Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
AMR-One Health Consortium, Calgary, Alberta, Canada.
Microbiol Spectr. 2024 Oct 3;12(10):e0053224. doi: 10.1128/spectrum.00532-24. Epub 2024 Aug 20.
Colistin resistance in is of public health significance for its use to treat multidrug-resistant Gram-negative infections. Amino acid variations in PmrB have been implicated in colistin resistance in . In this cross-sectional study, 288 generic isolates from surveillance of broiler chicken and feedlot cattle feces, retail meat, wastewater, and well water were whole-genome sequenced. Phylogroup designation and screening for two amino acid substitutions in PmrB putatively linked to colistin resistance (Y358N, E123D) were performed . Three additional data sets of publicly available assemblies were similarly scrutinized: (i) isolates from studies identifying the Y358N or E123D substitutions, (ii) colistin-susceptible isolates reported in the literature, and (iii) a random sampling of 14,700 assemblies available in the National Center for Biotechnology Information public database. Within all data sets, ≥95% of phylogroup B1 and C isolates have the PmrB Y358N variation. The PmrB E123D amino acid substitution was only identified in phylogroup B2 isolates, of which 94%-100% demonstrate the substitution. Both PmrB amino acid variations were infrequent in other phylogroups. Among published colistin susceptible isolates, colistin minimum inhibitory concentrations (MICs) were not higher in isolates bearing the E123D and Y358N amino acid variations than in isolates without these PmrB substitutions. The E123D and Y358N PmrB amino acid substitutions in appear strongly associated with phylogroup. The previously observed associations between Y358N and E123D amino acid substitutions in PmrB and colistin resistance in may be spurious.
Colistin is a critical last-resort treatment for extensively drug-resistant Gram-negative infections in humans. Therefore, accurate identification of the genetic mechanisms of resistance to this antimicrobial is crucial to effectively monitor and mitigate the spread of resistance. Examining over 16,000 whole-genome sequenced isolates, this study identifies that PmrB E123D and Y358N amino acid substitutions previously associated with colistin resistance in are strongly associated with phylogroup and are alone not sufficient to confer a colistin-resistant phenotype. This is a critical clarification, as both substitutions are identified as putative mechanisms of colistin resistance in many publications and a common bioinformatic tool. Given the potential spurious nature of initial associations of these substitutions with colistin resistance, this study's findings emphasize the importance of appropriate experimental design and consideration of relevant biological factors such as phylogroup when ascribing causal mechanisms of resistance to chromosomal variations.
多药耐药革兰氏阴性感染的治疗中使用粘菌素导致 中的粘菌素耐药性具有公共卫生意义。PmrB 中的氨基酸变异与 中的粘菌素耐药性有关。在这项横断面研究中，对来自肉鸡和育肥牛粪便、零售肉、废水和井水监测的 288 个通用 分离株进行了全基因组测序。对假定与粘菌素耐药性相关的两个 PmrB 氨基酸取代（Y358N、E123D）进行了 菌系指定和筛选。同样仔细检查了另外三个公开可得的 基因组数据集：（i）鉴定 Y358N 或 E123D 取代的研究中的 分离株，（ii）文献中报道的粘菌素敏感 分离株，以及（iii）在国家生物技术信息中心公共数据库中可获得的 14,700 个组装体的随机抽样。在所有数据集内，≥95%的 B1 和 C 菌系 PmrB Y358N 变异。仅在 B2 菌系中鉴定到 PmrB E123D 氨基酸取代，其中 94%-100%显示取代。其他菌系中这两种 PmrB 氨基酸变异均很少见。在已发表的粘菌素敏感分离株中，带有 E123D 和 Y358N 氨基酸变异的分离株的粘菌素最小抑菌浓度（MIC）并不高于没有这些 PmrB 取代的分离株。 中的 PmrB E123D 和 Y358N 氨基酸取代与菌系密切相关。先前观察到的 PmrB 中 Y358N 和 E123D 氨基酸取代与 中粘菌素耐药性之间的关联可能是虚假的。
粘菌素是治疗人类广泛耐药革兰氏阴性感染的关键最后手段。因此，准确识别这种抗生素的耐药性的遗传机制对于有效监测和减轻耐药性的传播至关重要。通过检查超过 16,000 个全基因组测序的 分离株，本研究表明，先前与 中的粘菌素耐药性相关的 PmrB E123D 和 Y358N 氨基酸取代与菌系密切相关，并且单独不足以赋予粘菌素耐药表型。这是一个重要的澄清，因为这两种取代均被确定为许多出版物中粘菌素耐药的假定机制，并且是一种常见的生物信息学工具。鉴于这些取代与粘菌素耐药性最初关联的潜在虚假性质，本研究的结果强调了在归因于染色体变异的耐药性因果机制时，适当的实验设计和考虑相关生物学因素（如菌系）的重要性。
