Nosocomial E. Coli Isolated from UTI Identified Using DNA Markers Based on PCR and Pathogenic Markers

Shler Ali Khorsheed

doi:10.55489/njmr.150220251087

Authors

Shler Ali Khorsheed Ministry Of Education, Open Educational College, Department of Biology, Kirkuk, Iraq

DOI:

https://doi.org/10.55489/njmr.150220251087

Keywords:

E. coli, UTI infection, DNA polymerase chain reaction

Abstract

Background: Urinary tract infections (UTIs) are among the most common bacterial infections, with Escherichia coli (E. coli) being the leading causative agent. The increasing resistance of E. coli to commonly used antibiotics, including β-lactam antibiotics, poses a significant clinical challenge. Understanding antimicrobial resistance patterns and genetic diversity among E. coli isolates is essential for effective treatment and infection control. This study aimed to determine the prevalence of E. coli in UTI cases, assess its resistance to multiple antibiotics, evaluate β-lactamase and extended-spectrum beta-lactamase (ESBL) production, and analyze genetic diversity using molecular techniques.

Materials and Methods: A total of 105 urine samples were collected from UTI patients at Rezali Hospital and General Hospital in Erbil (January–June 2024). Disk diffusion was used for antibiotic susceptibility testing, while MIC values were determined for penicillin and cephalosporin. β-lactamase production was assessed using the iodine titration method, ESBLs were confirmed using a disk proximity test, and RAPD markers were used for genetic diversity.

Results: E. coli accounted for 48.51% of UTIs, showing high resistance to tetracycline (75.71%) and ceftriaxone (95.14%), and complete resistance to ampicillin and amoxicillin. β-lactamase production was detected in 84.62% of isolates, while 5.77% were ESBL producers. Genetic analysis indicated strain diversity, suggesting multiple nosocomial sources.

Conclusion: The study highlights multidrug-resistant E. coli in UTIs, emphasizing the need for continuous surveillance and antibiotic stewardship programs to prevent treatment failures.

References

Al Samarai MA, Khorshed SA. Risk factors in diabetes and pregnant women with urinary tract infections compared to younger aged females. Int J Med Sci. 2018;1(3):26-38. DOI: https://doi.org/10.32441/ijms.v1i3.99 DOI: https://doi.org/10.32441/ijms.v1i3.99

Abdulghani MA, Khorshed SA, Hajer A, Abdulghani M. Urinary tract infection in females in Kirkuk city, Iraq: Association between risk factors and bacterial types. Our Dermatol Online. 2017;8(3):242-249. DOI: https://doi.org/10.7241/ourd.20173.72 DOI: https://doi.org/10.7241/ourd.20173.72

Zhanel GG, Karlowsky JA, Harding GK, Carrie A, Mazzulli T, Low DE, Hoban DJ. A Canadian national surveillance study of urinary tract isolates from outpatients: Comparison of the activities of trimethoprim-sulfamethoxazole, ampicillin, mecillinam, nitrofurantoin, and ciprofloxacin. Antimicrob Agents Chemother. 2000 Apr;44(4):1089-1092. DOI: https://doi.org/10.1128/AAC.44.4.1089-1092.2000 PMid:10722520 PMCid:PMC89821 DOI: https://doi.org/10.1128/AAC.44.4.1089-1092.2000

Chaïbi EB, Sirot D, Paul G, Labia R. Inhibitor-resistant TEM beta-lactamases: Phenotypic, genetic, and biochemical characteristics. J Antimicrob Chemother. 1999 Apr;43(4):447-458. DOI: https://doi.org/10.1093/jac/43.4.447 PMid:10350372 DOI: https://doi.org/10.1093/jac/43.4.447

Abraham EP, Chain E. An enzyme from bacteria able to destroy penicillin. Nature. 1940;146:837-840. DOI: https://doi.org/10.1038/146837a0 DOI: https://doi.org/10.1038/146837a0

Bush K, Jacoby GA, Medeiros AA. A functional classification scheme for beta-lactamases and its correlation with molecular structure. J Antimicrob Chemother. 1995;39(6):1211-1233. DOI: https://doi.org/10.1128/AAC.39.6.1211 PMid:7574506 PMCid:PMC162717 DOI: https://doi.org/10.1128/AAC.39.6.1211

Medeiros AA. Evolution and dissemination of beta-lactamases accelerated by generations of beta-lactam antibiotics. Clin Infect Dis. 1997;24(Suppl 1):S19-S45. DOI: https://doi.org/10.1093/clinids/24.Supplement_1.S19 PMid:8994778 DOI: https://doi.org/10.1093/clinids/24.Supplement_1.S19

Livermore DM. Beta-lactamases in laboratory and clinical resistance. J Clin Microbiol Rev. 1995;8(4):557-584. DOI: https://doi.org/10.1128/CMR.8.4.557 PMid:8665470 PMCid:PMC172876 DOI: https://doi.org/10.1128/CMR.8.4.557

Kholes JR. Penicillin resistance: The chemistry of beta-lactamase inhibition. Acc Chem Res. 1985;18:97-104. DOI: https://doi.org/10.1021/ar00112a001 DOI: https://doi.org/10.1021/ar00112a001

Gomes TR, Muniyappa L, Krishnappa A, Suryanarayana V, Isloor S, Prakash B, Hugar P. Genotypic characterization of avian E. coli by random amplified polymorphic DNA. Int J Poult Sci. 2005;4:378-381. DOI: https://doi.org/10.3923/ijps.2005.378.381

Caetano-Anollés G, Bassam BJ, Gresshoff PM. DNA amplification fingerprinting using very short oligonucleotide primers. BioTechnology. 1991;9:553-557. DOI: https://doi.org/10.1038/nbt0691-553 PMid:1367225 DOI: https://doi.org/10.1038/nbt0691-553

Lin AW, Usera MA, Barrett TJ, Goldsby RA. Application of random amplified polymorphic DNA analysis to differentiate strains of Salmonella enteritidis. J Clin Microbiol. 1996;34(4):870-876. DOI: https://doi.org/10.1128/jcm.34.4.870-876.1996 PMid:8815099 PMCid:PMC228908 DOI: https://doi.org/10.1128/jcm.34.4.870-876.1996

Alos JI, Lambert T, Courvalin P. Comparison of two molecular methods for tracing nosocomial transmission of E. coli in a neonatal unit. J Clin Microbiol. 1993;31(7):1704-1709. DOI: https://doi.org/10.1128/jcm.31.7.1704-1709.1993 PMid:8102374 PMCid:PMC265618 DOI: https://doi.org/10.1128/jcm.31.7.1704-1709.1993

Welsh J, McClelland MM. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990;18(24):7213-7218. DOI: https://doi.org/10.1093/nar/18.24.7213 PMid:2259619 PMCid:PMC332855 DOI: https://doi.org/10.1093/nar/18.24.7213

Tingey SV, Rafalski JA, Williams JGK. Application of random amplified polymorphic DNA technology to plant breeding. In: Caetano-Anollés G, Gresshoff PM, editors. DNA Markers, Protocols, Applications & Overview. Wiley-Liss; 1993. p. 75-83. DOI: https://doi.org/10.1007/978-94-017-6951-8_3 DOI: https://doi.org/10.1007/978-94-017-6951-8_3

Gomes TR, Muniyappa L, Krishnappa A, Suryanarayana V, Isloor S, Prakash B, Hugar P. Genotypic characterization of avian E. coli by random amplified polymorphic DNA. Int J Poult Sci. 2005;4:378-381. DOI: https://doi.org/10.3923/ijps.2005.378.381 DOI: https://doi.org/10.3923/ijps.2005.378.381

Mahon CR, Manuselis G. Textbook of Diagnostic Microbiology. 2nd ed. W.B. Saunders; 2000.

Atlas RM, Alfred EB, Lawrence CP. Laboratory Manual Experimental Microbiology. Mosby-Year, Inc.; 1995.

World Health Organization (WHO). Techniques for the detection of beta-lactamase producing strains of Neisseria gonorrhoeae. Techniques Report. 1978;616:137-143.

Shler KA, Abdulghani MA. Comparison of antibiotic sensitivity between extended spectrum beta-lactamase producers and ESBL-negative Escherichia coli clinical isolates. Int J Med Sci. 2018;1(1):36-42. DOI: https://doi.org/10.32441/ijms.v1i1.36 DOI: https://doi.org/10.32441/ijms.v1i1.36

Roeder V, Broda P. Rapid preparation of DNA from filamentous fungi. J Appl Microbiol. 1987;1:17-20. DOI: https://doi.org/10.1111/j.1472-765X.1985.tb01479.x DOI: https://doi.org/10.1111/j.1472-765X.1985.tb01479.x

Khorshed SA. Molecular epidemiology and characterization of extended spectrum beta-lactamase producing E. coli in female patients with urinary tract infection. Int J Med Sci. 2018;1(2):62-63. DOI: https://doi.org/10.32441/ijms.v1i2.78 DOI: https://doi.org/10.32441/ijms.v1i2.78

Weigand F, Baum M, Udupa S. DNA molecular marker techniques. Technical Manual No. 20. International Center for Agricultural Research in the Dry Areas, Aleppo, Syria; 1993.

Udupa SM, Weigand F, Saxena MC, Cahl G. Genotyping with RAPD and microsatellite markers resolves pathotype diversity in the Ascochyta blight pathogen of chickpea. Theor Appl Genet. 1998;97(3):299-307. DOI: https://doi.org/10.1007/s001220050899 DOI: https://doi.org/10.1007/s001220050899

Franz M, Horl WH. Common errors in diagnosis and management of urinary tract infections: Pathophysiology and diagnostic techniques. Nephrol Dial Transplant. 1999;14(11):2746-2753. DOI: https://doi.org/10.1093/ndt/14.11.2746 PMid:10534527 DOI: https://doi.org/10.1093/ndt/14.11.2746

Naveen R, Mathai E. Some virulence characteristics of uropathogenic E. coli in different patient groups. Indian J Med Res. 2005;122:143-147.

Al-Nammi AAS. Synergetic effect of some beta-lactamase inhibitors with beta-lactam antibiotics on some gram-negative bacteria and other beta-lactamase producers. MSc Thesis, College of Science, University of Almustansirya, Iraq; 2001.

Howell SA, Barnard RJ, Humphreys F. Application of molecular typing methods to dermatophyte species that cause skin and nail infections. J Med Microbiol. 1999;48(1):33-40. DOI: https://doi.org/10.1099/00222615-48-1-33 PMid:9920123 DOI: https://doi.org/10.1099/00222615-48-1-33

McOskar CC, Fitzpatrick AN. Nitrofurantoin mechanisms of action and implications for resistance development in common uropathogens. J Antimicrob Chemother. 1994;33(1):23-30. DOI: https://doi.org/10.1093/jac/33.suppl_A.23 PMid:7928834 DOI: https://doi.org/10.1093/jac/33.suppl_A.23

Hooper DC. Urinary tract agents: Nitrofurantoin and methenamine. Antimicrob Agents Chemother. 2000;44(6):1675-1683.

Kahlmeter G, Menday P, Cars O. Non-hospital antimicrobial usage and resistance in community-acquired Escherichia coli urinary tract infection. J Antimicrob Chemother. 2003 Dec;52(6):1005-10. DOI: https://doi.org/10.1093/jac/dkg488. Epub 2003 Nov 12. PMID: 14613955. DOI: https://doi.org/10.1093/jac/dkg488

Ena J, Lopez-Perezagua MM, Martinez-Peinddo C, Cia-Barrio MA, Uiz-Lopez I. Emergence of ciprofloxacin resistance in E. coli isolates after widespread use of fluoroquinolones. Diagn Microbiol Infect Dis. 1998;30(2):103-107. DOI: https://doi.org/10.1016/S0732-8893(97)00216-2 PMid:9554177 DOI: https://doi.org/10.1016/S0732-8893(97)00216-2

Bras AC. Prevalence and bacterial susceptibility of hospital-acquired urinary tract infection. Acta Cir Bras. 2003;18 Suppl 5:1-7. DOI: https://doi.org/10.1590/S0102-86502003001200013

Shler AK. Detection of Surgical Wound Infections among Patients in Azadi Teaching Hospital in Kirkuk, using Polymerase Chain Reaction Technique. Transylvanian. 2019;XXVII:45.

Potz NA, Hope R, Warner M, Jonson AP, Livermore DM. Prevalence and mechanism of cephalosporin resistance in Enterobacteriaceae in London and South-East England. J Antimicrob Chemother. 2006;58(2):320-326. DOI: https://doi.org/10.1093/jac/dkl217 PMid:16735428

Craig CR, Stitzel RE. Modern pharmacology with clinical applications. 6th ed. Lippincott Williams & Wilkins; 2004.

Tawfiq SM. Diffusion of modern antibiotics resistance in some gram-negative bacteria which cause urinary tract infection in children between 0-3 years. MSc Thesis, College of Science-Almustansirya University, Iraq. 2005.

Bras AC. Prevalence and bacterial susceptibility of hospital-acquired urinary tract infection. Acta Cir Bras. 2003;18 Suppl 5:1-7. DOI: https://doi.org/10.1590/S0102-86502003001200013 DOI: https://doi.org/10.1590/S0102-86502003001200013

Wiedemann B, Kliebe C, Kresken M. The epidemiology of β-lactamases. J Antimicrob Chemother. 1989;24:1-22. DOI: https://doi.org/10.1093/jac/24.suppl_B.1 PMid:2691474 DOI: https://doi.org/10.1093/jac/24.suppl_B.1

Bauman RW. Microbiology. Alange Medical Book; 2004.

Marcusson LL, Olofsson SK, Lindgren PK, Cars O, Hughes D. Mutant prevention concentrations of ciprofloxacin for urinary tract infection isolates of E. coli. J Antimicrob Chemother. 2005;55:938-943. DOI: https://doi.org/10.1093/jac/dki136 PMid:15860549 DOI: https://doi.org/10.1093/jac/dki136

Al-Nammi AAS. Synergetic effect of some β-lactamase inhibitors with β-lactam antibiotics on some gram-negative bacteria and other β-lactamase producers. MSc Thesis, College of Science, University of Almustansirya, Iraq. 2001.

Kunin CM. Resistance to antimicrobial drugs: a worldwide calamity. Ann Intern Med. 1993;118:557-561. DOI: https://doi.org/10.7326/0003-4819-118-7-199304010-00011 PMid:8442626 DOI: https://doi.org/10.7326/0003-4819-118-7-199304010-00011

Potz NA, Hope R, Warner M, Jonson AP, Livermore DM. Prevalence and mechanism of cephalosporin resistance in Enterobacteriaceae in London and South-East England. J Antimicrob Chemother. 2006;58(2):320-326. DOI: https://doi.org/10.1093/jac/dkl217 PMid:16735428 DOI: https://doi.org/10.1093/jac/dkl217

EARSS. EARSS Annual Report. Bithoven: RIVM; 2005. Available from: https://www.rivm.nl/bibliotheek/rapporten/210624001.pdf

Ryoo NH, Kim EC, Hong SG, Park YJ, Lee K, Bae K, Song EH, Jeong SH. Dissemination of SHV-12 and CTX-M-type ESBLs among clinical isolates of E. coli and Klebsiella pneumoniae and emergence of GES-3 in Korea. J Antimicrob Chemother. 2005;56:698-702. DOI: https://doi.org/10.1093/jac/dki324 PMid:16141280 DOI: https://doi.org/10.1093/jac/dki324

Bercker K, Badohorh D, Deiwick S, Peters G, Fegeler W. Molecular genotyping of Candida species with special respect to Candida (Torulopsis) glabrata strains. J Med Microbiol. 2000;49:575-581. DOI: https://doi.org/10.1099/0022-1317-49-6-575 PMid:10847212 DOI: https://doi.org/10.1099/0022-1317-49-6-575

Sotto A. Risk factors for antibiotic-resistant E. coli isolated from hospitalized patients with UTI. A prospective study. J Clin Microbiol. 2001;39(2):438-444. DOI: https://doi.org/10.1128/JCM.39.2.438-444.2001 PMid:11158087 PMCid:PMC87756 DOI: https://doi.org/10.1128/JCM.39.2.438-444.2001

El-Badawy MEM. Localization and characterization of quantitative trait loci for fusarium head blight resistance in wheat by means of molecular markers. PhD Thesis, Technischen Universität München. 2001.

Rafalski JA. Random amplified polymorphic DNA (RAPD) analysis. In: Caetano-Anolles G, Gresshoff PM, editors. DNA markers: Protocols, applications, and overview. Wiley-Liss; 1997. p. 75-83.

Iqbal MJ, Aziz N, Saeed NA, Zafar Y, Malik KA. Genetic diversity evaluation of some elite cotton varieties by RAPD analysis. Theor Appl Genet. 1997;94:139-144. DOI: https://doi.org/10.1007/s001220050392 PMid:19352756 DOI: https://doi.org/10.1007/s001220050392