Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.
Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, Australia.
PLoS One. 2016 Oct 13;11(10):e0163612. doi: 10.1371/journal.pone.0163612. eCollection 2016.
Australia has a low tuberculosis incidence rate with most cases occurring among recent immigrants. Given suboptimal cluster resolution achieved with 24-locus mycobacterium interspersed repetitive unit (MIRU-24) genotyping, the added value of whole genome sequencing was explored. MIRU-24 profiles of all Mycobacterium tuberculosis culture-confirmed tuberculosis cases diagnosed between 2009 and 2013 in New South Wales (NSW), Australia, were examined and clusters identified. The relatedness of cases within the largest MIRU-24 clusters was assessed using whole genome sequencing and phylogenetic analyses. Of 1841 culture-confirmed TB cases, 91.9% (1692/1841) had complete demographic and genotyping data. East-African Indian (474; 28.0%) and Beijing (470; 27.8%) lineage strains predominated. The overall rate of MIRU-24 clustering was 20.1% (340/1692) and was highest among Beijing lineage strains (35.7%; 168/470). One Beijing and three East-African Indian (EAI) clonal complexes were responsible for the majority of observed clusters. Whole genome sequencing of the 4 largest clusters (30 isolates) demonstrated diverse single nucleotide polymorphisms (SNPs) within identified clusters. All sequenced EAI strains and 70% of Beijing lineage strains clustered by MIRU-24 typing demonstrated distinct SNP profiles. The superior resolution provided by whole genome sequencing demonstrated limited M. tuberculosis transmission within NSW, even within identified MIRU-24 clusters. Routine whole genome sequencing could provide valuable public health guidance in low burden settings.
澳大利亚的结核病发病率较低，大多数病例发生在最近移民中。鉴于 24 个基因座分枝杆菌散布重复单位（MIRU-24）基因分型的聚类分辨率不理想，探索了全基因组测序的增值作用。对 2009 年至 2013 年间在澳大利亚新南威尔士州（NSW）诊断的所有分枝杆菌培养确诊结核病病例的 MIRU-24 图谱进行了检查并确定了聚类。使用全基因组测序和系统发育分析评估了最大 MIRU-24 聚类中病例之间的相关性。在 1841 例培养确诊的结核病病例中，91.9%（1692/1841）具有完整的人口统计学和基因分型数据。东非印度裔（474；28.0%）和北京（470；27.8%）谱系菌株占主导地位。MIRU-24 聚类的总体率为 20.1%（340/1692），在北京谱系菌株中最高（35.7%；168/470）。一个北京和三个东非印度裔（EAI）克隆复合体负责大多数观察到的聚类。对 4 个最大聚类（30 个分离株）的全基因组测序显示，在鉴定的聚类中存在多种单核苷酸多态性（SNP）。所有测序的 EAI 菌株和 70%的北京谱系菌株通过 MIRU-24 分型聚类表现出明显的 SNP 谱。全基因组测序提供的更高分辨率表明，即使在鉴定的 MIRU-24 聚类中，新南威尔士州的结核分枝杆菌传播也有限。在低负担环境中，常规全基因组测序可以提供有价值的公共卫生指导。
