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


Results
Three 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.


Conclusion
We report in our study, the intestinal carrying of C. freundii clone ST169 coproducing OXA-48 and VIM-1 identified in leukemic patients.
['Lalaoui|Rym|R|', 'Djukovic|Ana|A|', 'Bakour|Sofiane|S|', 'Hadjadj|Linda|L|', 'Sanz|Jaime|J|', 'Salavert|Miguel|M|', 'López-Hontangas|Jose Luis|JL|', 'Sanz|Miguel A|MA|', 'Ubeda|Carles|C|', 'Rolain|Jean-Marc|JM|']
D001426:Bacterial Proteins D016971:Citrobacter freundii D004756:Enterobacteriaceae Infections D016680:Genome, Bacterial D023281:Genomics D006801:Humans D007938:Leukemia D062486:Public Health Surveillance D013030:Spain D001618:beta-Lactamases
Citrobacter freundii OXA-48 VIM-1 Carbapenemase Whole genome sequencing