Molecular typing and integron detection of multidrug-resistant Klebsiella pneumoniae clinical isolates recovered from Baquba Teaching Hospital in Iraq
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Abstract
Klebsiella pneumoniae is a gram-negative bacterium that causes severe illnesses and is antibiotic-resistant. This study aimed to determine the antibiotic resistance profile and prevalence of classII and III Iintegrons and ERIC -PCR among clinical isolates of K. pneumoniae. The study was conducted between September 2022 and January 2023. Fifty isolates were obtained from 230 specimens (wounds, burns, blood, fluid, ears,urine and sputum). Macroscopic, microscopic, and biochemical assays were used to identify all K.pneumoniae isolates, which were confirmed with the genetically by 16S rRNA. All isolates were examined for various types of clinically significant antibiotic drugs. The results of resistance to antibiotics indicated resistance to Amoxilline-clavulanc acid(98%), Meropenem (38%), Ceftazidime (96%), Amikacin (48%), Trimethopri-sulfamethoxazole (58.62%) and Levofloxacin (46%).The testing for antibiotic susceptibility of the K.pneumoniaeisolate showed that 24 (48%) of the isolates were multi-drug resistant (MDR). K.pneumoniae β-lactamase producers (ESBL) appeared33(66%). Enterobacterial repetitive intergenic consensus (ERIC) amplification of 16 clinical K. pneumoniae isolates showed 14 (87.5 %) of Each of them revealed at least one amplification band. ERIC-PCR typing found two groups, A and B, with identical antimicrobial resistance patterns within the same group. While IntegronII showed that 1(6.25 %) of K. pneumoniae isolates was integrase gene positive. Class III integrons were seen in all isolates at a rate of 16 (100%).Continuous monitoring and characterization of integrons and their associated gene cassettes could be helpful in controlling the rate of antibiotic resistance by planning to take preventive measures to hinder the spread of resistant strains
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Keywords
Antibiotic resistance, ERIC–PCR, Integrons, Klebsiella pneumoniae, Multidrug-resistance stains
References
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Al-Baz, A. A., Maarouf, A., Marei, A.&Abdallah, A. L. (2022). Prevalence and Antibiotic Resistance profiles of carbapenem-resistant Klebsiella pneumoniae Isolated from Tertiary Care Hospital, Egypt. The Egyptian Journal of Hospital Medicine, 88(1), 2883-2890.
Allison, Paul D. (2012). Logistic regression using SAS: Theory and application: SAS institute.
Ali, F. A. & Ismael, R. M. (2017). Dissemination of Klebsiella pneumonia and Klebsiella oxytocaharboring bla TEM genes isolated from different clinical samples in Erbil City. Diyala Journal of Medicine, 12(2), 40-51.
Ayatollahi,J., Sharifyazdi, M., Fadakarfard, R. & Shahcheraghi, S. H. (2020). Antibiotic resistance pattern of Klebsiella pneumoniae in obtained samples from Ziaee Hospital of Ardakan, Yazd, Iran during 2016 to 2017. Iberoamerican Journal of Medicine, 2(2), 32-36.
Assafi, M. S., Ali, F. F., Polis, R. F., Sabaly, N. J., & Qarani, S. M. (2022). An Epidemiological and multidrug resistance study for E. coli Isolated from urinary tract infection (Three years of study). Baghdad Science Journal, 19(1), 0007
Caniça, M., Manageiro, V., Abriouel, H., Moran-Gilad, J., & Franz, C. M. (2019). Antibiotic resistance in food-borne bacteria. Trends in Food Science and Technology, 84, 41-44
Dayih,H. A.(2018) Molecular diversity of Escherichia coli isolatesfrom different local sources and theirrelationship resistance to antibiotics Diyala University. College of Education for Pure Sciences. Department of Biology.
Gebremariam, G., Legese, H., Woldu, Y., Araya, T., Hagos, K., & GebreyesusWasihun,A. (2019). Bacteriological profile, risk factors and antimicrobial susceptibility patterns of symptomatic urinary tract infection among students of Mekelle University, northern Ethiopia. BMC infectious diseases, 19(1), 950.
Ghellai,L., Hassaine, H., Klouche, N., Khadir, A., Aissaoui, N., Nas, F., & Zingg, W. (2014). Detection of biofilm formation of a collection of fifty strains of Staphylococcus aureus isolated in Algeria at the University Hospital of Tlemcen. Journal of Bacteriology Research, 6(1), 1-6.
Hasan, R. N., Jasim, S. A., & Ali, Y. H. (2022). Detection of fimH, kpsMTII, hlyA, and traT genes in Escherichia coli isolated from Iraqi patients with cystitis. Gene Reports, 26, 101468.
Hassan,P. A., & Khider, A. K. (2020). Correlation of biofilm formation and antibiotic resistance among clinical and soil isolates of Acinetobacter baumannii in Iraq. Acta Microbiologicaet Immunologica Hungarica, 67(3), 161-170
Humphries, Romney, Bobenchik, April M, Hindler, Janet A, & Schuetz, Audrey N. (2021). Overview of changes to the clinical and laboratory standards institute performance standards for antimicrobial susceptibility testing, M100. Journal of clinical microbiology, 59(12).
Husham A. A.2022. Molecular and Biochemical community with COVID-19 patients.MSC Thesis/ University of Diyala/ College of Science/ Department of Biology
Jahanbin, F., Marashifard, M., Jamshidi, S., Zamanzadeh, M., Dehshiri, M., Hosseini, S. A. A. M., & Khoramrooz, S. S. (2020). Investigation of Integron-Associated Resistance Gene Cassettes in Urinary Isolates of Klebsiella pneumoniae in Yasuj, Southwestern Iran During 2015–16. Avicennajournal of medical biotechnology, 12(2), 124
Karampatakis, T., Tsergouli, K.,& Behzadi, P. (2023). Carbapenem-resistant Klebsiella pneumoniae: virulence factors, molecular epidemiology and latest updates in treatment options. Antibiotics, 12(2), 234
Kuinkel, S., Acharya, J., Dhungel, B., Adhikari, S., Adhikari, N., Shrestha, U. T., & Ghimire, P. (2021). Biofilm formation and phenotypic detection of ESBL, MBL, KPC and AmpC enzymes and their coexistence in Klebsiella spp. isolated at the National Reference Laboratory, Kathmandu, Nepal. Microbiology Research, 12(3), 49.
Laibi, C. N. B. J. R. (2021). Molecular investigation of integrons in Klebsiella pneumoniae isolated from urinary tract infections in Thi-Qar province, Iraq. Turkish Journal of Physiotherapy and Rehabilitation, 32(3), 10564-10569.
Lai, C. K., Ng, R. W., Leung, S. S., Hui, M., & Ip, M. (2022). Overcoming the rising incidence and evolving mechanisms of antibiotic resistance by novel drug delivery approaches–an overview. Advanced Drug Delivery Reviews, 181, 114078
Li, R., Cheng, J., Dong, H., Li, L., Liu, W., Zhang, C., ...& Qin, S. (2020). Emergence of a novel conjugative hybrid virulence multidrug-resistant plasmid in extensively drug-resistant Klebsiella pneumoniae ST15. International journal of antimicrobial agents, 55(6), 105952.
Mahmud, Z. H., Uddin, S. Z., Moniruzzaman, M., Ali, S., Hossain, M., Islam, M. T., . & Parveen, S. (2022). Healthcare Facilities as Potential Reservoirs of Antimicrobial Resistant Klebsiella pneumoniae: An Emerging Concern to Public Health in Bangladesh. Pharmaceuticals, 15(9), 1116.
Mohamed.I.Q./2022. Molecular investigation of biofilm and quorum sensing genes in Klebsiella pneumoniae isolated from different clinical cases.MSC Thesis/University of Diyala/ College of Science/ Department of Biology
Mohammadalipour,Z.; Kargar, M. & Doosi, A. (2017). High Frequency of Class 2 and 3 Integrons Related to Drug Resistance in Clinical Isolates of Diarrheagenic E.coli n Iran. Novel Biomed.5(1):30-6.
Mohammed, A. (2021). Biofilm formation and antibiotic resistance in Klebsiella pneumoniae: a meta-analysis study
Muslim.R. E(2022). Phenotypic and Genotypic Characterization of Extended-Spectrum-β-Lactamase, AmpC, and Carbapenemase ProducingGram negative Bacteria Isolated from Intensive Care Unit Patients in Wasit Province./ Wasit University/College of Medicine Department of Medical Microbiology
Naji Hasan, R., & Abdal Kareem Jasim, S. (2021). Detection of Panton-Valentine leukocidin and MecA Genes in Staphylococcus aureus isolated from Iraqi Patients. Archives of Razi Institute, 76(4), 1054-1059.
Parsaie Mehr, V., Shokoohizadeh, L., Mirzaee, M., & Savari, M. (2017). Molecular typing of Klebsiella pneumoniae isolates by enterobacterial repetitive intergenic consensus (ERIC)–PCR. Infection Epidemiology and Microbiology, 3(4), 112-116
Raoof, M. A. & Fayidh, M. A. Investigation of biofilm formation efficiency in ESβLs of pathogenic Escherichia coli Isolates.
Rowe-Magnus, D. A., Guerout, A. M., Ploncard, P., Dychinco, B., Davies, J., & Mazel, D. (2001). The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons. Proceedings of the National Academy of Sciences, 98(2), 652-657
Samir, P., El-Baz, A. M., & Kenawy, H. I. (2023). The linkage between prevalence of integron I and reduced susceptibility to biocides in MDR Klebsiellapneumoniae isolated from neonates. IranianJournal of Microbiology, 15(1), 27.
Seifi, K., Kazemian, H., Heidari, H., Rezagholizadeh, F., Saee, Y., Shirvani, F & Houri, H. (2016). Evaluation of biofilm formation among Klebsiella pneumoniae isolates and molecular characterization by ERIC-PCR. Jundishapur Journal of Microbiology, 9(1).
Shadkam, S., Goli, H. R., Mirzaei, B., Gholami, M. & Ahanjan, M. (2021). Correlation between antimicrobial resistance and biofilm formation capability among Klebsiella pneumoniae strains isolated from hospitalized patients in Iran. Annals of Clinical Microbiology and Antimicrobials, 20(1), 1-7.
Sharma,Jyoti, Sharma, Meera, & Ray, Pallab (2010). Detection of TEM and SHV genes in Escherichia coli and Klebsiella pneumoniae isolates in a tertiary care hospital from India. Indian Journal of Medical Research, 132(3), 332-337 .
Slettengren, M., Mohanty, S., Kamolvit, W., Van Der Linden, J., & Brauner, A. (2020). Making medical devices safer: impact of plastic and silicone oil on microbial biofilm formation.Journal of Hospital Infection, 106(1), 155-162.
Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J Comput Biol. 7(1-2):203-14.
Al-Baz, A. A., Maarouf, A., Marei, A.&Abdallah, A. L. (2022). Prevalence and Antibiotic Resistance profiles of carbapenem-resistant Klebsiella pneumoniae Isolated from Tertiary Care Hospital, Egypt. The Egyptian Journal of Hospital Medicine, 88(1), 2883-2890.
Allison, Paul D. (2012). Logistic regression using SAS: Theory and application: SAS institute.
Ali, F. A. & Ismael, R. M. (2017). Dissemination of Klebsiella pneumonia and Klebsiella oxytocaharboring bla TEM genes isolated from different clinical samples in Erbil City. Diyala Journal of Medicine, 12(2), 40-51.
Ayatollahi,J., Sharifyazdi, M., Fadakarfard, R. & Shahcheraghi, S. H. (2020). Antibiotic resistance pattern of Klebsiella pneumoniae in obtained samples from Ziaee Hospital of Ardakan, Yazd, Iran during 2016 to 2017. Iberoamerican Journal of Medicine, 2(2), 32-36.
Assafi, M. S., Ali, F. F., Polis, R. F., Sabaly, N. J., & Qarani, S. M. (2022). An Epidemiological and multidrug resistance study for E. coli Isolated from urinary tract infection (Three years of study). Baghdad Science Journal, 19(1), 0007
Caniça, M., Manageiro, V., Abriouel, H., Moran-Gilad, J., & Franz, C. M. (2019). Antibiotic resistance in food-borne bacteria. Trends in Food Science and Technology, 84, 41-44
Dayih,H. A.(2018) Molecular diversity of Escherichia coli isolatesfrom different local sources and theirrelationship resistance to antibiotics Diyala University. College of Education for Pure Sciences. Department of Biology.
Gebremariam, G., Legese, H., Woldu, Y., Araya, T., Hagos, K., & GebreyesusWasihun,A. (2019). Bacteriological profile, risk factors and antimicrobial susceptibility patterns of symptomatic urinary tract infection among students of Mekelle University, northern Ethiopia. BMC infectious diseases, 19(1), 950.
Ghellai,L., Hassaine, H., Klouche, N., Khadir, A., Aissaoui, N., Nas, F., & Zingg, W. (2014). Detection of biofilm formation of a collection of fifty strains of Staphylococcus aureus isolated in Algeria at the University Hospital of Tlemcen. Journal of Bacteriology Research, 6(1), 1-6.
Hasan, R. N., Jasim, S. A., & Ali, Y. H. (2022). Detection of fimH, kpsMTII, hlyA, and traT genes in Escherichia coli isolated from Iraqi patients with cystitis. Gene Reports, 26, 101468.
Hassan,P. A., & Khider, A. K. (2020). Correlation of biofilm formation and antibiotic resistance among clinical and soil isolates of Acinetobacter baumannii in Iraq. Acta Microbiologicaet Immunologica Hungarica, 67(3), 161-170
Humphries, Romney, Bobenchik, April M, Hindler, Janet A, & Schuetz, Audrey N. (2021). Overview of changes to the clinical and laboratory standards institute performance standards for antimicrobial susceptibility testing, M100. Journal of clinical microbiology, 59(12).
Husham A. A.2022. Molecular and Biochemical community with COVID-19 patients.MSC Thesis/ University of Diyala/ College of Science/ Department of Biology
Jahanbin, F., Marashifard, M., Jamshidi, S., Zamanzadeh, M., Dehshiri, M., Hosseini, S. A. A. M., & Khoramrooz, S. S. (2020). Investigation of Integron-Associated Resistance Gene Cassettes in Urinary Isolates of Klebsiella pneumoniae in Yasuj, Southwestern Iran During 2015–16. Avicennajournal of medical biotechnology, 12(2), 124
Karampatakis, T., Tsergouli, K.,& Behzadi, P. (2023). Carbapenem-resistant Klebsiella pneumoniae: virulence factors, molecular epidemiology and latest updates in treatment options. Antibiotics, 12(2), 234
Kuinkel, S., Acharya, J., Dhungel, B., Adhikari, S., Adhikari, N., Shrestha, U. T., & Ghimire, P. (2021). Biofilm formation and phenotypic detection of ESBL, MBL, KPC and AmpC enzymes and their coexistence in Klebsiella spp. isolated at the National Reference Laboratory, Kathmandu, Nepal. Microbiology Research, 12(3), 49.
Laibi, C. N. B. J. R. (2021). Molecular investigation of integrons in Klebsiella pneumoniae isolated from urinary tract infections in Thi-Qar province, Iraq. Turkish Journal of Physiotherapy and Rehabilitation, 32(3), 10564-10569.
Lai, C. K., Ng, R. W., Leung, S. S., Hui, M., & Ip, M. (2022). Overcoming the rising incidence and evolving mechanisms of antibiotic resistance by novel drug delivery approaches–an overview. Advanced Drug Delivery Reviews, 181, 114078
Li, R., Cheng, J., Dong, H., Li, L., Liu, W., Zhang, C., ...& Qin, S. (2020). Emergence of a novel conjugative hybrid virulence multidrug-resistant plasmid in extensively drug-resistant Klebsiella pneumoniae ST15. International journal of antimicrobial agents, 55(6), 105952.
Mahmud, Z. H., Uddin, S. Z., Moniruzzaman, M., Ali, S., Hossain, M., Islam, M. T., . & Parveen, S. (2022). Healthcare Facilities as Potential Reservoirs of Antimicrobial Resistant Klebsiella pneumoniae: An Emerging Concern to Public Health in Bangladesh. Pharmaceuticals, 15(9), 1116.
Mohamed.I.Q./2022. Molecular investigation of biofilm and quorum sensing genes in Klebsiella pneumoniae isolated from different clinical cases.MSC Thesis/University of Diyala/ College of Science/ Department of Biology
Mohammadalipour,Z.; Kargar, M. & Doosi, A. (2017). High Frequency of Class 2 and 3 Integrons Related to Drug Resistance in Clinical Isolates of Diarrheagenic E.coli n Iran. Novel Biomed.5(1):30-6.
Mohammed, A. (2021). Biofilm formation and antibiotic resistance in Klebsiella pneumoniae: a meta-analysis study
Muslim.R. E(2022). Phenotypic and Genotypic Characterization of Extended-Spectrum-β-Lactamase, AmpC, and Carbapenemase ProducingGram negative Bacteria Isolated from Intensive Care Unit Patients in Wasit Province./ Wasit University/College of Medicine Department of Medical Microbiology
Naji Hasan, R., & Abdal Kareem Jasim, S. (2021). Detection of Panton-Valentine leukocidin and MecA Genes in Staphylococcus aureus isolated from Iraqi Patients. Archives of Razi Institute, 76(4), 1054-1059.
Parsaie Mehr, V., Shokoohizadeh, L., Mirzaee, M., & Savari, M. (2017). Molecular typing of Klebsiella pneumoniae isolates by enterobacterial repetitive intergenic consensus (ERIC)–PCR. Infection Epidemiology and Microbiology, 3(4), 112-116
Raoof, M. A. & Fayidh, M. A. Investigation of biofilm formation efficiency in ESβLs of pathogenic Escherichia coli Isolates.
Rowe-Magnus, D. A., Guerout, A. M., Ploncard, P., Dychinco, B., Davies, J., & Mazel, D. (2001). The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons. Proceedings of the National Academy of Sciences, 98(2), 652-657
Samir, P., El-Baz, A. M., & Kenawy, H. I. (2023). The linkage between prevalence of integron I and reduced susceptibility to biocides in MDR Klebsiellapneumoniae isolated from neonates. IranianJournal of Microbiology, 15(1), 27.
Seifi, K., Kazemian, H., Heidari, H., Rezagholizadeh, F., Saee, Y., Shirvani, F & Houri, H. (2016). Evaluation of biofilm formation among Klebsiella pneumoniae isolates and molecular characterization by ERIC-PCR. Jundishapur Journal of Microbiology, 9(1).
Shadkam, S., Goli, H. R., Mirzaei, B., Gholami, M. & Ahanjan, M. (2021). Correlation between antimicrobial resistance and biofilm formation capability among Klebsiella pneumoniae strains isolated from hospitalized patients in Iran. Annals of Clinical Microbiology and Antimicrobials, 20(1), 1-7.
Sharma,Jyoti, Sharma, Meera, & Ray, Pallab (2010). Detection of TEM and SHV genes in Escherichia coli and Klebsiella pneumoniae isolates in a tertiary care hospital from India. Indian Journal of Medical Research, 132(3), 332-337 .
Slettengren, M., Mohanty, S., Kamolvit, W., Van Der Linden, J., & Brauner, A. (2020). Making medical devices safer: impact of plastic and silicone oil on microbial biofilm formation.Journal of Hospital Infection, 106(1), 155-162.
Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J Comput Biol. 7(1-2):203-14.
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Molecular typing and integron detection of multidrug-resistant Klebsiella pneumoniae clinical isolates recovered from Baquba Teaching Hospital in Iraq. (2023). Journal of Applied and Natural Science, 15(4), 1354-1362. https://doi.org/10.31018/jans.v15i4.4950
