Whole genome sequencing revealed a high level of antimicrobial resistance genes and virulence factors in a multidrug-resistant Citrobacter freundii BAU_TM8 strain isolated from a domesticated duck in Bangladesh

Abstract

Citrobacter freundii is a prevalent source of nosocomial infections and a well-known cause of diarrheal diseases, and in recent years, it has also become increasingly resistant to a variety of 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 variety, molecular epidemiology, and underlying factors linked to the antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) of the isolate. The 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 complete 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. The sequence types of this strain was ST669, and the pathogenicity index of the strain was 0.919, indicating a highly virulent strain. 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 distance. The C. freundii BAU_TM8 strain consisted of 40 AGRs encoding resistance to 19 antimicrobial categories, showing about 85% similarity with the phenotypic properties of the isolate. 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. The ubiquitous occurrence of ARGs and VFGs in the C. freundii BAU_TM8 strain detected in this study highlights the growing concern of antimicrobial resistance in humans, animals, and environments.