Phenotypic, genotypic characterization and antimicrobial resistance profiling of uropathogenic Escherichia coli in a tertiary care hospital, Puducherry, India
-
Sherief Shebeena
,
Latha Ragunathan
,
Kavitha Kannaiyan
,
Thiyagarajan Sanjeevi
,
Pramodhini Subramanian
,
Aravind C Sasi
,
Jaishma Rajni
,
Jenifer Raj
,
Mohamed Asarudeen
Abstract
Background and Objectives: Uropathogenic Escherichia coli (E. coli) (UPEC) accounts for 70-95% of community-acquired urinary tract infections (UTIs) and a significant proportion of nosocomial UTIs. This study aimed to characterize the phenotypic and genotypic characteristics of E. coli isolates from symptomatic UTI patients and evaluate their antimicrobial susceptibility patterns.
Materials and Methods: A hospital-based observational study was conducted at Aarupadai Veedu Medical College and Hospital, Puducherry, India, from August 2022 to April 2024. A total of 106 UPEC isolates were obtained from symptomatic UTI patients. Antimicrobial susceptibility testing (AST) was performed using the Kirby-Bauer method, and virulence genes (hlyA, fimH, papC) were detected using PCR.
Results: The mean age of patients was 49.7 years, with a female predominance (69.8%). Diabetes mellitus was the most common comorbidity (29.2%). Fever (60.4%) and dysuria (38.7%) were the most common symptoms. AST showed high susceptibility (>90%) to amikacin, nitrofurantoin, meropenem, and piperacillin/tazobactam, while >60% resistance was observed to cefotaxime and ceftazidime. Phenotypically, 30.2% of the isolates produced mannose-resistant hemagglutinins, and 17.9% produced hemolysin. ESBL production was found in 46.3%. Biofilm production was moderate in 65.1%, weak in 30.2% and strong in 4.7% and significantly correlated with multidrug resistance (p<0.05). Genotypically, 80.2% had fimH, 51.9% had papC and 20.8% had hlyA. papC was associated with reduced cefotaxime susceptibility (p<0.05).
Conclusion: The study highlights the significance of phenotypic and genotypic characterization in understanding UPEC virulence and resistance patterns, and emphasizes the need for targeted empiric therapy to improve UTI management.
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2. Chakraborty A, Adhikari P, Shenoy S, Saralaya V. Molecular characterization of uropathogenic Escherichia coli isolates at a tertiary care hospital in South India. Indian J Med Microbiol 2017; 35: 305-310.
3. Ali Faraz MA, Mendem S, Swamy MV, Shubham P. Prevalence of urinary tract infections and related antimicrobial resistance in India: a systematic review and meta-analysis. Int J Pharm Sci Res 2021; 12: 4314-4321.
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5. Hyun M, Lee JY, Kim HA. Differences of virulence factors and antimicrobial susceptibility according to phylogenetic group in uropathogenic Escherichia coli strains isolated from Korean patients. Ann Clin Microbiol Antimicrob 2021; 20: 77.
6. El-Baz R, Said HS, Abdelmegeed ES, Barwa R. Characterization of virulence determinants and phylogenetic background of multiple and extensively drug-resistant Escherichia coli isolated from different clinical sources in Egypt. Appl Microbiol Biotechnol 2022; 106: 1279-1298.
7. Mohammad Zadeh F, Zarei H, Honarmand Jahromy S. Type 1 and 3 fimbriae phenotype and genotype as suitable markers for uropathogenic bacterial pathogenesis via attachment, cell surface hydrophobicity, and biofilm formation in catheter-associated urinary tract infections (CAUTIs). Iran J Basic Med Sci 2021; 24: 1098-1106.
8. Smith MA, Puckrin R, Lam PW, Lamb MJ, Simor AE, Leis JA. Association of increased Colony-Count Threshold for urinary pathogens in hospitalized patients with antimicrobial treatment. JAMA Intern Med 2019; 179: 990-992.
9. Kubone PZ, Mlisana KP, Govinden U, Abia AL, Essack SY. Antibiotic susceptibility and molecular characterization of uropathogenic Escherichia coli associated with community-acquired urinary tract infections in urban and rural settings in South Africa. Trop Med Infect Dis 2020; 5: 176.
10. Hojati Z, Zamanzad B, Hashemzadeh M, Molaie R, Gholipour A. The FimH gene in uropathogenic Escherichia coli strains isolated from patients with urinary tract infection. Jundishapur J Microbiol 2015; 8(2): e17520.
11. Ehsan B, Haque A, Qasim M, Ali A, Sarwar Y. High prevalence of extensively drug-resistant and extended-spectrum beta-lactamases (ESBLs) producing uropathogenic Escherichia coli isolated from Faisalabad, Pakistan. World J Microbiol Biotechnol 2023; 39: 132.
12. Shaikh S, Fatima J, Shakil S, Rizvi SM, Kamal MA. Antibiotic resistance and extended-spectrum beta-lactamases: Types, epidemiology and treatment. Saudi J Biol Sci 2015; 22: 90-101.
13. Naveen R, Mathai E. Some virulence characteristics of uropathogenic Escherichia coli in different patient groups. Indian J Med Res 2005; 122: 143-147.
14. Harika K, Shenoy VP, Narasimhaswamy N, Chawla K. Detection of biofilm production and its impact on antibiotic resistance profile of bacterial isolates from chronic wound infections. J Glob Infect Dis 2020; 12: 129-134.
15. Ramírez Castillo FY, Guerrero Barrera AL, Harel J, Avelar González FJ, Vogeleer P, Arreola Guerra JM, et al. Biofilm formation by Escherichia coli isolated from urinary tract infections from Aguascalientes, Mexico. Microorganisms 2023; 11: 2858.
16. Bhugra A, Gachinmath S. Significant bacteriuria among requested repeat urine samples and its clinical correlation. Iran J Microbiol 2021; 13: 592-601.
17. Odoki M, Almustapha Aliero A, Tibyangye J, Nyabayo Maniga J, Wampande E, Drago Kato C, et al. Prevalence of bacterial urinary tract infections and associated factors among patients attending hospitals in Bushenyi district, Uganda. Int J Microbiol 2019; 2019: 4246780.
18. Dadi BR, Abebe T, Zhang L, Mihret A, Abebe W, Amogne W. Distribution of virulence genes and phylogenetics of uropathogenic Escherichia coli among urinary tract infection patients in Addis Ababa, Ethiopia. BMC Infect Dis 2020; 20: 108.
19. Pardeshi P. Prevalence of urinary tract infections and current scenario of antibiotic susceptibility pattern of bacteria causing UTI. Indian J Microbiol Res 2018; 5: 334-338.
20. Ahmed AE, Abdelkarim S, Zenida M, Baiti MAH, Alhazmi AAY, Alfaifi BAH, et al. Prevalence and associated risk factors of urinary tract infection among diabetic patients: a cross-sectional study. Healthcare (Basel) 2023; 11: 861.
21. Paudel L, Manandhar N, Sah S, Khadka S, Neupane S, Joshi SK. Prevalence of urinary tract infection and associated risk factors among women in Sindhupalchowk district, Nepal. Int J Community Med Public Health 2018; 5: 2714-2719.
22. Dilleban J, Venkateshan N, Anand Raj P, Andrews E, Anu Sahaya Supria K. Prevalence of urinary tract infection among women in Virudhunagar, Tamil Nadu: Treatment Approach and Perspectives. Uttar Pradesh J Zool 2024; 45: 160-167.
23. Medina M, Castillo-Pino E. An introduction to the epidemiology and burden of urinary tract infections. Ther Adv Urol 2019; 11: 1756287219832172.
24. Kadry AA, Al-Kashef NM, El-Ganiny AM. Distribution of genes encoding adhesins and biofilm formation capacity among Uropathogenic Escherichia coli isolates in relation to the antimicrobial resistance. Afr Health Sci 2020; 20: 238-247.
25. Alshaikh SA, El-Banna T, Sonbol F, Farghali MH. Correlation between antimicrobial resistance, biofilm formation, and virulence determinants in uropathogenic Escherichia coli from Egyptian hospital. Ann Clin Microbiol Antimicrob 2024; 23: 20.
26. Tabasi M, Asadi Karam MR, Habibi M, Yekaninejad MS, Bouzari S. Phenotypic assays to determine virulence factors of uropathogenic Escherichia coli (UPEC) isolates and their correlation with antibiotic resistance pattern. Osong Public Health Res Perspect 2015; 6: 261-268.
27. Zeb Z, Azam S, Rehman N, Khan I, Afzal S, Sehra GE, et al. Phenotypic and molecular characterization of virulence factors of extra-intestinal pathogenic Escherichia coli isolated from patients of Peshawar, Pakistan. Pak J Pharm Sci 2021; 34: 85-94.
28. Basu S, Mukherjee SK, Hazra A, Mukherjee M. Molecular characterization of uropathogenic Escherichia coli: nalidixic acid and ciprofloxacin resistance, virulent factors and phylogenetic background. J Clin Diagn Res 2013; 7: 2727-2731.
29. Radera S, Srivastava S, Agarwal J. Virulence genotyping and multidrug resistance pattern of Escherichia coli isolated from community-acquired and hospital-acquired urinary tract infections. Cureus 2022; 14(9): e29404.
2. Chakraborty A, Adhikari P, Shenoy S, Saralaya V. Molecular characterization of uropathogenic Escherichia coli isolates at a tertiary care hospital in South India. Indian J Med Microbiol 2017; 35: 305-310.
3. Ali Faraz MA, Mendem S, Swamy MV, Shubham P. Prevalence of urinary tract infections and related antimicrobial resistance in India: a systematic review and meta-analysis. Int J Pharm Sci Res 2021; 12: 4314-4321.
4. Alqasim A, Jaffal AA, Almutairi N, Arshad M, Alyousef AA. Isolation, phenotypic and genotypic characterization of Escherichia coli from the bloodstream samples in Riyadh, Saudi Arabia. J King Saud Univ Sci 2020; 32: 1464-1469.
5. Hyun M, Lee JY, Kim HA. Differences of virulence factors and antimicrobial susceptibility according to phylogenetic group in uropathogenic Escherichia coli strains isolated from Korean patients. Ann Clin Microbiol Antimicrob 2021; 20: 77.
6. El-Baz R, Said HS, Abdelmegeed ES, Barwa R. Characterization of virulence determinants and phylogenetic background of multiple and extensively drug-resistant Escherichia coli isolated from different clinical sources in Egypt. Appl Microbiol Biotechnol 2022; 106: 1279-1298.
7. Mohammad Zadeh F, Zarei H, Honarmand Jahromy S. Type 1 and 3 fimbriae phenotype and genotype as suitable markers for uropathogenic bacterial pathogenesis via attachment, cell surface hydrophobicity, and biofilm formation in catheter-associated urinary tract infections (CAUTIs). Iran J Basic Med Sci 2021; 24: 1098-1106.
8. Smith MA, Puckrin R, Lam PW, Lamb MJ, Simor AE, Leis JA. Association of increased Colony-Count Threshold for urinary pathogens in hospitalized patients with antimicrobial treatment. JAMA Intern Med 2019; 179: 990-992.
9. Kubone PZ, Mlisana KP, Govinden U, Abia AL, Essack SY. Antibiotic susceptibility and molecular characterization of uropathogenic Escherichia coli associated with community-acquired urinary tract infections in urban and rural settings in South Africa. Trop Med Infect Dis 2020; 5: 176.
10. Hojati Z, Zamanzad B, Hashemzadeh M, Molaie R, Gholipour A. The FimH gene in uropathogenic Escherichia coli strains isolated from patients with urinary tract infection. Jundishapur J Microbiol 2015; 8(2): e17520.
11. Ehsan B, Haque A, Qasim M, Ali A, Sarwar Y. High prevalence of extensively drug-resistant and extended-spectrum beta-lactamases (ESBLs) producing uropathogenic Escherichia coli isolated from Faisalabad, Pakistan. World J Microbiol Biotechnol 2023; 39: 132.
12. Shaikh S, Fatima J, Shakil S, Rizvi SM, Kamal MA. Antibiotic resistance and extended-spectrum beta-lactamases: Types, epidemiology and treatment. Saudi J Biol Sci 2015; 22: 90-101.
13. Naveen R, Mathai E. Some virulence characteristics of uropathogenic Escherichia coli in different patient groups. Indian J Med Res 2005; 122: 143-147.
14. Harika K, Shenoy VP, Narasimhaswamy N, Chawla K. Detection of biofilm production and its impact on antibiotic resistance profile of bacterial isolates from chronic wound infections. J Glob Infect Dis 2020; 12: 129-134.
15. Ramírez Castillo FY, Guerrero Barrera AL, Harel J, Avelar González FJ, Vogeleer P, Arreola Guerra JM, et al. Biofilm formation by Escherichia coli isolated from urinary tract infections from Aguascalientes, Mexico. Microorganisms 2023; 11: 2858.
16. Bhugra A, Gachinmath S. Significant bacteriuria among requested repeat urine samples and its clinical correlation. Iran J Microbiol 2021; 13: 592-601.
17. Odoki M, Almustapha Aliero A, Tibyangye J, Nyabayo Maniga J, Wampande E, Drago Kato C, et al. Prevalence of bacterial urinary tract infections and associated factors among patients attending hospitals in Bushenyi district, Uganda. Int J Microbiol 2019; 2019: 4246780.
18. Dadi BR, Abebe T, Zhang L, Mihret A, Abebe W, Amogne W. Distribution of virulence genes and phylogenetics of uropathogenic Escherichia coli among urinary tract infection patients in Addis Ababa, Ethiopia. BMC Infect Dis 2020; 20: 108.
19. Pardeshi P. Prevalence of urinary tract infections and current scenario of antibiotic susceptibility pattern of bacteria causing UTI. Indian J Microbiol Res 2018; 5: 334-338.
20. Ahmed AE, Abdelkarim S, Zenida M, Baiti MAH, Alhazmi AAY, Alfaifi BAH, et al. Prevalence and associated risk factors of urinary tract infection among diabetic patients: a cross-sectional study. Healthcare (Basel) 2023; 11: 861.
21. Paudel L, Manandhar N, Sah S, Khadka S, Neupane S, Joshi SK. Prevalence of urinary tract infection and associated risk factors among women in Sindhupalchowk district, Nepal. Int J Community Med Public Health 2018; 5: 2714-2719.
22. Dilleban J, Venkateshan N, Anand Raj P, Andrews E, Anu Sahaya Supria K. Prevalence of urinary tract infection among women in Virudhunagar, Tamil Nadu: Treatment Approach and Perspectives. Uttar Pradesh J Zool 2024; 45: 160-167.
23. Medina M, Castillo-Pino E. An introduction to the epidemiology and burden of urinary tract infections. Ther Adv Urol 2019; 11: 1756287219832172.
24. Kadry AA, Al-Kashef NM, El-Ganiny AM. Distribution of genes encoding adhesins and biofilm formation capacity among Uropathogenic Escherichia coli isolates in relation to the antimicrobial resistance. Afr Health Sci 2020; 20: 238-247.
25. Alshaikh SA, El-Banna T, Sonbol F, Farghali MH. Correlation between antimicrobial resistance, biofilm formation, and virulence determinants in uropathogenic Escherichia coli from Egyptian hospital. Ann Clin Microbiol Antimicrob 2024; 23: 20.
26. Tabasi M, Asadi Karam MR, Habibi M, Yekaninejad MS, Bouzari S. Phenotypic assays to determine virulence factors of uropathogenic Escherichia coli (UPEC) isolates and their correlation with antibiotic resistance pattern. Osong Public Health Res Perspect 2015; 6: 261-268.
27. Zeb Z, Azam S, Rehman N, Khan I, Afzal S, Sehra GE, et al. Phenotypic and molecular characterization of virulence factors of extra-intestinal pathogenic Escherichia coli isolated from patients of Peshawar, Pakistan. Pak J Pharm Sci 2021; 34: 85-94.
28. Basu S, Mukherjee SK, Hazra A, Mukherjee M. Molecular characterization of uropathogenic Escherichia coli: nalidixic acid and ciprofloxacin resistance, virulent factors and phylogenetic background. J Clin Diagn Res 2013; 7: 2727-2731.
29. Radera S, Srivastava S, Agarwal J. Virulence genotyping and multidrug resistance pattern of Escherichia coli isolated from community-acquired and hospital-acquired urinary tract infections. Cureus 2022; 14(9): e29404.
| Files | ||
| Issue | Vol 17 No 3 (2025) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v17i3.18818 | |
| Keywords | ||
| Urinary tract infection Uropathogenic Escherichia coli Antibiotic susceptibility testing Antimicrobial resistance | ||
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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
How to Cite
1.
Shebeena S, Ragunathan L, Kannaiyan K, Sanjeevi T, Subramanian P, Sasi A, Rajni J, Raj J, Asarudeen M. Phenotypic, genotypic characterization and antimicrobial resistance profiling of uropathogenic Escherichia coli in a tertiary care hospital, Puducherry, India. Iran J Microbiol. 2025;17(3):366-375.
