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Description:
Several species of the genus Campylobacter (C.) are zoonotic pathogens, especially C. jejuni and C. coli, the leading causes of foodborne diseases worldwide. Although both species colonize many hosts including poultry, livestock and wild animals, persistence mechanisms enabling the bacteria to adapt towards new ecological niches are not yet fully understood. In this work, novel k-mer-based methods enabling high-throughput analysis of whole-genome sequencing (WGS) data of C. jejuni and C. coli have been developed, extended and applied to investigate the adaptive potential of the distinct species towards different ecological niches and changing environments. A k-mer-based microbial genome-wide association study (GWAS) was set up to identify host-specific genomic signatures of C. jejuni isolated from chicken, cattle, pig and clinical human samples. GWAS revealed a strong association of both, the core and the accessory genome of C. jejuni, with distinct host animal species. Moreover, multiple adaptive trajectories defining the evolution of C. jejuni lifestyle preferences in different ecosystems were identified. In a second approach, WGS data of Campylobacter isolates that showed ambiguous probing results using different polymerase chain reaction (PCR)-based species classification methods during routine-diagnostics were investigated. The Campylobacter genomes were analyzed with respect to their genomic make-up. For this purpose, a k-mer-based method was developed in order to identify recombination events between C. jejuni and C. coli. The identified genes encode proteins that were commonly associated with important pathways involved in chromosome maintenance and DNA repair, membrane transport and stress defense. Overall, the results presented in this work promote molecular surveillance and rapid diagnostics of Campylobacter. In addition, host-specific allelic variants identified among different phylogenetic backgrounds might serve as important maker genes in future source attribution models for fast and precise ...