- Visibility 142 Views
- Downloads 114 Downloads
- Permissions
- DOI 10.18231/j.ijmr.12671.1937092237
-
CrossMark
Genetic analysis of virulence factors of MDR Klebsiella pneumoniae spp. pneumoniae isolated from clinical specimens - study from a tertiary care hospital
- Author Details:
-
Bhavita Thakorbhai Prajapati
-
Anant Prabhakar Marathe *
-
Asmabanu Mahammed Hanif Shaikh
-
Shital Sangani
Bhavita Thakorbhai Prajapati
Anant Prabhakar Marathe *
Asmabanu Mahammed Hanif Shaikh
Shital Sangani
Background: Klebsiella pneumoniae is a predominant nosocomial pathogen owing to its potent virulence factors, viz, capsule, fimbriae, siderophores, efflux pump, regulatory secretions, and secretory system. As most nosocomial K. pneumoniae infections are MDR/XDR, treatment remains limited. The understanding of the different virulence mechanisms and their genetic control becomes imperative.
Aims and Objective: To determine the prevalence and distribution of virulence genes among Klebsiella pneumoniae isolates.
Materials and Methods: In the present study, virulence genes were analysed with the help of whole-genome sequencing. A total of 41 K. pneumoniae isolates from various nosocomial infections were collected, identified by VITEK 2 and MALDI-TOF-MS, and confirmed by whole genome sequencing. Virulence genes were studied using the Virulence Finder database, a web-based bioinformatics tool that identifies virulence genes in bacterial isolates.
Results: The genes for Type I fimbriae were found in all clinical specimens. Variation was observed in type III fimbriae isolated from bloodstream Infections. Besides the virulence factors seen in Enterobacterales, the K. pneumoniae also possessed virulence factors like enterobactin, aerobactin, salmochelin, and yersiniabactin siderophores. Additional secretory system Types 1 and 3 were detected in our strains, and variation was observed in Type 2.
Conclusion: Our study provides insights into the virulence factors of K. pneumoniae, revealing regional diversity and identifying predominant genes associated with hypervirulent strains. We found type 3 fimbriae genes in most isolates, linked to biofilm formation, and detected MDR nosocomial hypervirulent strains with K2 and K64 capsular types. Notably, the ST395 strain, prevalent in our region, exhibited multiple virulence factors, making it a highly virulent strain.
References
- Ashurst JV, Dawson A. Klebsiella pneumoniae. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2025
- Chen IR, Lin SN, Wu XN, Chou SH, Wang FD, Lin YT. Clinical and microbiological characteristics of bacteremic pneumonia caused by Klebsiella pneumoniae. Front Cell Infect Microbiol. 2022;12:903682.
- Huang X, Yao X, Hou Y, Zhang D, Xie R, Shi C, et al. Global trends of antimicrobial resistance and virulence of Klebsiella pneumoniae from different host sources. Commun Med (Lond). 2025;5(1):383.
- Asri NAM, Ahmad S, Mohamud R, Hanafi NM, Zaidi NFM, Irekeola AA, et al. Global prevalence of nosocomial multidrug- resistant Klebsiella pneumoniae: a systematic review and meta- analysis. Antibiotics (Basel). 2021;10(12):1508.
- Lodhi M, Lakshminarayana GP. Occurrence of nosocomial multi- drug resistant Klebsiella pneumoniae in India: a systemic review and meta-analysis. IP Int J Med Microbiol Trop Dis. 2024;10(1):17–
- Monteiro ASS, Cordeiro SM, Reis JN. Virulence factors in Klebsiella pneumoniae: a literature review. Indian J Microbiol. 2024;64(2):389–401.
- Malekzadegan Y, Khashei R, Sedigh Ebrahim-Saraie H, Hosseini MS. Distribution of virulence genes and their association with antimicrobial resistance among uropathogenic Escherichia coli isolates from Iranian patients. BMC Infect Dis. 2018;18:572.
- Marathe AP, Shaikh AMH, Prajapati BT, Sangani S. Species identification of lactose non-fermenting isolates from ventilator- associated pneumonia using VITEK 2 and matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a comparative study with next-generation sequencing. J Appl Biol Biotech. 2025;13(5):146–50.
- Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis JJ, et al. Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. Nucleic Acids Res. 2023;51(D1):D678–89.
- Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124.
- Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2005;33(Database issue):D325–8.
- Wick RR, Heinz E, Holt KE, Wyres KL. Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes. J Clin Microbiol. 2018;56(6):e00197-18.
- Rendueles O. Deciphering the role of the capsule of Klebsiella pneumoniae during pathogenesis: A cautionary tale. Mol Microbiol. 2020;113(5):883–8.
- Chen J, Zhang H, Liao X. Hypervirulent Klebsiella pneumoniae. Infect Drug Resist. 2023;16:5243–9. 418 Prajapati et al. / Indian Journal of Microbiology Research 2025;12(3):410–418
- Liao Y, Gong J, Yuan X, Wang X, Huang Y, Chen X. Virulence factors and carbapenem-resistance mechanisms in hypervirulent Klebsiella pneumoniae. Infect Drug Resist. 2024;17:1551–9.
- Huang X, Li X, An H, Wang J, Ding M, Wang L, et al. Capsule type defines the capability of Klebsiella pneumoniae in evading Kupffer cell capture in the liver. PLoS Pathog. 2022;18(8):e1010693.
- Diab H, Rahy K, Jisr T, El Chaar M, Abboud E, Tokajian S. Phenotypic and molecular characterization of multi-drug resistant Klebsiella spp. isolates recovered from clinical settings. Infect Genet Evol. 2024;119(105583):105583.
- Hussain A, Mazumder R, Ahmed A, Saima U, Phelan JE, Campino S, et al. Genome dynamics of high-risk resistant and hypervirulent Klebsiella pneumoniae clones in Dhaka, Bangladesh. Front Microbiol. 2023;14:1184196.
- Ngoc BVT, Brisse S, Tuyet TD, Viet DVT, Holt KE, Vu TN, et al. Klebsiella pneumoniae with capsule type K64 is overrepresented among invasive disease in Vietnam. F1000Res. 2025;10:454.
- El Fertas-Aissani R, Messai Y, Alouache S, Bakour R. Virulence profiles and antibiotic susceptibility patterns of Klebsiella pneumoniae strains isolated from different clinical specimens. Pathol Biol (Paris). 2013;61(5):209–16.
- Maleki NS, Babazadeh F, Arzanlou M, Teimourpour R, Dogaheh HP. Serotyping and molecular profiles of virulence-associated genes among Klebsiella pneumoniae isolates from teaching hospitals of Ardabil, Iran: a cross-sectional study. Health Sci Rep. 2023;6(9):e1557.
- Di Martino P, Cafferini N, Joly B, Darfeuille-Michaud A. Klebsiella pneumoniae type 3 pili facilitate adherence and biofilm formation on abiotic surfaces. Res Microbiol. 2003;154(1):9–16.
- Hider RC, Kong X. Chemistry and biology of siderophores. Nat Prod Rep. 2010;27(5):637–57.
- Nahar N, Rashid RB. Phylogenetic analysis of antibiotic resistance genes and virulence genes of Klebsiella species in silico. Dhaka Univ J Pharm Sci. 2017;16(1):119–27.
- Lam MMC, Wyres KL, Judd LM, Wick RR, Jenney A, Brisse S, et al. Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae. Genome Med. 2018;10(1):77.
- Kocsis B. Hypervirulent Klebsiella pneumoniae: An update on epidemiology, detection and antibiotic resistance. Acta Microbiol Immunol Hung. 2023;70(4):278–87.
- Ali MR, Yang Y, Dai Y, Lu H, He Z, Li Y, et al. Prevalence of multidrug-resistant hypervirulent Klebsiella pneumoniae without defined hypervirulent biomarkers in Anhui, China: a new dimension of hypervirulence. Front Microbiol. 2023;14:1247091.
- Lawlor MS, O'connor C, Miller VL. Yersiniabactin is a virulence factor for Klebsiella pneumoniae during pulmonary infection. Infect Immun. 2007;75(3):1463–72.
- Lan P, Yan R, Lu Y, Zhao D, Shi Q, Jiang Y, et al. Genetic diversity of siderophores and hypermucoviscosity phenotype in Klebsiella pneumoniae. Microb Pathog. 2021;158(105014):105014.
- Bachman MA, Oyler JE, Burns SH, Caza M, Lépine F, Dozois CM, et al. Klebsiella pneumoniae yersiniabactin promotes respiratory tract infection through evasion of lipocalin 2. Infect Immun. 2011;79(8):3309–16.
- Padilla E, Llobet E, Doménech-Sánchez A, Martínez-Martínez L, Bengoechea JA, Albertí S. Klebsiella pneumoniae AcrAB efflux pump contributes to antimicrobial resistance and virulence. Antimicrob Agents Chemother. 2010;54(1):177–83.
- ALmiyah SAF. Detection of AcrA and AcrB efflux pumps in multidrug-resistant Klebsiella pneumonia that isolated from wounds infection patients in Al-Diwaniyah province. Arch Razi Inst. 2023;78(1):269–76.
- Liu W, Li M, Cao S, Ishaq HM, Zhao H, Yang F, et al. The biological and regulatory role of type VI secretion system of Klebsiella pneumoniae. Infect Drug Resist. 2023;16:6911–22.
- Storey D, McNally A, Åstrand M, Santos J, Rodriguez-Escudero I, Elmore B, et al. Klebsiella pneumoniae type VI secretion system- mediated microbial competition is PhoPQ controlled and reactive oxygen species dependent. PLoS Pathog. 2020;16(3):e1007969.
- Tambassi M, Passarini E, Menozzi I, Berni M, Bracchi C, Dodi A, et al. Klebsiella pneumoniae carrying multiple alleles of antigen 43- encoding gene of Escherichia coli associated with biofilm formation. Eur J Clin Microbiol Infect Dis. 2023;42(3):371–7.
- Shafik SM, Abbas HA, Yousef N, Saleh MM. Crippling of Klebsiella pneumoniae virulence by metformin, N-acetylcysteine and secnidazole. BMC Microbiol. 2023;23(1):229. Cite this article: Prajapati BT, Marathe AP, Shaikh AMH, Sangani S. Genetic analysis of virulence factors of MDR Klebsiella pneumoniae spp. pneumoniae isolated from clinical specimens - study from a tertiary care hospital. Indian J Microbiol Res. 2025;12(3):410–418.