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Background <p>Urinary tract infections (UTIs), primarily caused by <i>Escherichia coli</i>, pose a global health challenge owing to rising antimicrobial resistance (AMR), particularly carbapenem-resistant (Carb-RT) and extended-spectrum beta-lactamase (ESBL)-producing uropathogenic <i>E. coli</i> (UPEC). This study analyzed AMR trends, virulence determinants, and molecular epidemiology of UPEC isolates from community and hospital settings in Pakistan.</p> Methods and results <p>A total of 2700 urine samples were screened in this study. UPEC isolates underwent antimicrobial susceptibility testing, PCR screening for ESBL/carbapenemase genes (<i>bla</i><sub>CTX−M</sub>, <i>bla</i><sub>TEM</sub>, <i>bla</i><sub>SHV</sub>, and <i>bla</i><sub>NDM</sub>), virulence factor detection, and multilocus sequence typing (MLST) of Carb-RT strains. Among the 390 UPEC isolates, third-generation cephalosporin resistance was higher in hospital (80.2%) than in community (37.9%) strains. Carbapenem resistance varied between community-acquired (CA-UTI: 7.4%) and hospital-acquired (HA-UTI: 34.2%) infections. The ESBL genes included <i>bla</i><sub>CTX−M</sub> (53.3%), <i>bla</i><sub>TEM</sub> (39.7%), and <i>bla</i><sub>SHV</sub> (13.35%), while <i>bla</i><sub>NDM</sub> accounted for 89% of carbapenem resistance. Virulence profiling showed the prevalence of adhesion genes <i>fim</i>H(89.5%), <i>pap</i>C (74.4%), and <i>pap</i>G (58.5%), iron acquisition markers <i>iut</i>A (66.4%) and <i>fyu</i>A (50%), and capsule gene <i>kps</i>MTII (60%). The hemolysin gene <i>hly</i>A was detected in 66.7% of isolates. MLST identified sequence types ST405 (19%), ST10 (18%), ST101 (18%), and ST131 (13%). <i>bla</i><sub>NDM</sub> was associated with major STs, except ST8051, indicating clonal resistance spread.</p> Conclusions <p>The high prevalence of Carb-RT UPEC with ESBLs and virulence genes in Pakistan poses a public health threat. The dominance of ST405 and ST131 highlights the need for genomic surveillance. These findings advocate for revised empirical therapies to combat AMR in healthcare and community settings.</p>

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Dynamics of urinary tract infections: a comprehensive study on antimicrobial susceptibility, virulence profiling and molecular epidemiology of uropathogenic Escherichia coli from Pakistan

  • 期刊论文

  • 发表日期：

    2025年7月10日

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  • Zia Ashraf,
  • Muhammad Hidayat Rasool,
  • Bilal Aslam,
  • Hasan Ejaz,
  • Fatima Mujahid,
  • Mohsin Khurshid

摘要

Background

Urinary tract infections (UTIs), primarily caused by Escherichia coli, pose a global health challenge owing to rising antimicrobial resistance (AMR), particularly carbapenem-resistant (Carb-RT) and extended-spectrum beta-lactamase (ESBL)-producing uropathogenic E. coli (UPEC). This study analyzed AMR trends, virulence determinants, and molecular epidemiology of UPEC isolates from community and hospital settings in Pakistan.

Methods and results

A total of 2700 urine samples were screened in this study. UPEC isolates underwent antimicrobial susceptibility testing, PCR screening for ESBL/carbapenemase genes (blaCTX−M, blaTEM, blaSHV, and blaNDM), virulence factor detection, and multilocus sequence typing (MLST) of Carb-RT strains. Among the 390 UPEC isolates, third-generation cephalosporin resistance was higher in hospital (80.2%) than in community (37.9%) strains. Carbapenem resistance varied between community-acquired (CA-UTI: 7.4%) and hospital-acquired (HA-UTI: 34.2%) infections. The ESBL genes included blaCTX−M (53.3%), blaTEM (39.7%), and blaSHV (13.35%), while blaNDM accounted for 89% of carbapenem resistance. Virulence profiling showed the prevalence of adhesion genes fimH(89.5%), papC (74.4%), and papG (58.5%), iron acquisition markers iutA (66.4%) and fyuA (50%), and capsule gene kpsMTII (60%). The hemolysin gene hlyA was detected in 66.7% of isolates. MLST identified sequence types ST405 (19%), ST10 (18%), ST101 (18%), and ST131 (13%). blaNDM was associated with major STs, except ST8051, indicating clonal resistance spread.

Conclusions

The high prevalence of Carb-RT UPEC with ESBLs and virulence genes in Pakistan poses a public health threat. The dominance of ST405 and ST131 highlights the need for genomic surveillance. These findings advocate for revised empirical therapies to combat AMR in healthcare and community settings.