Genomic and transcriptomic data of presumptive Klebsiella pneumoniae isolates for resistance mechanisms

<p dir="ltr">The second objective of the study was to select ten presumptive Klebsiella pneumoniae isolates that tested negative for carbapenemase and mcr genes for further genomic characterization. These ten clinical isolates were subjected to both DNA and RNA sequencing. The sequencing was conducted at the National Institute for Communicable Diseases (NICD) and Inqaba Biotech, respectively. The term "presumptive" was used because isolates A5, G3, and G5 were later identified as Enterobacter species based on DNA data. The DNA files were used for identifying resistance genes, virulence genes, phylogenetics, multi-locus sequence typing (MLST), and confirmation of species identification.</p><p dir="ltr">Due to cost constraints, RNA sequencing was performed on only half of the isolates, specifically Kp_14, Kp_24, A5, G5, and H3. The RNA was extracted from isolates grown in the presence of antibiotics: Kp_14 and Kp_24 were exposed to carbapenem, while A5, G5, and H3 were exposed to colistin. This approach was used to obtain the differentially expressed genes for carbapenem and colistin resistance. The reference genome used for the analysis was K. pneumoniae MGH64. Data extracted from these RNA files include differential expression genes (as detailed in the attached spreadsheet) and epigenetic information.</p>