Detection of a clinical carbapenem-resistant Citrobacter portucalensis strain and the dissemination of C. portucalensis in clinical settings

A clinical carbapenem-resistant Citrobacter portucalensis was characterised by whole-genome sequencing (WGS). Strain 3839 was identified by VITEK®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. 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 blaNDM-1, blaSHV-12, blaCMY-150, blaOXA-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 blaNDM-1 gene was carried by an IncX3 plasmid that was identical to a plasmid detected in a C. freundii strain. The genetic context of blaNDM-1 was IS30–blaNDM-1–bleMBL–trpF–dsbD–cutA1–groES–groEL–IS91. To our knowledge, this is the first report of carbapenem-resistant C. portucalensis isolated from a clinical sample. The blaNDM-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.