Phenotypic and genome-based characterization of Klebsiella species from different One Health sources in South Africa reveals the presence of multidrug-resistant isolates.

The emergence of antimicrobial-resistant and livestock-associated Klebsiella represents a serious public health concern, necessitating comprehensive genomic investigations. Bacterial strains were isolated from different domestic animals located in KwaZulu-Natal and Eastern Cape Provinces in South Africa. Antibiotic susceptibility testing was performed using the Kirby-Bauer disk diffusion method. Biofilm formation and hypermucoviscosity were investigated. Genomic DNA of the isolates was extracted, and whole-genome sequencing was performed using an Illumina MiSeq platform. Here, we report the isolation, molecular detection, virulence and antimicrobial resistance (AMR) determinants, as well as phylogenetic analyses of 16 Klebsiella strains using whole-genome sequence (WGS) analysis. Ten Klebsiella pneumoniae strains, three Klebsiella variicola and three Klebsiella aerogenes were detected. The assembled contigs were analyzed for AMR and virulence genes, K and O types, and multi-locus sequence type (MLST). To compare the sequenced strains to other previously sequenced Klebsiella species, a distance-based phylogeny method was used to confirm the taxonomic designation of the 16 Klebsiella genomes in an extended context of 169 genomes from the different Klebsiella species. Genomic analysis identified several antibiotic resistance genes conferring resistance to beta-lactams (bla SHV-11-like , bla SHV-40/56/79/85/89-like , bla SHV-110/81-like , bla SHV-119 , bla SHV-164/59-like, and bla LEN-16-like), quinolones (oqxA, oqxA-like, oqxB, oqxB-like), tetracyclines [tet(A)], and fosfomycin (fosA-like). All isolates harbored genes conferring resistance to at least three antibiotic classes, thus classifying them as multidrug-resistant (MDR). Nine sequence types (ST-76, ST-128, ST-494, ST-617, ST-2465, ST-4039, ST-5470, ST-5478, and ST-5497) were identified using the MLST K. pneumoniae scheme in the Klebsiella collection. The latter three STs are being reported for the first time in the current study. MLST analysis revealed that the three K. variicola isolates belonged to ST-696 using the MLST K. variicola scheme. Although no hypervirulent strains were identified, the 16 Klebsiella isolates were in vitro biofilm producers and contained one to five intact prophages. The detection of MDR K. pneumoniae highlights the critical significance of genomic surveillance in monitoring the dissemination of antimicrobial resistance in livestock pathogens and within the food chain. The report of novel sequence types (ST-5470, ST-5478, and ST-5497) in K. pneumoniae present new allelic profiles, indicating the ongoing evolution and diversification within the species.