Complete Genome Sequences of Multidrug-Resistant Campylobacter jejuni Strain 14980A (Turkey Feces) and Campylobacter coli Strain 14983A (Housefly from a Turkey Farm), Harboring a Novel Gentamicin Resistance Mobile Element

Abstract

Multidrug resistance (MDR) in foodborne pathogens is a major food safety and public health issue. Here we describe whole-genome sequences of two MDR strains of Campylobacter jejuni and Campylobacter coli from turkey feces and a housefly from a turkey farm. Both strains harbor a novel chromosomal gentamicin resistance mobile element.

GENOME ANNOUNCEMENT

Campylobacter jejuni and C. coli are leading bacterial agents for human foodborne disease, with poultry serving as a major vehicle (1). They frequently exhibit resistance to various antimicrobials, especially tetracycline (2). Resistance to the aminoglycoside gentamicin was rare, but has recently increased markedly (http://www.cdc.gov/narms/pdf/2011-annual-report-narms-508c.pdf, http://www.fda.gov/downloads/AnimalVeterinary/SafetyHealth/AntimicrobialResistance/NationalAntimicrobialResistanceMonitoringSystem/UCM453387.pdf). Here we report the whole-genome sequence of C. jejuni strain 14980A, isolated in July 2014 from turkey feces in a commercial turkey house (conventional production) in North Carolina, and C. coli strain 14983A, isolated on the same date from a housefly (Musca domestica) in the same turkey house. The fly isolate C. coli 14983A was resistant to all tested antibiotics (tetracycline, streptomycin, erythromycin, kanamycin, ciprofloxacin, nalidixic acid, gentamicin) while C. jejuni strain 14980A was resistant to all but erythromycin.

The Roche GS-FLX, Illumina MiSeq and PacBio RSII platforms were used to complete both genomes. Roche 454 shotgun and paired-end reads were assembled into single chromosomal scaffolds using the Roche Newbler assembler (v2.6); however, neither scaffold could be closed due to chromosomal repeats. Therefore, PacBio sequencing was used to generate single contigs for both genomes, and also generated single contigs for both megaplasmids. A final base call validation was performed using Illumina MiSeq reads. Illumina reads were also used to characterize hypervariable GC tracts, as described (3). The final coverage for both strains was >200×.

The two strains have circular genomes of 1,797 kb (14983A) and 1,709 kb (14980A). C. coli strain 14983A harbors three plasmids (180.5, 4.4, and 3.1 kb) and has sequence type (ST) 1067, while C. jejuni strain 14980A contains a single plasmid (50.7 kb) and has ST-1839. Protein-, rRNA-, and tRNA-encoding genes were identified as described (3), using a BLASTp identity of 50% to define a positive protein match. Nine predicted functional/degenerate IS elements were identified in C. coli strain 14983A and two in C. jejuni strain 14980A.

Genes or point mutations associated with the antibiotic resistance profiles were identified. Both megaplasmids harbor tet(O) associated with tetracycline resistance (4), along with either aphA-3 (C. jejuni strain 14980A) or aphA-7 (C. coli strain 14983A) that confers kanamycin resistance (5–7). Ciprofloxacin and nalidixic acid resistance in both strains was due to a Thr 86 → Ile substitution within GyrA (8, 9). Similarly, streptomycin resistance was associated with a substitution within RpsL: Lys 43 → Arg in C. coli strain 14983A and Lys 88 → Arg in C. jejuni strain 14980A (10, 11). Erythromycin resistance in C. coli strain 14983A was conferred by an A → G transition in all three copies of the 23S rRNA gene (equivalent to A2059 → G in Escherichia coli [12, 13]). An unique characteristic of both strains was a novel IS1595-family chromosomal mobile element, inserted at a different site in each strain (linked to fabG in C. jejuni strain 14980A and rplM in C. coli strain 14983A), harboring the gentamicin resistance determinant aph(2′′)-If (14). Although the element in 14983A also harbored an IS605-family element, the two elements were essentially identical (2-bp divergence).

Accession number(s).

The complete genome/plasmid sequences of C. coli strain 14983A and C. jejuni strain 14980A have been deposited in GenBank under the accession numbers CP017025 to CP017028 and CP017029 to CP017030, respectively.