Genomic Insights into Multi-Drug-Resistant, Klebsiella pneumoniae Isolated from an Infertile Woman: A Comprehensive Analysis of Antibiotic Resistance and Virulence Factors

Abstract

Objectives: Klebsiella pneumoniae is a significant global health concern due to its ability to cause diverse infections and its increasing multidrug resistance. This study analyzed the whole-genome sequence of multidrug-resistant K. pneumoniae strain CP4, isolated from a vaginal swab of an infertile woman, to characterize its virulence factors, antibiotic resistance mechanisms, and epidemiological features. Methods: The Kirby-Bauer disk diffusion assay was used to screen antibiotic resistance. Whole genome sequencing was conducted using the Illumina MiSeq platform and followed by comprehensive bioinformatic analysis. Results: Antibiotic susceptibility testing revealed that the K. pneumoniae strain CP4 exhibited resistance to 11 of 18 tested antibiotics, including carbapenems, and displayed a Multiple Antibiotic Resistance (MAR) index of 0.611. Whole-genome sequencing identified an array of putative virulence and metal-resistant genes, classifying it as a human pathogen with a probability score of 0.887. The strain was characterized as sequence type 327 with K16 capsular and O1/O2v1 somatic antigens. The antibiotic resistome included 38 putative genes conferring resistance to a spectrum of antibiotics. Moreover, point mutations were identified in several genes that ResFinder predicted to be associated with resistance to fluoroquinolones, cephalosporins, and carbapenems. Additionally, K. pneumoniae strain CP4 harbored six putative plasmid-replicon types and 454 putative mobile genetic element-associated protein hits among predicted ORFs. Several putative antibiotic resistance genes, including tet(A), floR, mph(A), and aph(6)-Id, were associated with insertion sequences, transposons, and integrons, indicating a potential for horizontal gene transfer. Conclusions: The genomic features of multidrug-resistant K. pneumoniae CP4 highlight its potential for antimicrobial resistance and virulence, emphasizing the need for continued genomic surveillance and targeted interventions. Keywords: Klebsiella pneumoniae, Whole Genome Sequencing, Antimicrobial Resistance, Pangenome analysis