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

Multidrug-resistant <i>Klebsiella pneumoniae</i> 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 <i>K</i>. <i>pneumoniae</i> 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 <i>bla</i>_TEM-1D, <i>bla</i>_SHV-11, <i>dfrA14</i>, <i>sul2</i>, <i>strA</i>, <i>strB</i>, and the ESBL-producing gene <i>bla</i>_CTX-M-15. In addition, ARM02 harbored 12 virulence genes, including the common pilus fibrillin subunit encoding gene <i>yagZ/ecpA</i> and a complete yersiniabactin siderophore system (<i>irp1</i>, <i>irp2</i>, <i>ybtAEPQSTUX</i>, and <i>fyuA</i>). 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 <i>K. pneumoniae</i>, which remain on the WHO's Priority Pathogens list, evolve and spread in LMICs, and how they contribute to the global AMR crisis.IMPORTANCEWe report the first genomic analysis of an extended-spectrum β-lactamase (ESBL)-producing <i>Klebsiella pneumoniae</i> ST37 isolate (ARM02) recovered from a hospitalized patient in Armenia. Genome sequencing identified several antimicrobial resistance (AMR) genes, including <i>bla</i>_CTX-M-15, <i>bla</i>_TEM-1D, and <i>bla</i>_SHV-11, which were directly linked to the observed resistance phenotypes. ARM02 also carried a variety of virulence genes, including a complete yersiniabactin siderophore system, which is associated with enhanced pathogenicity. Phylogenetic analysis revealed that ARM02 was closely related to strains from the United States, but it harbored a unique accessory genome, suggesting independent evolution and local spread in Armenia. This highlights the critical need for robust genomic surveillance and targeted interventions in low- and middle-income countries. This study provides crucial insights into the genetic diversity and potential local transmission of ST37 <i>K. pneumoniae</i> in Armenia and calls for larger-scale genomic surveillance to better understand and control its spread.