@article {Ghanem2017,
	title = {Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum},
	journal = {Journal of Clinical Microbiology},
	volume = {56},
	year = {2017},
	month = {oct},
	abstract = {\textlessp\textgreater \textlessnamed-content content-type="genus-species"\textgreaterMycoplasma gallisepticum\textless/named-content\textgreater is the most virulent and economically important \textlessnamed-content content-type="genus-species"\textgreaterMycoplasma\textless/named-content\textgreater species for poultry worldwide. Currently, \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater 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 \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater whole genomes. Here, we proposed the development of a core genome multilocus sequence typing (cgMLST) scheme for \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater strains and field isolates. For development of this scheme, a diverse collection of 37 \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater genomes was used to identify cgMLST targets. A total of 425 \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater conserved genes (49.85\% of \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater genome) were selected as core genome targets. A total of 81 \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater genomes from 5 countries on 4 continents were typed using \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater 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 \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater strains of the same outbreak. \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation among \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater 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. \textless/p\textgreater},
	keywords = {cgMLST, genomes, Mycoplasma gallisepticum, strain typing, whole-genome sequence},
	issn = {0095-1137},
	doi = {10.1128/JCM.01145-17},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/29070657 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5744223 https://jcm.asm.org/lookup/doi/10.1128/JCM.01145-17},
	author = {Ghanem, Mostafa and Wang, Leyi and Yan Zhang and Edwards, Scott and Lu, Amanda and Ley, David and El-Gazzar, Mohamed},
	editor = {Fenwick, Brad}
}
