Comparative Performance of Genomic Methods for the Detection of Pyrazinamide Resistance and Heteroresistance in Mycobacterium tuberculosis.
Comparative Performance of Genomic Methods for the Detection of Pyrazinamide Resistance and Heteroresistance in Mycobacterium tuberculosis.
复制标题
DOI：
10.1128/jcm.01907-21
复制
发表时间：
2022-01-19
影响因子：
9.4
通讯作者：
Metcalfe JZ
中科院分区：
文献类型：
--
作者：
Whitfield MG;Engelthaler DM;Allender C;Folkerts M;Heupink TH;Limberis J;Warren RM;Van Rie A;Metcalfe JZ
吡津酰胺是药物敏感和耐药结核病治疗方案的重要组成部分。虽然大约50%的利福平耐药菌株对吡嗪酰胺也有耐药性，但由于检测的挑战性，不会常规进行吡津胺敏感性测试。我们调查了基因分型和表型方法的诊断准确性，并探讨了吡嗪酰胺异质性耐药的发生。我们使用Sanger和pncA基因的靶向深度测序(TDS)、全基因组测序(WGS)和表型药物敏感性测试，评估了在南非EXIT-RIF队列中登记的358名个体的吡津胺敏感性。我们计算了不同方法的诊断准确性，并调查了pncA异质性耐药的患病率和临床影响。使用Köser分类和专家规则将真实的吡嗪酰胺敏感性状态分配给每个分离物。我们在检测pncA固定突变的基因分型方法中观察到100%的符合率；只有TDS自信地识别出三个分离株(0.8%)有微小的变异。对于355株(99.2%)可确定为真吡嗪酰胺状态的菌株，表型DST的敏感性为96.5%(95%可信区间，93.8~99.3%)，特异性为100%(95%CI，100~100%)，Sanger测序法和WGS的敏感性为97.1%(95%CI，94.6~99.6%)，特异性为97.8%(95%CI，95.7~99.9%)，TDS的敏感性为98.8%(95%CI，95.7%~99.9%)，特异度为97.8%(95%CI，95.7%~99.9%)。在所有被评估的基因分型方法中，我们证明了吡嗪酰胺敏感性试验的高度敏感性和特异性。与其他一线药物相比，结核分枝杆菌分离株对吡嗪酰胺的异质性耐药发生率较低。
Pyrazinamide is an important component of both drug-susceptible and drug-resistant tuberculosis treatment regimens. Although approximately 50% of rifampin-resistant isolates are also resistant to pyrazinamide, pyrazinamide susceptibility testing is not routinely performed due to the challenging nature of the assay. We investigated the diagnostic accuracy of genotypic and phenotypic methods and explored the occurrence of pyrazinamide heteroresistance. We assessed pyrazinamide susceptibility among 358 individuals enrolled in the South African EXIT-RIF cohort using Sanger and targeted deep sequencing (TDS) of the pncA gene, whole-genome sequencing (WGS), and phenotypic drug susceptibility testing. We calculated the diagnostic accuracy of the different methods and investigated the prevalence and clinical impact of pncA heteroresistance. True pyrazinamide susceptibility status was assigned to each isolate using the Köser classification and expert rules. We observed 100% agreement across genotypic methods for detection of pncA fixed mutations; only TDS confidently identified three isolates (0.8%) with minor variants. For the 355 (99.2%) isolates that could be assigned true pyrazinamide status with confidence, phenotypic DST had a sensitivity of 96.5% (95% confidence interval [CI], 93.8 to 99.3%) and specificity of 100% (95% CI, 100 to 100%), both Sanger sequencing and WGS had a sensitivity of 97.1% (95% CI, 94.6 to 99.6%) and specificity of 97.8% (95% CI, 95.7 to 99.9%), and TDS had sensitivity of 98.8% (95% CI, 97.2 to 100%) and specificity of 97.8% (95% CI, 95.7 to 99.9%). We demonstrate high sensitivity and specificity for pyrazinamide susceptibility testing among all assessed genotypic methods. The prevalence of pyrazinamide heteroresistance in Mycobacterium tuberculosis isolates was lower than that identified for other first-line drugs.