LAUSR

OBJECTIVE A clinically isolated carbapenem-resistant Citrobacter portucalensis was characterized by whole genome sequencing (WGS). METHODS Strain 3839 was identified by Vitek 2.0 and matrix-associated laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Antibiotic susceptibility testing was performed by microbroth dilution method. WGS followed by bioinformatics analysis was conducted. RESULTS Strain 3839 was initially identified as C. freundii by Vitek and MALDI-TOF MS, and later was demonstrated as C. portucalensis by WGS analysis. Through average-nucleotide identity analysis, we further detected 55 C. portucalensis genomes which were misidentified as C. freundii in GenBank, and at least 22 were clinical-associated, suggesting that the occurrence of C. portucalensis in the clinical setting might be underestimated by the conventional method. Strain 3839 was extremely 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, aac(6')Ib-cr, tetA, tet34, and catB3. Forty-five insertion sequences, 8 phages, and 1 integron gene cassette were identified in this strain. The blaNDM-1 gene was carried by an IncX3 plasmid, which 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. CONCLUSION To our knowledge, this is the first report of carbapenem-resistant C. portucalensis isolated from clinical samples. The blaNDM-1 gene carried by C. portucalensis may transmit among Citrobacter spp. mediated by plasmids. Together with the underestimation of clinical occurrence caused by the misidentification, our study warrants the necessity of preventing the dissemination of such emerging drug-resistant species in clinical settings.