Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA.
J Clin Microbiol. 2013 Sep;51(9):2991-9. doi: 10.1128/JCM.00984-13. Epub 2013 Jul 10.
The ability to identify bacterial pathogens at the subspecies level in clinical diagnostics is currently limited. We investigated whether splitting Escherichia coli species into clonal groups (clonotypes) predicts antimicrobial susceptibility or clinical outcome. A total of 1,679 extraintestinal E. coli isolates (collected from 2010 to 2012) were collected from one German and 5 U.S. clinical microbiology laboratories. Clonotype identity was determined by fumC and fimH (CH) sequencing. The associations of clonotype with antimicrobial susceptibility and clinical variables were evaluated. CH typing divided the isolates into >200 CH clonotypes, with 93% of the isolates belonging to clonotypes with ≥ 2 isolates. Antimicrobial susceptibility varied substantially among clonotypes but was consistent across different locations. Clonotype-guided antimicrobial selection significantly reduced "drug-bug" mismatch compared to that which occurs with the use of conventional empirical therapy. With trimethoprim-sulfamethoxazole and fluoroquinolones, the drug-bug mismatch was predicted to decrease 62% and 78%, respectively. Recurrent or persistent urinary tract infection and clinical sepsis were significantly correlated with specific clonotypes, especially with CH40-30 (also known as H30), a recently described clonotype within sequence type 131 (ST131). We were able to clonotype directly from patient urine samples within 1 to 3 h of obtaining the specimen. In E. coli, subspecies-level identification by clonotyping can be used to significantly improve empirical predictions of antimicrobial susceptibility and clinical outcomes in a timely manner.
目前，在临床诊断中识别细菌病原体亚种的能力有限。我们研究了将大肠杆菌种分为克隆群（克隆型）是否可以预测抗菌药物敏感性或临床结果。从一家德国和五家美国临床微生物学实验室收集了 1679 株肠外大肠杆菌分离株（收集于 2010 年至 2012 年）。通过 fumC 和 fimH（CH）测序确定克隆型身份。评估了克隆型与抗菌药物敏感性和临床变量的关联。CH 分型将分离株分为 >200 个 CH 克隆型，其中 93%的分离株属于至少有 2 个分离株的克隆型。克隆型之间的抗菌药物敏感性差异很大，但在不同地点是一致的。与常规经验性治疗相比，基于克隆型的抗菌药物选择显著减少了“药物-细菌”不匹配。对于复方磺胺甲噁唑和氟喹诺酮类药物，药物-细菌不匹配分别预计会减少 62%和 78%。复发性或持续性尿路感染和临床败血症与特定的克隆型显著相关，特别是与 CH40-30（也称为 H30）相关，这是一种最近在 131 型序列型（ST131）中描述的克隆型。我们能够在获得标本后 1 至 3 小时内直接从患者尿液样本中克隆型。在大肠杆菌中，通过克隆型进行亚种水平鉴定可以及时显著提高抗菌药物敏感性和临床结果的经验预测。
