High frequency of multidrug-resistant sequence type 131 subclade C1-M27 among Escherichia coli isolates from urine samples of hospitalized patients in Northern Iran

Urinary tract infections (UTIs) are a major public health concern, with Escherichia coli being the primary pathogen responsible for most cases. Among its clonal lineages, sequence type (ST) 131 is globally prevalent, consisting of clade A, B, and C. Subclade C, especially C1-M27 and C2, is strongly associated with extended-spectrum β-lactamases (ESBLs). This study focused on a subset of E. coli ST131 isolates, aiming to determine their clade and subclade distribution and clonal relationships. A total of 179 non-duplicate E. coli isolates were recovered from urine samples of hospitalized patients with urinary tract infections (UTIs) between 2021 and 2024. ST131 clades were identified by multiplex PCR. The presence of antimicrobial resistance genes ( bla CTX-M-15 , bla CTX-M-14, bla TEM , bla SHV, and bla NDM ), clonal analysis via ERIC-PCR, and O types were confirmed by PCR. Of a total of 179 E. coli strains, 113 (63.1%) were identified as ST131; predominantly O25b (85%) and O16 (15%). PCR-based clade assignment identified all three major ST131 clades, with clade C (55%), followed by clade B (30%) and clade A (15%). Within clade C, subclade C1 was predominant, including the C1-M27 lineage (73%; 38/52). Subclade C2 exhibited the highest proportion of MDR isolates (90%) among clade-specific resistance profiles. ERIC-PCR revealed substantial genetic heterogeneity, grouping isolates into 14 clusters and seven singletons. This study indicates that the high-risk clone E. coli ST131 and its subclade C1 are important contributors to UTIs in our region. Distinct resistance patterns between C1 and C2 highlight ST131’s adaptability, underscoring the need for ongoing genomic surveillance and strict antimicrobial stewardship.