Whole-Genome Sequence of Multidrug-Resistant Campylobacter coli Strain COL B1-266, Isolated from the Colombian Poultry Chain

Abstract

Campylobacter coli is considered one of the main causes of food-borne illness worldwide. We report here the whole-genome sequence of multidrug-resistant Campylobacter coli strain COL B1-266, isolated from the Colombian poultry chain. The genome sequences encode genes for a variety of antimicrobial resistance genes, including aminoglycosides, β-lactams, lincosamides, fluoroquinolones, and tetracyclines.

GENOME ANNOUNCEMENT

Campylobacter spp. are spiral-shaped bacteria capable of surviving in a wide range of environments, causing disease in humans and animals (1) and are also considered one of the main causes of food-borne illness worldwide (2, 3). In industrialized countries Campylobacter coli is the most common cause of community-acquired inflammatory enteritis (4). Other studies have suggested that the consumption of undercooked poultry and/or the inappropriate handling of raw poultry are risk factors for human campylobacteriosis (5, 6). Although most Campylobacter sp. infections are self-limiting, severe infections can occur and can even be fatal for very young children, the elderly, and immunosuppressed people (7). Some strains of Campylobacter spp. are increasingly resistant to most clinically important antibiotics, generating concern among public health authorities. The Campylobacter sp. described here is part of a comprehensive prevalence survey from the Colombian Integrated Program for Antimicrobial Resistance Survival (COIPARS), a national initiative to evaluate and to mitigate the spread of antimicrobial resistance associated to zoonotic pathogens in Colombia (8, 9). The isolate COL B1-266 is a multidrug-resistant member of a Campylobacter coli pulsed-field gel electrophoresis (PFGE) cluster composed of eight isolates from different stages of the poultry chain production (including drinking water at the farm, hatchery, and broiler farm and carcasses at slaughterhouses), suggesting dissemination through the poultry chain. This study was developed with the collaboration of two commercial producers in Colombia.

Here, we report the first whole-genome sequence of a Colombian multidrug-resistant strain, Campylobacter coli COL B1-266. Genomic DNA was isolated from an overnight culture using the PureLink Genomic DNA minikit (Invitrogen), and DNA libraries were prepared using the SureSelect QXT sample preparation kit (Agilent). The libraries were prepared according to the manufacturer’s instructions and sequenced on an Illumina HiScanSQ instrument with 2 × 151-bp paired-end reads, according to standard Illumina protocols. The genome was assembled using the reference-guided assembler ARGO, developed at NCBI, and the de-novo assembler SPAdes (10) to create initial assemblies of the reads. These were combined to produce the final assembly using a conservative process that incorporates pieces of de-novo assembly in the reference-guided assembly. The genome sequence of strain COL B1-266 consisted of 121 contigs, yielding total sequences of 1,948,500 bp. The overall G+C content of the isolate was determined to be 31%. The contigs were annotated using the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) and have been deposited at GenBank. The results of the genome annotation revealed 2,106 genes, 2,062 coding sequences, 120 pseudogenes, 3 rRNAs, 38 tRNAs, and 3 noncoding RNAs.

A search for resistance-associated genes present in the isolate was performed using ResFinder version 2.1 (11) and enriched using RAST version 2.0 (12) with default parameters. We found antimicrobial resistance genes for aminoglycosides (Aph 3′-III, Aad A2, and Sat1), β-lactams (blaOXA-61: beta-lactamase EC 3.5.2.6 or Cam-1), lincosamides (InuC), fluoroquinolones (gyrA and gyrB), tetracyclines (EF-G and TetO), and some genes associated with increased drug resistance (Efflux pumps: MFS, MacA, MacB, RND, and OM).

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession number LKIV00000000. The version described in this paper is the second version. The BioProject accession is PRJNA296596.