Search Results (284)

Background: Unambiguous clinical interpretation of PCR results for urinary tract infections (UTIs) remains a challenge. Here we compare and correlate multiplex qPCR results (quantification cycle values) with traditional microbial culture results (colony forming units) for clinical samples. Methods: Serial dilutions [10⁸ to 10⁰ colony forming units (CFU)/mL] were performed on five Gram-negative and two Gram-positive UTI-causing bacterial pathogens. For each dilution, quantitative cultures on solid media to confirm CFU/mL values and a real-time PCR UTI panel employing a nanofluidic Open Array^TM platform producing quantification cycle (Cq) values were performed. Cq values were correlated with CFU/mL values, generating a semi-quantitative interpretive scale for clinical samples. The clinical utility of the scale was then assessed using PCR and culture data from 168 clinical urine samples. Results: For Gram-negative bacteria, Cq values of <23, 23 to 28, and >28 corresponded with ≥10⁵ CFU/mL, <10⁵ CFU/mL and negative cultures, respectively. For Gram-positive bacteria, Cq values of <26, 26 to 30, and >30 corresponded with ≥10⁵ CFU/mL, <10⁵ CFU/mL and negative cultures, respectively. Among 168 urine specimens (including 138 Gram-negative and 30 Gram-positive bacteria), there was 83.3% agreement (n = 140/168) and 16.6% non-agreement (n = 28/168) between culture CFU/mL and qPCR Cq. Gram-negative bacteria had higher agreement (87.6%, 121/138) than Gram-positive bacteria (63.3%, 19/30). Conclusions: This study demonstrates that qPCR Cq results can be directly correlated with traditional urine quantitative culture results and reliably identify the clinically relevant cutoff of 10⁵ CFU/mL for detected uropathogens. Full article

The discovery of a resident urinary microbiome has significantly altered the understanding of urolithiasis, expanding its etiology beyond metabolic and dietary factors to include microbial contributions. This review highlights how specific uropathogens—particularly Proteus mirabilis, Klebsiella pneumoniae, and Escherichia coli—facilitate stone formation through mechanisms such as urease activity, citrate degradation, urine alkalinization, biofilm development, and inflammatory signaling. We critically examine how antibiotic therapies, while essential for treating urinary tract infections (UTIs), disrupt microbial homeostasis by depleting beneficial taxa like Lactobacillus and enabling colonization by lithogenic and resistant strains. Recurrent or broad-spectrum antibiotic use is linked to persistent dysbiosis and increased risk of stone recurrence. Additionally, this paper explores emerging microbiome-targeted strategies—such as probiotics, prebiotics, bacteriotherapy, and precision antimicrobials—as potential interventions to restore microbial balance and mitigate stone risk. Recognizing the urinary microbiome as a therapeutic target opens new avenues for personalized, microbiota-conscious strategies in the prevention and management of kidney stone disease. Full article

Background/Objectives: Alternative therapies for urinary tract infections (UTIs) have been explored, but their efficacy remains inconsistent. With rising antibiotic resistance, this study aimed to evaluate simplified postbiotic formulations derived from heat-killed probiotics for long-term protection against primary and recurrent UTIs in a murine model. Methods: We compared a multi-strain (seven-strain) versus a single-strain postbiotic in preventing Escherichia coli-induced UTIs and recurrent polymicrobial UTIs, assessed protection persistence after treatment discontinuation, and established a novel sustained UTI model via intravesical co-inoculation of three uropathogens. Mice were allocated to three experimental groups: a placebo group (PBS), Postbiotic I group (a seven-strain heat-killed probiotic formulation), and Postbiotic II group (a single-strain heat-killed probiotic). After two weeks of treatment, mice were challenged with uropathogenic E. coli (UPEC) and treated for seven days. Following a 14-day washout and bacterial clearance, they were rechallenged with multidrug-resistant UPEC, Klebsiella pneumoniae, and Staphylococcus pseudintermedius. Results: Both postbiotics significantly accelerated bacterial clearance in primary UTIs (p < 0.05). In recurrent UTIs, placebo-treated mice exhibited persistent bacteriuria, while Postbiotic I maintained a significantly higher sterile urine rate (50–80%, p < 0.01) post-treatment. Histopathological analysis confirmed reduced bladder and kidney inflammation (p < 0.05) with Postbiotic I. Conclusions: These findings demonstrate the superior efficacy of Postbiotic I in mitigating UTIs, with sustained protection post-treatment, supporting its potential as a long-term, non-antibiotic strategy. Additionally, our reproducible chronic UTI model, achieved through the co-inoculation of three uropathogens, provides a valuable tool for future research on chronic UTI pathogenesis and treatment. Full article

Antibiotics are frequently used in the poultry industry, which has led to the emergence of bacterial strains that are resistant to antimicrobial treatments. The main objectives of this research were to conduct a multimodal risk assessment, to determine the extent of contamination of chicken meat with Escherichia coli, assess the prevalence of strains resistant to extended-spectrum cephalosporins (ESC), and characterise the genes associated with resistance and virulence. A standardised procedure involving enrichment in buffered peptone water and isolation of E. coli on MacConkey agar was carried out on 100 chicken carcasses. Subsequently, the sensitivity of the strains was tested against 21 antibiotic discs. Additionally, ESBL production was detected using a double synergy test. Specific PCRs were employed to identify resistance to critical antibiotics in human medicine (such as cephalosporins, carbapenems, fluoroquinolones, and colistin), as well as the presence of virulence genes. The contamination rate of chicken meat with E. coli was 82%. The prevalence of ESC-resistant isolates was 91.2%. Furthermore, 76.5% of the isolates exhibited ESBL production, with the different beta-lactamase genes (bla_CTXM, bla_TEM, and bla_SHV). The mcr-1 gene, associated with colistin resistance, was detected in four strains (5.9%). Some isolates also carried resistance genes such as sul1, sul2, sul3, tetA, tetB, qnrB, and qnrS. In addition, several virulence genes were detected. In our study, we were able to link the expression of AMR to the iron metabolic regulatory elements using a multimodal machine learning approach; this mechanism could be targeted to mitigate the bacteria virulence and resistance. The high prevalence of ESBL-producing and multi-resistant E. coli strains in poultry presents significant human health risks, with the focus on antibiotic-resistant uropathogenic strains since poultry meat could be an important source of uropathogenic strains, underscoring the danger of hard-to-treat urinary tract infections, stressing the need for controlled antibiotic use and thorough monitoring. Full article

Urinary tract infections (UTIs) are among the most prevalent infectious diseases in older women, especially those over 65 years of age. Physiological changes related to aging, comorbidities, and frequent use of medical devices such as urinary catheters increase susceptibility. Increasing antimicrobial resistance further complicates treatment strategies. This study aims to describe the epidemiological profile of UTI in women over 65 years of age, focusing on the characterization of etiological agents, observed antimicrobial resistance patterns, and commonly reported risk factors. We conducted a retrospective analysis of microbiological and clinical data from elderly women diagnosed with UTIs. Bacterial isolates were identified and antimicrobial susceptibility profiles were evaluated over a specified period. A statistical analysis was performed to determine the prevalence of different pathogens and antibiotic resistance trends. Escherichia coli was the predominant uropathogen, consistent across different clinical scenarios and patient conditions. The four most common bacterial strains—E. coli, Klebsiella pneumoniae, Proteus mirabilis, and Enterococcus faecalis—aligned with global epidemiological data. In Escherichia coli a significant increase in resistance to nitrofurantoin was observed, possibly indicating excessive empirical use, while resistance to other antibiotics, such as amoxicillin/clavulanic acid and ertapenem, remained stable or decreased. Institutional antibiotic stewardship programs likely contributed to this trend. The study highlights E. coli as the main etiological agent in elderly women with UTIs. The observed resistance patterns emphasize the need for localized antimicrobial surveillance and personalized therapeutic approaches. Continuous microbiological monitoring and rational use of antibiotics are crucial to optimize treatment outcomes and control the development of resistance. Full article

Background: Urinary tract infection (UTI) is predominantly caused by uropathogenic Escherichia coli (UPEC). Previous studies have reported that the fimbriae of UPEC are involved in virulence and antimicrobial resistance. We aimed to analyze the fimbrial gene profiles of UPEC and investigate the specificity of these expressions in symptomatic UTI, urinary device use, and levofloxacin (LVFX) resistance/extended-spectrum beta-lactamase (ESBL) production. Methods: A total of 120 UPEC strains were isolated by urine culture between 2019 and 2023 at our institution. They were subjected to an antimicrobial susceptibility test and polymerase chain reaction (PCR) to identify 14 fimbrial genes and their association with clinical outcomes or antimicrobial resistance. Results: The prevalence of the papG2 gene was significantly higher in the symptomatic UTI group by multivariate analyses (OR 5.850, 95% CI 1.390–24.70, p = 0.016). The prevalence of the c2395 gene tended to be lower in the symptomatic UTI group with urinary devices (all p < 0.05). In LVFX-resistant UPEC strains from both the asymptomatic bacteriuria (ABU) and the symptomatic UTI group, the expression of the papEF, papG3, c2395, and yadN genes tended to be lower (all p < 0.05). Conclusion: The fimbrial genes of UPEC are associated with virulence and LVFX resistance, suggesting that even UPEC with fewer motility factors may be more likely to ascend the urinary tract in the presence of the urinary devices. These findings may enhance not only the understanding of the virulence of UPEC but also the management of UTI. Full article

The presented in silico and phylogenetic analysis of putative endolysins potentially produced by phages infecting uropathogenic Escherichia coli (UPEC) demonstrates their remarkable diversity. These proteins exhibit significant variations in sequence length, molecular weight, isoelectric point, and stability, as well as diverse functional domains determining their enzymatic activity, including lysin, lysozyme, hydrolase, amidase, and peptidase functions. Due to their predicted lytic properties, endolysins hold great promise in combating UPEC bacteria, including those within biofilms, which are often highly resistant to conventional treatments. Despite their potential, several challenges hinder the full utilization of endolysins. These include the relatively small number of identified proteins, challenges in the annotation process, and the scarcity of studies evaluating their efficacy in vitro and in vivo against Gram-negative bacteria. In this work, we emphasize these challenges while also underlining the potential of endolysins as an effective tool against UPEC infections. Their effectiveness could be significantly enhanced when combined with agents that disrupt the outer membrane of these bacteria, making them a promising alternative or complement to existing antimicrobial strategies. Further research is necessary to fully explore their therapeutic potential. Full article

Urinary tract infections (UTI) are among the most frequent bacterial infections in children, representing a significant cause of morbidity with potential long-term complications, including renal scarring and chronic kidney disease. This review explores the multifaceted roles of vitamins A, D, E, and C in the prevention and management of pediatric UTI. Vitamin A supports mucosal barrier integrity and immune modulation, reducing pathogen adhesion and colonization. Vitamin C exhibits antioxidant and antimicrobial properties, acidifying urine to inhibit bacterial growth and enhancing the efficacy of antibiotics. Vitamin D strengthens innate immunity by promoting antimicrobial peptide production, such as cathelicidins, and improves epithelial barrier function, while vitamin E mitigates oxidative stress, reducing renal inflammation and tissue damage. The interplay between oxidative stress, immune response, and nutritional factors is emphasized, highlighting the potential of these vitamins to restore antioxidant balance and prevent renal injury. Complementary strategies, including probiotics and phytotherapeutic agents, further enhance therapeutic outcomes by addressing microbiome diversity and providing additional antimicrobial effects. While these approaches show promise in mitigating UTI recurrence and reducing dependence on antibiotics, evidence gaps remain regarding optimal dosing, long-term outcomes, and their integration into pediatric care. By adopting a holistic approach incorporating vitamin supplementation and conventional therapies, clinicians can achieve improved clinical outcomes, support antibiotic stewardship, and reduce the risk of renal complications in children with UTI. Full article

Urinary tract infections (UTIs) are a leading cause of illness in children and adults of all ages, with uropathogenic Escherichia coli (UPEC) being the primary agent responsible. During colonization and subsequent infection of the urinary tract (UT), UPEC requires the expression of genes associated with virulence, such as those that encode the fimbrial adhesins FimH, PapG, and CsgA, as well as the presence of the TosA protein and the flagellar appendages of the bacteria. However, for colonization and infection to be successful, UPEC must overcome the host’s immunological barriers, such as physical barriers, expressed peptides and proteins, and immune cells found in the UT. In this context, the UT functions as an integral system where these factors act to prevent the colonization of uropathogens. Significant genetic diversity exists among UPEC strains, and the clonal complex ST131 represents one of the key lineages. This lineage has a high content of virulence genes, multiple mechanisms of antibiotic resistance, and a high frequency of extended-spectrum β-lactamases (ESBLs). New knowledge regarding protein structures known as adhesins and their role in the infection process can help identify therapeutic targets and aid in the design of vaccines. These vaccines could be based on the development of chimeric fusion proteins (FimH + CsgA + PapG), which may significantly reduce the incidence of UTIs in pediatric and adult patients. Full article

Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are a major healthcare challenge, necessitating effective antimicrobial therapy for treatment. However, the prevalence of antimicrobial resistance among UPEC strains is escalating, particularly among patients experiencing recurrent infection. The rise in UPEC strains that exhibit resistance to multiple antimicrobial agents, including the spread of extended-spectrum beta-lactamase (ESBL)-producing UPEC, intensifies the complexity of managing UTIs. Genetic variations within UPEC strains play a major role in their ability to resist antimicrobial agents and adapt to changing environments. Unveiling and understanding the genomic landscape of emerging UPEC strains is essential for comprehending the genetic basis of their resilience. Moreover, monitoring these genetic strains is crucial for identifying patterns of resistance dissemination, guiding infection control measures, and informing the development of targeted therapeutics. Full article

Urinary tract infections (UTIs) are a prevalent global health issue, often requiring antibiotic treatment, which contributes to antimicrobial resistance. This narrative review explores the potential of probiotics and plant-based foods as alternative or complementary preventive strategies against UTIs. Fermented foods, such as yogurt, kefir, and kombucha, contain probiotic strains that can modulate the gut and urogenital microbiota, enhancing resistance to uropathogens. Likewise, plant-based foods, including cranberry, garlic, bearberry, juniper, and nettle, possess bioactive compounds with antimicrobial, anti-inflammatory, and diuretic properties. Laboratory and clinical studies suggest that these natural interventions may reduce the incidence of UTIs by inhibiting pathogen adhesion, modulating immune responses, and promoting urinary tract health. However, despite promising findings, inconsistencies in study methodologies, dosage standardization, and long-term efficacy warrant further investigation. Future research should focus on optimizing probiotic formulations, standardizing plant-based supplement dosages, and assessing potential food–drug interactions to establish evidence-based guidelines for UTI prevention. Full article

Background: Urinary tract infections (UTIs) are among the most common bacterial infections in children, and the antibiotic susceptibility in the youngest patients remains poorly understood. This study aimed to describe the distribution of uropathogens and their antibiotic susceptibility, focusing on oral formulations. Methods: Data from the first microbiological isolation, between January 2007 and December 2023, at Istituto Gaslini, in young infants (aged <6 months), were analyzed. Results: We isolated 2473 infants’ first pathogen, with a median age in the sample of 2.8 months and 62.6% male. A total of 2498 bacterial isolates were identified, of which 88.8% were Gram-negative and 11.2% were Gram-positive. Escherichia coli (53%) was the most frequent isolate, followed by Klebsiella pneumoniae (12.3%) and Enterococcus spp. (9.6%). No significant differences were observed between males and females, but infants younger than 3 months exhibited a significantly different pathogen distribution compared to older infants. The pathogen distribution showed significant changes before and after 2015, with a marked increase in Klebsiella pneumoniae isolates post-2015. Escherichia coli showed increases in resistance to amoxicillin-clavulanate and ciprofloxacin after 2015. Conclusions: Escherichia coli remains the most common uropathogen; however, Klebsiella pneumoniae has not only shown a high prevalence but also significant resistance, particularly in recent years. Full article

Iron uptake plays an important role in the persistence of Escherichia coli in the host and for its survival in the environment, and it is known that E. coli has a variety of siderophore systems for iron uptake. We investigated the ability to produce siderophores, the genetic diversity of the siderophores and their correlation with virulence-associated genes (VAGs), phylogroups and bacteriocin production in E. coli strains isolated from different sources: uropathogenic E. coli (UPEC) from urine of patients with urinary tract infections, avian pathogenic E. coli (APEC) from organs of birds with signs of colibacillosis, fecal E. coli (FEC) from feces of healthy cattle and E. coli from organic fertilizers based on poultry and cattle manure (OFEC). A high variability in siderophore production was found among the UPEC strains studied, while the OFEC strains showed the highest siderophore production among all groups. Genes for aerobactin and yersiniabactin receptors were most frequently found in the UPEC strain, followed by the APEC, FEC and OFEC strains. The greatest diversity of siderophore receptors was found in the APEC strain. We also found that iutA-positive E. coli isolated from animals contained more VAGs than iutA-negative strains. The profiles of the siderophore genes of APEC and OFEC from poultry manure were very similar, indicating that APEC can be transmitted via organic fertilizers, suggesting that poultry manure is an environmental risk. The data obtained complement the information on the prevalence of siderophore producers and contribute to our knowledge on the biodiversity of E. coli pathotypes. Full article

Background: Urinary tract infections are a global health concern, with uropathogenic Escherichia coli (UPEC) accounting for 80–90% of cases. Given the rise in antimicrobial resistance, our aim was to elucidate the genetic mechanisms behind low-level resistance to ciprofloxacin and fosfomycin (LLCR and LLFR) in UPEC strains, using whole-genome sequencing (WGS) to identify point mutations in chromosomal and plasmid genes. Methods: A cohort UPEC was collected from kidney transplant recipients at the Virgen del Rocío University Hospital, Spain. Minimum inhibitory concentrations were determined for ciprofloxacin and fosfomycin to categorize strains into LLCR and LLFR. Twenty strains were selected for WGS, with genome annotations. Point mutations were identified and analyzed using alignment tools, and protein stability changes were predicted. Results: LLCR strains exhibited mutations in key quinolone resistance-determining regions of the gyrA gene, in 83% of cases. The qnrS1 plasmid gene was found in 17% of LLCR strains. LLFR strains showed mutations in the glpT and cyaA genes. Mutations in the uhp gene family were linked to the fosfomycin-resistant phenotype, suggesting a multi-step resistance evolution mechanism. Conclusions: This study highlights the complex interplay between chromosomal and plasmid genes in UPEC’s resistance to ciprofloxacin and fosfomycin. The findings contribute to understanding low-level resistance mechanisms and may guide the development of novel therapeutic strategies to combat multidrug-resistant strains. Full article

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide. They occur in the urinary system when a microorganism, commonly present on the perineal skin or rectum, reaches the bladder through the urethra, and adheres to the luminal surface of uroepithelial cells, forming biofilms. The treatment of UTIs includes antibiotics, but their indiscriminate use has favored the development of multidrug-resistant bacteria strains, which represent a serious challenge to today’s microbiology. The pathogenesis of the infection and antibiotic resistance synergistically contribute to hindering the eradication of the disease while favoring the establishment of persistent infections. The repeated requirement for antibiotic treatment and the limited therapeutic options have further contributed to the increase in antibiotic resistance and the occurrence of potential relapses by therapeutic failure. To limit antimicrobial resistance and broaden the choice of non-antibiotic preventive approaches, this review reports studies focused on the bacteriostatic/bactericidal activity, inhibition of bacterial adhesion and quorum sensing, restoration of uroepithelial integrity and immune response of molecules, vitamins, and compounds obtained from plants. To date, different supplementations are recommended by the European Association of Urology for the management of UTIs as an alternative approach to antibiotic treatment, while a variety of bioactive compounds are under investigation, mostly at the level of in vitro and preclinical studies. Although the evidence is promising, they are far from being included in the clinical practice of UTIs. Full article