Background The objectives of this study were to define the phylogenetic groups in urinary and commensal E. coli isolated from urine and stool samples of hospitalized children and to determine the pattern of resistance to antibiotics.

Method A total of 100 urine and stool samples were processed during the study period from September 2009 to August 2010. Samples were cultured using standard microbiological techniques. Biochemical testing was used to identify the organisms, E. coli isolates were tested for phylogenic grouping by using triplex PCR and antibiotic susceptibility test done by the Kirby Bauer method.

Results Phylogenic group B2 and D were predominant in urinary samples (54% and 34% respectively). Phylogenic group A, D and B2 were found in decreasing order of 41%, 26% and 16% respectively in the stool samples.

Following resistance patterns were observed in urinary E. coli isolates vs. commensal E. coli, respectively: nitrofurantoin(2% vs. 8%); imipenem (2% vs. 1%); amikacin (4% vs. 3%); ciprofloxacin(8% vs. 5%); nalidixic acid (8% vs. 27%); amoxicillin (16% vs. 20%); ceftazidime (12% vs.7%); amoxicillin-clavulanic acid (14% vs. 9%); gentamicin (22% vs. 12%); cefpodoxime (48% vs. 19%); cefotaxime (45% vs. 27%); co-trimoxazole (61% vs. 82%); and aztreonam (78% vs. 16%); Multi-drug resistance (MDR = resistance in>3 drugs) was most commonly associated with UPEC isolates.

Conclusion Although group B2 E. coli strains were uncommon in stool samples, as they are highly virulent they still represent a potential reservoir for urinary tract infection. Resistance to most antimicrobials is high both in UPEC and commensal strains.