Core genome multi-locus sequence typing of Mycoplasma hyorhinis

Mycoplasma hyorhinis is a common commensal and opportunistic pathogen in swine, particularly affecting piglets by causing polyserositis and polyarthritis, and contributing to the Porcine Respiratory Disease Complex. Its role in systemic infection and various clinical manifestations such as meningitis, conjunctivitis, and otitis remain poorly understood. Currently, there are no commercial vaccines in Europe, and management of infection largely relies on antibiotics and biosecurity measures. To better understand and track M. hyorhinis infections, advanced genotyping methods like multi-locus sequence typing and variable number tandem repeat analysis have been developed. However, these techniques show only moderate discriminatory power for differentiating closely related strains. In this study, a core genome multi-locus sequence typing scheme was developed and applied to 81 M. hyorhinis strains from Austrian and German pig herds. The core genome multilocus sequence typing scheme demonstrated superior discriminatory power compared to traditional multi-locus sequence typing methods, revealing high genetic diversity among strains and differences in detection sites. Furthermore, core genome multilocus sequence typing allowing the identification of clonal clusters. The core genome multi-locus sequence typing approach was further compared with core genome single nucleotide polymorphism typing, confirming the high resolution of core genome multi-locus sequence typing for epidemiological studies. Overall, this study highlights the usefulness of core genome multi-locus sequence typing in tracking M. hyorhinis outbreaks and understanding its population structure in pig herds.