High resolution discrimination of clinical Mycobacterium tuberculosis complex strains based on single nucleotide polymorphisms.
High resolution discrimination of clinical Mycobacterium tuberculosis complex strains based on single nucleotide polymorphisms.
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DOI：
10.1371/journal.pone.0039855
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Niemann S
中科院分区：
文献类型：
--
作者：
Homolka S;Projahn M;Feuerriegel S;Ubben T;Diel R;Nübel U;Niemann S
最近，结核分枝杆菌复合群（MTBC）种群结构的多样性已被详细描述。基于地理分离和特定宿主病原体共同进化形成MTBC毒力性状，至少有20个主要谱系/基因型已经进化，最终导致菌株遗传背景对传播性、临床表现/结果和抗性发展的明显影响。因此，高分辨率基因分型表征菌株在较大的研究是强制性的宿主-病原体相互作用的机制，以提高结核病（TB）的控制。单核苷酸多态性（SNPs）是临床分离株谱系分类的最可靠的标志物，因为其同源性低，但其使用受到低区分能力或需要分析大量基因以实现更高分辨率的阻碍。因此，我们进行了26个基因的从头测序（约100个）。20000 bp/菌株），以定义高度区分的基因组。总的来说，检测到161个多态性，其中59个是基因型特异性的，而13个定义更深的分支，如欧美血统。在基于群体的菌株收集（一年，汉堡市，德国）中对11个基因的最可变集合的无偏研究证实了SNP分析的有效性，因为所有菌株都以高准确度分类。总之，我们定义了一种诊断算法，该算法允许通过仅对五个基因进行测序分析首次以高置信度鉴定17个MTBC系统发育谱系。总之，在我们的研究中开发的诊断算法很可能为基于低成本高分辨率序列/SNP的具有非常高特异性的MTBC分化打开大门。可以建立高通量测定法，这将是大的关联研究所需的，这些研究是结核病感染期间宿主-病原体相互作用的详细调查所必需的。
Recently, the diversity of the Mycobacterium tuberculosis complex (MTBC) population structure has been described in detail. Based on geographical separation and specific host pathogen co-evolution shaping MTBC virulence traits, at least 20 major lineages/genotypes have evolved finally leading to a clear influence of strain genetic background on transmissibility, clinical presentation/outcome, and resistance development. Therefore, high resolution genotyping for characterization of strains in larger studies is mandatory for understanding mechanisms of host-pathogen-interaction and to improve tuberculosis (TB) control. Single nucleotide polymorphisms (SNPs) represent the most reliable markers for lineage classification of clinical isolates due to the low levels of homoplasy, however their use is hampered either by low discriminatory power or by the need to analyze a large number of genes to achieve higher resolution. Therefore, we carried out de novo sequencing of 26 genes (approx. 20000 bp per strain) in a reference collection of MTBC strains including all major genotypes to define a highly discriminatory gene set. Overall, 161 polymorphisms were detected of which 59 are genotype-specific, while 13 define deeper branches such as the Euro-American lineage. Unbiased investigation of the most variable set of 11 genes in a population based strain collection (one year, city of Hamburg, Germany) confirmed the validity of SNP analysis as all strains were classified with high accuracy. Taken together, we defined a diagnostic algorithm which allows the identification of 17 MTBC phylogenetic lineages with high confidence for the first time by sequencing analysis of just five genes. In conclusion, the diagnostic algorithm developed in our study is likely to open the door for a low cost high resolution sequence/SNP based differentiation of the MTBC with a very high specificity. High throughput assays can be established which will be needed for large association studies that are mandatory for detailed investigation of host-pathogen-interaction during TB infection.
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