Biostatistics and Modeling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada.
Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, Canada.
Can J Microbiol. 2019 Nov;65(11):842-850. doi: 10.1139/cjm-2019-0235. Epub 2019 Jul 29.
Whole genome sequencing (WGS) is rapidly replacing other molecular techniques for identifying and subtyping bacterial isolates. The resolution or discrimination offered by WGS is significantly higher than that offered by other molecular techniques, and WGS readily allows infrequent differences that occur between 2 closely related strains to be found. In this investigation, WGS was used to identify the changes that occurred in the genomes of 13 strains of bacterial foodborne pathogens after 100 serial subcultures. Pure cultures of Shiga-toxin-producing , , , and were subcultured daily for 100 successive days. The 1st and 100th subcultures were whole-genome sequenced using short-read sequencing. Single nucleotide polymorphisms (SNPs) were identified between the 1st and final culture using 2 different approaches, and multilocus sequence typing of the whole genome was also performed to detect any changes at the allelic level. The number of observed genomic changes varied by strain, species, and the SNP caller used. This study provides insight into the genomic variation that can be detected using next-generation sequencing and analysis methods after repeated subculturing of 4 important bacterial pathogens.
全基因组测序（WGS）正在迅速取代其他用于鉴定和细分细菌分离株的分子技术。WGS 提供的分辨率或区分度明显高于其他分子技术，并且 WGS 可以轻松发现 2 个密切相关菌株之间发生的罕见差异。在这项研究中，我们使用 WGS 来鉴定在 13 株食源性致病菌的基因组中发生的变化，这些细菌在 100 次连续传代后发生了变化。产志贺毒素的 、 、 和 纯培养物每天进行传代培养，连续进行了 100 天。使用短读长测序对第 1 次和第 100 次传代培养物进行全基因组测序。使用 2 种不同的方法在第 1 次和最终培养物之间鉴定单核苷酸多态性（SNP），并对全基因组进行多位点序列分型，以检测等位基因水平的任何变化。观察到的基因组变化数量因菌株、物种和 SNP 调用者而异。这项研究深入了解了在重复传代 4 种重要细菌病原体后，使用下一代测序和分析方法可以检测到的基因组变异。
