Comprehensive Genomic Characterization of a Drug-Resistant Klebsiella pneumoniae Clinical Isolate in Iraq Using Whole Genome Sequencing.

Background: Klebsiella pneumoniae is a Gram-negative encapsulated opportunistic pathogen, which presents a major threat to public health due to its ability for multi-antibiotic drug resistance. It is responsible for 30% of Gram-negative bacterial infections, including nosocomial infections, pneumonia, septicemia, and urinary tract infections. The study aimed to analyze the key phenotypic and genetic features of clinical K. pneumoniae isolates.

Methods: Between 2022 and 2023, a total of 91 strains of Klebsiella pneumoniae were collected from Al-Imamian Al-Kadhimiyain Medical City (IKMC) and characterized using the VITEK-2 technique. Whole-genome sequencing (WGS) was employed to characterize the extreme drug-resistant strain. The whole genome was extracted and sequenced using the Next Generation Sequencing (NGS) technique. The genome of our bacterial isolate was analyzed using different bioinformatics tools such as Galaxy workflow, SPAdes, PROKKA, and Staramr.

Results: The analysis identified Klebsiella pneumoniae serotype K36:O2a and sequencing type ST-437, containing 15 different plasmids carrying 54 resistance genes and more than 100 virulence genes with one region of CRISPR and no Cas. The sample obtained four intact bacteriophages and two questionable ones. Seven insertion sequences were revealed in the analysis as part of Other Mobile Genetic Elements (OMG). Additionally, the 16SrRNA phylogenetic tree identified a higher relationship of the bacteria to the strains from the USA and India than from Iraq.

Conclusion: It is the first study in Iraq to utilize WGS to comprehensively characterize an opportunistic pathogen. The study emphasizes the need for WGS to track the development of resistance and virulence patterns in clinical strains of K. pneumoniae.