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

Abstract

<i>Klebsiella</i> 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 <i>Klebsiella</i> 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 <i>Klebsiella</i> species. The nine sequenced <i>Klebsiella</i> spp. isolates were identified as <i>K. pneumoniae</i> (n = 2) originated from sheep faeces, <i>K. variicola</i> (n = 2) and <i>K. michiganensis</i> (n = 5) isolated from water (river stream). The genomes of <i>K. variicola</i> and <i>K. michiganensis</i> contained antibiotic resistance genes for fosfomycin (<i>fosA</i>), nalidixic acid (<i>oqxAB</i>), and β-lactamase (<i>bla</i> _LEN24/16 or <i>bla</i> _OXY-1-3), aminoglycoside (<i>aph(3')-Ia_5</i>), efflux pump [<i>mdf(A</i>)] and tetracycline [<i>tet(34</i>)]. Furthermore, <i>K. michiganensis</i> strains harboured the aminoglycoside <i>aph(3')-Ia</i> gene. <i>K. pneumoniae</i> strains KPT2 and KPT4 contained a plasmid AB595 that encodes for tetracycline (<i>tetA</i>), sulphonamide (<i>sul</i>), and aminoglycoside (<i>aph(3')-Ia</i>). Core virulence genes encoding siderophores (<i>ent</i>, <i>fep</i>, <i>iutA</i>), adhesins (<i>fim</i>, <i>ecp</i>), and quorum sensing (<i>luxS</i>) were present across <i>Klebsiella</i> spp. isolates. Additional flagellar-related genes, including those for motor assembly (<i>fliE, fliF, fliG, fliH, fliI</i>, and <i>fliJ</i>) and motility (<i>motA</i> and <i>motB</i>), were exclusive in the <i>K. pneumoniae</i> strain KPT4, highlighting their crucial role in biofilm formation and survival under antibiotic stress. The identification of ARGs, including <i>bla</i> _SHV-194, <i>fosA6</i>, <i>oqxAB</i>, and <i>tet(A)</i>, in <i>K. pneumoniae</i> 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 <i>Klebsiella</i> species reservoirs and underscore the need for integrated One Health surveillance in low-resource farming communities.