Escherichia coli is a major causative agent of extra-intestinal infections and highly clonal. Our goal was to use the newly developed septatyping method to determine the clonal structure of E. coli population in routinely collected urine samples from a clinical microbiology lab, evaluate the patterns of antibiotic resistance of individual clones, their temporal stability and prevalence in samples with clinically significant load. Isolated E. coli were assigned a clonotype using septatyping, which is a quantitative real-time PCR test consisting of seven reactions that identify the absence or presence of clone-specific SNP’s in two loci – fumC and fimH. The eighth reaction is a reference control, detecting E. coli specific loci, uidA. We identified 40 (out of 128 possible) clonotypes from 647 E. coli isolates. The most prevalent was the 561 clonotype, aka H30 clone (114 isolates, 17.6%), followed by clones 571, 760, 620 and 271 (7-8% of isolates per clone). Clonal structure of E. coli remained relatively stable over the 3-year period (less than 2% difference). Furthermore, clones varied significantly in their antibiotic susceptibility profiles. For example, 561 (H30) is a highly multi-drug resistant clone, whereas 760 and 530 are highly susceptible to all tested antibiotics. Such differential susceptibility can be extremely useful for choosing the proper course of treatment for the patient. When we compared the clonal structure of E. coli isolated from samples with low bacterial load (<10⁴ cfu/ml, usually discarded as contamination) and high load (≥10⁴, clinically significant), most of the clonotypes were evenly split between the two groups. The fact that the same clones can grow both to low and to high numbers in patients’ urine indicates that the cutoff of 10⁴ cfu/ml may need revision as a clinically significant level.

Escherichia coli (E. coli) is the major causative agent of urinary tract infections (UTI) and is highly clonal. One of the major clones is a multidrug-resistant H30 clone, which has spread worldwide and is almost exclusively resistant to fluoroquinolones, accounting for 50% of all ciprofloxacin-resistant uropathogenic E. coli. The goal of this study was to determine if H30 clone is prevalent among fecal E. coli, which might explain its high occurrence in extraintestinal infections. We obtained 555 fecal samples from female volunteers and screened them for the H30 clone using a multiplex quantitative PCR test, ST200. This test contains primers for uidA (E. coli specific loci), and primer-probe combinations for ST131, ST69, and fimH30. The combination of positive ST131 and fimH30 probes identifies the H30 clone. The results of fecal screenings were compared to the data on H30 found among urine isolates from women with UTIs. Out of 555 fecal samples, 531 (96%) had detectable presence of E. coli ranging from 10⁴ to 10⁷ cfu/ml. H30 clone was found only in 25/555 samples (4.5%), while it was significantly more prevalent in urine (7.7%, P=0.008). The prevalence of H30 clone in younger (<50 years old) versus older (>50 years old) women didn’t differ significantly for fecal samples (6.1% vs 8.1%, P=0.24). However H30 was significantly more prevalent in older women’s urine samples (5.9% vs 8.6 %, P=0.014). Overall, 44/555 (7.9 %) fecal samples contained ciprofloxacin-resistant isolates. Similarly to urine, H30 clone accounted for almost half of isolates (21/44, 47.7 %),  although resistance of fecal H30 isolates to fluorquinolones was slightly decreased in comparison to urine H30 isolates (84% vs 95%). In summary, the H30 clone preferentially causes UTIs in elderly women and is the major reservoir of ciprofloxacin-resistant E. coli in gut microflora, potentially leading to higher infection rates due to mismatched antibiotic therapy.