Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
Faculty of Veterinary Medicine, Alexandria University, Rasheed El-Mahmoudeya, Markaz Rasheed, El Beheira Governorate, Egypt.
J Clin Microbiol. 2017 Dec 26;56(1). doi: 10.1128/JCM.01145-17. Print 2018 Jan.
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.
是全世界对家禽最具毒性和经济重要性的物种。目前，基于 5 个基因座序列分析的菌株分化对于准确的暴发调查仍然不足。最近，许多人类和动物病原体的全基因组序列（WGS）已成功用于微生物暴发调查。然而，大量的序列数据和细菌基因组内不同基因的多样性特性导致缺乏用于全基因组之间比较的标准可重复方法。在这里，我们提出了为 菌株和现场分离株开发核心基因组多位点序列分型（cgMLST）方案。为了开发该方案，使用了多样化的 37 个基因组来鉴定 cgMLST 靶标。共选择了 425 个保守基因（基因组的 49.85%）作为核心基因组靶标。使用 cgMLST 对来自 5 个国家的 81 个基因组进行了分型。cgMLST 生成的系统发育树分析显示出与地理和时间信息的高度一致性。此外，cgMLST 的高区分能力允许区分同一暴发的 菌株。cgMLST 代表一种标准化、准确、高度区分和可重复的方法，用于区分 分离株。cgMLST 提供稳定且可扩展的命名法，允许在全球范围内的实验室之间进行比较和共享分型结果。cgMLST 为在地方和全球层面利用下一代测序技术在应用禽类支原体流行病学中的巨大力量提供了机会。
