Genomic characterization of an ESBL-producing Klebsiella pneumoniae ST37 recovered from a hospitalized patient in Armenia

Multidrug-resistant Klebsiella pneumoniae continues to challenge healthcare services globally. However, our understanding of its occurrence, genomic characteristics, and epidemiology in low- and middle-income countries (LMICs) remains severely limited. In this study, we report the whole-genome sequencing of an extended-spectrum β-lactamase (ESBL)-producing, sequence type (ST) 37 K. pneumoniae isolate (ARM02) recovered from a patient in Armenia. Antibiotic susceptibility testing revealed that ARM02 was resistant to four of the 11 antibiotics tested, including ampicillin, amoxicillin-clavulanic acid, cefepime, and ceftazidime. Genome sequencing analysis identified seven antimicrobial resistance (AMR) genes in ARM02, including blaTEM-1D, blaSHV-11, dfrA14, sul2, strA, strB, and the ESBL-producing gene blaCTX-M-15. In addition, ARM02 harbored 12 virulence genes, including the common pilus fibrillin subunit encoding gene yagZ/ecpA and a complete yersiniabactin siderophore system (irp1, irp2, ybtAEPQSTUX, and fyuA). Moreover, we also detected five insertion sequences and two plasmid replicons in the ARM02 genome. Phylogenetic analysis showed that ARM02 shared a common ancestor with the USA strains SRR5283489 and SRR5973349, diverging around 2007 (95% onfidence interval, 2004 to 2011). However, ARM02 carried a unique accessory genome, indicating independent evolution and spread. Our findings highlight the co-existence of virulence and resistance genes in the Armenian ST37 strain and emphasize the critical need for genomic surveillance in LMICs. This is crucial for understanding how gram-negative bacterial pathogens, such as ESBL-producing K. pneumoniae, which remain on the WHO’s Priority Pathogens list, evolve and spread in LMICs, and how they contribute to the global AMR crisis.