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

## TL;DR

This study identifies antibiotic-resistant Klebsiella species in South African rural environments, highlighting their public health risks and the need for better surveillance.

## Contribution

The study provides genomic evidence that rural agricultural settings are reservoirs of multidrug-resistant Klebsiella species.

## Key findings

- Klebsiella isolates from sheep and water sources showed resistance genes like fosA, oqxAB, and blaLEN24/16.
- K. pneumoniae strains contained plasmid AB595 with tetracycline, sulphonamide, and aminoglycoside resistance genes.
- Virulence genes for adhesion, siderophores, and motility were identified, emphasizing their role in antibiotic resistance.

## Abstract

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 (blaLEN24/16 or blaOXY-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 blaSHV-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.