Genomic characterisation and antimicrobial resistance of Klebsiella species isolated from small stock and environmental sources in South Africa

Klebsiella species pose a significant public health concern due to their association with various infections and the rising levels of antibiotic resistance. This study examined the antibiotic resistance profiles of nine Klebsiella species obtained from the culture collection at North-West University’s Potchefstroom campus in South Africa using whole genome sequencing. The average nucleotide identity (ANI), plasmid types, and the identification of antibiotic resistance and virulence genes were performed on Klebsiella species. The nine sequenced Klebsiella spp. isolates were identified as K. pneumoniae (n = 2) originated from sheep faeces, K. variicola (n = 2) and K. michiganensis (n = 5) isolated from water (river stream). The genomes of K. variicola and K. michiganensis contained antibiotic resistance genes for fosfomycin ( fosA ), nalidixic acid ( oqxAB ), and β-lactamase ( bla LEN24/16 or bla OXY-1-3 ), aminoglycoside ( aph(3’)-Ia_5 ), efflux pump [ mdf(A )] and tetracycline [ tet(34 )]. Furthermore, K. michiganensis strains harboured the aminoglycoside aph(3’)-Ia gene. K. pneumoniae strains KPT2 and KPT4 contained a plasmid AB595 that encodes for tetracycline ( tetA ), sulphonamide ( sul ), and aminoglycoside ( aph(3’)-Ia ). Core virulence genes encoding siderophores ( ent , fep , iutA ), adhesins ( fim , ecp ), and quorum sensing ( luxS ) were present across Klebsiella spp. isolates. Additional flagellar-related genes, including those for motor assembly ( fliE, fliF, fliG, fliH, fliI , and fliJ ) and motility ( motA and motB ), were exclusive in the K. pneumoniae strain KPT4, highlighting their crucial role in biofilm formation and survival under antibiotic stress. The identification of ARGs, including bla SHV-194 , fosA6 , oqxAB , and tet(A) , in K. pneumoniae isolates from sheep further highlights the circulation of antimicrobial resistance determinants in low-resource settings, where surveillance is limited and exposure to untreated animal waste is prevalent. This study provides genomic evidence that rural agricultural environments serve as underappreciated multidrug-resistant and potentially virulent Klebsiella species reservoirs and underscore the need for integrated One Health surveillance in low-resource farming communities.