Whole genome-based characterization of virulence and antimicrobial resistance determinants in clinical Campylobacter jejuni isolates from Minnesota, 2018–2021

ABSTRACT Campylobacter jejuni is a leading cause of foodborne gastroenteritis globally and is classified by the Centers for Disease Control and Prevention as a serious public health threat due to increasing resistance to fluoroquinolones and macrolides. This study used whole-genome sequencing to characterize the virulence and antimicrobial resistance profiles of 2,783 clinical C. jejuni isolates (98.4% stool, 1.2% unknown source, 0.4% blood, and one from rectal swab) collected from Minnesota residents from 2018 through 2021. More than 90% of the isolates had genes related to stress defense ( rpoN and htrB ), cytolethal distending toxin ( cdtA , cdtB , and cdtC ), and cell adhesion and invasion ( ciaB , cadF , and flaC ). A diverse array of antimicrobial resistance genes were detected, with beta-lactam resistance genes having a particularly high prevalence. Five gyrA point mutations associated with quinolone resistance were present in 29% of isolates, with the T861 substitution being the most prevalent. Phenotypically, tetracycline resistance was most common (52.3%), followed by quinolone resistance (30.7%), while resistance to other antimicrobial classes—macrolide (2.4%) and aminoglycoside (1.8%)—was uncommon. To evaluate the correlation between genotypic and phenotypic antimicrobial resistance profiles, the antimicrobial susceptibility testing results from a subset of isolates were compared with genotypic resistance profiles. The results showed a strong overall correlation, particularly for tetracycline and quinolones, though 24 discrepancies were detected. In the majority of discrepancies ( n = 21), genomic antimicrobial resistance markers were absent in isolates that were phenotypically resistant, suggesting possible unknown resistance mechanisms or limitations in current sequencing analysis methods. The remaining three discrepancies occurred in isolates that had the tet (O) resistance gene but were susceptible to tetracycline phenotypically. These findings highlight the value of whole-genome sequencing in improving antimicrobial resistance surveillance and understanding virulence-associated factors in C. jejuni , supporting its integration into routine monitoring practices to better manage and understand antimicrobial resistance in foodborne pathogens. IMPORTANCE This study characterizes the virulence and antimicrobial resistance profiles of Campylobacter isolates using whole-genome sequencing (WGS) data generated through routine foodborne disease surveillance. A subset of isolates was also tested for phenotypic antimicrobial susceptibility testing, allowing us to evaluate resistance patterns and assess genotype-phenotype concordance. This comparison provides important evidence regarding the reliability and limitations of using WGS-detected resistance determinants to predict antimicrobial susceptibility. The 5 years of accumulated surveillance data provide a comprehensive, population-level understanding of circulating Campylobacter strains in Minnesota, USA, and establish an important regional baseline for monitoring changes over time. These findings can be compared with national surveillance data to identify geographic similarities and differences and provide a valuable regional context for public health decision-making and antimicrobial stewardship.