bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.09.03.749063

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

Hasan, Z.·Ahmed, S.·Tupur, S.·Yasmin, M.
View original source ↗Export metadata ↓

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

Explore related subjects

microbiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Hasan, Z., Ahmed, S., Tupur, S., Yasmin, M.. 2026-09-07. Genomic Insights into Multi-Drug-Resistant, Klebsiella pneumoniae Isolated from an Infertile Woman: A Comprehensive Analysis of Antibiotic Resistance and Virulence Factors. https://doi.org/10.64898/2026.09.03.749063

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

Periodontitis is an archetypical mucosal inflammatory disease in which microbiome dysbiosis at the tooth-epithelial interface interacts with host genetic and behavioral risk factors to drive immune-mediated tissue destruction. Although subgingival microbiome compositional shifts are thought to parallel disease severity, microbiome variation at the population-level and its relationship to periodontal clinical phenotypes and disease-modifying factors remain poorly defined. Here, we use unsupervised manifold learning to map the compositional landscape of the subgingival microbiome in 1,355 adults spanning periodontal health to severe periodontitis. We identified eight latent microbiome states organized along a branching continuum from eubiosis to dysbiosis. An intermediate microbial configuration marked ecological destabilization and bifurcation into two distinct periodontitis-associated dysbiotic trajectories, distinguished by links to gingival inflammation and smoking. Although the microbiome trajectories broadly tracked periodontal destruction, a minority of individuals showed discordant microbiome-clinical phenotypes, with some individuals with periodontitis retaining otherwise eubiotic microbiomes enriched for low-abundance pathobionts, while some cases of health or mild disease had highly dysbiotic communities, suggesting distinct host susceptibility. Together, these findings define a population-scale ecological landscape of the subgingival microbiome, reveal divergent trajectories to periodontal dysbiosis, and highlight heterogeneity in the relationship between microbial community structure and clinical disease expression.

microbiology↗
bioRxiv2026

The iron-binding siderophore enterobactin is required for the response of multi-drug resistant Klebsiella pneumoniae to zinc limitation

To persist during infection Klebsiella pneumoniae must overcome nutrient iron and zinc limitation imposed by the host immune system through a process called nutritional immunity. Secreted small molecule siderophores are a major virulence determinant of Klebsiella pneumoniae pathogenesis and are presumed to overcome nutritional immunity by binding iron for bacterial acquisition. In this work, we set out to identify how a multi-drug resistant K. pneumoniae grows in zinc limited environments. Using unbiased transcriptomics, proteomics, and an arrayed transposon screen, we identified that synthesis and uptake of the siderophore enterobactin is required to allow for growth in low zinc conditions. Iron-specific chelators did not replicate this phenotype and addition of supplemental iron through heme in growth media could not complement severe growth defects of enterobactin mutant K. pneumoniae experiencing zinc limitation. Finally, zinc starvation induced enterobactin production independent of the canonical zinc uptake regulator (Zur) transcription factor suggesting an unidentified regulatory mechanism by which Gram-negative pathogens may respond to zinc stress. Together, these studies expand the role of enterobactin beyond iron regulation and highlight a previously unreported link between iron and zinc homeostasis in Klebsiella pneumoniae.

microbiology↗
bioRxiv2026

A microbiota-derived protease links phage susceptibility to host epithelial responses

Bacteriophages are major ecological drivers of gut microbial ecology, yet whether bacterial mechanisms that determine phage susceptibility have consequences for the mammalian host remains poorly understood. Here, we identify dipeptidyl peptidase 11 (Dpp11a), the predominant active serine protease of the prevalent gut commensal Phocaeicola vulgatus, as an unexpected bacterial defence factor. Dpp11a protects against environmental proteases and confers resistance to bacteriophage infection. Metatranscriptomic analyses further reveal increased expression of both dpp11a and P. vulgatus-associated phage transcripts in ulcerative colitis stool samples, indicating that both components of this interaction are transcriptionally active in disease-associated human microbiomes. Using the microfluidic gut-on-a-chip co-culture model HuMiX, we show that the absence of Dpp11 is accompanied by altered epithelial tight-junction remodelling during phage-bacterial infection. Together, our findings reveal that the consequences of bacterial phage defence can extend beyond phage-bacterium interactions to the mammalian epithelium.

microbiology↗