Mycoplasma gallisepticum Genome sequencing and assembly and core genome MLST development

Mycoplasma gallisepticum (MG) is the most pathogenic avian mycoplasma species to poultry. Currently, MG strain differentiation based on the sequence analysis of 5 loci is proved to be insufficient for accurate outbreak investigation. Recently, whole genome sequence (WGS) of many human and animal pathogens has been successfully used for microbial outbreak investigation. However, the massive sequence data and the diverse properties of different genes within bacterial genomes resulted in the lack of standard reproducible method for comparison between MG whole genomes. Here, we proposed the development of core genome multilocus sequence typing (cgMLST) scheme for typing of MG strains and field isolates. For development of this scheme, a diverse collection of 37 MG genomes was used to identify the cgMLST targets. A total of 425 MG conserved genes (49.85% of MG genome) were selected as core genome targets for this scheme. A total of 81 MG genomes from 5 countries in 4 continents were typed using MG-cgMLST. Analysis 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 MG strains of the same outbreak. MG-cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation between MG isolates. cgMLST provides stable and expandable nomenclature, allowing for comparing and sharing the typing results between different 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.