Hospital-Based Surveillance of Klebsiella pneumoniae and Other Klebsiella species in Southern Saudi Arabia (2012–2024): Escalating Carbapenem and DTR Resistance with Species-Specific Phenotypes and Genotypes

Yahya Shabi,1 Abdullah M Algarni,2 Khalifa Binkhamis,3 Ali Al Bshabshe,4 Tarik Alazraqi,5 Safia Abdullah Mohammed,5 Sara Habbash,5 Abdulah J Alqahtani,1 Nada A Basheer,6 Abdulaziz H Alhazmi,7 Glenn Patriquin,8 Abdulah OS Bawazeer,6 Esmahan Ibrahim Tahtouh5 1Department of Microbiology and Clinical Parasitology, College of Medicine, King Khalid University, Abha, Saudi Arabia; 2Department of Family Medicine, Aseer Central Hospital, Abha, Saudi Arabia; 3Department of Pathology, College of Medicine, King Saud University, Riyadh, Saudi Arabia; 4Department of Medicine, College of Medicine, King Khalid University, Abha, Saudi Arabia; 5Department of Internal Medicine, Aseer Central Hospital, Abha, Saudi Arabia; 6Department of Microbiology, Aseer Central Hospital, Abha, Saudi Arabia; 7Medical and Scientific Affairs, Cepheid, Riyadh, Saudi Arabia; 8Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, NS, CanadaCorrespondence: Yahya Shabi, Email [email protected]: Klebsiella species, particularly Klebsiella pneumoniae, are major healthcare-associated infections showing increasing resistance to carbapenems and other antibiotics. In Saudi Arabia, rising antimicrobial resistance (AMR) and the emergence of difficult-to-treat resistance (DTR) phenotypes pose significant clinical challenges.Methods: A 12-year retrospective surveillance study (2012– 2024) of 9790 non-duplicate Klebsiella isolates from Aseer Central Hospital in southern Saudi Arabia. Species-level identification, antimicrobial susceptibility testing for each isolate was done. Molecular characterization of carbapenemase genes for selected isolates were performed. Temporal resistance trends were assessed using logistic regression.Results: K. pneumoniae accounted for 93.0% of isolates, with non-pneumoniae species showing distinct resistance profiles. Carbapenem resistance surged from 12.4% in 2012 to 69.3% in 2021, while DTR prevalence rose to 50.7%. ICU and inpatient settings exhibited the highest resistance rates. Molecular testing revealed widespread bla_OXA-48-like (35.7%), bla_NDM (17.9%), and emerging bla_KPC (14.3%) genes, with 25% of isolates co-harboring multiple carbapenemases. Progression from colonization to bloodstream infection occurred in 1.7% of K. pneumoniae cases, primarily from respiratory and urinary sources.Conclusion: This study highlights escalating carbapenem and DTR resistance among Klebsiella species in southern Saudi Arabia, driven by species-specific mechanisms and widespread carbapenemase gene dissemination. Findings underscore the need for species-level diagnostics, expanded molecular surveillance, and integrated stewardship strategies to curb the spread of multidrug-resistant Klebsiella.Keywords: Klebsiella pneumoniae, carbapenem-resistant enterobacterales, difficult-to-treat resistance, antimicrobial resistance surveillance, carbapenemase genes, Saudi Arabia