Guérillot Romain, Gonçalves da Silva Anders, Monk Ian, Giulieri Stefano, Tomita Takehiro, Alison Eloise, Porter Jessica, Pidot Sacha, Gao Wei, Peleg Anton Y, Seemann Torsten, Stinear Timothy P, Howden Benjamin P
Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
mSphere. 2018 Jan 24;3(1). doi: 10.1128/mSphere.00550-17. eCollection 2018 Jan-Feb.
Mutations in the beta-subunit of bacterial RNA polymerase (RpoB) cause resistance to rifampin (Rif), a critical antibiotic for treatment of multidrug-resistant . studies have shown that RpoB mutations confer decreased susceptibility to other antibiotics, but the clinical relevance is unknown. Here, by analyzing 7,099 genomes, we demonstrate that the most prevalent RpoB mutations promote clinically relevant phenotypic plasticity resulting in the emergence of stable lineages, associated with increased risk of therapeutic failure through generation of small-colony variants (SCVs) and coresistance to last-line antimicrobial agents. We found eight RpoB mutations that accounted for 93% (469/505) of the total number of Rif mutations. The most frequently selected amino acid substitutions affecting residue 481 (H481N/Y) were associated with worldwide expansions of Rif clones spanning decades. Recreating the H481N/Y mutations confirmed no impact on growth, but the H481N mutation promoted the emergence of a subpopulation of stable Rif SCVs with reduced susceptibility to vancomycin and daptomycin. Recreating the other frequent RpoB mutations showed similar impacts on resistance to these last-line agents. We found that 86% of all Rif isolates in our global sample carried the mutations promoting cross-resistance to vancomycin and 52% to both vancomycin and daptomycin. As four of the most frequent RpoB mutations confer only low-level Rif, equal to or below some international breakpoints, we recommend decreasing these breakpoints and reconsidering the appropriate use of rifampin to reduce the fixation and spread of these clinically deleterious mutations. Increasing antibiotic resistance in the major human pathogen is threatening the ability to treat patients with these infections. Recent laboratory studies suggest that mutations in the gene commonly associated with rifampin resistance may also impact susceptibility to other last-line antibiotics in ; however, the overall frequency and clinical impact of these mutations are unknown. By mining a global collection of clinical genomes and by mutagenesis experiments, this work reveals that common rifampin-induced mutations promote phenotypic plasticity that has led to the global emergence of stable, multidrug-resistant lineages that are associated with increased risk of therapeutic failure through coresistance to other last-line antimicrobials. We recommend decreasing susceptibility breakpoints for rifampin to allow phenotypic detection of critical mutations conferring low resistance to rifampin and reconsidering the appropriate use of rifampin to reduce the fixation and spread of these deleterious mutations globally.
细菌RNA聚合酶（RpoB）β亚基的突变会导致对利福平（Rif）产生耐药性，利福平是治疗多重耐药菌的关键抗生素。研究表明，RpoB突变会降低对其他抗生素的敏感性，但其临床相关性尚不清楚。在此，通过分析7099个基因组，我们证明最常见的RpoB突变会促进具有临床相关性的表型可塑性，导致稳定菌系的出现，通过产生小菌落变体（SCV）和对一线抗菌药物的共耐药性，增加治疗失败的风险。我们发现8个RpoB突变占利福平突变总数的93%（469/505）。影响第481位残基（H481N/Y）的最常选择的氨基酸替代与跨越数十年的利福平克隆在全球范围内的扩张有关。重新创建H481N/Y突变证实对生长没有影响，但H481N突变促进了对万古霉素和达托霉素敏感性降低的稳定利福平SCV亚群的出现。重新创建其他常见的RpoB突变对这些一线药物的耐药性也有类似影响。我们发现，在我们的全球样本中，所有利福平分离株中有86%携带促进对万古霉素交叉耐药的突变，52%携带对万古霉素和达托霉素均耐药的突变。由于最常见的4个RpoB突变仅赋予低水平的利福平耐药性，等于或低于一些国际断点，我们建议降低这些断点，并重新考虑利福平的适当使用，以减少这些临床有害突变的固定和传播。主要人类病原体中抗生素耐药性的增加正威胁着治疗这些感染患者的能力。最近的实验室研究表明，通常与利福平耐药性相关的基因中的突变也可能影响对其他一线抗生素的敏感性；然而，这些突变的总体频率和临床影响尚不清楚。通过挖掘全球临床基因组集合并进行诱变实验，这项工作揭示了常见的利福平诱导的突变促进了表型可塑性，导致了稳定的多重耐药菌系在全球出现，这些菌系通过对其他一线抗菌药物的共耐药性增加了治疗失败的风险。我们建议降低利福平的敏感性断点，以便对赋予低水平利福平耐药性的关键突变进行表型检测，并重新考虑利福平的适当使用，以减少这些有害突变在全球的固定和传播。
