Background

Fecal microbiota transplantation (FMT) aims to cure Clostridioides difficile infection (CDI) through reestablishing a healthy microbiome and restoring colonization resistance. Although often effective after one infusion, patients with continued microbiome disruptions may require multiple FMTs. In this N-of-1 study, we use a systems biology approach to evaluate CDI in a patient receiving chronic suppressive antibiotics with four failed FMTs over two years.

Methods

Seven stool samples were obtained between 2016-18 while the patient underwent five FMTs. Stool samples were cultured for C. difficile and underwent microbial characterization and functional gene analysis using shotgun metagenomics. C. difficile isolates were characterized through ribotyping, whole genome sequencing, metabolic pathway analysis, and minimum inhibitory concentration (MIC) determinations.

Results

Growing ten strains from each sample, the index and first four recurrent cultures were single strain ribotype F078-126, the fifth was a mixed culture of ribotypes F002 and F054, and the final culture was ribotype F002. One single nucleotide polymorphism (SNP) variant was identified in the RNA polymerase (RNAP) β-subunit RpoB in the final isolated F078-126 strain when compared to previous F078-126 isolates. This SNV was associated with metabolic shifts but phenotypic differences in fidaxomicin MIC were not observed. Microbiome differences were observed over time during vancomycin therapy and after failed FMTs.

Conclusion

This study highlights the importance of antimicrobial stewardship in patients receiving FMT. Continued antibiotics play a destructive role on a transplanted microbiome and applies selection pressure for resistance to the few antibiotics available to treat CDI.

中文翻译：

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难治性艰难梭菌感染的系统生物学评估，包括粪便微生物群移植的多次失败

背景

粪便微生物群移植 (FMT) 旨在通过重建健康的微生物群和恢复定植抗性来治愈艰难梭菌感染 (CDI)。虽然一次输注后通常有效，但微生物组持续破坏的患者可能需要多次 FMT。在这项 N-of-1 研究中，我们使用系统生物学方法来评估一名接受慢性抑制性抗生素的患者的 CDI，该患者在两年内有四次 FMT 失败。

方法

2016-18 年间获得了 7 个粪便样本，而患者接受了 5 次 FMT。针对艰难梭菌培养粪便样本，并使用鸟枪宏基因组学进行微生物表征和功能基因分析。通过核糖分型、全基因组测序、代谢途径分析和最小抑制浓度 (MIC) 测定对艰难梭菌分离株进行了表征。

结果

从每个样品中培养十个菌株，索引和前四个重复培养物是单菌株核糖型 F078-126，第五个是核糖型 F002 和 F054 的混合培养物，最终培养物是核糖型 F002。与之前的 F078-126 分离株相比，在最终分离的 F078-126 菌株的 RNA 聚合酶 (RNAP) β-亚基 RpoB 中鉴定出一个单核苷酸多态性 (SNP) 变体。该 SNV 与代谢变化有关，但未观察到非达霉素 MIC 的表型差异。在万古霉素治疗期间和 FMT 失败后，随着时间的推移观察到微生物组差异。

结论

本研究强调了抗菌药物管理在接受 FMT 的患者中的重要性。持续使用的抗生素对移植的微生物组具有破坏性作用，并对少数可用于治疗 CDI 的抗生素施加选择压力。