Genomic characterization of Citrobacter freundii strains coproducing OXA-48 and VIM-1 carbapenemase enzymes isolated in leukemic patient in Spain

Abstract

BackgroundThe emergence of carbapenemase-producing (CP) Citrobacter freundii poses a significant threat to public health, especially in high-risk populations. In this study, whole genome sequencing was used to characterize the carbapenem resistance mechanism of three C. freundii clinical isolates recovered from fecal samples of patients with acute leukemia (AL) from Spain.Materials and methodsTwelve fecal samples, collected between 2013 and 2015 from 9 patients with AL, were screened for the presence of CP strains by selecting them on MacConkey agar supplemented with ertapenem (0.5 mg/L). Bacteria were identified by MALDI-TOF mass spectrometry and were phenotypically characterized. Whole genome sequencing of C. freundii isolates was performed using the MinION and MiSeq Illumina sequencers. Bioinformatic analysis was performed in order to identify the molecular support of carbapenem resistance and to study the genetic environment of carbapenem resistance encoding genes.ResultsThree carbapenem-resistant C. freundii strains (imipenem MIC≥32 mg/L) corresponding to three different AL patients were isolated. Positive modified Carba NP test results suggested carbapenemase production. The genomes of each C. freundii tested were assembled into a single chromosomal contig and plasmids contig. In all the strains, the carbapenem resistance was due to the coproduction of OXA-48 and VIM-1 enzymes encoded by genes located on chromosome and on an IncHI2 plasmid, respectively. According to the MLST and the SNPs analysis, all strains belonged to the same clone ST169.ConclusionWe report in our study, the intestinal carrying of C. freundii clone ST169 coproducing OXA-48 and VIM-1 identified in leukemic patients.

Whole Genome Sequencing of a Citrobacter freundii Strain Isolated from the Hospital Environment: An Extremely Multiresistant NDM-1 and VIM-48 Coproducing Isolate

“…26 Whereas various MBL genes, including bla NDM-1 , bla VIM-1 , bla VIM-4 , and bla IMP-8 , in association with other carbapenemase genes (non-MBL) particularly bla OXA-48 and bla KPC-2 have been detected in C. freundii. [27][28][29][30] Likewise, we report in our study the second detection in the world of the bla VIM-48 gene, which was first found in Pseudomonas putida isolated from chicken in China. 31 It has been reported that VIM-48 increases the enzymatic activity, thermostability, and resistance to carbapenems.…”

mCIM test as a reliable assay for the detection of CRE in the Gulf region

“…Interestingly, there are eleven isolates in this study that carried two different types of carbapenemase genes, three of them were from 2015. The uncommon co-carriage of genes encoding different classes of carbapenemases genes were already described in the literature and reported in the western region of Saudi Arabia [35–38]. As migration and population mobility are increasingly important determinants of infection transmission, these issues will require greater policy attention at the multilateral level.…”

Dissemination of Carbapenemases (OXA-48, NDM and VIM) Producing Enterobacteriaceae Isolated from the Mohamed VI University Hospital in Marrakech, Morocco

“…The study of Arana et al also highlighted several remarkable findings, such as clonal and polyclonal dissemination of C. freundii across different geographical areas and hospitals. OXA-48 and VIM-1 enzymes encoded were also detected in C. freundii from patients with acute leukemia in Spain [ 45 ].…”