Boxrud, D. | Search bioRxiv

bioRxiv2026

Whole genome-based Characterization of Virulence and Antimicrobial Resistance Determinants in Clinical Campylobacter jejuni Isolates from Minnesota, 2018-2021

Campylobacter jejuni is a leading cause of foodborne gastroenteritis globally and is classified by the CDC 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 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 was detected, with beta-lactam resistance genes having a particularly high prevalence. The gyrA point mutation associated with quinolone resistance was present in 29% of isolates. 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. 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 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 factors in C. jejuni, supporting its integration into routine monitoring practices to better manage and understand antimicrobial resistance in foodborne pathogens.

microbiology↗

bioRxiv2019

Emergence of a novel Salmonella enterica serotype Reading clone is linked to its expansion in commercial turkey production, resulting in unanticipated human illness in North America

Concurrent separate human outbreaks of Salmonella enterica serotype Reading occurred in 2017-2019 in the United States and Canada, which were both linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of S. Reading from turkeys, and to determine the genomic context of outbreaks involving this rarely isolated Salmonella serotype. A total of 988 isolates of U.S. origin were examined using whole genome-based approaches, including current and historical isolates from humans, meat, and live food animals. Broadly, isolates clustered into three major clades, with one apparently highly adapted turkey clade. Within the turkey clade isolates clustered into three subclades, including an "emergent" clade that only contained isolates dated 2016 or later, including many of the isolates from these outbreaks. Genomic differences were identified between emergent and other turkey subclades suggesting that the apparent success of currently circulating subclades clade is, in part, attributable to plasmid acquisitions conferring antimicrobial resistance, gain of phage-like sequences with cargo virulence factors, and mutations in systems that may be involved in beta-glucuronidase activity and resistance towards colicins. U.S. and Canadian outbreak isolates were found interspersed throughout the emergent subclade and the other circulating subclade. The emergence of a novel S. Reading turkey subclade, coinciding temporally with expansion in commercial turkey production and with U.S. and Canadian human outbreaks, indicates that emergent strains with higher potential for niche success were likely vertically transferred and rapidly disseminated from a common source. ImportanceIncreasingly, outbreak investigations involving foodborne pathogens are confounded by the inter-connectedness of food animal production and distribution, necessitating high-resolution genomic investigations to determine their basis. Fortunately, surveillance and whole genome sequencing, combined with the public availability of these data, enable comprehensive queries to determine underlying causes of such outbreaks. Utilizing this pipeline, it was determined that a novel clone of Salmonella Reading has emerged that coincides with increased abundance in raw turkey products and two outbreaks of human illness in North America. The rapid dissemination of this highly adapted and conserved clone indicates that it was likely obtained from a common source and rapidly disseminated across turkey production. Key genomic changes may have contributed to its apparent continued success in the barn environment, and ability to cause illness in humans.

microbiology↗