Analysis of Antimicrobial Resistance Patterns in Escherichia coli And Molecular Characterization Across Karachi's Different Districts
DOI:
https://doi.org/10.65761/pjcr.2026.299Keywords:
Antimicrobial Resistance, Escherichia coli, Karachi, Multidrug Resistance, Clinical Microbiology, Public Health.Abstract
Background: Antimicrobial resistance (AMR) among Escherichia coli is an increasing clinical and public-health concern, particularly in settings where antimicrobial use and resistance surveillance remain challenging. Local phenotypic and molecular data are important for guiding empirical treatment and antimicrobial stewardship.
Objective: To characterize antimicrobial resistance patterns among clinical E. coli isolates from Karachi, Pakistan, and detect selected antimicrobial-resistance genes using polymerase chain reaction (PCR).
Methods: A laboratory-based observational study was conducted from January to December 2025 using 177 non-duplicate clinical E. coli isolates recovered from urine (n=145), pus (n=21), and blood (n=11) specimens. Antimicrobial susceptibility was determined using the Kirby–Bauer disk diffusion method and interpreted according to applicable Clinical and Laboratory Standards Institute criteria. Resistance patterns were analyzed according to specimen type, age group, sex, and residential district. Selected isolates were subjected to PCR targeting tetA, sul1, and sul2, with amplicons of 502, 430, and 190 bp, respectively.
Results: Among 2,210 antimicrobial susceptibility test results, resistance was highest to cefuroxime (89.3%), ampicillin (85.3%), and ciprofloxacin (76.0%). Resistance was comparatively low to fosfomycin (2.0%), meropenem (4.7%), and nitrofurantoin (6.7%), while no resistance was detected against amikacin or polymyxin B/colistin. Pus isolates demonstrated high resistance to ampicillin and ceftazidime (90.5% each), while blood isolates showed substantial resistance to ampicillin (81.8%). District-level differences were not statistically significant (χ²=0.49, p=0.92). PCR detected tetA, sul1, and sul2 resistance determinants.
Conclusion: Clinical E. coli isolates in Karachi demonstrated substantial resistance to commonly used antibiotics, while selected agents retained comparatively good activity. Continued local surveillance integrating phenotypic and molecular approaches is warranted to support antimicrobial stewardship and evidence-based empirical therapy.
References
1. Holmes AH, Moore LSP, Sundsfjord A, Steinbakk M, Regmi S, Karkey A, et al. Understanding the mechanisms and drivers of antimicrobial resistance. Lancet. 2016;387(10014):176-87. doi:10.1016/S0140-6736(15)00473-0.
2. Kaper JB, Nataro JP, Mobley HLT. Pathogenic Escherichia coli. Nat Rev Microbiol. 2004;2(2):123-40. doi:10.1038/nrmicro818.
3. Nordmann P, Naas T, Poirel L. Global spread of carbapenemase-producing Enterobacteriaceae. Emerg Infect Dis. 2011;17(10):1791-8. doi:10.3201/eid1710.110655.
4. Tenover FC. Mechanisms of antimicrobial resistance in bacteria. Am J Infect Control. 2006;34(5 Suppl 1). doi:10.1016/j.ajic.2006.05.219.
5. Madigan MT, Bender KS, Buckley DH, Sattley WM, Stahl DA. Brock biology of microorganisms. 16th ed. Pearson; 2021.
6. Murray PR, Rosenthal KS, Pfaller MA. Medical microbiology. 9th ed. Elsevier; 2021.
7. Willey JM, Sherwood LM, Woolverton CJ. Prescott's microbiology. 10th ed. McGraw-Hill Education; 2017.
8. Todar K. Todar's online textbook of bacteriology. Madison (WI): University of Wisconsin-Madison, Department of Bacteriology; 2004-2006. Available from: https://www.textbookofbacteriology.net
9. Tortora GJ, Funke BR, Case CL. Microbiology: an introduction. 13th ed. Pearson; 2020.
10. World Health Organization. Antimicrobial resistance [Internet]. Geneva: World Health Organization; 2023 [cited 2026 Sep 7]. Available from: https://www.who.int/news-room/fact-sheets/detail/antimicrobial-resistance
11. Croxen MA, Law RJ, Scholz R, Keeney KM, Wlodarska M, Finlay BB. Recent advances in understanding enteric pathogenic Escherichia coli. Clin Microbiol Rev. 2013;26(4):822-80. doi:10.1128/CMR.00022-13.
12. Nataro JP, Kaper JB. Diarrheagenic Escherichia coli. Clin Microbiol Rev. 1998;11(1):142-201. doi:10.1128/CMR.11.1.142.
13. Donnenberg MS, Whittam TS. Pathogenesis and evolution of virulence in enteropathogenic and enterohemorrhagic Escherichia coli. J Clin Invest. 2001;107(5):539-48. doi:10.1172/JCI12404.
14. Wang X, Quinn PJ. Lipopolysaccharide: biosynthetic pathway and structure modification. Prog Lipid Res. 2010;49(2):97-107. doi:10.1016/j.plipres.2009.06.002.
15. Foxman B. The epidemiology of urinary tract infection. Nat Rev Urol. 2010;7(12):653-60. doi:10.1038/nrurol.2010.190.
16. World Health Organization. Antimicrobial resistance: global report on surveillance. Geneva: World Health Organization; 2014. Available from: https://www.who.int/publications/i/item/9789241564748
17. Tarr PI, Gordon CA, Chandler WL. Shiga-toxin-producing Escherichia coli and haemolytic uraemic syndrome. Lancet. 2005;365(9464):1073-86. doi:10.1016/S0140-6736(05)71144-2.
18. Johnson JR, Russo TA. Molecular epidemiology of extraintestinal pathogenic (uropathogenic) Escherichia coli. Int J Med Microbiol. 2005;295(6-7):383-404. doi:10.1016/j.ijmm.2005.07.005.
19. World Health Organization. Global action plan on antimicrobial resistance. Geneva: World Health Organization; 2015. Available from: https://www.who.int/publications/i/item/9789241509763
20. Centers for Disease Control and Prevention. Antibiotic resistance threats in the United States, 2019. Atlanta (GA): US Department of Health and Human Services, CDC; 2019.
21. O'Neill J. Tackling drug-resistant infections globally: final report and recommendations. London: Review on Antimicrobial Resistance; 2016.
22. Prestinaci F, Pezzotti P, Pantosti A. Antimicrobial resistance: a global multifaceted phenomenon. Pathog Glob Health. 2015;109(7):309-18. doi:10.1179/2047773215Y.0000000030.
23. Ventola CL. The antibiotic resistance crisis: part 1: causes and threats. P T. 2015;40(4):277-83.
24. Laxminarayan R, Sridhar D, Blaser M, Wang M, Woolhouse M. Achieving global targets for antimicrobial resistance. Science. 2016;353(6302):874-5. doi:10.1126/science.aaf9286.
25. Founou RC, Founou LL, Essack SY. Clinical and economic impact of antibiotic resistance in developing countries: a systematic review and meta-analysis. PLoS One. 2017;12(12). doi:10.1371/journal.pone.0189621.
26. Van Boeckel TP, Brower C, Gilbert M, Grenfell BT, Levin SA, Robinson TP, et al. Global trends in antimicrobial use in food animals. Proc Natl Acad Sci U S A. 2015;112(18):5649-54. doi:10.1073/pnas.1503141112.
27. Klein EY, Van Boeckel TP, Martinez EM, Pant S, Gandra S, Levin SA, et al. Global increase and geographic convergence in antibiotic consumption between 2000 and 2015. Proc Natl Acad Sci U S A. 2018;115(15). doi:10.1073/pnas.1717295115.
Downloads
Published
Issue
Section
License
Copyright (c) 2026 Muhammad Sahal, Zeba Parween Imran, Muhammad Owais Sarfaraz, Syeda Sadaf Akber, Farhan Essa, Muhammad Uneeb
This work is licensed under a Creative Commons Attribution 4.0 International License.
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
