Citrobacter freundii has acquired resistance to several antimicrobial drugs, including last-resort antibiotics affecting, therefore, clinical efficacy and causing high rates of mortality. In this study, we investigate the whole genome sequence of a carbapenem-resistant C. freundii strain isolated from the hospital environment in Tunisia. A total of 210 samples were taken using sterile swabs, from inanimate surfaces, medical devices, and care staff, during the period extended between March and April 2019. After the microbiological analysis of samples and antimicrobial susceptibility testing, only one strain identified as C. freundii showing resistance to carbapenems was selected for the whole genome sequencing. The genome analysis revealed a high-level resistance to most antibiotics. Interestingly, we have noted the coexistence of bla_NDM-1 and bla_VIM-48 metallo-β-lactamase (MBL) encoding genes conferring resistance to carbapenems. Other β-lactamases encoding genes have also been detected, including bla_TEM-1, bla_CMY-48, and bla_OXA-1. Moreover, genes conferring resistance to aminoglycoside [aac(3)-IId, ant(3″)-Ia, aadA, aac(6′)-Ib], macrolide [mph(A)], sulfonamide (sul1), trimethoprim (dfrA1), tetracycline [tet(D)], chloramphenicol [cat(B3)], rifamycin (arr-3), and quinolone (qnrB) have been revealed. The multi-locus sequence typing analysis showed that this isolate could not be assigned to an existing sequence type (ST), but it is almost identical to ST22. The plasmid investigation revealed the presence of five plasmids belonging to diverse incompatibility groups (IncFII, IncHI1A, IncHI1B, IncN, and IncX3). To the best of our knowledge, our findings report the first detection of NDM-1 and VIM-48 coproducing C. freundii in Tunisia and the second detection in the world of the bla_VIM-48.

中文翻译：

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从医院环境中分离出的弗氏柠檬酸杆菌菌株的全基因组测序：一种极多耐药的 NDM-1 和 VIM-48 共生分离物

弗氏柠檬酸杆菌对几种抗菌药物产生了耐药性，包括最后的抗生素，因此会影响临床疗效并导致高死亡率。在这项研究中，我们调查了从突尼斯医院环境中分离出的耐碳青霉烯类弗氏梭菌菌株的全基因组序列。在 2019 年 3 月至 2019 年 4 月期间，使用无菌拭子从无生命的表面、医疗设备和护理人员中采集了 210 个样本。在对样本进行微生物分析和抗菌素敏感性测试后，只有一个菌株被确定为C.弗氏全基因组测序选择对碳青霉烯类具有抗性。基因组分析揭示了对大多数抗生素的高水平抗性。有趣的是，我们注意到bla _NDM-1和bla _VIM-48金属-β-内酰胺酶 (MBL) 编码基因的共存赋予了对碳青霉烯类的抗性。还检测到其他编码 β-内酰胺酶的基因，包括bla _TEM-1、bla _CMY-48和bla _OXA-1。此外，赋予氨基糖苷类抗性的基因 [ aac (3)-IId, ant (3")-Ia, aad A, aac (6')-Ib], 大环内酯 [ mph(A)]、磺胺 ( sul 1)、甲氧苄啶 ( dfr A1)、四环素 [ tet (D)]、氯霉素 [ cat (B3)]、利福霉素 ( arr -3) 和喹诺酮 ( qnr B)。多位点序列分型分析表明，该分离株不能归属于现有的序列类型（ST），但与 ST22 几乎相同。质粒调查揭示了属于不同不相容组（IncFII、IncHI1A、IncHI1B、IncN 和 IncX3）的五种质粒的存在。据我们所知，我们的研究结果报告了在突尼斯首次检测到 NDM-1 和 VIM-48 共产C. freundii以及在bla世界中的第二次检测_维姆-48。