engleski

Whole-Genome Analyses of Campylobacter upsaliensis and C. helveticus Isolated from Dogs and Cats and in Silico Investigation of Their Pathogenic Potentials

Campylobacter species are commonly isolated from faeces of dogs and cats with C. upsaliensis (CU) and C. helveticus (CH) being the most frequently isolated. These two species are usually not considered pathogenic in dogs and cats and are closely related to each other and to C. jejuni, the most common cause of bacterial gastroenteritis in humans in the developed world. Interestingly, despite their close genetic relationship, in humans CU is considered a pathogen while CH is not. This study aimed to describe whole genomes of CU and CH isolated from dogs and cats and to in silico investigate their pathogenic potential with comparison to several published genomes of C. jejuni and C. coli. Genomic DNA was extracted from three isolates of each of CU and CH recovered from the faeces of healthy dogs and cats. Sequencing was performed using an Illumina MiSeq to generate 250 base-paired reads. Reads were trimmed for both length and quality. Contigs were assembled using the Velvet assembler. The concatenated contigs generated for each assembly were quality ranked (by number, size, maximum length and N50), and the three top-ranked assemblies were annotated using the Prokka annotation tool. Ribosomal MLST nucleotide sequences were used as a proxy for the core genome to compare the phylogeny of CU and CH with other species in the Campylobacter genus and visualised as a NeighborNet using SplitsTree. Annotated draft genomes were clustered using OrthoMCL, and pathogenic traits were investigated in silico using PathogenFinder and VirulentPred software. The CU and CH draft genomes were ~ 1.732 Mb and ~ 1.844 Mb in size, and comprised on average 110 and 151 contigs, and on average 1782 and 1942 predicted genes, respectively. Of these, CU had on average 497 and CH 622 hypothetical proteins. Using OrthoMCL, a core genome of 1459 and 1751 genes resulted for CU and CH, respectively. NeighborNet trees based on ribosomal MLST nucleotide sequences and the core genome confirmed the close phylogenetic relationship of CH and CU within the Campylobacter genus. PathogenFinder predicted all isolates as human pathogens with probabilities of 88.3–91.5%. Both PathogenFinder and VirulentPred identified many pathogenic proteins in CU and CH of different functions (e.g., chemotaxis, transporter and motility systems) but considerably fewer than in C. jejuni and C. coli. This study provides many insights into the pathogenic potential of pet-associated emerging Campylobacter pathogens and is, to our knowledge, the first to report a draft genome of CH.

genome ; companion animals ; zoonosis ; Campylobacter ; emerging pathogens ; pathogenicity ;

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