Supplemental files_Paul Katongole et al.XLSX

<b>Introduction</b>:<b> </b>Uropathogenic <i>E.coli</i> (UPEC) remains the most common cause of urinary tract infections (UTIs). They account for over 80-90% of all community acquired and 30-50% of all hospital acquired UTIs. <i>E.coli</i> strains have been found to belong to evolutionary origins known as phylogenetic groups. In 2013, Clermont classified <i>E. coli </i>strains into eight phylogenetic groups using quadruplex PCR method. The aim of this study was to identify the phylogenetic groups of <i>UPEC </i>strains in Uganda<i> </i>using Clermont’s quadruplex PCR method and to assess their antibiotic susceptibility patterns in Uganda. <b>Methods: </b>In this cross-sectional study, 140 stored Uropathogenic <i>E.coli </i>isolates from the clinical microbiology laboratory, department of Medical Microbiology, College of Health sciences Makerere University were subjected to phylogenetic typing by a quadruplex PCR method. Antimicrobial susceptibility testing was performed by disk diffusion method according to CLSI 2014. Phenotypic detection of ESBL, AmpC and Carbapenemases was done according to CLSI guidelines and Laboratory SOPs. <b>Results: </b>Phylogenetic group B2 (40%) was the most predominant followed by A (6.23%), Clade I and II (5%), D and E (each 2.14%), B1 (1.43%) and F and C (each 0.71%). The most common resistant antibiotic was Trimethoprim sulphamethoxazole (90.71%) and the least was imipenem (1.43%). 73.57% of isolates were multiple drug resistant (MDR). Antibiotic resistance was mainly detected in phylogenetic group B2 (54%). <b>Conclusions: </b>Our findings showed the high prevalence of MDR <i>E. coli </i>isolates with dominance of phylogenetic group B2. About 9 % of <i>E. coli </i>isolates belonged to the newly described phylogroups C, E, F, and clade I and II