Abstract：
BACKGROUND: Single-nucleotide variants (SNVs) in Mycobacterium tuberculosis (M. tuberculosis) genomes can predict multidrug resistance (MDR) but not all phenotype-genotype correlations can be explained. We investigated SNVs in efflux pumps (EPs) in the context of M. tuberculosis drug resistance.
METHODS: We analysed 2221 M. tuberculosis genomes from 1432 susceptible and 200 MDR, 172 pre-extensively drug resistant (XDR) and 417 XDR isolates. Analysis of 47 EP genes was conducted using MTB-VCF, an in-house bioinformatics pipeline. SNVs were categorized according to their SIFT/Polyphen scores. Resistance genotypes were also called using the TB-Profiler tool.
RESULTS: Genome comparisons between susceptible and drug resistant (DR) isolates identified 418 unique SNVs in EP of which; 53.5% were in MDR, 68.9% in pre-XDR and 61.3% in XDR isolates. Twenty EPs had unique SNVs with a high SIFT/PolyPhen score, comprising 38 unique SNVs. Sixteen SNVs across 12 EP genes were significantly associated with drug resistance and enriched in pre-XDR and XDR strains. These comprised 12 previously reported SNVs (in Rv0191, Rv0507, Rv0676, Rv1217, Rv1218, Rv1273, Rv1458, Rv1819, and Rv2688) and 4 novel SNVs (in Rv1877 and Rv2333). We investigated their presence in genomes of 52 MDR isolates with phenotype-genotype discrepancies to rifampicin (RIF), isoniazid (INH), or fluoroquinolones. SNVs associated with RIF and INH (Rv1217_1218, Rv1819, Rv0450, Rv1458, Rv3827, Rv0507, Rv0676, Rv1273, and Rv2333), and with fluoroquinolone (Rv2688) resistance were present in these discrepant strains.
CONCLUSIONS: Considering SNVs in EPs as part of M. tuberculosis genome-based resistance interpretation may add value, especially in evaluation of XDR resistance in strains with phenotype-genotype discrepancies.
METHODS: We analysed 2221 M. tuberculosis genomes from 1432 susceptible and 200 MDR, 172 pre-extensively drug resistant (XDR) and 417 XDR isolates. Analysis of 47 EP genes was conducted using MTB-VCF, an in-house bioinformatics pipeline. SNVs were categorized according to their SIFT/Polyphen scores. Resistance genotypes were also called using the TB-Profiler tool.
RESULTS: Genome comparisons between susceptible and drug resistant (DR) isolates identified 418 unique SNVs in EP of which; 53.5% were in MDR, 68.9% in pre-XDR and 61.3% in XDR isolates. Twenty EPs had unique SNVs with a high SIFT/PolyPhen score, comprising 38 unique SNVs. Sixteen SNVs across 12 EP genes were significantly associated with drug resistance and enriched in pre-XDR and XDR strains. These comprised 12 previously reported SNVs (in Rv0191, Rv0507, Rv0676, Rv1217, Rv1218, Rv1273, Rv1458, Rv1819, and Rv2688) and 4 novel SNVs (in Rv1877 and Rv2333). We investigated their presence in genomes of 52 MDR isolates with phenotype-genotype discrepancies to rifampicin (RIF), isoniazid (INH), or fluoroquinolones. SNVs associated with RIF and INH (Rv1217_1218, Rv1819, Rv0450, Rv1458, Rv3827, Rv0507, Rv0676, Rv1273, and Rv2333), and with fluoroquinolone (Rv2688) resistance were present in these discrepant strains.
CONCLUSIONS: Considering SNVs in EPs as part of M. tuberculosis genome-based resistance interpretation may add value, especially in evaluation of XDR resistance in strains with phenotype-genotype discrepancies.
摘要：
背景：结核分枝杆菌（MTB）基因组中的单核苷酸变异（SNV）可以预测多药耐药性（MDR），但不能解释所有表型-基因型相关性。我们在MTB耐药性的背景下研究了外排泵（EP）中的SNV。
方法：我们分析了来自1432个易感和200个MDR的2221个MTB基因组，172个pre-XDR（广泛耐药）和417个XDR分离株。使用MTB-VCF对47个EP基因进行分析，内部生物信息学管道。根据其SIFT/Polyphen评分对SNV进行分类。也使用TB-Profiler工具调用抗性基因型。
结果：易感和DR分离株之间的基因组比较在EP中确定了418个独特的SNV；53.5％在MDR中，XDR前68.9%，XDR分离株61.3%。二十EP具有独特的SNV，具有较高的SIFT/PolyPhen评分，包括38个独特的SNV。12个EP基因中的16个SNV与耐药性显着相关，并在preXDR和XDR菌株中富集。这些是先前报道的12个SNV（在Rv0191，Rv0507，Rv0676，Rv1217，Rv1218，Rv1273，Rv1458，Rv1819和Rv2688中）和四个新颖的SNV（在Rv1877和Rv2333中）。我们调查了52个与利福平（RIF）表型基因型不一致的MDR分离株中的16个SNV，异烟肼（异烟肼）和氟喹诺酮。与RIF和INH关联的SNV（Rv1217_1218、Rv1819、Rv0450、Rv1458、Rv3827、Rv0507、Rv0676、Rv1273和Rv2333），在这些不同的菌株中存在对氟喹诺酮(Rv2688)的耐药性。
结论：将外排泵中的SNV作为基于MTB基因组的抗性解释的一部分，可能会增加价值，尤其是在评估具有表型-基因型差异的菌株的XDR抗性方面。
方法：我们分析了来自1432个易感和200个MDR的2221个MTB基因组，172个pre-XDR（广泛耐药）和417个XDR分离株。使用MTB-VCF对47个EP基因进行分析，内部生物信息学管道。根据其SIFT/Polyphen评分对SNV进行分类。也使用TB-Profiler工具调用抗性基因型。
结果：易感和DR分离株之间的基因组比较在EP中确定了418个独特的SNV；53.5％在MDR中，XDR前68.9%，XDR分离株61.3%。二十EP具有独特的SNV，具有较高的SIFT/PolyPhen评分，包括38个独特的SNV。12个EP基因中的16个SNV与耐药性显着相关，并在preXDR和XDR菌株中富集。这些是先前报道的12个SNV（在Rv0191，Rv0507，Rv0676，Rv1217，Rv1218，Rv1273，Rv1458，Rv1819和Rv2688中）和四个新颖的SNV（在Rv1877和Rv2333中）。我们调查了52个与利福平（RIF）表型基因型不一致的MDR分离株中的16个SNV，异烟肼（异烟肼）和氟喹诺酮。与RIF和INH关联的SNV（Rv1217_1218、Rv1819、Rv0450、Rv1458、Rv3827、Rv0507、Rv0676、Rv1273和Rv2333），在这些不同的菌株中存在对氟喹诺酮(Rv2688)的耐药性。
结论：将外排泵中的SNV作为基于MTB基因组的抗性解释的一部分，可能会增加价值，尤其是在评估具有表型-基因型差异的菌株的XDR抗性方面。
