Whole genome sequencing and 16S rRNA amplicon study of Arcobacter spp in sewage
Arcobacter spp. are emerging food- and waterborne pathogens frequently detected in wastewater treatment plants (WWTPs), yet their diversity, antibiotic resistance, and genomic traits in WWTPs remain poorly characterized. We conducted a systematic investigation of Arcobacter spp. in a Finnish WWTP using combined amplicon sequencing and isolate-based genomic approaches. Arcobacter spp. were highly abundant in raw sewage and substantially reduced during treatment, with A. cryaerophilus and A. suis dominating. A considerable proportion of amplicon sequence variants unclassified to species-level revealed potentially unexplored Arcobacter diversity. For the first time, we demonstrate intragenomic variability in 16S rRNA gene copies of A. cryaerophilus, emphasizing the need to integrate culture-based and culture-independent approaches when studying bacterial diversity. Phenotypic testing revealed high proportions of non-wild type isolates for ampicillin, cefotaxime, tetracycline, and erythromycin. Genomic analyses showed antibiotic resistance profiles were primarily mediated by chromosomally encoded determinants. In contrast, a broad arsenal of chromosomal and plasmid-borne resistance genes to heavy metals, biocides, and organic solvents was detected. This study provides new insights into species-level diversity, resistance mechanisms, and ecological adaptations of Arcobacter in anthropogenically influenced environments.