Employing whole genome sequencing to elucidate the pathogenic and Antimicrobial resistance potential of Klebsiella Oxytoca clinical isolates from Mulago Referral National Hospital in Uganda

Abstract

Introduction: Klebsiella oxytoca (K. oxytoca) comprises a complex of related Gram negative opportunistic bacterial pathogens with scantly explored emerging antimicrobial resistance globally. Evidence shows shared virulence and antimicrobial resistance with some strains of the K. pneumoniae complex. Objectives: This study aimed to unveil the genomic features determining the pathogenic and antimicrobial resistance (AMR) potential of K. oxytoca isolates from Mulago Referral Hospital in Uganda using both genomic and specific gene analyses. Materials and methods: Eight isolates were subcultured, six of which were phenotypically tested for AMR using a panel of 11 antibiotics including Trimethoprim/sulfamethoxazole (TXM), clindamycin (CN), ciprofloxacin (CIP), tetracycline (TE), chloramphenicol (C), imipenem (IPM), cefuroxime (CXM), ampicillin (AMP), ceftriaxone (CRO), cefepime (FEP) and amoxicillin/clavulanate (AMC). Then, whole sequencing was performed for all eight isolates using the Illumina Novaseq 6000 platform, followed by bioinformatic analysis of virulence and AMR profiles. Results: Eight of the genomes were confirmed to belong to the Klebsiella oxytoca complex, four belonged to K. oxytoca sensu stricto, three to K. michiganensis and one Raoulella ornithinolytica, some carrying novel alleles for housekeeping genes. Virulence factor analysis revealed that all except one of the isolates contain uncharacterized capsular polysaccharides and O-antigens. Genome mining recovered biosynthetic gene clusters (BGCs) for enterobactin, yersiniabactin, kleboxymicin (tilimycin) and a potentially novel enterotoxin (namely 3-(4,5-dihydro-2-(2-hydroxyphenyl)thiazol-4-yl)-3-hydroxy-2,2-dimethylpropanoic acid), with similar mode of action to tilimycin in silico. AMR findings showed that all the isolates are resistant to ampicilin with extended spectrum of beta-lactamases (ESBL), determined by Bla- genes. One isolate, K. michiganensis strain RSM7756, carries plasmids with multiple insertion sequences and extensive AMR to multiple antibiotics, including fluoroquinolones. Conclusion: Isolates from Mulago National Referral Hospital have the potential to cause infection and resist conventional drugs of all generations. The K. oxytoca complex presents significant pathogenic and antimicrobial resistance profiles whose clinical importance could have been overlooked