Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum.

is the most virulent and economically important species for poultry worldwide. Currently, strain differentiation based on sequence analysis of 5 loci remains insufficient for accurate outbreak investigation. Recently, whole-genome sequences (WGS) of many human and animal pathogens have been successfully used for microbial outbreak investigations. However, the massive sequence data and the diverse properties of different genes within bacterial genomes results in a lack of standard reproducible methods for comparisons among whole genomes. Here, we proposed the development of a core genome multilocus sequence typing (cgMLST) scheme for strains and field isolates. For development of this scheme, a diverse collection of 37 genomes was used to identify cgMLST targets. A total of 425 conserved genes (49.85% of genome) were selected as core genome targets. A total of 81 genomes from 5 countries on 4 continents were typed using cgMLST. Analyses of phylogenetic trees generated by cgMLST displayed a high degree of agreement with geographical and temporal information. Moreover, the high discriminatory power of cgMLST allowed differentiation between strains of the same outbreak. cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation among isolates. cgMLST provides stable and expandable nomenclature, allowing for comparison and sharing of typing results among laboratories worldwide. cgMLST offers an opportunity to harness the tremendous power of next-generation sequencing technology in applied avian mycoplasma epidemiology at both local and global levels.