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Uropathogenic <jats:italic>E. coli<\/jats:italic> causes 80% of uncomplicated community acquired UTIs, particularly in pre-menopausal women. Considering this high prevalence and the potential to spread antimicrobial resistant genes, the current study was conducted to investigate the presence of clinically important strains of <jats:italic>E. coli<\/jats:italic> in Pakistani women having uncomplicated cystitis and pyelonephritis. Women belonging to low-income groups were exclusively included in the study. Seventy-four isolates from urine samples were processed, phylotyped, and screened for the presence of two Single Nucleotide Polymorphisms (SNPs) particularly associated with a clinically important clonal group A of <jats:italic>E. coli<\/jats:italic> (CgA) followed by antibiotic susceptibility testing and genome sequence analysis.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Phylogroup B2 was most prevalent in patients and 44% of isolates were positive for the presence of CgA specific SNPs in Fumarate hydratase and DNA gyrase subunit B genes. Antibiotic susceptibility testing showed widespread resistance to trimethoprim-sulfamethoxazole and extended-spectrum beta-lactamase production. The infection analysis revealed the phylogroup B2 to be more pathogenic as compared to the other groups. The genome sequence of <jats:italic>E. coli<\/jats:italic> strain U17 revealed genes encoding virulence, multidrug resistance, and host colonization mechanisms.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Our research findings not only validate the significant occurrence of multidrug-resistant clonal group A <jats:italic>E. coli<\/jats:italic> (CgA) in premenopausal Pakistani women suffering from cystitis and pyelonephritis but also reveal the presence of genes associated withvirulence, and drug efflux pumps. The detection of highly pathogenic, antimicrobial-resistant phylogroup B2 and CgA <jats:italic>E. coli<\/jats:italic> strains is likely to help in understanding the epidemiology of the pathogen and may ultimately help to reduce the impact of these strains on human health. Furthermore, the findings of this study will particularly help to reduce the prevalence of uncomplicated UTIs and the cost associated with their treatment in women belonging to low-income groups.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-024-03221-8","type":"journal-article","created":{"date-parts":[[2024,3,7]],"date-time":"2024-03-07T05:01:28Z","timestamp":1709787688000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Multidrug resistance among uropathogenic clonal group A E. 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