使用全基因组测序检测结核病实验室交叉污染。
Detection of tuberculosis laboratory cross-contamination using whole-genome sequencing.
机构信息
Department of Hospital Infection Control, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China; Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China.
Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA.
出版信息
Tuberculosis (Edinb). 2019 Mar;115:121-125. doi: 10.1016/j.tube.2018.10.012. Epub 2019 Mar 9.
OBJECTIVE
Detection of tuberculosis laboratory cross-contamination using whole-genome sequencing.
METHODS
A total of 22 M. tuberculosis strains with high genotypic homology from one hospital were collected during the drug resistance surveillance. Genome sequencing and epidemiological investigation were conducted to determine the occurrence of cross-contamination.
RESULTS
The pair wise comparison between the genomes in each cluster indicated that 15 (71.4%) of 21 strains with available genomic data had no SNP differences with at least one other strain within the same cluster. The analysis of the specimen collection time found that, among the 16 strains collected on the same day, 14 (87.5%) of them had no SNP differences with one another strain; meanwhile, among the strains within the same cluster whose SNP distance was 0, 93.3% (14/15) of them had the same collection time, suggesting that these findings were most likely caused by cross contamination.
CONCLUSION
A high proportion of M. tuberculosis strains with genotypic homology from the single institute that shared the same process time period was most likely caused by the cross contamination. Whole genome sequencing analysis can help to determine the occurrence of cross contamination.
目的
利用全基因组测序检测结核分枝杆菌实验室交叉污染。
方法
收集某医院同一耐药监测时间段内具有高度基因同源性的 22 株结核分枝杆菌。进行基因组测序和流行病学调查，以确定是否发生交叉污染。
结果
每个聚类中基因组之间的两两比较表明，在有可用基因组数据的 21 株菌株中，有 15 株（71.4%）与同一聚类中的至少一株其他菌株没有 SNP 差异。对标本采集时间的分析发现，在同一天采集的 16 株菌株中，有 14 株（87.5%）彼此之间没有 SNP 差异；同时，在 SNP 距离为 0 的同一聚类内的菌株中，有 93.3%（14/15）的菌株具有相同的采集时间，表明这些发现最有可能是由交叉污染引起的。
结论
来自同一机构且具有相同处理时间的高度基因同源性结核分枝杆菌菌株的比例很高，很可能是由交叉污染引起的。全基因组测序分析有助于确定交叉污染的发生。
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