Data Sheet 1_The emergence and spread of blaNDM-1, blaKPC-2, mcr-10 genes, and the tmexCD2-toprJ2 gene cluster in extensively drug-resistant clinical Raoultella ornithinolytica.zip

BackgroundRaoultella ornithinolytica is an infrequent opportunistic pathogen capable of causing multi-site infections and frequently harboring a broad array of resistance determinants, thereby complicating antimicrobial therapy. Here we report the genomic characterization of the extensively drug-resistant strain FAHZZU6693, which concurrently harbors blaNDM-1, blaKPC-2, mcr-10 genes and tmexCD2-toprJ2 resistance cluster.
MethodsMatrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and average nucleotide identity (ANI) were employed to confirm the species identity as R. ornithinolytica. Antimicrobial susceptibility testing (AST) delineated the corresponding antimicrobial phenotypes. S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blotting and whole-genome sequencing (WGS) elucidated the isolate’s complete molecular architecture.
ResultsGlobally, R. ornithinolytica strains harboring related resistance genes exhibit diverse geographical distribution. Strain FAHZZU6693 is resistant to most antibiotics, except amikacin and chloramphenicol. The blaNDM-1, blaKPC-2, mcr-10 genes and the tmexCD2-toprJ2 cluster in this strain are plasmid-borne. These occur in conserved genetic contexts: xerC-mcr-10-ISEc36-ISEc27-ISEcl1 and umuC-IS881-tmexC2-tmexD2-toprJ2-umuC. Further analysis indicates that the insertion sequence ISEc27 and the gene element umuC play a crucial role in the dissemination of the mcr-10 gene and the tmexCD2-toprJ2 gene cluster.
ConclusionsThis study combines database analysis to comprehensively describe the distribution of R. ornithinolytica strains carrying the target genes and characterizes the genomic features of a clinically Multi-drug resistant strain, providing a theoretical foundation for preventing the spread of such bacteria.

背景：解鸟氨酸拉乌尔菌（Raoultella ornithinolytica）是一种罕见的机会致病菌，可引发多部位感染，且常携带大量耐药决定因子，进而使抗菌治疗复杂化。本研究报道了一株泛耐药菌株FAHZZU6693的基因组特征，该菌株同时携带blaNDM-1、blaKPC-2、mcr-10基因及tmexCD2-toprJ2耐药基因簇。
方法：采用基质辅助激光解吸电离飞行时间质谱（Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, MALDI-TOF MS）与平均核苷酸同源性（average nucleotide identity, ANI）验证该菌株的物种分类地位，确认为解鸟氨酸拉乌尔菌；通过抗菌药物敏感性试验（Antimicrobial susceptibility testing, AST）明确其对应的抗菌表型；结合S1核酸酶脉冲场凝胶电泳（S1 nuclease pulsed-field gel electrophoresis, S1-PFGE）、Southern印迹杂交与全基因组测序（whole-genome sequencing, WGS），解析该分离株的完整分子结构特征。
结果：全球范围内，携带相关耐药基因的解鸟氨酸拉乌尔菌菌株呈现多样化的地理分布特征。菌株FAHZZU6693对绝大多数抗菌药物均表现耐药，仅对阿米卡星与氯霉素敏感。该菌株携带的blaNDM-1、blaKPC-2、mcr-10基因以及tmexCD2-toprJ2基因簇均位于质粒上，且位于保守的遗传背景中：xerC-mcr-10-ISEc36-ISEc27-ISEcl1 以及 umuC-IS881-tmexC2-tmexD2-toprJ2-umuC。进一步分析显示，插入序列ISEc27与基因元件umuC在mcr-10基因及tmexCD2-toprJ2基因簇的传播过程中发挥关键作用。
结论：本研究结合数据库分析，全面阐述了携带目标耐药基因的解鸟氨酸拉乌尔菌菌株的分布情况，并对一株临床多重耐药菌株的基因组特征进行了系统表征，为防控此类细菌的传播提供了理论依据。