Comparative genomics of five different resistance plasmids coexisting in a clinical multi-drug resistant <em>Citrobacter freundii</em> isolate

Abstract

BackgroundPlasmid-mediated multi-drug resistance (MDR) has been widely found in Citro-bacter freundii. C. freundii P10159 was isolated from a human case of postoperative urinary tract infection in a Chinese teaching hospital.MethodsThe complete nucleotide sequences of five resistance plasmids pP10159-1, pP10159-2, pP10159-3, pP10159-4 and pP10159-5 from C. freundii P10159 were determined through high-throughput genome sequencing, and then compared with related plasmids sequences. Plasmid transfer, CarbaNP test of carbapenemase activity, and bacterial antimicrobial susceptibility test were performed to characterize resistance phenotypes mediated by these plasmids.ResultspP10159-1 carrying blaNDM-1and pP10159-2 harboring blaIMP-4 plus qnrS1 were almost identical to IncX3 plasmid pNDM-HN380 and IncN1 plasmid pP378-IMP, respectively. The blaKPC-2-carrying plasmids pP10159-3, pHS062105-3 and pECN49-KPC were highly similar to each other, and constituted a novel group of plasmids belonging to an unknown incomparability group. The MDR plasmids pP10159-4 and pP10159-5 had the backbones highly similar to IncHI4 plasmid pNDM-CIT and type 2 IncC plasmid pR55, respectively, but their accessory resistance regions differed from pNDM-CIT and pR55, respectively. The five plasmids from the P10159 isolate contained a total of 24 different genes or gene loci, which contributed to resistance to 13 distinct antibiotic molecules or toxic compounds.ConclusionThis is the first report of co-occurrence of five different resistance plasmids, with determination of their complete sequences. Data presented here provide a deeper insight into co-selection and maintenance of multiple plasmids and an extremely large number of resistance genes in a single bacterial isolate.

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

“…Carbapenemase production in C. freundii is poorly documented, only a few studies reported the expression of such enzymes in this species [6, 18–20]. The coproduction of carbapenemase enzymes was already described in some Enterobacteriaceae species such as Klebsiella pneumoniae (KPC-2 + VIM-2 or NDM-1 + VIM-1) [19, 21, 22] and Enterobacter cloacae (NDM-1 + VIM-1) [19] as well as in C. freundii (KPC-2 + NDM-1, NDM-1 + VIM-1) [19, 20].…”

“…Citrobacter freundii is a gram-negative bacterium which is rarely the causative agent of infections but it has been associated with different infections including respiratory, urinary, gastrointestinal and bloodstream infections [5, 6]. The emergence of MDR C. freundii, especially those carbapenemase producing strains, poses a significant threat to public health worldwide, especially in immunocompromised patients such as leukemia patients, which are mostly dependent on antibiotics [5, 6].…”

First Report of Coexistence of Three Different MDR Plasmids, and That of Occurrence of IMP-Encoding Plasmid in Leclercia adecarboxylata

“…Bacteria were spotted on Muller-Hinton agar (BD Biosciences, NJ, United States) plates containing 1000 μg/ml rifampin together with 10 μg/ml azithromycin, 2 μg/ml meropenem or 20 μg/ml tetracycline, for selecting an E. coli transconjugant that carried mph (A) (p16005813A), bla IMP (B) (p16005813B), or tet (C) (p16005813C), respectively. Plasmid electroporation experiments were carried out as described previously (Ouyang et al, 2018). Bacteria were spotted on Super Optimal Broth agar plates containing 10 μg/ml azithromycin, 2 μg/ml meropenem or 20 μg/ml tetracycline, for selecting an E. coli electroporant that carried p16005813A, p16005813B, or p16005813C, respectively.…”

<p>Genetic characterization of a novel sequence type of multidrug-resistant <em>Citrobacter freundii</em> strain recovered from wastewater treatment plant</p>

“…C. freundii strain IFO 13545 has the ability to produce bioflocculant which can be used in fields of water supply, wastewater treatment, and food production.6 Although C. freundii was previously recognized as a bacterium of low virulence, it has been demonstrated to be the causative agent of a wide spectrum of infections including diarrhea, pneumonia and septicemia 7,8. Moreover, there has been a growing body of literature that reported the plasmid-mediated multidrug resistance in C. freundii , indicating its threat to human health 9,10…”