Escherichia coli is the most common cause of urinary tract infection (UTI). The pathogenic isolates are becoming increasingly resistant to antibiotics; with a worldwide dissemination of resistant sequence types (ST). We characterized three different uropathogenic E. coli populations, from non-hospitalized patients to describe the genetic kinship between resistant and susceptible isolates. We studied the populations by use of multi-locus sequence typing (MLST) and abbreviated-multi locus variable number of tandem repeat analysis (a-MLVA). Urine samples submitted for testing, by general practitioners, were identified at Dept. of Clinical Microbiology at Hvidovre Hospital, Denmark, from Oct. 2011 to July 2012. We included 94 fully susceptible, 94 resistant (non-ESBL) and 98 Extended Spectrum Beta-lactamases- (ESBL)-producing E. coli isolates. The ESBL population was dominated vastly by ST131 (51 %), ST38 (9 %) and ST69 (6 %). In the resistant group ST69 (18 %), ST73 (11 %) and ST131 (15 %) were the largest clusters. In the susceptible population more STs and a-MLVA codes were identified compared to the other groups and ST73 and ST95 were found as the only clusters with 16 % and 6 %, respectively. Ninety-eight per cent of the ESBL-producing E. coli isolates were CTX-M-producers. ST131 dominated the population of community-associated uropathogenic ESBL-producing E. coli, but was less frequent among non-ESBL-producing E. coli. The fully susceptible E. coli population was a much more diverse group than the resistant and ESBL-producing E. coli populations. Overall, these findings suggest that dominant ESBL-producing lineages are derived from UPEC lineages already established in the general UPEC population.

Studies on human and mouse gastrointestinal microbiota have correlated the composition of the microbiota to a variety of diseases, as well as proved it vital to prevent colonization with resistant bacteria, a phenomenon known as colonization resistance. Antibiotics dramatically modify the gut community and there are examples of how antibiotic usage lead to colonization with resistant bacteria [e.g., dicloxacillin usage selecting for ESBL-producing E. coli carriage], as shown by Hertz et al. Here, we investigated the impact of five antibiotics [cefotaxime, cefuroxime, dicloxacillin, clindamycin, and ciprofloxacin] on the intestinal microbiota in mice. Five different antibiotics were each given to groups of five mice. The intestinal microbiotas were profiled by use of the IS-pro analysis; a 16S–23S rDNA interspace [IS]-region-based profiling method. For the mice receiving dicloxacillin and clindamycin, we observed dramatic shifts in dominating phyla from day 1 to day 5. Of note, diversity increased, but overall bacterial load decreased. For ciprofloxacin, cefotaxime, and cefuroxime there were few overall changes. We speculate that antibiotics with efficacy against the abundant anaerobes in the gut, particularly Bacteroidetes, can in fact be selected for resistant bacteria, disregarding the spectrum of activity.

Background: Most Gram-negative community-acquired and nosocomial infections are caused by Escherichia coli and Klebsiella pneumoniae, among which increasing resistance due to extended-spectrum β-lactamase (ESBL) is a major problem. We present data from the first Danish nationwide prevalence study on ESBL-producing E. coli, K. pneumoniae, and Proteus mirabilis in blood and urine cultures from hospitals and the community. Methods: During September and October 2007, 13 of 15 Danish departments of clinical microbiology collected data and strains. Confirmatory ESBL test-positive isolates were sent to a central laboratory for species and ESBL-phenotype confirmation, extended susceptibility testing, phylogenetic grouping of E. coli strains, and ESBL gene characterization. Results: During the study, blood samples from 18,259 patients and urine samples from 47,504 patients were subjected to culture. Among 14,674 cultured isolates, 352 were confirmed to be ESBL-producers. Thus, the crude ESBL prevalence was 2.4% (range 1.5% of E. coli in community urine to 6.6% of K. pneumoniae in hospital urine). An average of 7.2 ESBL-producers per 100,000 consumed bed-days was calculated. Of the 352 reported ESBL-producers, 205 E. coli, 73 K. pneumoniae, and 1 P. mirabilis, were available for testing. CTX-M enzymes dominated, both in hospitals and in the community, occurring in 92% of E. coli and 88% of K. pneumoniae, and with CTX-M-15 constituting 60% and 77%, respectively. Conclusions: Compared to 2003 data the ESBL prevalence in Denmark has increased significantly. In the ESBL-producers, reduced susceptibility towards both gentamicin and ciprofloxacin was seen among 43% E. coli and 55% K. pneumoniae, leaving clinicians in these cases with only a carbapenem for the treatment of serious infections. Part of this study was presented at the 20^th European Congress of Clinical Microbiology and Infectious Diseases, abstract P-1617.

The purpose of the study was to evaluate how use of antibiotics precedes the presence of ESBL-producing E.coli in general practice. The authors performed a triple-case-control study where three case groups were individually compared to a single control group of uninfected individuals. Urine samples were prospectively collected and retrospective statistical analyses were done. This study included 98 cases with urinary tract infection (UTI) caused by ESBL-producing E. coli, 174 with antibiotic-resistant (non-ESBL) E. coli, 177 with susceptible E. coli and 200 with culture negative urine samples. Case groups had significantly higher use of antibiotics than the control group within 30 days before infection (p < 0.0001). The ESBL group had significantly more hospital admissions than the other case groups (p < 0.05). Hospital admission was an independent risk factor for community onset UTI by ESBL-producing E. coli. Exposure to antibiotics was a risk factor for UTI with E. coli, while prior antibiotic usage was not an indisputable predictor for infection with ESBL-producing E.coli in general practice.

The ability of different antibiotics to select for extended-spectrum β-lactamase (ESBL)-producing Escherichia coli remains a topic of discussion. In a mouse intestinal colonization model, we evaluated the selective abilities of nine common antimicrobials (cefotaxime, cefuroxime, dicloxacillin, clindamycin, penicillin, ampicillin, meropenem, ciprofloxacin, and amdinocillin) against a CTX-M-15-producing E. coli sequence type 131 (ST131) isolate with a fluoroquinolone resistance phenotype. Mice (8 per group) were orogastrically administered 0.25 ml saline with 10 ⁸ CFU/ml E. coli ST131. On that same day, antibiotic treatment was initiated and given subcutaneously once a day for three consecutive days. CFU of E. coli ST131, Bacteroides , and Gram-positive aerobic bacteria in fecal samples were studied, with intervals, until day 8. Bacteroides was used as an indicator organism for impact on the Gram-negative anaerobic population. For three antibiotics, prolonged colonization was investigated with additional fecal CFU counts determined on days 10 and 14 (cefotaxime, dicloxacillin, and clindamycin). Three antibiotics (cefotaxime, dicloxacillin, and clindamycin) promoted overgrowth of E. coli ST131 ( P < 0.05). Of these, only clindamycin suppressed Bacteroides , while the remaining two antibiotics had no negative impact on Bacteroides or Gram-positive organisms. Only clindamycin treatment resulted in prolonged colonization. The remaining six antibiotics, including ciprofloxacin, did not promote overgrowth of E. coli ST131 ( P > 0.95), nor did they suppress Bacteroides or Gram-positive organisms. The results showed that antimicrobials both with and without an impact on Gram-negative anaerobes can select for ESBL-producing E. coli , indicating that not only Gram-negative anaerobes have a role in upholding colonization resistance. Other, so-far-unknown bacterial populations must be of importance for preventing colonization by incoming E. coli .

Objectives: To compare the therapeutic effect of pivmecillinam and other common oral antibiotics for community-acquired urinary tract infections (UTIs) caused by Extended Spectrum Beta-Lactamase (ESBL)- or non-ESBL-producing Escherichia coli.
Methods: Retrospective cohort study from 2010 to mid-2016 with data from the regional Laboratory Database and three national databases on antibiotic prescriptions, hospital admission, and mortality, respectively. Primary care patients (≥18 years) empirically treated for UTI caused by non-ESBL- or ESBL-producing E. coli (non-ESBL and ESBL E. coli) were included. Seven antibiotics, commonly used empirically for UTI, were investigated. Treatment failure measured as the redemption of a new antibiotic prescription or admission to hospital due to UTI. Cox proportional hazard ratios and adjusted risk differences along with 95% confidence intervals were calculated for 14 and 30 days, respectively. Results: Thirty-six thousand two hundred and ninety-three (95.7%) and 1624 (4.3%) cases were included in the non-ESBL and ESBL groups, respectively. Male sex, high age, ESBL production, and resistance to empirical therapy were found to independently increase the risk of treatment failure. Compared to pivmecillinam, ciprofloxacin had significantly lower treatment failure for non-ESBL E. coli, but significantly higher treatment failure in ESBL E. coli. There was no significant difference between nitrofurantoin and pivmecillinam. Conclusion: All antibiotics seem to have a higher risk of treatment failure for UTI caused by ESBL-producing E. coli as compared to non-ESBL-producing E. coli. At present, nitrofurantoin and pivmecillinam seem to be the most relevant orally available therapies for E. coli UTI. Local resistance data should guide which of the two that should be the contemporary first-line option.