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Background: Uropathogens are microorganisms that cause urinary tract infections (UTIs). Owing to higher blood glucose levels and compromised immune functions, treatment of uropathogens in diabetic patients is a challenge. Aim: This study aims to assess the prevalence of uropathogens and their antibiotic susceptibility among diabetic patients at St. John of God Hospital at Duayaw Nkwanta (SJGHDN) in the Ahafo region of Ghana. Methods: The cross-sectional study recruited 175 diabetic patients at SJGHDN between August and September 2023. Questionnaires were used to collect patients' background information. Fasting Blood Sugar (FBS) was assessed by using a glucometer. Urine samples were examined for the presence of uropathogens. A sterile inoculating loop with a calibrated volume of 2 µl was used for plating. Each colony equals 500 CFU/mL. Significant uropathogen was determined by multiplying the counted colonies by 500 to obtain CFU/mL. Positive uropathogen was defined as CFU ≥ 105/mL. Significant uropathogen was defined as ≥200 colonies per sample. The disc diffusion method was used to determine antibiotic susceptibility. Results: Out of the 175 patients, 19.4% expressed various uropathogens with Escherichia coli being the predominant. Suboptimal glucose level was the most significant risk factor (p = 0.038). Glucosuria (p = 0.036), hazy urine (p = 0.028), positive leukocyte esterase (p = 0.001), and pus cells in urine sediment (p = 0.020) were significant indicators of uropathogen occurrence. Klebsiella pneumonia and Proteus mirabilis were resistant to ≥4 antibiotics. Amikacin, nitrofurantoin, levofloxacin, ciprofloxacin, and ceftriaxone demonstrated efficacy against the isolates. Conclusion: This study underscores the notable prevalence of uropathogens in diabetic patients and the alarming levels of antibiotic resistance observed. The results highlight the critical need for vigilant monitoring and customized treatment approaches, particularly for diabetic patients exhibiting risk factors such as elevated urine glucose levels, cloudy urine, and presence of leukocyte esterase and pus cells in urine sediment. The significant resistance to frequently used antibiotics like co-trimoxazole and tetracycline points to the necessity of routine susceptibility testing and the use of alternative antibiotics for effective treatment. These findings can assist healthcare providers in more effectively managing and preventing UTIs in diabetic populations.
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One of the most prevalent infectious diseases identified in both communities and hospitalized patients is urinary tract infection (UTI). Enterococcus is evolved into a clinically pertinent uropathogen due to its evolving resistance to multiple antimicrobial agents.This study, detects antimicrobial susceptibility patterns of Enterococcus species and molecular detection of Enterococcus faecalis from patients with urinary tract infections. In this cross-sectional observational study, 165 urine samples were obtained from clinically diagnosed patients with UTIs of different ages and gender. Enterococcus species were identified by standard microbiological procedure and PCR (by using species-specific primers for Enterococcus faecalis). A modified Kirby Bauer Disc diffusion method was used to identify the antimicrobial susceptibility pattern following Clinical and Laboratory Standards Institute (CLSI) guidelines. Out of 165 urine samples, 134 samples yielded positive cultures. Enterococcus species were isolated from 23 (17.1%) urine samples. Among all Enterococcus, 16 (69.6%) isolates were E. faecalis, detected by PCR assay. A higher (30.4%) proportion of Enterococcus-positive patients were from the age group 48-57 years and female patients (78.2%) had a higher prevalence. Enterococcal infection was found in 56.5% of non-catheterized patients and 43.5% of catheterized patients. Vancomycin and linezolid (78.3%) and meropenem (73.9%) sensitivity was prevalent among all Enterococcus species. They showed 100% resistance towards ceftriaxone, cefixime 95.7%, cefuroxime 91.3%, azithromycin 82.6%. This research indicated the occurrence of Enterococcus species and the advent of multidrug-resistant E. faecalis in patients with UTIs. Routine speciation and antimicrobial susceptibility testing of Enterococcus in various clinical samples is encouraged.
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Background: Aerococcus urinae and Aerococcus sanguinicola are emerging pathogens linked with urinary tract infections. We present a case series of A. urinae and A. sanguinicola isolates characterizing the spectrum of clinical presentation, microbiological characteristics and antimicrobial sensitivities. Methods: Retrospective chart review was performed on patients who grew positive cultures for A. urinae and A. sanguinicola identified on MALDI-TOF in Saskatchewan from January to June 2023. Demographic and clinical variables, antimicrobial susceptibility and prescription were documented. Results: This cohort (n = 115) had a median age 82 years. A. urinae and A. sanguinicola infections spanned from urinary tract infection (n = 96) to urosepsis (n = 6). These infections were predominantly monomicrobial (73.9%) and were susceptible to ceftriaxone, penicillin G and vancomycin. Antimicrobials were seldom prescribed within the urinary tract infection cohort (31.2%). Conclusion: Untreated A. urinae and A. sanguinicola infections can precipitate into urosepsis. The reported antimicrobial susceptibility for these Aerococcus isolates should be utilized to provide appropriate antimicrobial coverage.
Aerococcus urinae and Aerococcus sanguinicola are bacteria that can cause urine infections. They are often overlooked and thought to be unable to cause serious blood infections, such as sepsis. We collected data on 87 cases of A. urinae and 28 cases of A. sanguinicola to show that these bacteria can cause urine and blood infections in elderly patients. We also looked at other studies and summarized that patients with serious blood infections from these bacteria often had a previous urine infection from these same bacteria. These bacteria can be resistant to a common antibiotic used to treat urine infections. It is important to test and report if these bacteria are resistant to this common antibiotic and doctors must be aware that they can cause serious blood infections if not treated with the correct antibiotics.
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Rapid detection and classification of pathogenic microbes for food hygiene, healthcare, environmental contamination, and chemical and biological exposures remain a major challenge due to nonavailability of fast and accurate detection methods. The delay in clinical diagnosis of the most frequent bacterial infections, particularly urinary tract infections (UTIs), which affect about half of the population at least once in their lifetime, can be fatal if not detected and treated appropriately. In this work, we have fabricated aluminum (Al) foil integrated pegylated gold nanoparticles (AuNPs) as a potential surface-enhanced Raman scattering (SERS) substrate, which is used for the detection and classification of uropathogens, namely, E. coli, S. aureus, and P. aeruginosa directly from the culture without any pretreatment. The substrate is first drop cast with bacterial pellets and then pegylated AuNPs, and the interaction of two on Al foil base gives identifiable characteristic Raman peaks with good reproducibility. With the use of chemometric methods such as principal component analysis (PCA), the Al foil-based SERS substrate offers a quick, effective detection and classification of three strains of UTI bacteria with the least bacterial concentration (105 cells mL-1) necessary for clinical diagnosis. In addition, this substrate was able to detect E. coli positive clinical samples by giving SERS fingerprint information directly from centrifuged urine samples within minutes. The stability of pegylated AuNPs provides for its application at the point of care with rapid and easy detection of uropathogens as well as the possibility of advancement in healthcare applications.
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Aluminio , Escherichia coli , Oro , Nanopartículas del Metal , Polietilenglicoles , Espectrometría Raman , Staphylococcus aureus , Oro/química , Nanopartículas del Metal/química , Aluminio/química , Polietilenglicoles/química , Escherichia coli/aislamiento & purificación , Staphylococcus aureus/aislamiento & purificación , Tamaño de la Partícula , Propiedades de Superficie , Ensayo de Materiales , Materiales Biocompatibles/química , Pseudomonas aeruginosa/aislamiento & purificación , Infecciones Urinarias/diagnóstico , Infecciones Urinarias/microbiología , HumanosRESUMEN
The emergence and spread of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli (E. coli) pose significant challenges to the treatment and control of urinary tract infections, particularly among vulnerable populations, such as the elderly living in nursing care homes. In this study, we investigated the occurrence of ESBL genes in commensal E. coli isolated from urine samples of 118 elderly individuals residing in Ghanaian nursing care homes. A total of 195 ESBL genes were detected among 41 E. coli isolated from the study participants. All the isolates harboured at least one ESBL gene, and the majority of them (70.1%) carried at least four ESBL genes. Among the ESBL genes detected, CTXM825 was the predominant (14.1%). In antimicrobial susceptibility testing, 65.9% of the isolates showed resistance to cefepime, a fourth-generation cephalosporin, while 56.1% showed resistance to cefotaxime, a third-generation cephalosporin. Additionally, 46.3% of the isolates were multidrug-resistant, indicating resistance to antibiotics from multiple classes. In summary, we observed relatively high rates of resistance to antibiotics as well as alarming rates of ESBL genes in the isolated pathogens. These findings emphasise the urgent need for antimicrobial stewardship and infection control programmes to mitigate the spread of multidrug-resistant pathogens in nursing care homes.
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Antibacterianos , Programas de Optimización del Uso de los Antimicrobianos , Infecciones por Escherichia coli , Escherichia coli , Casas de Salud , Infecciones Urinarias , beta-Lactamasas , Humanos , Escherichia coli/genética , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Anciano , Femenino , beta-Lactamasas/genética , Masculino , Ghana/epidemiología , Infecciones Urinarias/microbiología , Infecciones Urinarias/tratamiento farmacológico , Infecciones por Escherichia coli/tratamiento farmacológico , Infecciones por Escherichia coli/microbiología , Infecciones por Escherichia coli/epidemiología , Antibacterianos/uso terapéutico , Antibacterianos/farmacología , Anciano de 80 o más Años , Prevalencia , Pruebas de Sensibilidad Microbiana , Sistema Urinario/microbiología , Farmacorresistencia Bacteriana Múltiple/genética , Proteínas de Escherichia coli/genéticaRESUMEN
Urinary tract infections (UTI) by antibiotic resistant and virulent K. pneumoniae are a growing concern. Understanding the genome and validating the genomic profile along with pangenome analysis will facilitate surveillance of high-risk clones of K. pneumoniae to underpin management strategies toward early detection. The present study aims to correlate resistome with phenotypic antimicrobial resistance and virulome with pathogenicity in Klebsiella spp. The present study aimed to perform complete genome sequences of Klebsiella spp. and to analyse the correlation of resistome with phenotypic antimicrobial resistance and virulome with pathogenicity. To understand the resistome, pangenome and virulome in the Klebsiella spp, the ResFinder, CARD, IS Finder, PlasmidFinder, PHASTER, Roary, VFDB were used. The phenotypic susceptibility profiling identified the uropathogenic kp3 to exhibit multi drug resistance. The resistome and in vitro antimicrobial profiling showed concordance with all the tested antibiotics against the study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA and magA genes. To the best of our knowledge, this is the first report on the presence of ste, stf, stc and sti major fimbrial operons of Salmonella enterica serotype Typhimurium in K. pneumoniae genome. The study identifies the discordance of virulome and virulence in Klebsiella spp. The complete genome analysis and phenotypic correlation identify uropathogenic K. pneumoniae kp3 as a carbapenem-resistant and virulent pathogen. The Pangenome of K. pneumoniae was open suggesting high genetic diversity. Diverse K serotypes were observed. Sequence typing reveals the prevalence of K. pneumoniae high-risk clones in UTI catheterised patients. The study also highlights the concordance of resistome and in vitro susceptibility tests. Importantly, the study identifies the necessity of virulome and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high-risk K. pneumoniae clones.
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BACKGROUND: This study aimed to characterise the infant penile (coronal sulcus) microbiome and the effects of early infant male circumcision (EIMC), following a standard surgical method (Mogen Clamp) and a non-surgical alternative (ShangRing). METHODS: We collected coronal sulcus swabs at baseline and on days 7 and 14 post-circumcision from infants assigned to receive EIMC by Mogen Clamp (n = 15) or ShangRing (n = 15), in a randomised trial in Rakai and Kakuuto, Uganda. We used 16S rRNA gene-based sequencing and broad-coverage qPCR to characterise the infant penile microbiome and assess the effects of EIMC in both study arms. FINDINGS: Prior to EIMC, the infant penile microbiome had a mixture of facultative and strict anaerobes. In both study arms, EIMC caused penile microbiome proportional abundance changes characterised by decreases in penile anaerobes [ShangRing Prevotella: -15.0%, (SD = 19.1); Mogen clamp Prevotella: -3.6% (11.2); ShangRing Veillonella: -11.3% (17.2); Mogen clamp Veillonella: -2.6% (11.8)] and increases in skin-associated facultative anaerobes [ShangRing Corynebacterium: 24.9%, (22.4); Mogen clamp Corynebacterium: 4.7% (21.3); ShangRing Staphylococcus: 21.1% (20.5); Mogen clamp Staphylococcus: 18.1% (20.1)]. Clostridium tetani was not detected during the study. INTERPRETATION: Mogen Clamp and ShangRing EIMC both changed the composition of the infant penile microbiome by reducing the proportional abundances of anaerobes and uropathogens, which is consistent with medical male circumcision findings in adults. C. tetani was not increased by either EIMC method. FUNDING: Bill and Melinda Gates Foundation.
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Circuncisión Masculina , Microbiota , Pene , ARN Ribosómico 16S , Humanos , Masculino , Pene/microbiología , Lactante , ARN Ribosómico 16S/genética , Recién Nacido , Uganda , Bacterias/genética , Bacterias/clasificación , Bacterias/aislamiento & purificaciónRESUMEN
The recognition of the Aerococcus urinae complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic resistance profiles. Here, we investigated the prevalence of macrolide resistance within urinary AUC isolates, shedding light on potential genetic mechanisms. Phenotypic testing revealed a high rate of macrolide resistance: 45%, among a total of 189 urinary AUC isolates. Genomic analysis identified integrative and conjugative elements (ICEs) as carriers of the macrolide resistance gene ermA, suggesting horizontal gene transfer as a mechanism of resistance. Furthermore, comparison with publicly available genomes of related pathogens revealed high ICE sequence homogeneity, highlighting the potential for cross-species dissemination of resistance determinants. Understanding mechanisms of resistance is crucial for developing effective surveillance strategies and improving antibiotic use. Furthermore, the findings underscore the importance of considering the broader ecological context of resistance dissemination, emphasizing the need for community-level surveillance to combat the spread of antibiotic resistance within the urinary microbiome.
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Background and Aims: Antibiotic resistance presents a significant global public health challenge, particularly for urinary tract infections (UTIs), and is notably severe in developing countries. Surveillance of the antimicrobial susceptibility patterns of UTI-causing bacteria is crucial for effective treatment selection. This study aimed to analyze these patterns in bacteria isolated from the urine samples of patients at Mughda Medical College Hospital, Dhaka, Bangladesh. Methods: A retrospective study (January 2019 to December 2020) at Mugdha Medical College and Hospital, Dhaka, examined clinical and laboratory data from patients with positive urine cultures (≥105 CFU/mL). The study classified patients into four age groups: children (1-<18 years), young adults (18-<33 years), middle-aged adults (33-50 years), and old adults (>50 years). The standard Kirby-Bauer method was used to assess antibiotic sensitivity to 28 common antibiotics. Results: Among 243 positive urine cultures in both community- and hospital-acquired UTIs, Escherichia coli was the most common uropathogen (65.84%), followed by Klebsiella spp. (12.34%), Enterococcus spp. (8.23%), and other types of bacteria. Conclusion: Old adults are particularly vulnerable to UTIs, with E. coli being the predominant causative agent in the study region. The observed antimicrobial resistance patterns underscore the necessity of judicious antibiotic selection to effectively treat UTIs across different age groups.
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AIMS: The main objective of this study was to modify a recently reported multi-purpose artificial urine (MP-AU) for culture and gene expression studies of uropathogenic Escherichia coli (UPEC) strains. METHODS AND RESULTS: We used liquid chromatography mass spectrometry (LC-MS) to identify and adjust the metabolic profile of MP-AU closer to that of pooled human urine (PHU). Modification in this way facilitated growth of UPEC strains with growth rates similar to those obtained in PHU. Transcriptomic analysis of UPEC strains cultured in enhanced artificial urine (enhanced AU) and PHU showed that the gene expression profiles are similar, with <7% of genes differentially expressed between the two conditions. CONCLUSIONS: Enhancing an MP-AU with metabolites identified in PHU allows the enhanced AU to be used as a substitute for the culture and in vitro gene expression studies of UPEC strains.
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Infecciones por Escherichia coli , Proteínas de Escherichia coli , Infecciones Urinarias , Escherichia coli Uropatógena , Humanos , Escherichia coli Uropatógena/genética , Perfilación de la Expresión Génica , Expresión Génica , Proteínas de Escherichia coli/genética , Factores de Virulencia/genéticaRESUMEN
Staphylococcus saprophyticus, a common contaminant of foods, causes urinary tract infections in humans. Here, we report the draft genomic sequence for S. saprophyticus ATCC 49453, which is currently being used in food safety research.
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Background: Urinary tract infections are the primary factors that cause mortality and morbidity in patients with underlying comorbid conditions and are responsible for most hospital admissions worldwide. Objectives: The study aims to identify the common bacterial uropathogens and determine their antimicrobial susceptibility pattern, including multidrug-resistant/extensively drug-resistant bacteria. Methods: The descriptive cross-sectional study was conducted among inpatients provisionally suspected of urinary tract infections in the medical ward of Koshi Hospital, Biratnagar, Nepal. Samples were inoculated in a cystine lysine electrolyte-deficient medium, and pure growth of significant bacteria was further subjected Gram staining, biochemical identification, and antimicrobial susceptibility testing as per laboratory standard procedure and Clinical Laboratory Standards Institute guidelines, respectively. Descriptive and inferential statistical analysis was performed to analyze the outcomes and a p-value < 0.05 was considered statistically significant. Results: A total of 305 patients urine specimens were examined, of which 251 (82.29%) samples resulted in significant bacterial growth in the culture. Escherichia coli (62.94%) was the most predominantly isolated organism, followed by Klebsiella pneumoniae (12.35%), Staphylococcus aureus (9.16%), and Pseudomonas aeruginosa (8.76%). Among antimicrobials, colistin had shown absolute susceptibility (100%) toward gram-negative uropathogens followed by carbapenem and aminoglycosides in a majority of uropathogens. Escherichia coli was found to be the leading drug-resistant bacteria (70%) among uropathogens. The presence of multidrug-resistant/extensively drug-resistant bacteria uropathogens was found to be significantly associated with diabetes mellitus and those with combined antimicrobial therapies. Diabetic patients were twice (OR~2) more likely to colonize and develop uropathogens as compared to non-diabetics. Conclusion: Escherichia coli was the most common uropathogens followed by Klebsiella pneumoniae in urinary tract infection patients. The polymyxin group (colistin) of antimicrobials was found to be effective in all multidrug-resistant and extensively drug-resistant uropathogens. The study recommends the need of optimized antimicrobial stewardship program to develop effective strategies in the management of urinary tract infections in diverse healthcare settings.
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Introducción: La infección del tracto urinario tiene impacto mundial por ser causa común de prescripción antibiótica empírica, por lo que la elección del tratamiento representa un desafío para el médico. Objetivos: Identificar los factores asociados a una adecuada prescripción antibiótica empírica en pacientes con infección del tracto urinario. Métodos: Se realizó un estudio analítico transversal. Se revisaron 275 resultados de urocultivos positivos de febrero a octubre del 2019, se excluyeron 97 debido a que no cumplieron los criterios de selección, quedaron 178 como población elegible. Se revisaron las historias clínicas de estos pacientes diagnosticados en los consultorios externos del Hospital Regional Hermilio Valdizán, Perú. Para el análisis bivariado se utilizó el test estadístico ji al 2, prueba de Fisher, la razón de prevalencia (RP), intervalos de confianza al 95 por ciento y p 0,05). Conclusiones: La prescripción antibiótica empírica en infecciones urinarias a menudo es inadecuada, por la complacencia durante el tratamiento. La prescripción empírica de antibióticos es adecuada en pacientes con diabetes y con riesgo de infección por el uropatógeno Klebsiella, ya que los pacientes con diabetes tienen riesgo de infección con cepas resistentes y los médicos son más cautelosos al recetar antibióticos(AU)
Introduction: Urinary tract infection has a global impact as it is a common cause of empirical antibiotic prescription, so the choice of treatment represents a challenge for the doctor. Objective: To identify the factors associated with an adequate empirical antibiotic prescription in patients with urinary tract infection. Methods: A cross-sectional analytical study was carried out in 275 positive urine culture results, which were reviewed from February to October 2019. Ninety-seven were excluded because they did not meet the selection criteria, 178 remained as an eligible population. The medical records were reviewed for these patients diagnosed in the outpatient clinics of Hermilio Valdizán Regional Hospital, Peru. For the bivariate analysis, chi-2 statistical test, Fisher's test, the prevalence ratio (PR) were used. 95percent confidence intervals and p 0.05). Conclusions: Empirical antibiotic prescription in urinary infections is often inadequate, due to complacency during treatment. Empirical prescription of antibiotics is appropriate in patients with diabetes and at risk of infection with the uropathogen Klebsiella, since patients with diabetes are at risk of infection with resistant strains and physicians are more cautious when prescribing antibiotics(AU)
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Humanos , Masculino , Femenino , Infecciones Urinarias/tratamiento farmacológico , Estudios TransversalesRESUMEN
Introduction: The occurrence of extended spectrum beta lactamase-producing uropathogens, especially in pregnant women can result in life-threatening condition and morbidity for both the mother and the newborn due to very limited drug options for treatment of these pathogens. The aim of this study was to determine the bacterial profile, associated factors, and their antimicrobial susceptibility patterns and to identify extended spectrum beta lactamase-producing bacterial uropathogens. Methods: A hospital-based cross-sectional study was conducted from July to September 2018 on a total of 177 pregnant women with and without symptoms of urinary tract infection at ALERT Hospital, Addis Ababa, Ethiopia. From these study participants, 72 have symptoms, whereas 105 have no symptoms. All urine samples were inoculated onto cysteine lactose electrolyte deficient medium and MacConkey agar. Colonies were counted to check the presence of significant bacteriuria. Pure isolates of bacterial pathogen were characterized and identified at species level by colony morphology, gram stain, and standard biochemical procedures. All Gram-negative isolates were put into Muller-Hinton agar plates for antibiotic susceptibility test by Kirby-Bauer disc diffusion technique. Extended spectrum beta lactamase was detected using double-disk synergy methods on Muller-Hinton agar. The data were double entered into epidemiological Information system and analyzed using Statistical Package for Social Science version 26. Results: The overall proportion of urinary tract infection among pregnant women was 14.7% (n = 26/177). Klebsiella pneumoniae was the predominant bacterial etiologic agent of urinary tract infection 26.9% (n = 7/26). The proportion of extended spectrum beta lactamase among Gram-negative isolates was 50% (n = 6/12). Among extended spectrum beta lactamase-producing isolates (100%), all are resistance to amikacin and gentamicin while intermediate level resistance rate of 66.7% was observed among trimethoprim-sulphamethoxazole. They were susceptible for some limited drugs, and these were Nitrofurantoin (83.3%) and Chloramphenicol (83.3%). Conclusions: Majority of extended spectrum beta lactamase-producing isolates exhibited co-resistance to other commonly prescribed antibiotics. This indicates that the option of treatment for these pathogens rapidly decreased from time to time which results serious life-threatening conditions, especially in mother and newborn unless the appropriate measure is taken.
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Pseudomonas aeruginosa is a widespread multidrug-resistant opportunistic human pathogen with an extremely high mortality rate that leads to urinary tract infection morbidities in particular. Variability and dynamics in genome features and ecological flexibility help these bacteria adapt to many environments and hosts and underlie their broad antibiotic resistance. Overall, studies aimed at obtaining a deeper understanding of the genome organization of UTI-associated P. aeruginosa strains are of high importance for sustainable health care worldwide. Herein, we report the draft assembly of entire genomes of two P. aeruginosa strains, PA18 and PA23, isolated from voided urine of patients with urinary tract diseases (hydronephrosis and urolithiasis, respectively) and determine the most important genetic features for pathogenesis and virulence. Whole-genome sequencing and annotation of genomes revealed high similarity between the two UTI strains along with differences in comparison with other uropathogenic P. aeruginosa and reference strains. The 6 981 635 bp and 6 948 153 bp draft genome sequences with GC contents of 65.9% and 65.8%, respectively, provide new insights into the virulence genetic factors and genes associated with antimicrobial resistance. The whole genome data of PA18 and PA23 have been deposited in the NCBI GenBank database (accession numbers JAQRBF000000000.1 and JAQRBG000000000.1, respectively).
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Infection by antibiotic-resistant extraintestinal pathogenic Escherichia coli may result in treatment failure and thus pose a serious public health threat. Here we report the complete closed genome sequence of three multidrug-resistant (MDR) human uropathogenic E. coli isolates using long-read sequencing technology and de novo assembly.
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OBJECTIVE: Aim: Analysis of trends in the microbial communities of the genitourinary system in patients with urolithiasis. PATIENTS AND METHODS: Materials and Methods: 165 urine samples from patients with urolithiasis was examined. The quantitative isolation of microflora was carried out using the bacteriological method. Microorganisms were identified using API biochemical test systems (bioMerieux, France). The percentage of the various types of microorganisms was determined. The reliability of differences in the frequency of various types of microorganisms isolation in a monoculture and the composition of microbial associations was determined by two-field tables with Fisher's Exact criterion. The GraphPad Prism 7 software was used. RESULTS: Results: 198 bacterial cultures of various types were isolated. In one case, a Candida culture was isolated. E. faecalis was the most frequently isolated culture (29.1% of the isolated strains number); E. coli (18.1% of the total number of isolated cultures; K. pneumoniae (11.1%). There were no significant differences in the rate of E. faecalis compared to E. coli. K. pneumonia was isolated significantly less frequently than E. faecalis. These types of microorganisms were also leaders in the formation of bacterial mixes. In addition, these species are involved in the urease activity of bacteria (directly or indirectly), which contributes to the formation of stones in the genitourinary system. CONCLUSION: Conclusions: E. faecalis is the species most often isolated from patients with purulent-inflammatory processes in patients with urolithiasis, both in the case of mono-infection and as part of mixed bacterial cultures.
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Nitrofurantoin (NF), a wide-spectrum antibiotic accessible since 1953, is utilized widely to treat urinary tract infections as it usually stays active against drug-resistant uropathogen. The use of Nitrofurantoin has increased exponentially since new guidelines have repositioned it as first-line therapy for uncomplicated lower urinary tract infection (UTI). To, although fluoroquinolones are usually used to re-evaluate the first- and second-line therapies for treating uncomplicated UTI, their level of utilization is thought to be inappropriately excessive and will eventually have a detrimental impact; thus, we hypothesize that NF might be the best choice for this condition, because of its low frequency of utilization and its high susceptibility in common UTI pathogens. It can be concluded from this review that NF can be considered as the most effective drug in the treatment of acute urinary infection, but due to the long-term side effects of this drug, especially in elderly patients, it is essential to introduce some criteria for prescribing NF in cases of chronic UTI.
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Nitrofurantoína , Infecciones Urinarias , Humanos , Anciano , Nitrofurantoína/uso terapéutico , Nitrofurantoína/efectos adversos , Infecciones Urinarias/tratamiento farmacológico , Antibacterianos/uso terapéutico , Antibacterianos/farmacología , Fluoroquinolonas/farmacologíaRESUMEN
Background: Urinary tract infections (UTIs) remain a diagnostic challenge and often promote antibiotic overuse. Despite urine culture being the gold standard for UTI diagnosis, some uropathogens may lead to false-negative or inconclusive results. Although PCR testing is fast and highly sensitive, its diagnostic yield is limited to targeted microorganisms. Metagenomic next-generation sequencing (mNGS) is a hypothesis-free approach with potential of deciphering the urobiome. However, clinically relevant information is often buried in the enormous amount of sequencing data. Methods: Precision metagenomics (PM) is a hybridization capture-based method with potential of enhanced discovery power and better diagnostic yield without diluting clinically relevant information. We collected 47 urine samples of clinically suspected UTI and in parallel tested each sample by microbial culture, PCR, and PM; then, we comparatively analyzed the results. Next, we phenotypically classified the cumulative microbial population using the Explify® data analysis platform for potential pathogenicity. Results: Results revealed 100% positive predictive agreement (PPA) with culture results, which identified only 13 different microorganisms, compared to 19 and 62 organisms identified by PCR and PM, respectively. All identified organisms were classified into phenotypic groups (0-3) with increasing pathogenic potential and clinical relevance. This PM can simultaneously quantify and phenotypically classify the organisms readily through bioinformatic platforms like Explify®, essentially providing dissected and quantitative results for timely and accurate empiric UTI treatment. Conclusion: PM offers potential for building effective diagnostic models beyond usual care testing in complex UTI diseases. Future studies should assess the impact of PM-guided UTI management on clinical outcomes.
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Metagenómica , Infecciones Urinarias , Humanos , Metagenómica/métodos , Infecciones Urinarias/diagnóstico , Infecciones Urinarias/epidemiología , Antibacterianos/uso terapéutico , Biología Computacional , Secuenciación de Nucleótidos de Alto RendimientoRESUMEN
Standard urine culture (SUC) is the current standard method for confirmation of a urinary tract infection (UTI). SUC identifies microorganisms in urine samples and semi-quantifies these as colony-forming units (CFUs) ml-1. In contrast, quantitative multiplex polymerase chain reaction (q-MPCR) is a culture-independent assay in which the microbes are quantified by targeting genomic sequences and reported as cells ml-1, calculated from copies ml-1. Using serial dilutions within the 104-105 cells ml-1 range, the usual reporting range of SUC, this study compared the quantification results based on SUC and q-MPCR for four uropathogens with the control hemocytometer counts. The results revealed a linear relationship and a 1:1 correlation between the q-MPCR and SUC results. Additional q-MPCR quantification of 36 uropathogenic non-fastidious and fastidious bacteria and yeast indicated a reproducible linear correlation in a 1:1 manner with the control counts over a range of cell densities (103-106 cells ml-1). The results confirm that the quantifications by q-MPCR in cells ml-1 and by SUC in CFUs ml-1 are comparable and answer to the lingering question of how the results of these two methods correlate. Moreover, q-MPCR provided accurate quantification of various microorganisms over wider cell density ranges without the time required for microbial growth.