Analysis of Antimicrobial Resistance Patterns in Escherichia coli And Molecular Characterization Across Karachi's Different Districts
TL;DR
Clinical E. coli isolates in Karachi demonstrated substantial resistance to commonly used antibiotics, while selected agents retained comparatively good activity, to support antimicrobial stewardship and evidence-based empirical therapy.
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.