Infant Escherichia coli urinary tract infection: is it associated with meningitis?

OBJECTIVES: Determine the prevalence of coexisting bacterial meningitis (BM) and sterile cerebrospinal fluid (CSF) with raised white cell count relative to age ('pleocytosis') in the presence of Escherichia coli urinary tract infection (UTI), with the addition of CSF E. coli PCR analysis. DESIGN: Single-centre, retrospective cohort study. SETTING: Tertiary paediatric hospital. PARTICIPANTS: Children aged 8 days to 2 years, with a pure growth of E. coli from urine and a CSF sample taken within 48 hours of a positive urine culture between 1 January 2014 and 30 April 2019. MAIN OUTCOME MEASURE: Prevalence of coexisting E. coli BM with UTI, defined as a pure growth E. coli from urine and a CSF culture with pure growth E. coli and/or positive E. coli PCR. RESULTS: 1903 patients had an E. coli UTI, of which 314 (16%) had a CSF sample taken within 48 hours. No cases of coexisting E. coli BM were identified. There were 71 (23%) cases of pleocytosis, 57 (80%) of these had PCR analysis, all of which were E. coli PCR not detected. Patients aged 1-6 months accounted for 72% of all lumbar punctures (LPs). CONCLUSION: The risk of E. coli UTI and coexisting E. coli BM is low. There is potential to reduce the number of routine LPs in infants with a diagnosis of E. coli UTI with the greatest impact in children up to 6 months of age. CSF E. coli PCR can help further reduce post-test probability of BM in the setting of pleocytosis.

Combination of bactericidal antibiotics and inhibitors of Universal stress protein A (UspA): a potential therapeutic alternative against multidrug resistant Escherichia coli in urinary tract infections.

The increasing incidence of multidrug resistant uropathogenic E. coli (MDR-UPEC), the most common opportunistic pathogen in urinary tract infections (UTI) pose a global health problem and demands searching for alternative therapeutics. Antibiotics generate oxidative stress in bacteria which results in overexpression of the universal stress protein, UspA that helps in bacterial survival. An in silico study showed that two compounds ZINC000104153710, and ZINC000000217308 effectively bound bacterial UspA. This study aimed to determine the activity of ZINC000104153710, and ZINC000000217308 against bacterial UspA function in MDR-UPEC in vitro. Twenty-five highly MDR-UPEC were screened against ZINC000104153710, and, ZINC000000217308 either alone or in combination with the bactericidal antibiotics; ciprofloxacin (CIP), ceftazidime(CAZ), gentamicin(GEN) respectively by determining minimum inhibitory concentrations (MICs) using a broth microdilution assay. Additionally, the effect of ZINC000104153710, and ZINC000000217308 in the absence and presence of antibiotics on the bacteria was monitored by bacterial growth curve assays, ROS production, structure of the organism by scanning electron microscopy (FESEM) and quantitating UspA using a western blot technique. A 2-8 fold reduction in MIC values against ZINC000104153710, and ZINC000000217308 was observed against all 25 MDR-UPEC isolates in the presence of antibiotics with no alteration in intracellular ROS production. Discrete changes in cell morphology was evident in bacteria treated with ZINC000104153710 or ZINC000000217308 and antibiotics individually by FESEM compared with untreated control. Reduction in the level of UspA protein in bacteria treated with combination of ZINC000104153710 or ZINC000000217308 with individual antibiotics established their ability to inhibit UspA whose expression was elevated in presence of antibiotics alone. Therefore this study validated ZINC000104153710, and ZINC000000217308 as potent inhibitors of bacterial UspA function and indicated their potential as alternative therapeutics to combat the MDR-UPEC.

Changes of urine isolates of Escherichia coli and Klebsiella pneumoniae biofilm affect monocytes' response.

The Gram negative rods as Escherichia coli and Klebsiella pneumoniae belong to the most common etiology agents of urinary tract infections. The aim of our study was to assess the diversity of biofilm formed in different urinary tract diseases and their impact on monocytes' adherence and activation. The bacteria were obtained from patients with different kidney problems. Some of the patients were after renal transplantation, some of them were not. Changes in the size and granularity of monocytes, as well as their adherence to biofilm, were assessed using FACSVerse flow cytometer after 1 h co-incubation of monocytes and bacterial biofilm in 37 °C. The obtained results were validated against monocytes incubated without bacteria. The isolates from patients with chronic kidney disease formed the most adherent biofilm regardless the presence or absence of inflammatory reaction. Adherence of monocytes also increased during therapy with immunosuppressive agents, but monocytes' response was different when cyclosporine or tacrolimus were used. Additionally the presence of inflammatory reaction in patients with kidney disease modified the monocytes response when the immunosuppressive drugs were used. Considering the obtained results, we conclude that the changes of monocytes' morphology in response to biofilm formed by Gram negative rods could become a tool to detect urinary tract infection, especially in those groups of patients, where the knowledge of ongoing inflammation is important and the standard tools fail to detect it.

Genetic and antimicrobial resistance profiles of non-O157 Shiga toxin-producing Escherichia coli from different sources in Egypt.

BACKGROUND: The Shiga toxin-producing Escherichia coli (STEC) represented a great risk to public health. In this study, 60 STEC strains recovered from broiler and duck fecal samples, cow's milk, cattle beef, human urine, and ear discharge were screened for 12 virulence genes, phenotypic and genotypic antimicrobial resistance, and multiple-locus variable-number tandem-repeat analysis (MLVA). RESULTS: The majority of strains harbored Shiga toxin 1 (stx1) and stx1d, stx2 and stx2e, and ehxA genes, while a minority harbored stx2c subtype and eaeA. We identified 10 stx gene combinations; most of strains 31/60 (51.7%) exhibited four copies of stx genes, namely the stx1, stx1d, stx2, and stx2e, and the strains exhibited a high range of multiple antimicrobial resistance indices. The resistance genes blaCTX-M-1 and blaTEM were detected. For the oxytetracycline resistance genes, most of strains contained tetA, tetB, tetE, and tetG while the tetC was present at low frequency. MLVA genotyping resolved 26 unique genotypes; genotype 21 was highly prevalent. The six highly discriminatory loci DI = 0.9138 are suitable for the preliminary genotyping of STEC from animals and humans. CONCLUSIONS: The STEC isolated from animals are virulent, resistant to antimicrobials, and genetically diverse, thus demands greater attention for the potential risk to human.

Antimicrobial Resistance Trends in Urine Escherichia coli Isolates From Adult and Adolescent Females in the United States From 2011 to 2019: Rising ESBL Strains and Impact on Patient Management.

BACKGROUND: Uncomplicated urinary tract infection (uUTI) is predominantly caused by Escherichia coli, which has increasing antimicrobial resistance (AMR) at the United States (US)-community level. As uUTI is often treated empirically, assessing AMR is challenging, and there are limited contemporary data characterizing period prevalence in the US. METHODS: This was a retrospective study of AMR using Becton, Dickinson and Company Insights Research Database (Franklin Lakes, New Jersey, US) data collected 2011-2019. Thirty-day, nonduplicate Escherichia coli urine isolates from US female outpatients (aged ≥12 years) were included. Isolates were evaluated for nonsusceptibility (intermediate/resistant) to trimethoprim-sulfamethoxazole, fluoroquinolones, or nitrofurantoin, and assessed for extended-spectrum ß-lactamase production (ESBL+) and for ≥2 or ≥3 drug-resistance phenotypes. Generalized estimating equations were used to model AMR trends over time and by US census region. RESULTS: Among 1 513 882 E. coli isolates, the overall prevalence of isolates nonsusceptible to trimethoprim-sulfamethoxazole, fluoroquinolones, and nitrofurantoin was 25.4%, 21.1%, and 3.8%, respectively. Among the isolates, 6.4% were ESBL+, 14.4% had ≥2 drug-resistance phenotypes, and 3.8% had ≥3. Modeling demonstrated a relative average yearly increase of 7.7% (95% confidence interval [CI], 7.2-8.2%) for ESBL+ isolates and 2.7% (95% CI, 2.2-3.2%) for ≥3 drug-phenotypes (both P < .0001). Modeling also demonstrated significant variation in AMR prevalence between US census regions (P < .001). CONCLUSIONS: Period prevalence of AMR among US outpatient urine-isolated E. coli was high, and for multidrug-resistance phenotypes increased during the study period with significant variation between census regions. Knowledge of regional AMR rates helps inform empiric treatment of community-onset uUTI and highlights the AMR burden to physicians.

High prevalence of multidrug resistant ESBL- and plasmid mediated AmpC-producing clinical isolates of Escherichia coli at Maputo Central Hospital, Mozambique.

BACKGROUND: Epidemiological data of cephalosporin-resistant Enterobacterales in Sub-Saharan Africa is still restricted, and in particular in Mozambique. The aim of this study was to detect and characterize extended-spectrum ß-lactamase (ESBL) - and plasmid-mediated AmpC (pAmpC)-producing clinical strains of Escherichia coli at Maputo Central Hospital (MCH), a 1000-bed reference hospital in Maputo, Mozambique. METHODS: A total of 230 clinical isolates of E. coli from urine (n = 199) and blood cultures (n = 31) were collected at MCH during August-November 2015. Antimicrobial susceptibility testing was performed by the disc diffusion method and interpreted according to EUCAST guidelines. Isolates with reduced susceptibility to 3rd generation cephalosporins were examined further; phenotypically for an ESBL-/AmpC-phenotype by combined disc methods and genetically for ESBL- and pAmpC-encoding genes by PCR and partial amplicon sequencing as well as genetic relatedness by ERIC-PCR. RESULTS: A total of 75 isolates with reduced susceptibility to cefotaxime and/or ceftazidime (n = 75) from urine (n = 58/199; 29%) and blood (n = 17/31; 55%) were detected. All 75 isolates were phenotypically ESBL-positive and 25/75 (33%) of those also expressed an AmpC-phenotype. ESBL-PCR and amplicon sequencing revealed a majority of blaCTX-M (n = 58/75; 77%) dominated by blaCTX-M-15. All AmpC-phenotype positive isolates (n = 25/75; 33%) scored positive for one or more pAmpC-genes dominated by blaMOX/FOX. Multidrug resistance (resistance ≥ three antibiotic classes) was observed in all the 75 ESBL-positive isolates dominated by resistance to trimethoprim-sulfamethoxazole, ciprofloxacin and gentamicin. ERIC-PCR revealed genetic diversity among strains with minor clusters indicating intra-hospital spread. CONCLUSION: We have observed a high prevalence of MDR pAmpC- and/or ESBL-producing clinical E. coli isolates with FOX/MOX and CTX-Ms as the major ß-lactamase types, respectively. ERIC-PCR analyses revealed genetic diversity and some clusters indicating within-hospital spread. The overall findings strongly support the urgent need for accurate and rapid diagnostic services to guide antibiotic treatment and improved infection control measures.

Reevaluating the true diagnostic accuracy of dipstick tests to diagnose urinary tract infection using Bayesian latent class analysis.

OBJECTIVE: Previous studies on diagnostic accuracy of dipstick testing for leukocyte esterase (LE) and nitrite to diagnose urinary tract infection (UTI) had used urine culture, which is an imperfect gold standard. Estimates of diagnostic accuracy obtained using the classical gold standard framework might not reflect the true diagnostic accuracy of dipstick tests. METHODS: We used the dataset from a prospective, observational study conducted in the emergency department of a teaching hospital in southern India. Patients with a clinical suspicion of UTI underwent dipstick testing for LE and nitrite, urine microscopy, and urine culture. Based on the results of urine microscopy and culture, UTI was classified into definite, probable, and possible. Patients with microscopic pyuria and a positive urine culture were adjudicated as definite UTI. Unequivocal imaging evidence of emphysematous pyelonephritis or perinephric collections was also considered definite UTI. We estimated the diagnostic accuracy of LE and nitrite tests using the classical analysis (assuming definite UTI as gold standard) and two different Bayesian latent class models (LCMs; 3-tests in 1-population and 2-tests in 2-populations models). RESULTS: We studied 149 patients. Overall, 64 (43%) patients had definite, 76 (51%) had probable, and 2 (1.3%) had possible UTI; 7 (4.6%) had alternate diagnoses. In classical analysis, LE was more sensitive than nitrite (87.5% versus 70.5%), while nitrite was more specific (24% versus 58%). The 3-tests in 1-population Bayesian LCM indicated a substantially better sensitivity and specificity for LE (98.1% and 47.6%) and nitrite (88.2% and 97.7%). True sensitivity and specificity of urine culture as estimated by the model was 48.7% and 73.0%. Estimates of the 2-tests in 2-populations model were in agreement with the 3-tests in 1-population model. CONCLUSIONS: Bayesian LCMs indicate a clinically important improvement in the true diagnostic accuracy of urine dipstick testing for LE and nitrite. Given this, a negative dipstick LE would rule-out UTI, while a positive dipstick nitrite would rule-in UTI in our study setting. True diagnostic accuracy of urine dipstick testing for UTI in various practice settings needs reevaluation using Bayesian LCMs.

Recurrent Escherichia coli Urinary Tract Infection Triggered by Gardnerella vaginalis Bladder Exposure in Mice.

Recurrent urinary tract infections (rUTI) caused by uropathogenic Escherichia coli (UPEC) are common and costly. Previous articles describing models of UTI in male and female mice have illustrated the procedures for bacterial inoculation and enumeration in urine and tissues. During an initial bladder infection in C57BL/6 mice, UPEC establish latent reservoirs inside bladder epithelial cells that persist following clearance of UPEC bacteriuria. This model builds on these studies to examine rUTI caused by the emergence of UPEC from within latent bladder reservoirs. The urogenital bacterium Gardnerella vaginalis is used as the trigger of rUTI in this model because it is frequently present in the urogenital tracts of women, especially in the context of vaginal dysbiosis that has been associated with UTI. In addition, a method for in situ bladder fixation followed by scanning electron microscopy (SEM) analysis of bladder tissue is also described, with potential application to other studies involving the bladder.

The prevalence and mechanism of triclosan resistance in Escherichia coli isolated from urine samples in Wenzhou, China.

BACKGROUND: The widespread application of triclosan contributes to its residual deposition in urine, which provides an environment of long-term exposure to triclosan for the intestinal Escherichia coli. We determined the triclosan and antibiotic resistance characteristics of E. coli strains isolated from urine samples and further investigated the resistance mechanism and molecular epidemic characteristics of triclosan-resistant E. coli isolates. METHODS: A total of 200 non-repetitive E. coli strains were isolated from urine samples and then identified. The minimum inhibitory concentrations (MICs) of triclosan and antibiotics, fabI mutation, efflux pump activity, the expression of 14 efflux pump encoding genes, and epidemiological characteristics were determined by the agar dilution method, polymerase chain reaction (PCR), carbonyl cyanide 3-chlorophenylhydrazone (CCCP) inhibition test, quantitative real-time polymerase chain reaction (RT-qPCR), multilocus sequence typing (MLST), and pulse-field gel electrophoresis (PFGE) for all triclosan-resistant isolates. Furthermore, we also investigated the effect of triclosan exposure in vitro on antibiotic susceptibility and the efflux pump encoding gene expressions of triclosan-susceptible strains via serial passage experiments. RESULTS: Of the 200 E. coli isolates, 2.5% (n = 5) were found to be resistant to triclosan, and multidrug resistance (MDR) and cross-resistance phenotypes were noted for these triclosan-resistant strains. The triclosan-sensitive strains also exhibited MDR phenotypes, probably because of the high resistance rate to AMP, CIP, LVX, and GEN. Gly79Ala and Ala69Thr amino acid changes were observed in the triclosan-resistant strains, but these changes may not mediate resistance of E. coli to triclosan, because mutations of these two amino acids has also been detected in triclosan-susceptible strains. Moreover, except for DC8603, all other strains enhanced the efflux pumps activity. As compared with ATCC 25922, except for fabI, increased expressions were noted for all efflux pump encoding genes such as ydcV, ydcU, ydcS, ydcT, cysP, yihV, acrB, acrD, and mdfA among the studied strains with varying PFGE patterns and STs types. Unexpectedly, 5 susceptible E. coli isolates showed rapidly increasing triclosan resistance after exposure to triclosan in vitro for only 12 days, while MDR or cross-resistance phenotypes and the overexpression of efflux pump genes were recorded among these triclosan-induced resistant isolates. CONCLUSIONS: This is the first study to report that short-term triclosan exposure in vitro increases triclosan resistance in susceptible E. coli isolates. After acquiring resistance, these strains may present MDR or cross-resistance phenotypes. Moreover, triclosan resistance mainly involves the overexpression of fabI and efflux pumps in E. coli isolates.

Virulence and resistance properties of E. coli isolated from urine samples of hospitalized patients in Rio de Janeiro, Brazil - The role of mobile genetic elements.

Extraintestinal pathogenic E. coli (ExPEC) is the most frequent etiological agent of urinary tract infections (UTIs). Particular evolutionary successful lineages are associated with severe UTIs and higher incidences of multidrug resistance. Most of the resistance genes are acquired by horizontal transfer of plasmids and other mobile genetic elements (MGEs), and this process has been associated with the successful dissemination of particular lineages. Here, we identified the presence of MGEs and their role in virulence and resistance profiles of isolates obtained from the urine of hospitalized patients in Brazil. Isolates belonging to the successful evolutionary lineages of sequence type (ST) 131, ST405, and ST648 were found to be multidrug-resistant, while those belonging to ST69 and ST73 were often not. Among the ST131, ST405, and ST648 isolates with a resistant phenotype, a high number of mainly IncFII plasmids was identified. The plasmids contained resistance cassettes, and these were also found within phage-related sequences and the chromosome of the isolates. The resistance cassettes were found to harbor several resistance genes, including blaCTX-M-15. In addition, in ST131 isolates, diverse pathogenicity islands similar to those found in highly virulent ST73 isolates were detected. Also, a new genomic island associated with several virulence genes was identified in ST69 and ST131 isolates. In addition, several other MGEs present in the ST131 reference strain EC958 were identified in our isolates, most of them exclusively in ST131 isolates. In contrast, genomic islands present in this reference strain were only partially present or completely absent in our ST131 isolates. Of all isolates studied, ST73 and ST131 isolates had the most similar virulence profile. Overall, no clear association was found between the presence of specific MGEs and virulence profiles. Furthermore, the interplay between virulence and resistance by acquiring MGEs seemed to be lineage dependent. Although the acquisition of IncF plasmids, specific PAIs, GIs, and other MGEs seemed to be involved in the success of some lineages, it cannot explain the success of different lineages, also indicating other (host) factors are involved in this process. Nevertheless, the detection, identification, and surveillance of lineage-specific MGEs may be useful to monitor (new) emerging clones.

Bacteriuria in Pregnancy in a Danish Contemporary Cohort of Women.

Introduction: The purpose of this study is to describe bacteriuria with regard to the uropathogens found in relation to the frequency of urine culture tests in a contemporary cohort of pregnant Danish women. Methods: A historical cohort study of 24,817 pregnant women registered in the Danish Fetal Medicine Database at Aarhus University Hospital, from 2010 to 2014. Social security numbers were linked to the microbiological database with the registration of 17,233 urine cultures in 8,807 women. Bacteriuria was defined as 1 × 105 CFU/ml, with a maximum of two urinary pathogens. Streptococcus agalactiae (GBS) was included with 1 × 104 CFU/ml. Data are presented as numbers and proportions in percent. Logistic regression on predictors are presented as crude and adjusted odds ratios (ORc/ORa) with 95% confidence intervals (CIs). Results: 42% had a urine sample culture test at the hospital-the majority only once during pregnancy. 96% of all urine culture tests were negative. The bacteriuria incidence was 5.6%. The most frequent uropathogenic bacteria isolated were Escherichia coli (49%), GBS (29%), and Enterococci (10%). We identified subgroups of women with increased likelihood of bacteriuria during pregnancy: age < 25 years, ORa 1.60 (CI 1.26 to 2.02, p < 0.001); age > 34 years, ORa 1.28 (CI 1.01 to 1.61, p = 0.040); Afro-Caribbean origin, ORa 1.872 (CI 1.13 to 3.07, p = 0.014); Asian origin, ORa 2.07 (CI 1.29 to 3.32, p = 0.002); and mixed ethnicity ORa 2.34 (CI 1.23 to 4.46, p = 0.010). Women delivering preterm were more likely to have an episode of bacteriuria during pregnancy OR 2.05 (CI 1.36 to 3.09, p = 0.001). Conclusions: 96% of urine culture tests in pregnant women are negative. Optimized urine sampling may change this. Escherichia coli and GBS are predominant uropathogens. Younger and elder women, certain ethnical groups, and women delivering preterm seem more likely to have bacteriuria during pregnancy.

Antiadhesive natural products against uropathogenic E. coli: What can we learn from cranberry extract?

ETHNOPHARMACOLOGICAL RELEVANCE: Extracts from Cranberry fruits (Vaccinium macrocarpon) are traditionally used against urinary tract infections, mainly due to antiadhesive activity against uropathogenic E. coli (UPEC), but the exact mode of action and compounds, responsible for the activity, are unknown. AIM OF THE STUDY: i. To investigate if cranberry extract acts only by a single component or must be assessed as a multi-active-compound preparation; ii to screen isolated cranberry-related natural products under in vitro conditions to pinpoint natural products with antiadhesive effects against UPEC, followed by in silico calculations (QSAR) to predict potential antiadhesive compounds; iii. investigations by using urine samples from cranberry treated volunteers for evaluation on the bacterial transcriptome and the mannose-binding side of FimH, iv. to investigate if besides Tamm Horsfall Protein induction in the kidney, the extract acts also directly against UPEC. MATERIAL AND METHODS: Antiadhesive activity of 105 compounds was determined by flow cytometric adhesion assay (UPEC UTI89 on T24 bladder cells). Urine samples from 16 volunteers treated with cranberry extract (p.o., 7 days, 900 mg/day) were used for ex vivo testing concerning influence on the bacterial transcriptome (Illumina RNA-seq) and interaction with the mannose binding domain of type-1 fimbriae. RESULTS: i. The antiadhesive effect of cranberry extract cannot be attributed to a single compound or to a single fraction. ii. Unglycosylated flavones and flavonols with bulky substitution of the B ring contribute to the antiadhesive activity. 3'-8″-biflavones and flavolignans (not related to cranberry fruits) were identified as potent antiadhesive compounds against UPEC. iii. QSAR yielded a model with good statistical performance and sufficient internal and external predictive ability. iv. Urine samples from male cranberry-treated volunteers indicated significant interaction with the mannose binding domain of type-1 fimbriae, which correlated with the amount of Tamm-Horsfall Protein in the test samples. v Cranberry extract did not influence the UPEC transcriptome; gene expression of bacterial adhesins (P-, S-fimbrae, curli) was not influenced by the urine samples, while a slight, but non-significant upregulation of type 1 fimbriae was observed. CONCLUSIONS: B-ring substituted flavones and flavonols from cranberry contribute to the antiadhesive activity against UPEC by inhibition of the FimH-mediated interaction with the host cell bladder epithelium.

Rapid label-free detection of intact pathogenic bacteria in situ via surface plasmon resonance imaging enabled by crossed surface relief gratings.

The unique plasmonic energy exchange occurring within metallic crossed surface relief gratings (CSRGs) has recently motivated their use as biosensors. However, CSRG-based biosensing has been limited to spectroscopic techniques, failing to harness their potential for integration with ubiquitous portable electronics. Here, we introduce biosensing via surface plasmon resonance imaging (SPRi) enabled by CSRGs. The SPRi platform is fully integrated including optics and electronics, has bulk sensitivity of 613 Pixel Intensity Unit (PIU)/Refractive Index Unit (RIU), a resolution of 10-6 RIU and a signal-to-noise ratio of ∼33 dB. Finite-Difference Time-Domain (FDTD) simulations confirm that CSRG-enabled SPRi is supported by an electric field intensity enhancement of ∼30 times, due to plasmon resonance at the metal-dielectric interface. In the context of real-world biosensing applications, we demonstrate the rapid (<35 min) and label-free detection of uropathogenic E. coli (UPEC) in PBS and human urine samples for concentrations ranging from 103 to 109 CFU mL-1. The detection limit of the platform is ∼100 CFU mL-1, three orders of magnitude lower than the clinical detection limit for diagnosis of urinary tract infection. This work presents a new avenue for CSRGs as SPRi-based biosensing platforms and their great potential for integration with portable electronics for applications requiring in situ detection.

Assessment of the Urinary Microbiome in Children Younger Than 48 Months.

BACKGROUND: The urinary tract was once thought to be sterile, and little is known about the urinary microbiome in children. This study aimed to examine the urinary microbiome of young children across demographic and clinical factors. METHODS: Children <48 months, undergoing a urinary catheterization for clinical purposes in the Pediatric Emergency Department were recruited and urine samples collected. Detailed demographic and clinical information were recorded. Urine samples underwent DNA extraction and 16S ribosomal RNA gene sequencing, urinalysis and urine culture. RESULTS: Eighty-five children were included; a urinary microbiome was identified in every child. Nine children had Escherichia coli urinary tract infections (UTIs) identified. Those with UTIs had a significantly decreased alpha diversity (t test, P < 0.001) and the composition of the microbiome clustered separately (P = 0.001) compared with those without UTIs. CONCLUSIONS: A urinary microbiome was identified in every child, even neonates. Differences in microbiome diversity and composition were observed in patients with a standard culture positive UTI. The urinary microbiome has just begun to be explored, and the implications on long-term disease processes deserve further investigation.

A snapshot of diversity: Intraclonal variation of Escherichia coli clones as commensals and pathogens.

Whole-genome sequencing has enabled detailed studies on bacterial evolution during infection, but there is limited knowledge on intraclonal variation. In this study, we sought to provide a snapshot of the intraclonal diversity of Escherichia coli as both commensal in the faecal environment and pathogen during urinary tract infection, respectively. This was performed by whole-genome sequencing and analyses of single nucleotide polymorphisms (SNPs) and gene-content variation in ten isolates belonging to the same clone and isolated from rectal swabs or urine samples. We identified only one clone in eight of the nine urines sampled (89 %). In both the commensal and pathogenic state, the within-host diversity was limited with intraclonal SNP diversity of 0-2 non-synonymous SNPs for each clone. The genetic diversity showed variation in gene content in a range of 2-15 genes in total for all clones, including genes positioned on plasmids, and in the K- and O-antigen cluster. The observed SNP- and gene variation shows that sampling of one colony would be enough for surveillance, outbreak investigations and clonal evolution. However, for studies of adaptation during or between colonization and infection, this variation is relevant to consider.

The synergistic triad between microcin, colibactin, and salmochelin gene clusters in uropathogenic Escherichia coli.

A functional synergy was previously demonstrated between microcin, salmochelin and colibactin islands in Escherichia coli strains from B2 phylogroup. We aimed to determine this association prevalence in uropathogenic E. coli, and whether it was predictive of the infection severity in a collection of 225 E. coli strains from urinary samples. The high prevalence of this triad, even if it wasn't correlated with infection severity, suggested that it might not be a virulence factor per se within the urinary tract, but would promote its colonization. This triad would enable the strain to dominate the rectal reservoir with a minimal genetic cost.

Characterization of cefotaxime-resistant urinary Escherichia coli from primary care in South-West England 2017-18.

OBJECTIVES: Third-generation cephalosporin-resistant Escherichia coli from community-acquired urinary tract infections are increasingly reported worldwide. We sought to determine and characterize the mechanisms of cefotaxime resistance employed by urinary E. coli obtained from primary care, over 12 months, in Bristol and surrounding counties in South-West England. METHODS: Cefalexin-resistant E. coli isolates were identified from GP-referred urine samples using disc susceptibility testing. Cefotaxime resistance was determined by subsequent plating onto MIC breakpoint plates. ß-Lactamase genes were detected by PCR. WGS was performed on 225 isolates and analyses were performed using the Center for Genomic Epidemiology platform. Patient information provided by the referring general practices was reviewed. RESULTS: Cefalexin-resistant E. coli (n=900) isolates were obtained from urines from 146 general practices. Following deduplication by patient approximately 69% (576/836) of isolates were cefotaxime resistant. WGS of 225 isolates identified that the most common cefotaxime-resistance mechanism was blaCTX-M carriage (185/225), followed by plasmid-mediated AmpCs (pAmpCs) (17/225), AmpC hyperproduction (13/225), ESBL blaSHV variants (6/225) or a combination of both blaCTX-M and pAmpC (4/225). Forty-four STs were identified, with ST131 representing 101/225 isolates, within which clade C2 was dominant (54/101). Ciprofloxacin resistance was observed in 128/225 (56.9%) of sequenced isolates, predominantly associated with fluoroquinolone-resistant clones ST131 and ST1193. CONCLUSIONS: Most cefalexin-resistant E. coli isolates were cefotaxime resistant, predominantly caused by blaCTX-M carriage. The correlation between cefotaxime resistance and ciprofloxacin resistance was largely attributable to the high-risk pandemic clones ST131 and ST1193. Localized epidemiological data provide greater resolution than regional data and can be valuable for informing treatment choices in the primary care setting.