Sadovska Darja, Nodieva Anda, Pole Ilva, Vīksna Anda, Ķimsis Jānis, Ozere Iveta, Norvaiša Inga, Bogdanova Ineta, Bandere Dace, Ranka Renāte
Latvian Biomedical Research and Study Centre, Riga, Latvia.
Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Stopiņi region, Upeslejas, Latvia.
Infect Drug Resist. 2024 Aug 1;17:3289-3307. doi: 10.2147/IDR.S468997. eCollection 2024.
Current tuberculosis treatment regimens primarily rely on phenotypic drug susceptibility testing and rapid molecular assays. Although whole-genome sequencing (WGS) offers a promising alternative, disagreements between phenotypic and molecular testing methods remain. In this retrospective study, we compared the phenotypic and WGS-predicted drug resistance profiles of paired isolates with small genetic distances (≤10 single nucleotide variants) obtained from patients with longitudinal single-episode or recurrent tuberculosis. Additionally, we investigated the distribution of drug-resistance-conferring variants among the identified genotypes.
Paired isolates from 46 patients with pulmonary tuberculosis (2002-2019) were analyzed. Spoligotyping was performed for all the isolates. WGS data were processed using TB-Profiler software to genotype the strains and detect variants in genes associated with drug resistance. The significance of these variants was evaluated using the variant catalog developed by the World Health Organization. Phenotypic drug susceptibility test results were obtained from patients' medical records.
Among the 46 isolate pairs, 25 (54.3%) harbored drug-resistance-associated variants, with 20 demonstrating identical WGS-predicted drug resistance profiles. Drug-resistant isolate pairs belonged to Lineages 2 and 4, with the most common sub-lineages being 2.2.1 (SIT1 and SIT190 spoligotypes), and 4.3.3 (SIT42). Agreement between phenotypic and WGS-based drug susceptibility testing was highest (>90%) for rifampicin, isoniazid, ethambutol, fluoroquinolones, streptomycin, and amikacin when calculated for isolates or isolate pairs. In most discordant cases, isolate pairs harbored variants that could cause low- or moderate-level resistance or were previously associated with variable minimum inhibitory concentrations. Notably, such discrepancies mostly occurred in one isolate from the pair. In addition, differences in resistance-related variant distributions among genotypes were observed for most of the analyzed drugs.
The simultaneous performance of phenotypic and WGS-based drug susceptibility testing creates the most accurate drug resistance profile for isolates and eliminates important limitations of each method.
目前的结核病治疗方案主要依赖表型药敏试验和快速分子检测。尽管全基因组测序（WGS）提供了一种有前景的替代方法，但表型和分子检测方法之间仍存在分歧。在这项回顾性研究中，我们比较了从纵向单发性或复发性结核病患者中获得的遗传距离较小（≤10个单核苷酸变异）的配对分离株的表型和WGS预测的耐药谱。此外，我们还研究了在已鉴定的基因型中赋予耐药性的变异的分布情况。
对46例肺结核患者（2002 - 2019年）的配对分离株进行分析。对所有分离株进行间隔寡核苷酸分型。使用TB-Profiler软件处理WGS数据，对菌株进行基因分型并检测与耐药相关基因中的变异。使用世界卫生组织开发的变异目录评估这些变异的意义。表型药敏试验结果来自患者的病历。
在46对分离株中，25对（54.3%）含有与耐药相关的变异，其中20对显示出相同的WGS预测耐药谱。耐药分离株对属于谱系2和4，最常见的亚谱系是2.2.1（SIT1和SIT190间隔寡核苷酸分型）和4.3.3（SIT42）。当对分离株或分离株对进行计算时，基于表型和WGS的药敏试验之间的一致性在利福平、异烟肼、乙胺丁醇、氟喹诺酮类、链霉素和阿米卡星方面最高（>90%）。在大多数不一致的病例中，分离株对含有可能导致低水平或中等水平耐药或先前与可变最低抑菌浓度相关的变异。值得注意的是，这种差异大多发生在一对中的一个分离株中。此外，对于大多数分析的药物，在基因型之间观察到耐药相关变异分布的差异。
同时进行基于表型和WGS的药敏试验可为分离株创建最准确的耐药谱，并消除每种方法的重要局限性。
