Frequency of cas genes in the CRISPR/Cas system in ESBL-producing Escherichia coli isolated from urinary tract infection
Subject Areas :
Bacteriology
Neda Merikhi
1
,
Jamileh Nowroozi
2
,
ali nazemi
3
,
Mehrdad Hashemi
4
,
Robab Rafiei Tabatabaei
5
1 - Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
2 - Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
3 - Department of Biology. Tonekabon Branch, Islamic Azad University, Tonekabon, Iran
4 - Department of genetics, Faculty of advanced sciences and technology, Islamic Azad University, Tehran medical sciences branch, Tehran, Iran
5 - Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
Received: 2022-11-29
Accepted : 2023-05-06
Published : 2023-06-05
Keywords:
Urinary tract infections,
Escherichia coli,
ESBL,
CRISPR/Cas system,
Abstract :
Background & Objectives: CRISPR system (clustered regularly interspaced short palindromic repeats) and Cas portions is a part of the immune system in microorganisms. The cas genes could be involved in reducing antibiotic resistance in bacteria. The aim of the study was to investigate the frequency of cas genes of the CRISPR/Cas system in Extended Spectrum Beta-Lactamase (ESBL) producing Escherichia coli isolated from urine culture of patients with urinary tract infection.
Materials & Methods: In this cross-sectional study, 437 positive urine culture samples were collected from Chalus hospitals. Escherichia coli strains were isolated based on standard biochemical tests and Enterobacteriaceae commercial diagnostic kit, as well as antibiotic sensitivity using disc diffusion method (Kerby Baer). Combined disk test was conducted for isolates that were resistant to at least one of the third-generation cephalosporins in the foregoing antibiotic susceptibility test. Molecular identification of cas1,cas2,cas3,cas7 and cas5 genes was performed using the PCR method.
Results: Out of 437 urin culture samples, 106 samples (24.3%) had E.coli infection. The highest antibiotic resistance was associated with ampicillin (99%). Among the resistant isolates, thirty isolates (88.3%) were ESBL producing. cas1 gene had the highest frequency (96.2%) and other cas genes had almost the same frequency.
Conclusion: The results of the present study showed that a significant percentage of E. coli isolates had ESBL phenotype, which may be due to the presence of broad-spectrum beta-lactamase genes in these samples. Besides, it was shown that there is no relationship between the presence of ESBL phenotype and the distribution of cas genes.
References:
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Louwen R, Staals RH, Endtz HP, van Baarlen P, van der Oost J. The role of CRISPR-Cas systems in virulence of pathogenic bacteria. Microbiology and Molecular Biology Reviews. 2014;78(1):74-88.
Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, et al. Evolution and classification of the CRISPR-Cas systems. Nature reviews Microbiology. 2011;9(6):467-77.
Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, et al. An updated evolutionary classification of CRISPR–Cas systems. Nature Reviews Microbiology. 2015;13(11):722-36.
Sternberg SH, Richter H, Charpentier E, Qimron U. Adaptation in CRISPR-Cas systems. Molecular cell. 2016;61(6):797-808.
Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie. 2015;117:119-28.
Goren M, Yosef I, Qimron U. Sensitizing pathogens to antibiotics using the CRISPR-Cas system. Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy. 2017;30:1-6.
Gholizadeh P, Aghazadeh M, Asgharzadeh M, Kafil HS. Suppressing the CRISPR/Cas adaptive immune system in bacterial infections. 2017;36(11):2043-51.
Tao S, Chen H, Li N, & Liang. The Application of the CRISPR-Cas System in Antibiotic Resistance. Infection and Drug Resistance. 2022, 15: 4155.
Mohr KI. History of antibiotics research. How to Overcome the Antibiotic Crisis. 2016:237-72.
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Philippon A, Labia R, Jacoby G. Extended-spectrum beta-lactamases. Antimicrobial agents and chemotherapy. 1989;33(8):1131.
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Hemmati TB, Mehdipour Moghaddam MJ, Salehi Z, Habibzadeh SM. Prevalence of CTX-M-Type β-lactamases in multi-drug resistant Escherichia coli isolates from north of Iran, Rasht. Biological Journal of Microorganism. 2015;3(12).
Mohajeri P, Darfarin G, Farahani A. Genotyping of ESBL producing Uropathogenic Escherichia coli in west of Iran. International journal of microbiology. 2014;2014.
Shams F, Hasani A, Pormohammad A, Rezaee MA, Reza M, Nahaie AH, et al. qnrA implicated quinolone resistance in Escherichia coli and Klebsiella pneumoniae clinical isolates from a University Teaching Hospital. Life Sci J. 2014;11(12s):1032-5.
Khoshvaght H, Haghi F, Zeighami H. Extended spectrum betalactamase producing Enteroaggregative Escherichia coli from young children in Iran. Gastroenterology and Hepatology from bed to bench. 2014;7(2):131.
Shayan S, Bokaeian M, Shahraki S. Prevalence and molecular characterization of AmpC-producing clinical isolates of Escherichia coli from southeastern Iran. Microbial Drug Resistance. 2014;20(2):104-7.
Wong-Beringer A. Therapeutic challenges associated with extended-spectrum, beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae. Pharmacotherapy. 2001;21(5):583-92.
Chaudhary U, Aggarwal R. Extended spectrum -lactamases (ESBL) - an emerging threat to clinical therapeutics. Indian journal of medical microbiology. 2004;22(2):75-80.
Alizade H. Escherichia coli in Iran: An Overview of Antibiotic Resistance: A Review Article. Iran J Public Health. 2018;47(1):1-12.
Haghighatpanah M, Nejad ASM, Mojtahedi A, Amirmozafari N, Zeighami H. Detection of extended-spectrum β-lactamase (ESBL) and plasmid-borne blaCTX-M and blaTEM genes among clinical strains of Escherichia coli isolated from patients in the north of Iran. Journal of global antimicrobial resistance. 2016;7:110-3.
Yousefipour M, Rasoulinejad M, Hadadi A, Esmailpour N, Abdollahi A, Jafari S, et al. Bacteria producing extended spectrum β-lactamases (ESBLs) in hospitalized patients: Prevalence, antimicrobial resistance pattern and its main determinants. Iranian journal of pathology. 2019;14(1):61.
Díez-Villaseñor C, Almendros C, García-Martínez J, Mojica FJ. Diversity of CRISPR loci in Escherichia coli. Microbiology (Reading, England). 2010;156(5):1351-61.
Touchon M, Rocha EP. The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PloS one. 2010;5(6):e11126.
Wang G, Song G, Xu Y. Association of CRISPR/Cas system with the drug resistance in Klebsiella pneumoniae. Infection and Drug Resistance. 2020;13:1929.
Touchon M, Charpentier S, Pognard D, Picard B, Arlet G, Rocha EP, et al. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology (Reading, England). 2012;158(12):2997-3004.
Burley KM, Sedgley CM. CRISPR-Cas, a prokaryotic adaptive immune system, in endodontic, oral, and multidrug-resistant hospital-acquired Enterococcus faecalis. Journal of endodontics. 2012;38(11):1511-5.
Palmer KL, Gilmore MS. Multidrug-resistant enterococci lack CRISPR-cas. mBio. 2010;1(4).
Touchon M, Charpentier S, Pognard D, Picard B, Arlet G, Rocha EP, et al. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology (Reading). 2012;158(Pt 12):2997-3004.
Pawluk A, Staals RH. Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. 2016;1(8):16085.
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Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of bacteriology. 1987;169(12):5429-33.
Louwen R, Staals RH, Endtz HP, van Baarlen P, van der Oost J. The role of CRISPR-Cas systems in virulence of pathogenic bacteria. Microbiology and Molecular Biology Reviews. 2014;78(1):74-88.
Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, et al. Evolution and classification of the CRISPR-Cas systems. Nature reviews Microbiology. 2011;9(6):467-77.
Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, et al. An updated evolutionary classification of CRISPR–Cas systems. Nature Reviews Microbiology. 2015;13(11):722-36.
Sternberg SH, Richter H, Charpentier E, Qimron U. Adaptation in CRISPR-Cas systems. Molecular cell. 2016;61(6):797-808.
Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie. 2015;117:119-28.
Goren M, Yosef I, Qimron U. Sensitizing pathogens to antibiotics using the CRISPR-Cas system. Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy. 2017;30:1-6.
Gholizadeh P, Aghazadeh M, Asgharzadeh M, Kafil HS. Suppressing the CRISPR/Cas adaptive immune system in bacterial infections. 2017;36(11):2043-51.
Tao S, Chen H, Li N, & Liang. The Application of the CRISPR-Cas System in Antibiotic Resistance. Infection and Drug Resistance. 2022, 15: 4155.
Mohr KI. History of antibiotics research. How to Overcome the Antibiotic Crisis. 2016:237-72.
Galindo-Méndez M. Antimicrobial Resistance in Escherichia coli. E. coli Infection: IntechOpen; 2020.
Lynch JP, 3rd, Clark NM, Zhanel GG. Evolution of antimicrobial resistance among Enterobacteriaceae (focus on extended spectrum β-lactamases and carbapenemases). Expert Opin Pharmacother. 2013;14(2):199-210.
Yang JH, Han SJ, Yoon EK, Lee WS. Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells. Nucleic acids research. 2006;34(6):1892-9.
Philippon A, Labia R, Jacoby G. Extended-spectrum beta-lactamases. Antimicrobial agents and chemotherapy. 1989;33(8):1131.
Terlizzi ME, Gribaudo G, Maffei ME. UroPathogenic Escherichia coli (UPEC) infections: virulence factors, bladder responses, antibiotic, and non-antibiotic antimicrobial strategies. Frontiers in microbiology. 2017;8:1566.
CLSI. Performance Standards for Antimicrobial Susceptibility Testing. 31st ed. CLSI supplement M100. Clinical and Laboratory Standards Institute. 2021.
Livermore DM, Brown DF. Detection of β-lactamase-mediated resistance. Journal of antimicrobial Chemotherapy. 2001;48(suppl_1):59-64.
Davari K, Nowroozi J, Hosseini F, Akhavan Sepahy A, Mirzaie S. Inhibitor discovery against beta lactamase CTX-M-9 from E. coli by molecular docking, MM/PBSA and molecular dynamics studies. Journal of Cellular and Molecular Research (Iranian Journal of Biology). 2019;32(1):33-46.
Lesani SS, Soleimani M, Shakib P, Zolfaghari MR. Prevalence of bla CTX-M, bla SHV, and bla TEM Genes in Escherichia coli Strains Isolated From Urinary Tract Infection Samples of Patients in the Intensive Care Unit in Qom, Iran. Gene, Cell and Tissue. 2020;7(2).
Khaledi A, Esmaeili D, Barzegar KEF, Ghamari N, Razipour H, Rostami H. Prevalence of extended-spectrum-β-lactamase-producing Escherichia coli isolates among uropathogensin a pediatrics hospital. Der Pharma Chemica. 2016;8(3):161-5.
Rezaie Kahkhaie K, Rezaie Kehkhaie A, Rezaie Kahkhaie L, Koochakzai M, Rezaie Keikhaie K, Nakhaee Moghaddam M. Isolation of Beta-Lactamase Producing Genes (shv, ctx-M1, ctx-M2, ctx-M3) in Escherichia Coli Isolated from Pregnant Woman Patients. World Journal of Peri and Neonatology. 2018;1(1):21-9.
Masoomi Jahandizi R, Aletaha M, Moosavi M. Evaluation of the Frequency of TEM beta-lactamase gene in patients with urinary tract infections in Bonab County. Cellular and Molecular Researches (Iranian Journal of Biology). 2019;32(3):438-48.
Hemmati TB, Mehdipour Moghaddam MJ, Salehi Z, Habibzadeh SM. Prevalence of CTX-M-Type β-lactamases in multi-drug resistant Escherichia coli isolates from north of Iran, Rasht. Biological Journal of Microorganism. 2015;3(12).
Mohajeri P, Darfarin G, Farahani A. Genotyping of ESBL producing Uropathogenic Escherichia coli in west of Iran. International journal of microbiology. 2014;2014.
Shams F, Hasani A, Pormohammad A, Rezaee MA, Reza M, Nahaie AH, et al. qnrA implicated quinolone resistance in Escherichia coli and Klebsiella pneumoniae clinical isolates from a University Teaching Hospital. Life Sci J. 2014;11(12s):1032-5.
Khoshvaght H, Haghi F, Zeighami H. Extended spectrum betalactamase producing Enteroaggregative Escherichia coli from young children in Iran. Gastroenterology and Hepatology from bed to bench. 2014;7(2):131.
Shayan S, Bokaeian M, Shahraki S. Prevalence and molecular characterization of AmpC-producing clinical isolates of Escherichia coli from southeastern Iran. Microbial Drug Resistance. 2014;20(2):104-7.
Wong-Beringer A. Therapeutic challenges associated with extended-spectrum, beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae. Pharmacotherapy. 2001;21(5):583-92.
Chaudhary U, Aggarwal R. Extended spectrum -lactamases (ESBL) - an emerging threat to clinical therapeutics. Indian journal of medical microbiology. 2004;22(2):75-80.
Alizade H. Escherichia coli in Iran: An Overview of Antibiotic Resistance: A Review Article. Iran J Public Health. 2018;47(1):1-12.
Haghighatpanah M, Nejad ASM, Mojtahedi A, Amirmozafari N, Zeighami H. Detection of extended-spectrum β-lactamase (ESBL) and plasmid-borne blaCTX-M and blaTEM genes among clinical strains of Escherichia coli isolated from patients in the north of Iran. Journal of global antimicrobial resistance. 2016;7:110-3.
Yousefipour M, Rasoulinejad M, Hadadi A, Esmailpour N, Abdollahi A, Jafari S, et al. Bacteria producing extended spectrum β-lactamases (ESBLs) in hospitalized patients: Prevalence, antimicrobial resistance pattern and its main determinants. Iranian journal of pathology. 2019;14(1):61.
Díez-Villaseñor C, Almendros C, García-Martínez J, Mojica FJ. Diversity of CRISPR loci in Escherichia coli. Microbiology (Reading, England). 2010;156(5):1351-61.
Touchon M, Rocha EP. The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PloS one. 2010;5(6):e11126.
Wang G, Song G, Xu Y. Association of CRISPR/Cas system with the drug resistance in Klebsiella pneumoniae. Infection and Drug Resistance. 2020;13:1929.
Touchon M, Charpentier S, Pognard D, Picard B, Arlet G, Rocha EP, et al. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology (Reading, England). 2012;158(12):2997-3004.
Burley KM, Sedgley CM. CRISPR-Cas, a prokaryotic adaptive immune system, in endodontic, oral, and multidrug-resistant hospital-acquired Enterococcus faecalis. Journal of endodontics. 2012;38(11):1511-5.
Palmer KL, Gilmore MS. Multidrug-resistant enterococci lack CRISPR-cas. mBio. 2010;1(4).
Touchon M, Charpentier S, Pognard D, Picard B, Arlet G, Rocha EP, et al. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology (Reading). 2012;158(Pt 12):2997-3004.
Pawluk A, Staals RH. Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. 2016;1(8):16085.
