First identification and genomic features of multidrug-resistant Citrobacter freundii ST669 strain isolated from a domesticated duck in Bangladesh

Abstract

ObjectivesCitrobacter freundii is a prevalent source of nosocomial infections and a well-known cause of diarrheal diseases. In recent years, it has also become increasingly resistant to various antimicrobials. In this study, we screened and characterized a multidrug-resistant (MDR) C. freundii isolate obtained from a domesticated diseased duck to better understand the genetic features, molecular epidemiology, and underlying factors linked to the antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) of the isolate. MethodsThe C. freundii BAU_TM8 strain was isolated using culturing, staining, biochemical, polymerase chain reaction, and Matrix-assisted laser desorption/ionization-time of flight methods. The MDR properties of the strain were determined by a disk diffusion test. The genomic sequence of C. freundii BAU_TM8 was performed using the Illumina NextSeq2000 platform. The ARGs, VFGs, and genomic functional characteristics of the C. freundii BAU_TM8 strain were identified using several open-source databases. ResultsThe sequence type of this strain was ST669, and the pathogenicity index of the strain was 0.919. Moreover, the strain had an estimated genome length of 5,797,806 bp, harboring 62 contigs, a G+C content of 54.32%, and five contig L50s with an N50 value of 443,947 bp. Using phylogenetic analysis, this strain was closely related to two strains isolated from human and environmental samples in the USA and China despite huge geographical distances. The C. freundii BAU_TM8 strain consisted of 40 AGRs encoding resistance to 19 antimicrobial categories, e.g., fluoroquinolones, macrolides, folate pathway antagonists, aminoglycosides, tetracyclines, cephalosporins, and others. According to the phenotypic assay and genome sequence, the sensitivity and specificity of resistance profiles of the strain were 100% and 20%, respectively. Moreover, the virulence factor database detected 66 VFGs in this strain. This strain contained 1581 subsystems, having 33% subsystem coverage and 2275 genes encoding amino acid derivatives, carbohydrate metabolism, protein metabolism, cofactors, vitamins, prosthetic groups, pigments, respiration, motility and chemotaxis, stress response, DNA metabolism, nucleosides and nucleotides, and others. ConclusionsTo the best of our knowledge, this is the first WGS report of C. freundii from a domesticated duck in Bangladesh. The ubiquitous occurrence of ARGs and VFGs in the C. freundii BAU_TM8 strain detected in this study highlights the growing concern about antimicrobial resistance in humans, animals, and environments.