Grandjean Louis, Gilman Robert H, Iwamoto Tomatada, Köser Claudio U, Coronel Jorge, Zimic Mirko, Török M Estee, Ayabina Diepreye, Kendall Michelle, Fraser Christophe, Harris Simon, Parkhill Julian, Peacock Sharon J, Moore David A J, Colijn Caroline
University College London, Institute of Child Health, London, United Kingdom.
Academic Health Sciences Centre, Imperial College, London, United Kingdom.
PLoS One. 2017 Dec 27;12(12):e0189838. doi: 10.1371/journal.pone.0189838. eCollection 2017.
Multidrug-resistant tuberculosis poses a major threat to the success of tuberculosis control programs worldwide. Understanding how drug-resistant tuberculosis evolves can inform the development of new therapeutic and preventive strategies.
Here, we use novel genome-wide analysis techniques to identify polymorphisms that are associated with drug resistance, adaptive evolution and the structure of the phylogenetic tree. A total of 471 samples from different patients collected between 2009 and 2013 in the Lima suburbs of Callao and Lima South were sequenced on the Illumina MiSeq platform with 150bp paired-end reads. After alignment to the reference H37Rv genome, variants were called using standardized methodology. Genome-wide analysis was undertaken using custom written scripts implemented in R software.
High quality homoplastic single nucleotide polymorphisms were observed in genes known to confer drug resistance as well as genes in the Mycobacterium tuberculosis ESX secreted protein pathway, pks12, and close to toxin/anti-toxin pairs. Correlation of homoplastic variant sites identified that many were significantly correlated, suggestive of epistasis. Variation in genes coding for ESX secreted proteins also significantly disrupted phylogenetic structure. Mutations in ESX genes in key antigenic epitope positions were also found to disrupt tree topology.
Variation in these genes have a biologically plausible effect on immunogenicity and virulence. This makes functional characterization warranted to determine the effects of these polymorphisms on bacterial fitness and transmission.
耐多药结核病对全球结核病控制项目的成功构成重大威胁。了解耐多药结核病的演变过程可为新的治疗和预防策略的制定提供依据。
在此，我们使用新颖的全基因组分析技术来识别与耐药性、适应性进化以及系统发育树结构相关的多态性。2009年至2013年间在利马郊区卡亚俄和利马南部收集的来自不同患者的471份样本，在Illumina MiSeq平台上进行测序，采用150bp双端读取。与参考H37Rv基因组比对后，使用标准化方法调用变异。使用在R软件中实现的自定义编写脚本进行全基因组分析。
在已知赋予耐药性的基因以及结核分枝杆菌ESX分泌蛋白途径、pks12中的基因以及靠近毒素/抗毒素对的基因中观察到高质量的同塑性单核苷酸多态性。同塑性变异位点的相关性表明许多位点显著相关，提示存在上位性。编码ESX分泌蛋白的基因变异也显著破坏了系统发育结构。还发现关键抗原表位位置的ESX基因突变破坏了树的拓扑结构。
这些基因的变异对免疫原性和毒力具有生物学上合理的影响。这使得进行功能表征以确定这些多态性对细菌适应性和传播的影响成为必要。
