Genetic characterization of an MDR/virulence genomic element carrying two T6SS gene clusters in a clinical Klebsiella pneumoniae isolate of swine origin

Objectives: Multiresistant Klebsiella pneumoniae isolates rarely cause infections in pigs. The aim of this study was to investigate a multiresistant porcine K. pneumoniae isolate for plasmidic and chromosomal antimicrobial resistance and virulence genes and their genetic environment. Methods: K. pneumoniae strain ZYST1 originated from a pig with pneumonia. Antimicrobial susceptibility testing was performed using broth microdilution. Conjugation experiments were conducted using Escherichia coli J53 as the recipient. The complete sequences of the chromosomal DNA and the plasmids were generated by WGS and analysed for the presence of resistance and virulence genes. Results: The MDR K. pneumoniae ST1 strain ZYST1 contained three plasmids belonging to incompatibility groups IncFII(k5)-FIB, IncI1 and IncX4, respectively. The IncFII(k5)-FIB plasmid carried the resistance genes aadA2, mph(A), sul1 and aph(3')-Ia, and the IncI1 plasmid carried aadA22 and erm(B). No resistance genes were present on the IncX4 plasmid. Plasmids related to the aforementioned three plasmids were also present in other Enterobacteriaceae species from humans, animals and the environment. Bioinformatic analyses identified a chromosomal 904 kb MDR element flanked by two copies of ISKpn26. This element included virulence factors, such as a type VI secretion system (T6SS) and genes for type 1 fimbriae, the toxin-antitoxin system HipA/HipB, antimicrobial resistance genes, such as bla(SHV-187), mdtk, catA and the multiple antibiotic resistance operon marRABC, and heavy metal resistance determinants, such as chrB/chrA and tehA/tehB. Conclusions: This study reports a novel 904 kb MDR/virulence genomic element and three important plasmids coexisting in a clinical K. pneumoniae isolate of animal origin.