Antibiotyping, RAPD- and ERIC-PCR fingerprinting of Klebsiella pneumoniae clinical isolates at a tertiary reference hospital in Denpasar, Bali, Indonesia
-
Ni Nengah Dwi Fatmawati
,
Felicia Aviana
,
Ronny Maharianto
,
Gede Ngurah Rsi Suwardana
,
Ni Made Adi Tarini
,
I Made Adi Sujaya
Abstract
Background and Objectives: Klebsiella pneumoniae is a healthcare-associated infections agent and could be an extended spectrum β-lactamase (ESBL) producer. Understanding the transmission of this bacterium in a hospital setting needs accurate typing methods. An antibiogram is used to detect the resistance pattern of the isolates. Random Amplified Polymorphic DNA (RAPD) and Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR are rapid, technically simple, and easy-to-interpret DNA typing methods. This study aimed to evaluate the use of antibiotyping, RAPD-, and ERIC-PCR to investigate the heterogeneity of K. pneumoniae isolated from clinical specimens.
Materials and Methods: The antibiograms of 46 K. pneumoniae clinical isolates were determined by Vitek® 2 Compact. All isolates underwent RAPD-PCR using AP4 primer and ERIC-PCR using ERIC-2 primer. The dendrogram was generated using the GelJ software and analyzed to determine its similarity. The analysis of antibiogram and the molecular typing diversity index was calculated using the formula of the Simpson’s diversity index.
Results: About 71.7% of the isolates were ESBL-producers, and more than 80% of isolates were susceptible to amikacin, ertapenem, and meropenem. The antibiotyping produced 32 diverse types with DI = 0.964. In Conclusion: Antibiotyping, RAPD- and ERIC-PCR showed powerful discrimination power among the isolates, supported the diversity of K. pneumoniae isolates in current study. These combination could be promising tools for clonal relationship determination, including in tracking the transmission of the outbreak’s agent in hospital setting.
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3. Cheng F, Li Z, Lan S, Liu W, Li X, Zhou Z, et al. Characterization of Klebsiella pneumoniae associated with cattle infections in southwest China using multi-locus sequence typing (MLST), antibiotic resistance and virulence-associated gene profile analysis. Braz J Microbiol 2018; 49 Suppl 1(Suppl 1): 93-100.
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6. Goh LPW, Marbawi H, Goh SM, bin Abdul Asis AK, Gansau JA. The prevalence of hospital-acquired infections in Southeast Asia (1990-2022). J Infect Dev Ctries 2023; 17: 139-146.
7. Abou-Dobara MI, Deyab MA, Elsawy EM, Mohamed HH. Antibiotic susceptibility and genotype patterns of Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa isolated from urinary tract infected patients. Pol J Microbiol 2010; 59: 207-212.
8. Stefańska I, Kwiecień E, Górzyńska M, Sałamaszyńska-Guz A, Rzewuska M. RAPD-PCR-based fingerprinting method as a tool for epidemiological analysis of Trueperella pyogenes infections. Pathogens 2022; 11: 562.
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11. Fatmawati NND, Suwardana GNR, Dharmika IAGW, Tarini NMA, Sujaya IN, Suranadi IW. Early detection of a possible multidrug-resistant Acinetobacter baumannii outbreak in the local hospital setting by using random amplified polymorphism DNA-polymerase chain reaction (RAPD-PCR), oxacillinase gene profiles, and antibiograms. Iran J Microbiol 2023; 15: 642-653.
12. Purighalla S, Esakimuthu S, Reddy M, Varghese GK, Richard VS, Sambandamurthy VK. Discriminatory power of three typing techniques in determining relatedness of nosocomial Klebsiella pneumoniae isolates from a tertiary hospital in India. Indian J Med Microbiol 2017; 35: 361-368.
13. Wong NA, Linton CJ, Jalal H, Millar MR. Randomly amplified polymorphic DNA typing: a useful tool for rapid epidemiological typing of Klebsiella pneumoniae. Epidemiol Infect 1994; 113: 445-454.
14. Wilson LA, Sharp PM. Enterobacterial repetitive intergenic consensus (ERIC) sequences in Escherichia coli: Evolution and implications for ERIC-PCR. Mol Biol Evol 2006; 23: 1156-1168.
15. Ashayeri-panah M, Eftekhar F, Feizabadi MM. Development of an optimized random amplified polymorphic DNA protocol for fingerprinting of Klebsiella pneumoniae. Lett Appl Microbiol 2012; 54: 272-279.
16. Heras J, Domínguez C, Mata E, Pascual V, Lozano C, Torres C, et al. GelJ--a tool for analyzing DNA fingerprint gel images. BMC Bioinformatics 2015; 16: 270.
17. Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J Clin Microbiol 1988; 26: 2465-2466.
18. Effah CY, Sun T, Liu S, Wu Y. Klebsiella pneumoniae: an increasing threat to public health. Ann Clin Microbiol Antimicrob 2020; 19: 1.
19. Salawudeen A, Raji YE, Jibo GG, Desa MNM, Neoh HM, Masri SN, et al. Epidemiology of multidrug-resistant Klebsiella pneumoniae infection in clinical setting in South-Eastern Asia: a systematic review and meta-analysis. Antimicrob Resist Infect Control 2023; 12: 142.
20. Beigverdi R, Jabalameli L, Jabalameli F, Emaneini M. Prevalence of extended-spectrum β-lactamase-producing Klebsiella pneumoniae: First systematic review and meta-analysis from Iran. J Glob Antimicrob Resist 2019; 18: 12-21.
21. Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, et al. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci U S A 2015; 112: E3574-E3581.
22. Wyres KL, Holt KE. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr Opin Microbiol 2018; 45: 131-139.
23. Arabzadeh B, Ahmadi Z, Ranjbar R. Molecular Characterization of Antibiotic Resistance and Genetic Diversity of Klebsiella pneumoniae Strains. Can J Infect Dis Med Microbiol 2022; 2022: 2156726.
24. Aladag MO, Uysal A, Dundar N, Durak Y, Gunes E. Characterization of Klebsiella pneumoniae strains isolated from urinary tract infections: Detection of ESBL characteristics, antibiotic susceptibility and RAPD genotyping. Pol J Microbiol 2013; 62: 401-409.
25. Power EG. RAPD typing in microbiology--a technical review. J Hosp Infect 1996; 34: 247-265.
26. Atienzar FA, Jha AN. The random amplified polymorphic DNA (RAPD) assay and related techniques applied to genotoxicity and carcinogenesis studies: a critical review. Mutat Res 2006; 613: 76-102.
27. Versalovic J, Koeuth T, Lupski R. Distribution of repetitive DNA sequences in eubacteria and application to fingerpriting of bacterial genomes. Nucleic Acids Res 1991; 19: 6823-6831.
28. Kundu J, Kansal S, Rathore S, Kaundal M, Angrup A, Biswal M, et al. Evaluation of ERIC-PCR and MALDI-TOF as typing tools for multidrug resistant Klebsiella pneumoniae clinical isolates from a tertiary care center in India. PLoS One 2022; 17(11): e0271652.
29. Wasfi R, Elkhatib WF, Ashour HM. Molecular typing and virulence analysis of multidrug resistant Klebsiella pneumoniae clinical isolates recovered from Egyptian hospitals. Sci Rep 2016; 6: 38929.
30. Saha O, Hoque MN, Islam OK, Rahaman MM, Sultana M, Hossain MA. Multidrug-resistant avian pathogenic Escherichia coli strains and association of their virulence genes in Bangladesh. Microorganisms 2020; 8: 1135.
2. Bengoechea JA, Sa Pessoa J. Klebsiella pneumoniae infection biology: living to counteract host defences. FEMS Microbiol Rev 2019; 43: 123-144.
3. Cheng F, Li Z, Lan S, Liu W, Li X, Zhou Z, et al. Characterization of Klebsiella pneumoniae associated with cattle infections in southwest China using multi-locus sequence typing (MLST), antibiotic resistance and virulence-associated gene profile analysis. Braz J Microbiol 2018; 49 Suppl 1(Suppl 1): 93-100.
4. Chung PY. The emerging problems of Klebsiella pneumoniae infections: carbapenem resistance and biofilm formation. FEMS Microbiol Lett 2016; 363: fnw219.
5. Mohd Asri NA, Ahmad S, Mohamud R, Mohd Hanafi N, Mohd Zaidi NF, Irekeola AA, et al. Global prevalence of nosocomial multidrug-resistant Klebsiella pneumoniae: a systematic review and meta-analysis. Antibiotics (Basel) 2021; 10: 1508.
6. Goh LPW, Marbawi H, Goh SM, bin Abdul Asis AK, Gansau JA. The prevalence of hospital-acquired infections in Southeast Asia (1990-2022). J Infect Dev Ctries 2023; 17: 139-146.
7. Abou-Dobara MI, Deyab MA, Elsawy EM, Mohamed HH. Antibiotic susceptibility and genotype patterns of Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa isolated from urinary tract infected patients. Pol J Microbiol 2010; 59: 207-212.
8. Stefańska I, Kwiecień E, Górzyńska M, Sałamaszyńska-Guz A, Rzewuska M. RAPD-PCR-based fingerprinting method as a tool for epidemiological analysis of Trueperella pyogenes infections. Pathogens 2022; 11: 562.
9. Gajic I, Kabic J, Kekic D, Jovicevic M, Milenkovic M, Mitic Culafic D, et al. Antimicrobial susceptibility testing: A comprehensivereview of currently used methods. Antibiotics (Basel) 2022; 11: 427.
10. Ashayeri-Panah M, Eftekhar F, Ghamsari MM, Parvin M, Feizabadi MM. Genetic profiling of Klebsiella pneumoniae: comparison of pulsed field gel electrophoresis and random amplified polymorphic DNA. Braz J Microbiol 2013; 44: 823-828.
11. Fatmawati NND, Suwardana GNR, Dharmika IAGW, Tarini NMA, Sujaya IN, Suranadi IW. Early detection of a possible multidrug-resistant Acinetobacter baumannii outbreak in the local hospital setting by using random amplified polymorphism DNA-polymerase chain reaction (RAPD-PCR), oxacillinase gene profiles, and antibiograms. Iran J Microbiol 2023; 15: 642-653.
12. Purighalla S, Esakimuthu S, Reddy M, Varghese GK, Richard VS, Sambandamurthy VK. Discriminatory power of three typing techniques in determining relatedness of nosocomial Klebsiella pneumoniae isolates from a tertiary hospital in India. Indian J Med Microbiol 2017; 35: 361-368.
13. Wong NA, Linton CJ, Jalal H, Millar MR. Randomly amplified polymorphic DNA typing: a useful tool for rapid epidemiological typing of Klebsiella pneumoniae. Epidemiol Infect 1994; 113: 445-454.
14. Wilson LA, Sharp PM. Enterobacterial repetitive intergenic consensus (ERIC) sequences in Escherichia coli: Evolution and implications for ERIC-PCR. Mol Biol Evol 2006; 23: 1156-1168.
15. Ashayeri-panah M, Eftekhar F, Feizabadi MM. Development of an optimized random amplified polymorphic DNA protocol for fingerprinting of Klebsiella pneumoniae. Lett Appl Microbiol 2012; 54: 272-279.
16. Heras J, Domínguez C, Mata E, Pascual V, Lozano C, Torres C, et al. GelJ--a tool for analyzing DNA fingerprint gel images. BMC Bioinformatics 2015; 16: 270.
17. Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J Clin Microbiol 1988; 26: 2465-2466.
18. Effah CY, Sun T, Liu S, Wu Y. Klebsiella pneumoniae: an increasing threat to public health. Ann Clin Microbiol Antimicrob 2020; 19: 1.
19. Salawudeen A, Raji YE, Jibo GG, Desa MNM, Neoh HM, Masri SN, et al. Epidemiology of multidrug-resistant Klebsiella pneumoniae infection in clinical setting in South-Eastern Asia: a systematic review and meta-analysis. Antimicrob Resist Infect Control 2023; 12: 142.
20. Beigverdi R, Jabalameli L, Jabalameli F, Emaneini M. Prevalence of extended-spectrum β-lactamase-producing Klebsiella pneumoniae: First systematic review and meta-analysis from Iran. J Glob Antimicrob Resist 2019; 18: 12-21.
21. Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, et al. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci U S A 2015; 112: E3574-E3581.
22. Wyres KL, Holt KE. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr Opin Microbiol 2018; 45: 131-139.
23. Arabzadeh B, Ahmadi Z, Ranjbar R. Molecular Characterization of Antibiotic Resistance and Genetic Diversity of Klebsiella pneumoniae Strains. Can J Infect Dis Med Microbiol 2022; 2022: 2156726.
24. Aladag MO, Uysal A, Dundar N, Durak Y, Gunes E. Characterization of Klebsiella pneumoniae strains isolated from urinary tract infections: Detection of ESBL characteristics, antibiotic susceptibility and RAPD genotyping. Pol J Microbiol 2013; 62: 401-409.
25. Power EG. RAPD typing in microbiology--a technical review. J Hosp Infect 1996; 34: 247-265.
26. Atienzar FA, Jha AN. The random amplified polymorphic DNA (RAPD) assay and related techniques applied to genotoxicity and carcinogenesis studies: a critical review. Mutat Res 2006; 613: 76-102.
27. Versalovic J, Koeuth T, Lupski R. Distribution of repetitive DNA sequences in eubacteria and application to fingerpriting of bacterial genomes. Nucleic Acids Res 1991; 19: 6823-6831.
28. Kundu J, Kansal S, Rathore S, Kaundal M, Angrup A, Biswal M, et al. Evaluation of ERIC-PCR and MALDI-TOF as typing tools for multidrug resistant Klebsiella pneumoniae clinical isolates from a tertiary care center in India. PLoS One 2022; 17(11): e0271652.
29. Wasfi R, Elkhatib WF, Ashour HM. Molecular typing and virulence analysis of multidrug resistant Klebsiella pneumoniae clinical isolates recovered from Egyptian hospitals. Sci Rep 2016; 6: 38929.
30. Saha O, Hoque MN, Islam OK, Rahaman MM, Sultana M, Hossain MA. Multidrug-resistant avian pathogenic Escherichia coli strains and association of their virulence genes in Bangladesh. Microorganisms 2020; 8: 1135.
| Files | ||
| Issue | Vol 16 No 3 (2024) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v16i3.15761 | |
| Keywords | ||
| Klebsiella pneumonia; Transmission; Antibiogram; Molecular typing; DNA fingerprinting | ||
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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
How to Cite
1.
Fatmawati NND, Aviana F, Maharianto R, Suwardana G, Tarini N, Sujaya I. Antibiotyping, RAPD- and ERIC-PCR fingerprinting of Klebsiella pneumoniae clinical isolates at a tertiary reference hospital in Denpasar, Bali, Indonesia. Iran J Microbiol. 2024;16(3):306-313.
