Department of Pediatrics, Baylor College of Medicine, Houston, Texas.
Inform Diagnostics, Irving, Texas; Department of Pathology, Baylor College of Medicine, Houston, Texas.
Gastroenterology. 2021 Nov;161(5):1433-1442.e2. doi: 10.1053/j.gastro.2021.07.012. Epub 2021 Jul 19.
BACKGROUND & AIMS: The decline in Helicobacter pylori cure rates emphasizes the need for readily available methods to determine antimicrobial susceptibility. Our aim was to compare targeted next-generation sequencing (NGS) and culture-based H pylori susceptibility testing using clinical isolates and paired formalin-fixed, paraffin-embedded (FFPE) gastric biopsies.
H pylori isolates and FFPE tissues were tested for susceptibility to amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline, and rifabutin using agar dilution and NGS targeted to 23S rRNA, gyrA, 16S rRNA, pbp1, rpoB and rdxA. Agreement was quantified using κ statistics.
Paired comparisons included 170 isolates and FFPE tissue for amoxicillin, clarithromycin, metronidazole, and rifabutin and 57 isolates and FFPE tissue for levofloxacin and tetracycline. Agreement between agar dilution and NGS from culture isolates was very good for clarithromycin (κ = 0.90012), good for levofloxacin (κ = 0.78161) and fair for metronidazole (κ = 0.55880), and amoxicillin (κ = 0.21400). Only 1 isolate was resistant to tetracycline (culture) and 1 to rifabutin (NGS). Comparison of NGS from tissue blocks and agar dilution from isolates from the same stomachs demonstrated good accuracy to predict resistance for clarithromycin (94.1%), amoxicillin (95.9%), metronidazole (77%), levofloxacin (87.7%), and tetracycline (98.2%). Lack of resistance precluded comparisons for tetracycline and rifabutin.
Compared with agar dilution, NGS reliably determined resistance to clarithromycin, levofloxacin, rifabutin, and tetracycline from clinical isolates and formalin-fixed gastric tissue. Consistency was fair for metronidazole and amoxicillin. Culture-based testing can predict treatment outcomes with clarithromycin and levofloxacin. Studies are needed to compare the relative ability of both methods to predict treatment outcomes for other antibiotics.
幽门螺杆菌治愈率的下降强调了需要有现成的方法来确定抗菌药物敏感性。我们的目的是比较靶向下一代测序（NGS）和基于培养的幽门螺杆菌药敏试验，使用临床分离株和配对的福尔马林固定、石蜡包埋（FFPE）胃活检组织。
使用琼脂稀释法和靶向 23S rRNA、gyrA、16S rRNA、pbp1、rpoB 和 rdxA 的 NGS 检测，对幽门螺杆菌分离株和 FFPE 组织进行阿莫西林、克拉霉素、甲硝唑、左氧氟沙星、四环素和利福布丁的药敏试验。使用κ统计量来量化一致性。
配对比较包括 170 个分离株和 FFPE 组织用于阿莫西林、克拉霉素、甲硝唑和利福布丁，以及 57 个分离株和 FFPE 组织用于左氧氟沙星和四环素。来自培养分离株的琼脂稀释法和 NGS 之间的一致性对于克拉霉素非常好（κ=0.90012），对于左氧氟沙星和甲硝唑好（κ=0.78161 和κ=0.55880），对于阿莫西林差（κ=0.21400）。仅 1 个分离株对四环素（培养）和 1 个分离株对利福布丁（NGS）耐药。来自同一胃部的组织块的 NGS 与分离株的琼脂稀释法比较，对克拉霉素（94.1%）、阿莫西林（95.9%）、甲硝唑（77%）、左氧氟沙星（87.7%）和四环素（98.2%）的耐药性预测具有良好的准确性。由于缺乏耐药性，四环素和利福布丁无法进行比较。
与琼脂稀释法相比，NGS 可靠地确定了来自临床分离株和福尔马林固定胃组织的克拉霉素、左氧氟沙星、利福布丁和四环素的耐药性。甲硝唑和阿莫西林的一致性一般。基于培养的检测可以预测克拉霉素和左氧氟沙星的治疗结果。需要研究这两种方法预测其他抗生素治疗结果的相对能力。
