Detection of a clinical carbapenem-resistant Citrobacter portucalensis strain and the dissemination of C. portucalensis in clinical settings
Detection of a clinical carbapenem-resistant Citrobacter portucalensis strain and the dissemination of C. portucalensis in clinical settings
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临床耐碳青霉烯类柠檬酸杆菌菌株的检测及其在临床环境中的传播
DOI：
10.1016/j.jgar.2021.04.027
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发表时间：
2021-09-17
影响因子：
4.6
通讯作者：
Zhou, Kai
中科院分区：
文献类型：
--
作者：
Cao, Xiaoli;Xie, Hui;Zhou, Kai
目的：采用全基因组测序（WGS）方法对一株临床耐碳青霉烯葡酸柠檬酸杆菌（Citrobacter portucalensis）进行鉴定。方法：采用VITEK (R) 2.0和基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF/MS）对菌株3839进行鉴定。采用微肉汤稀释法进行药敏试验。WGS后进行生物信息学分析。结果：菌株3839经VITEK和MALDI-TOF/MS鉴定为弗伦地柠檬酸杆菌，WGS鉴定为葡聚糖柠檬酸杆菌。通过平均核苷酸同源性分析，我们在GenBank中检测到55个C. portucalensis基因组被错误识别为C. freundii，其中至少22个与临床相关，这表明传统方法可能低估了C. portucalensis在临床环境中的发生率。菌株3839广泛耐药，WGS检测到多种耐药决定因子，包括bla（NDM-1）、bla（SHV-12）、bla（CMY-150）、bla（OXA-1）、qnrB9、qnrA1、aac（6’）-Ib-cr、aph(6)-Id_1、aph（3’）-Ib、tetA、tet34和catB3。共鉴定出45个插入序列元件、8个噬菌体和1个整合子基因盒。bla（NDM-1）基因由IncX3质粒携带，该质粒与在C. freundii菌株中检测到的质粒相同。bla（NDM-1）的遗传背景为IS30-bla(NDM-1)-ble(MBL)-trpF-dsbD-cutA1-groES-groEL-IS91。结论：据我们所知，这是第一次从临床样本中分离到碳青霉烯耐药的葡卡菌。C. portucalensis携带的bla（NDM-1）基因可通过质粒介导在柠檬酸杆菌间传播。再加上由于错误识别而导致的对其临床发生的低估，我们的研究证明了在临床环境中防止这种新出现的耐药物种传播的必要性。(C) 2021年由Elsevier Ltd代表国际抗微生物化疗学会出版。
Objectives: A clinical carbapenem-resistant Citrobacter portucalensis was characterised by whole-genome sequencing (WGS).Methods: Strain 3839 was identified by VITEK (R) 2.0 and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Antimicrobial susceptibility testing was performed by microbroth dilution. WGS followed by bioinformatics analysis was performed.Results: Strain 3839 was initially identified as Citrobacter freundii by VITEK and MALDI-TOF/MS, and was subsequently demonstrated to be C. portucalensis by WGS analysis. Through average nucleotide identity analysis, we detected 55 C. portucalensis genomes misidentified as C. freundii in GenBank, and at least 22 were clinically-associated, suggesting that the occurrence of C. portucalensis in the clinical setting might be underestimated by the conventional method. Strain 3839 was extensively drug-resistant and the presence of multiple resistance determinants was detected by WGS, including bla(NDM-1), bla(SHV-12), bla(CMY-150), bla(OXA-1), qnrB9, qnrA1, aac(6')-Ib-cr, aph(6)-Id_1, aph(3 '')-Ib, tetA, tet34 and catB3. A total of 45 insertion sequence (IS) elements, 8 phages and 1 integron gene cassette were identified. The bla(NDM-1) gene was carried by an IncX3 plasmid that was identical to a plasmid detected in a C. freundii strain. The genetic context of bla(NDM-1) was IS30-bla(NDM-1)-ble(MBL)-trpF-dsbD-cutA1-groES-groEL-IS91.Conclusion: To our knowledge, this is the first report of carbapenem-resistant C. portucalensis isolated from a clinical sample. The bla(NDM-1) gene carried by C. portucalensis may transmit among Citrobacter spp. mediated by plasmids. Together with underestimation of its clinical occurrence caused by misidentification, our study warrants the necessity of preventing the dissemination of such emerging drug-resistant species in clinical settings. (C) 2021 Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.