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Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant in situ populations.

ABSTRACT: Urinary tract infections (UTIs) are one of the most commonly acquired bacterial infections in humans, and uropathogenic Escherichia coli strains are responsible for over 80% of all cases. The standard method for identification of uropathogens in clinical laboratories is cultivation, primarily using solid growth media under aerobic conditions, coupled with morphological and biochemical tests of typically a single isolate colony. However, these methods detect only culturable microorganisms, and characterization is phenotypic in nature. Here, we explored the genotypic identity of communities in acute uncomplicated UTIs from 50 individuals by using culture-independent amplicon pyrosequencing and whole-genome and metagenomic shotgun sequencing. Genus-level characterization of the UTI communities was achieved using the 16S rRNA gene (V8 region). Overall UTI community richness was very low in comparison to other human microbiomes. We strain-typed Escherichia-dominated UTIs using amplicon pyrosequencing of the fimbrial adhesin gene, fimH. There were nine highly abundant fimH types, and each UTI sample was dominated by a single type. Molecular analysis of the corresponding clinical isolates revealed that in the majority of cases the isolate was representative of the dominant taxon in the community at both the genus and the strain level. Shotgun sequencing was performed on a subset of eight E. coli urine UTI and isolate pairs. The majority of UTI microbial metagenomic sequences mapped to isolate genomes, confirming the results obtained using phylogenetic markers. We conclude that for the majority of acute uncomplicated E. coli-mediated UTIs, single cultured isolates are diagnostic of the infection. IMPORTANCE In clinical practice, the diagnosis and treatment of acute uncomplicated urinary tract infection (UTI) are based on analysis of a single bacterial isolate cultured from urine, and it is assumed that this isolate represents the dominant UTI pathogen. However, these methods detect only culturable bacteria, and the existence of multiple pathogens as well as strain diversity within a single infection is not examined. Here, we explored bacteria present in acute uncomplicated UTIs using culture-independent sequence-based methods. Escherichia coli was the most common organism identified, and analysis of E. coli dominant UTI samples and their paired clinical isolates revealed that in the majority of infections the cultured isolate was representative of the dominant taxon at both the genus and the strain level. Our data demonstrate that in most cases single cultured isolates are diagnostic of UTI and are consistent with the notion of bottlenecks that limit strain diversity during UTI pathogenesis.

SUBMITTER: Willner D

PROVIDER: S-EPMC3940035 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

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Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant in situ populations.

Willner Dana D Low Serene S Steen Jason A JA George Narelle N Nimmo Graeme R GR Schembri Mark A MA Hugenholtz Philip P

mBio 20140225 2

Urinary tract infections (UTIs) are one of the most commonly acquired bacterial infections in humans, and uropathogenic Escherichia coli strains are responsible for over 80% of all cases. The standard method for identification of uropathogens in clinical laboratories is cultivation, primarily using solid growth media under aerobic conditions, coupled with morphological and biochemical tests of typically a single isolate colony. However, these methods detect only culturable microorganisms, and ch ...[more]

PMID: 24570371

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Project description:BackgroundMost diagnostic tests for acute uncomplicated urinary tract infections (UTIs) have been previously studied in so-called single-test evaluations. In practice, however, clinicians use more than one test in the diagnostic work-up. Since test results carry overlapping information, results from single-test studies may be confounded. The primary objective of the Amsterdam Cystitis/Urinary Tract Infection Study (ACUTIS) is to determine the (additional) diagnostic value of relevant tests from patient history and laboratory investigations, taking into account their mutual dependencies. Consequently, after suitable validation, an easy to use, multivariable diagnostic rule (clinical index) will be derived.MethodsWomen who contact their GP with painful and/or frequent micturition undergo a series of possibly relevant tests, consisting of patient history questions and laboratory investigations. Using urine culture as the reference standard, two multivariable models (diagnostic indices) will be generated: a model which assumes that patients attend the GP surgery and a model based on telephone contact only. Models will be made more robust using the bootstrap. Discrimination will be visualized in high resolution histograms of the posterior UTI probabilities and summarized as 5th, 10th, 25th 50th, 75th, 90th, and 95th centiles of these, Brier score and the area under the receiver operating characteristics curve (ROC) with 95% confidence intervals. Using the regression coefficients of the independent diagnostic indicators, a diagnostic rule will be derived, consisting of an efficient set of tests and their diagnostic values. The course of the presenting complaints is studied using 7-day patient diaries. To learn more about the natural history of UTIs, patients will be offered the opportunity to postpone the use of antibiotics.DiscussionWe expect that our diagnostic rule will allow efficient diagnosis of UTIs, necessitating the collection of diagnostic indicators with proven added value. GPs may use the rule (preferably after suitable validation) to estimate UTI probabilities for women with different combinations of test results. Finally, in a subcohort, an attempt is made to identify which indicators (including antibiotic treatment) are useful to prognosticate recovery from painful and/or frequent micturition.

Project description:Objective To investigate whether symptomatic treatment with non-steroidal anti-inflammatory drugs (NSAIDs) is non-inferior to antibiotics in the treatment of uncomplicated lower urinary tract infection (UTI) in women, thus offering an opportunity to reduce antibiotic use in ambulatory care.Design Randomised, double blind, non-inferiority trial.Setting 17 general practices in Switzerland.Participants 253 women with uncomplicated lower UTI were randomly assigned 1:1 to symptomatic treatment with the NSAID diclofenac (n=133) or antibiotic treatment with norfloxacin (n=120). The randomisation sequence was computer generated, stratified by practice, blocked, and concealed using sealed, sequentially numbered drug containers.Main outcome measures The primary outcome was resolution of symptoms at day 3 (72 hours after randomisation and 12 hours after intake of the last study drug). The prespecified principal secondary outcome was the use of any antibiotic (including norfloxacin and fosfomycin as trial drugs) up to day 30. Analysis was by intention to treat.Results 72/133 (54%) women assigned to diclofenac and 96/120 (80%) assigned to norfloxacin experienced symptom resolution at day 3 (risk difference 27%, 95% confidence interval 15% to 38%, P=0.98 for non-inferiority, P<0.001 for superiority). The median time until resolution of symptoms was four days in the diclofenac group and two days in the norfloxacin group. A total of 82 (62%) women in the diclofenac group and 118 (98%) in the norfloxacin group used antibiotics up to day 30 (risk difference 37%, 28% to 46%, P<0.001 for superiority). Six women in the diclofenac group (5%) but none in the norfloxacin group received a clinical diagnosis of pyelonephritis (P=0.03).Conclusion Diclofenac is inferior to norfloxacin for symptom relief of UTI and is likely to be associated with an increased risk of pyelonephritis, even though it reduces antibiotic use in women with uncomplicated lower UTI.Trial registration ClinicalTrials.gov NCT01039545.

Project description:BACKGROUND:Uncomplicated urinary tract infections (UTIs) can often be diagnosed based solely on symptoms and should be treated with a short course of narrow spectrum antibiotics. However, clinicians often order urine analyses and prescribe long courses of broad spectrum antibiotics. OBJECTIVE:The objectives of our study are: 1) Understand how primary care providers and residents clinically approach UTIs and 2) to understand specific opportunities, based on provider type, to target future antibiotic stewardship interventions. DESIGN AND PARTICIPANTS:We conducted semi-structured qualitative interviews of community primary care providers (n = 15) and internal medicine residents (n = 15) in St. Louis, Missouri from 2018-2019. A 5-point Likert scale was used to evaluate participant preferences for possible interventions. Interviews were transcribed, de-identified, and coded by two independent researchers using a combination inductive and deductive approach. KEY RESULTS:Several common themes emerged. Both providers and residents ordered urine tests to "confirm" presence of urinary tract infections. Antibiotic prescription decisions were often based on historical practice and anecdotal experience rather than local susceptibility data or clinical practice guidelines. Community providers were more comfortable treating patients over the phone than residents and tended to prescribe longer courses of antibiotics. Both community providers and residents voiced frustrations with guidelines being difficult to easily incorporate due to length and extraneous information. Preferences for receiving and incorporating guidelines into practice varied. Both groups felt benchmarking would improve prescribing practices but had reservations about implementation. Community providers preferred pragmatic clinical decision support systems and nurse triage algorithms. Residents preferred order sets. CONCLUSIONS:Significant opportunities exist to optimize urinary tract infection management among residents and community providers. Multifaceted interventions that include provider education, synthesis of guidelines, and pragmatic clinical decision support systems are needed to improve antibiotic prescribing and diagnostic testing; optimal interventions to improve UTI management may vary based on provider training level.

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Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant in situ populations.

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Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant in situ populations.

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