). Default parameters were used for all software unless otherwise noted. After quality checks and trimming with tools (CutAdapt v2.2 with Python v3.7.9) in PATRIC, short reads (n = 2,686,576) and long reads (n = 20,000; N₅₀ = 5423) were assembled with 670× depth using Unicycler v. 0.4.8 (default normal bridging mode, rotation) in PATRIC (4). The complete genome of C. coli P4581 is 1,808,117 bp in length, containing one chromosome (1,693,479 bp) and one plasmid, pCC001, (114,638 bp). The G+C contents of the chromosome and plasmid were 31.43% and 26.3%, respectively. The strain P4581 genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP v4.11) (5). The annotated chromosome contained 1,777 coding genes, 53 pseudogenes, 44 tRNAs, 9 rRNAs, and 2 antibiotic resistance genes, tetO, and oxa-₆₁. The Mash distance between C. coli strain P4581 and representative C. coli strain OR12 (CP013733) was 0.00973, which equated to an average nucleotide identity (ANI) of 99.03% as estimated using MinHash v2.3 (6). The annotated plasmid, pCC001, contained 146 coding genes, including transfer-related genes and 56 repeat regions. Plasmid pCC001 shared 97% sequence identity (query coverage, 78%) with C. coli strain YH503 plasmid pCO5503 (CP046318.1) and 87% sequence identity (query coverage, 87%) with C. jejuni CC19PF065 plasmid pPF065-186 (CP068568). The genomic features are presented in Table 1. Taxonomic computation of C. coli strain P4581 revealed “a chimeric genome of C. coli and C. jejuni” using the Kraken2 algorithm in the Taxonomic Classification Services in PATRIC (7).

TABLE 1.

Summary of genetic features of C. coli strain P4581

Genetic element	Size (bp)	G+C content (%)	No. Coding sequences	No. of rRNAs	No. of tRNAs	GenBank accession no.
Chromosome	1,693,479	31.43	1,777	9	44	CP086657
Plasmid	114,638	26.3	146	0	0	CP086658

Data availability.

The genome sequences have been deposited in GenBank under the accession numbers CP086657 and CP086658. The raw reads have been deposited in the Sequence Read Archive (SRA) under the accession numbers SRR17194716 and SRR17194717.