Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients.
Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients.
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DOI：
10.1371/journal.pone.0082551
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Niemann S
中科院分区：
文献类型：
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作者：
Merker M;Kohl TA;Roetzer A;Truebe L;Richter E;Rüsch-Gerdes S;Fattorini L;Oggioni MR;Cox H;Varaine F;Niemann S
多药耐药结核分枝杆菌复合群（MTBC）菌株是结核病（TB）控制的主要威胁。对耐多药结核病患者的治疗时间长，效果差，导致大量治疗失败。进一步耐药的发展导致广泛耐药（XDR）变体。然而，有关治疗失败的个体原因（例如诱导的突变爆发）以及患者体内细菌进化的数据很少。为了解决这个问题，我们研究了从三名接受纵向治疗的耐多药结核病患者中获得的系列MTBC分离株的患者内演变，最终导致广泛耐药结核病。连续分离株显示出相同的IS 6110指纹图谱，表明不存在外源性再感染。我们利用全基因组测序（WGS）来筛选分别来自患者A的三个分离株和来自患者B和C的四个分离株的变异。随后通过桑格测序在多达15个系列分离株中验证获得的多态性。我们确定了8个（患者A）和9个（患者B）多态性，这些多态性在治疗过程中以逐步的方式发生，并与抵抗或潜在的代偿机制有关。对于这两名患者，我们的分析显示了长期共存的克隆亚群，显示不同的耐药等位基因组合。其中，抗性最强的克隆被固定在种群中。相比之下，患者C的基线和随访分离株分别由11个独特的多态性区分，表明IS 6110 RFLP分型未检测到XDR菌株的外源性再感染。我们的研究表明，在纵向治疗下，MDR-MTBC菌株的患者内微进化比以前预期的更复杂。然而，未检测到突变体表型。不同亚群的存在可能混淆表型和分子耐药试验。此外，高分辨率WGS分析对于准确检测外源性再感染是必要的，因为经典基因分型在高发病率环境中缺乏区分能力。
Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains represent a major threat for tuberculosis (TB) control. Treatment of MDR-TB patients is long and less effective, resulting in a significant number of treatment failures. The development of further resistances leads to extensively drug-resistant (XDR) variants. However, data on the individual reasons for treatment failure, e.g. an induced mutational burst, and on the evolution of bacteria in the patient are only sparsely available. To address this question, we investigated the intra-patient evolution of serial MTBC isolates obtained from three MDR-TB patients undergoing longitudinal treatment, finally leading to XDR-TB. Sequential isolates displayed identical IS6110 fingerprint patterns, suggesting the absence of exogenous re-infection. We utilized whole genome sequencing (WGS) to screen for variations in three isolates from Patient A and four isolates from Patient B and C, respectively. Acquired polymorphisms were subsequently validated in up to 15 serial isolates by Sanger sequencing. We determined eight (Patient A) and nine (Patient B) polymorphisms, which occurred in a stepwise manner during the course of the therapy and were linked to resistance or a potential compensatory mechanism. For both patients, our analysis revealed the long-term co-existence of clonal subpopulations that displayed different drug resistance allele combinations. Out of these, the most resistant clone was fixed in the population. In contrast, baseline and follow-up isolates of Patient C were distinguished each by eleven unique polymorphisms, indicating an exogenous re-infection with an XDR strain not detected by IS6110 RFLP typing. Our study demonstrates that intra-patient microevolution of MDR-MTBC strains under longitudinal treatment is more complex than previously anticipated. However, a mutator phenotype was not detected. The presence of different subpopulations might confound phenotypic and molecular drug resistance tests. Furthermore, high resolution WGS analysis is necessary to accurately detect exogenous re-infection as classical genotyping lacks discriminatory power in high incidence settings.
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影响因子：
3
作者：
Ngamphiw C;Kulawonganunchai S;Assawamakin A;Jenwitheesuk E;Tongsima S
通讯作者：
Tongsima S
影响因子：
30.8
作者：
Comas, Inaki;Borrell, Sonia;Roetzer, Andreas;Rose, Graham;Malla, Bijaya;Kato-Maeda, Midori;Galagan, James;Niemann, Stefan;Gagneux, Sebastien
通讯作者：
Gagneux, Sebastien
影响因子：
56.9
作者：
Oliver, A;Cantón, R;Blázquez, J
通讯作者：
Blázquez, J
DOI：
10.1099/mic.0.053983-0
发表时间：
2012-02
期刊：
Microbiology (Reading, England)
影响因子：
--
作者：
Fivian-Hughes AS;Houghton J;Davis EO
通讯作者：
Davis EO
影响因子：
30.8
作者：
通讯作者：
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