Jie Wu1, Chongguang Yang2, Liping Lu3, Wanqin Dai4. 1. 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. Electronic address: wujie@51mch.com. 2. 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. 3. Department of Tuberculosis Control, Songjiang District Center for Disease Control and Prevention, Shanghai, China. 4. Clinical Laboratory, Shanghai Songjiang District Central Hospital, Shanghai, China.
Abstract
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.
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.