A new study has uncovered the secrets of a particular strain of the bacterium Klebsiella pneumoniae, revealing a potentially deadly genetic capacity for both antimicrobial resistance and virulence.
The research, presented at the recent Minoritised Life Scientists Future Forum at the ICC in Birmingham, delivered with support from AMI, makes use of bioinformatic programmes to probe the potential mechanisms and characteristics within the specific K pneumoniae strain (007) that makes it resistant to antibiotics.
Kenechukwu Egwuonwu, a student at Birmingham City University, won a poster prize for his study which highlighted the genomic features contributing to the multidrug resistance and virulence of K. pneumoniae and emphasize the need for continuous surveillance and novel therapeutic approaches, such as bacteriophage therapy or combination treatments, to combat MDR infection.
Antibiotic resistance genes
“The genome analysis revealed the presence of multiple antibiotic resistance genes, including those conferring resistance to β-lactams, aminoglycosides, and fluoroquinolones,” he says.
“Plasmid analysis indicated the presence of conjugative elements, suggesting a high potential for horizontal gene transfer. Profiling Virulence factors identified genes associated with biofilm formation and type VI secretion system, which can contribute to pathogenicity. Phylogenetic analysis placed the isolate within a globally disseminated high-risk clone ST15.”
To characterise the genome of Klebsiella pneumoniae strain 007, Kenechukwu began by sequencing it using Illumina technology on the NovaSeq 6000 platform, with 2 x 250 bp kits. This generated high-quality raw reads in the form of FASTQ files (R1_007.fasta.gz & R2_007.fasta.gz), as well as an assembled genome file (K007.fasta).
How it compares
He uploaded the assembled genome to the Comprehensive Genome Analysis service on PATRIC (now part of BV-BRC), where it was annotated and compared to other K. pneumoniae genomes. The results indicated strong genome quality, and BV-BRC went on to identify antibiotic resistance genes, virulence factors, and their sources.
Kenechukwu also looked into genes associated with biofilm formation and explored the bacterium’s subsystems in more detail. To confirm the strain’s identity, he turned to the Type (Strain) Genome Server (TYGS) for a full phylogenetic analysis. He uploaded the genome, and TYGS provided a whole-genome-based taxonomic classification, supported by nomenclature and taxonomic insights from its sister database, the List of Prokaryotic Names.
To investigate the plasmid landscape of this strain, he then performed plasmid multilocus sequence typing (pMLST) using tools from the Center for Genomic Epidemiology, which highlighted various resistance genes, virulence factors, mobile genetic elements, and plasmid replicons.
Strain lineage
“I also wanted to understand the strain’s lineage, so I ran an in silico multilocus sequence typing (MLST) analysis using MLST 2.0. I provided both the raw FASTQ reads and the assembled FASTA file, which allowed me to determine the sequence type (ST) of the isolate,” he says.
“To further characterise the plasmids, I used PlasmidFinder 2.1, which identified known plasmid replicons present in the genome. To delve deeper into the genome’s mobile genetic content, I used MobileElementFinder to detect insertion sequences, transposons, and integrative conjugative elements. Finally, I visualised the structure of the plasmids using Proksee, which helped me map out key features like resistance genes, replication origins, and other mobile elements in a clear, intuitive format.”
Path to virulence
The study provides a clear overview of the strain’s ability to transport nutrients, maintain homeostasis, and potentially contribute to virulence through specific factors, he says.
“Phylogenetic tree inferred with FastME 2.1.6.1 from GBDP distances calculated from genome sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values > 60% from 100 replications, with an average branch support of 65.8%,” he says.
“The proteins with functional assignments included 1,471 proteins and proteins with pathways were mapped to KEGG pathway. The relatively high number of hypothetical proteins (809) suggests that there may be novel or poorly understood functions in this strain. Along with the functional and pathway-annotated proteins, which indicate key metabolic and survival mechanisms, potentially linked to virulence or antimicrobial resistance.”
Concerning traits
The genomic characterisation of Klebsiella pneumoniae strain 007 reveals a strain with both the genetic capacity for antimicrobial resistance and virulence—traits that are particularly concerning when found in combination, Kenechukwu says.
“The fact that ST15, the sequence type to which this strain belongs, has a global clinical presence and is increasingly recognised as a high-risk clone highlights the urgency of monitoring and controlling its spread,” he says.
“Its association with extended-spectrum β-lactamases (ESBLs) like CTX-M-15 and carbapenemases such as NDM-1 and OXA-48 makes it particularly difficult to treat, as these enzymes render many frontline antibiotics ineffective. In a real-world clinical setting, this translates to longer hospital stays, higher treatment costs, and an increased risk of mortality—especially for vulnerable patients.
Genetic reservoir
“What makes ST15 especially problematic is its ability to carry highly recombinogenic plasmids, which facilitate the horizontal transfer of resistance and virulence genes between bacteria. This means that even if ST15 itself is contained, it can serve as a genetic reservoir, helping to spread these traits to other pathogens. Its prevalence in high-income countries with strong healthcare systems is also significant—it suggests that this strain can thrive even in environments with rigorous infection control measures. This challenges the assumption that advanced healthcare infrastructure alone is sufficient to prevent the spread of resistant organisms.
“In practical terms, these findings reinforce the need for enhanced genomic surveillance, strict antimicrobial stewardship, and quick diagnostic methods in both hospital and community settings. Understanding strains like 007 is critical not just for managing infections today, but for preparing for the continued evolution and global movement of multidrug-resistant pathogens.”
Way forward
Kenechukwu suggests that future work should focus on both experimental validation and broader contextual analysis. Functional assays—including antimicrobial susceptibility testing, biofilm quantification, and virulence assays using in vitro or in vivo models—would help confirm the predicted resistance and pathogenicity profiles.
Comparative genomics across a wider collection of global ST15 isolates could reveal unique or emerging features of strain 007, while pangenome and phylogenomic analyses would place it in an evolutionary and epidemiological context. Resolving plasmid structures through long-read sequencing and assessing their mobility would clarify the mechanisms driving gene transfer, especially if resistance and virulence genes are co-located.
Transcriptomic or proteomic profiling could provide insight into gene expression under clinically relevant conditions, shedding light on functional activity beyond genetic presence. Further, incorporating strain 007 into regional surveillance initiatives could determine whether it represents a broader trend or potential outbreak clone.
Understanding the threat
Finally, exploring the genomic context of resistance genes and assessing environmental or host adaptation strategies would offer a more complete understanding of this strain’s clinical relevance and potential to persist and spread.
The research was led and supported by supervisor, Mr Kashif Haq.
Kenechukwu says: ”From day one to dissertation submission, my supervisor, Mr Kashif Haq, has been a constant source of wisdom, support, and the occasional reality check. Thank you for guiding me through this journey with patience, insight, and just the right amount of academic pressure. I couldn’t have done it without you!”
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