Genomic determinants of virulence and antimicrobial resistance in colistin resistant Klebsiella pneumoniae isolates from Mulago National Referral Hospital

Abstract

Introduction: Multidrug resistance and high virulence in K. pneumoniae are of particular concern and have emerged as critically alarming threats to the global community. Worringly, K.pneumoniae has become resistant to colistin, the last resort antibiotic for carbapenem resistant K. pneumoniae making the treatment of the infections more challenging. The objectives of this study were to determine hypermucoid K.pneumoniae isolates, delineate the virulence and antimicrobial resistance determinants of colistin resistant K.pneumoniae and determine the phylogenetic relatedness of each K.pneumoniae strain. Methodology: All 31 archived multidrug resistant K. pneumoniae isolates were retrieved and instantly inoculated on MacConkey agar for recovery followed by re-identification using conventional biochemical methods. The isolates were then subjected to phenotypic characterization of the hypermucoid K.pneumoniae using string test. Additionally, the isolates were subjected to antibiotic susceptibility against 16 antibiotics.. Genomic DNA isolation from the overnight culture of the isolates was performed using CTAB method. Then library preparation and sequencing were done using illumina novaseq platform. Results: The isolates were found to be multidrug resistant and colistin resistance was detected in 7/31 (22.58%) isolates. The sequence analysis of the commonly known genes involved in colistin resistance revealed several non-synonmous mutations in nucleotide sequences of pmrA/pmrB, phoP/phoQ and mgrB genes rendering resistance to colistin. Interestingly, the isolates also harbored mcr-1 gene in the chromosome. More so, the isolates harbored several virulent genes as several virulence factors genes such as fim genes for adherence, enterobactin, salmocherin aerobactin, clpvi for effector delivery system or waaA genes for LPS were found in colistin resistant K. pneumoniae strains.Conclusion: The study clearly show the occurrence of colistin resistance and high virulence genes in clinical isolates which is alarming and warrants attention as it can lead to untreatable and invasive K. pneumoniae infections. It is therefore imperative to conduct active surveillance in order to prevent the transmission and spread of highly viurulent or multidrug resistant strains, focusing not only on antimicrobial resistance but also on identifying virulence determinants.