Genomic Characteristics of Clinical Strains of Klebsiella pneumoniae
Abstract
Background. Klebsiella pneumoniae is a clinically significant pathogen associated with a broad spectrum of infectious diseases, characterized by genetic diversity and the formation of successful clones. The aim of the study was to analyze the molecular genetic characteristics of clinical K. pneumoniae strains ( n = 35) isolated from the lower respiratory tract, blood, and urine of patients in Moscow, Vologda, and Yakutsk in 2021–2023 and deposited in the collection of the State Clinical Hospital «Obolensk». Material and methods . Bacteria were identified using a MALDI-TOF Biotyper (Bruker, Germany), and antimicrobial susceptibility was determined using a Vitek 2 Compact (BioMireux, France) and serial dilution in broth. Antibiotic resistance and virulence genes ( rmpA, iroN, iroD, uge, wabG, kfu, fimH, allS, and allR ) were detected via PCR. Whole genome analysis (GenoLab M) was performed using BLAST, PubMLST, and other methods. Results . Strains were isolated from neurosurgical and COVID-19 patients in Moscow. The ST512 (KL37/107) and ST395 (KL2/39) genetic lineages were predominant, with ST874 (KL45), ST147 (KL64), ST336 (KL25), ST11 (KL27), and ST1773 (KL123) being less common. The following antibiotic resistance genes were identified: bla SHV-106/121/28/182 , bla TEM-1B , bla CTX-M-15 , bla KPC-3 , bla NDM-1 , bla OXA-48 , armA, aph (3›)-VI; aac (3)-IIa/d, aac (6›)-Ib-cr; aph (3›)-Ia/VI, aadA2, sul1/2, fosA, catA1/B3, msrE, mphA, ermB, tetA . The strains isolated in Vologda from patients with COVID-19 complicated by pneumonia were classified as ST874(K45), ST395(K64), and carried the genes bla NDM-1/5 ; bla TEM-1B , bla SHV-121 , bla CTX-M-15 , armA, aph (3›)-VI; aac (3)-IId, aac (6›)-Ib-cr; aadA2, sul1/2; fosA; msrE; rmtB; catA1 and mphA . The strains isolated in Yakutsk were classified as ST307 (KL102), ST23 (KL57), ST147 (KL64), and less frequently as ST395 (KL108) and ST3551 (KL64). They carried the genes bla SHV-11/67/106/75/28/182 , bla OXA-48 , bla OXA-1 , bla CTX-M-15, bla TEM-1B , aac (3)-IIa, aac (6›)-Ib-cr, aph (6)- Id, aadA1, rmtF, fosA/6, sul2, catA1/B3, tetA, rmtF . The following genes were identified: efflux pumps oqxAB, KpnFEHG, LptD, msbA, qacE1, H-NS, emrR, CRP, baeR , and marA; porins OmpK37, OmpK36, and OmpA ; and the outer membrane vesicle protein MdtQ . Resistance to fluoroquinolones is also caused by mutations in the gyrA (D87N) and parC (S80I) genes. The virulence genes wabG, fimH , and uge_2 were detected in all strains; rmpA was detected in 5 strains belonging to ST395, 23, and 147 from Moscow and Yakutsk; ugeE was detected in 4 strains of the capsular type KL64 (ST395 and 874) from Vologda. Conclusion . Consequently, the resistomes and virulomes of the studied K. pneumoniae strains were characterized, and their affiliation with successful international clones was established.