Schwanbeck Julian, Laukien Friederike, Riedel Thomas, Bunk Boyke, Halama Philipp, Spröer Cathrin, Overmann Jörg, Cooper Paul, Kusumawati R Lia, Groß Uwe, Bohne Wolfgang, Zautner Andreas E
Institut Für Medizinische Mikrobiologie Und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany.
Present Address: BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, MN, USA.
BMC Microbiol. 2025 Jul 29;25(1):458. doi: 10.1186/s12866-025-04164-4.
Rifaximin (RFX) has recently been suggested as an alternative treatment option for Clostridioides difficile infection. This study reports the survey on RFX susceptibility within a C. difficile test cohort that represents the five clinically relevant phylogenetic clades.
Agar dilution assays were conducted to determine the minimum inhibitory concentrations (MICs) of RFX for 129 clinical C. difficile isolates from Germany (86), Indonesia (29), and Ghana (14). Genome sequence data were obtained for 50 representative isolates, including all those with a minimum inhibitory concentration MIC[RFX] of ≥ 32.0 µg/mL, to identify the underlying rpoB gene resistance alleles, determine the multilocus sequence typing (MLST) sequence types (STs), and infer phylogenetic relatedness.
10.1% of the isolates were found to be resistant to RFX. The resistance rate varies by region, with 4.7% in Germany, 27.6% in Indonesia, and 7.1% in Ghana. Three distinct rpoB alleles were associated with RFX resistance. The presence of a specific rpoB allele correlates with the MLST-based ST of the isolate, indicating that the rifaximin-resistant isolates belong to phylogenetic clades 1, 2, and 4. These isolates are represented by six different ribotypes: 010, 017, 027, 046, 084, and 131. Furthermore, we identified seven amino acid substitutions resulting from SNPs in the rpoB gene through alignment analysis. These substitutions are found in both RFX-resistant and susceptible isolates, suggesting that they are neutral mutations in relation to RFX susceptibility. These observations also indicate that RFX resistance arose independently in different clades.
A substantial rate of RFX resistance, particularly among Indonesian isolates, was observed. This may be attributed to the prolonged use of rifampicin, especially in the treatment of tuberculosis. RFX resistance has been linked to specific amino acid substitutions in the β-subunit of RNA polymerase encoded by the rpoB gene. To the best of our knowledge, one of the identified RFX resistance-associated rpoB alleles (H502N, R505K, I750M) has not been previously described, whereupon, the amino acid substitutions I750M as well as I750V, E1037Q, A1205V, N1207A, A1208T, and D1232E were identified as neutral mutations that do not confer resistance to RFX.
利福昔明（RFX）最近被提议作为艰难梭菌感染的一种替代治疗选择。本研究报告了在一个代表五个临床相关系统发育分支的艰难梭菌检测队列中对RFX敏感性的调查。
采用琼脂稀释法测定了来自德国（86株）、印度尼西亚（29株）和加纳（14株）的129株临床艰难梭菌分离株对RFX的最低抑菌浓度（MIC）。获得了50株代表性分离株的基因组序列数据，包括所有最低抑菌浓度MIC[RFX]≥32.0μg/mL的分离株，以鉴定潜在的rpoB基因抗性等位基因，确定多位点序列分型（MLST）序列类型（STs），并推断系统发育相关性。
发现10.1%的分离株对RFX耐药。耐药率因地区而异，德国为4.7%，印度尼西亚为27.6%，加纳为7.1%。三个不同的rpoB等位基因与RFX耐药相关。特定rpoB等位基因的存在与基于MLST的分离株ST相关，表明利福昔明耐药分离株属于系统发育分支1、2和4。这些分离株由六种不同的核糖体分型代表：010、017、027、046、084和131。此外，通过比对分析，我们在rpoB基因中鉴定出由单核苷酸多态性导致的七个氨基酸替换。这些替换在RFX耐药和敏感分离株中均有发现，表明它们是与RFX敏感性相关的中性突变。这些观察结果还表明，RFX耐药在不同分支中独立出现。
观察到相当比例的RFX耐药，尤其是在印度尼西亚的分离株中。这可能归因于利福平的长期使用，特别是在治疗结核病时。RFX耐药与rpoB基因编码的RNA聚合酶β亚基中的特定氨基酸替换有关。据我们所知，鉴定出的与RFX耐药相关的rpoB等位基因之一（H502N、R505K、I750M）此前尚未被描述，因此，氨基酸替换I750M以及I750V、E1037Q、A1205V、N1207A、A1208T和D1232E被鉴定为不赋予RFX耐药性的中性突变。
