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Background: Group B Streptococcus (GBS) is a major cause of sepsis and meningitis in newborns. The Centers for Disease Control and Prevention (CDC) recommends to pregnant women, between 35 and 37 weeks of gestation, universal vaginal-rectal screening for GBS colonization, aimed at intrapartum antibiotic prophylaxis (IAP). The latter is the only currently available and highly effective method against early onset GBS neonatal infections. Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, the preventive measures implemented to mitigate the effects of SARS-CoV-2 infection led to the reduction in the access to many health facilities and services, including the obstetric and perinatal ones. The purpose of the present study was to evaluate the prevalence of maternal GBS colonization, as well as use of IAP and incidence of episodes of neonatal GBS infection when antibiotic prophylaxis has not been carried out in colonized and/or at risk subjects, in a population of pregnant women during (years 2020–2021) and after (year 2022) the COVID-19 pandemic, also with the aim to establish possible epidemiological and clinical differences in the two subjects' groups. Methods: We retrospectively analyzed the clinical data of pregnant women admitted to, and delivering, at the Gynaecology and Obstetrics Unit, Department of Sciences for Health Promotion and Mother and Child Care, of the University Hospital of Palermo, Italy, from 01.01.2020 to 31.12.2022. For each of them, we recorded pertinent socio-demographic information, clinical data related to pregnancy, delivery and peripartum, and specifically execution and status of vaginal and rectal swab test for GBS detection, along with eventual administration and modality of IAP. The neonatal outcome was investigated in all cases at risk (positive maternal swabs status for GBS, either vaginal or rectal, with or without/incomplete IAP, preterm labor and/or delivery, premature rupture of membranes ≥ 18 h, previous pregnancy ended with neonatal early onset GBS disease [EOD], urine culture positive for GBS in any trimester of current gestation, intrapartum temperature ≥ 38 °C and/or any clinical/laboratory signs of suspected chorioamnionitis). The data concerning mothers and neonates at risk, observed during the pandemic (years 2020–2021), were compared with those of both subjects' groups with overlapping risk factors recorded in the following period (year 2022). The chi squared test has been applied in order to find out the relationship between pregnant women with GBS colonization receiving IAP and outcome of their neonates. Results: The total source population of the study consisted of 2109 pregnant women, in addition to their 2144 newborns. Our analysis, however, focused on women and neonates with risk factors. The vaginal-rectal swab for GBS was performed in 1559 (73.92%) individuals. The test resulted positive in 178 cases overall (11.42% of those undergoing the screening). Amongst our whole sample of 2109 subjects, 298 women had an indication for IAP (vaginal and/or rectal GBS colonization, previous pregnancy ended with neonatal GBS EOD, urine culture positive for GBS in any trimester of current gestation, and unknown GBS status at labor onset with at least any among delivery at < 37 weeks' gestation, amniotic membranes rupture ≥ 18 h and/or intrapartum temperature ≥ 38.0 °C), and 64 (21.48%) received adequate treatment; for 23 (7.72%) it was inadequate/incomplete, while 211 (70.8%) did not receive IAP despite maternal GBS colonization and/or the presence of any of the above mentioned risk factors. Comparing the frequency of performing vaginal-rectal swabs in the women admitted in the two time periods, the quote of those screened out of the total in the pandemic period (years 2020–2021) was higher than that of those undergoing GBS screening out of the total admitted in the year 2022 (75.65% vs. 70.38%, p = 0.009), while a greater number (not statistically significant, p = 0.12) of adequate and complete IAP was conducted in 2022, than in the previous biennium (26.36 vs. 18.62%). During the whole 3 years study period, as expected, none of the newborns of mothers with GBS colonization and/or risk factors receiving IAP developed EOD. Conversely, 13 neonates with EOD, out of 179 (7.3%) born to mothers with risk factors, were observed: 3 among these patients' mothers performed incomplete IAP, while the other 10 did not receive IAP. Neither cases of neonatal meningitis, nor deaths were observed. The incidence rate in the full triennium under investigation, estimated as the ratio between the number of babies developing the disease out of the total of 2144 newborns, was 6.06‰; among those born to mothers with risk factors, if comparing the two time periods, the incidence was 8.06% in the pandemic biennium, while 5.45% in the following year, evidencing thus no statistical significance (p = 0.53). Conclusions: The present study revealed in our Department an increased prevalence of pregnant women screened for, and colonized by GBS, in the last decade. However, an overall still low frequency of vaginal-rectal swabs performed for GBS, and low number of adequate and complete IAP despite the presence of risk factors have been found, which did not notably change during the two time periods. Moreover, significant EOD incidence rates have been reported among children of mothers carrying risk factors, although also in this case no statistically significant differences have been observed during and after the pandemic. Such data seem to be in contrast to those reported during the COVID-19, showing a decrease in the access to health facilities and increased mortality/morbidity rates also due to the restrictive measures adopted to mitigate the effects of the pandemic. These findings might be explained by the presence within the same metropolitan area of our Department of a COVID hospital and birthing center, which all the patients with SARS-CoV-2 infection referred to, and likely leading to a weaker concern of getting sick perceived by our patients. Although IAP is an easy procedure to implement, however adherence and uniformity in the management protocols are still not optimal. Therefore, the prophylactic measures adopted to date cannot be considered fully satisfactory, and should be improved. Better skills integration and obstetrical-neonatological collaboration, in addition to new effective preventive tools, like vaccines able to prevent invasive disease, may allow further reduction in morbidity and mortality rates related to GBS perinatal infection. [ABSTRACT FROM AUTHOR]

Current microbiome investigations of patients with pressure ulcers (PU) are mainly based on wound swabs and/or biopsy sequencing, leaving the colonization scenario unclear. Urinary microbiota has been never studied. As a part of the prospective ESCAFLOR study, we studied urinary microbiota of spinal cord injury (SCI) patients with PU without any urinary tract infection at the inclusion, collected at two times (at admission [D0] and after 28 days [D28]) during the patient's care, investigated by 16S rDNA metagenomics next generation sequencing. Subgroup analyses were carried out between patients with wounds showing improved evolution versus stagnated/worsened wounds at D28. Analysis was done using EPISEQ® 16S and R software. Among the 12 studied patients, the urinary microbiota of patients with improved wound evolution at D28 (n = 6) presented a significant decrease of microbial diversity. This modification was associated with the presence of Proteobacteria phylum and an increase of Escherichia‐Shigella (p = 0.005), as well as the presence of probiotic anaerobic bacteria Lactobacillus and Bifidobacterium. In contrast, Proteus abundance was significantly increased in urine of patients with stagnated/worsened wound evolution (n = 6) (p = 0.003). This study proposes urinary microbiota as a complementary factor indirectly associated with the wound evolution and patient cure. It opens new perspectives for further investigations based on multiple body microbiome comparison to describe the complete scenario of the transmission dynamics of wound‐colonizing microorganisms. [ABSTRACT FROM AUTHOR]

Introduction: Abnormal levels of heavy metals (HM) and trace elements (TE) affect body metabolism and can induce carcinogenesis. This study aims to evaluate the role of HM and TE in carcinoma urinary bladder (CAUB). Methods: Patients with biopsy-proven CAUB (n = 100) were taken as the study group, while age-and sex-matched healthy volunteers were taken as control (n = 100). Blood and urine samples were compared for Arsenic (As), Copper (Cu), Manganese (Mn), Selenium (Se), Cadmium (Cd), Lead (Pb), and Mercury (Hg) levels. Serum glutathione peroxidase (GSH-Px), superoxide dismutase (SOD), and lipid peroxidation (LPO) levels were assessed to know the redox status between the two groups. Results: A significantly higher blood level of As, Mn, and Pb was observed in CAUB cases as compared to controls. Blood Se level was significantly lower in CAUB patients. On comparing urinary levels, CAUB patients had a higher As, Mn, and Pb levels compared to controls. Further, 68% and 59% of patients had their blood and urinary HM and TE levels above the permitted level, respectively. CAUB cases also had a lower GSH-Px (113.5 ± 44.7 vs. 163.9 ± 120.5, P = 0.0002), lower SOD levels (11.35 ± 5.6 vs. 13.75 ± 3.9, P = 0.008), and a higher LPO levels (15.5 ± 14.7 vs. 11.18 ± 11.2, P = 0.02) in the serum. Conclusions: A significantly higher concentration of As, Mn, and Pb was noted in the blood and urine of CAUB patients compared to controls. CAUB cases also had lower serum GSH-Px and SOD levels with a concomitant increased serum LPO assay suggesting underlying oxidative stress. [ABSTRACT FROM AUTHOR]

A retrospective analysis of urine culture results was conducted for adult patients treated between 1 January 2017 and 31 December 2021 at the Department of Gastroenterology in Rzeszow (southern Poland). A total of 102 patients were sampled for microbiological tests during the analyzed period, with microbial growth found in 30 samples. The purpose of our study was to determine the predominant bacterial species present in the urine of patients hospitalized in the Department of Gastroenterology, as well as their drug susceptibility. The data obtained from medical records included, for example, urine culture results and the antibiotic susceptibility of the isolated microorganisms. The material for the study was collected according to the current procedures. During the analyzed period, urine was collected from a total of 102 patients, and 30 positive samples were found. The predominant pathogen was Escherichia coli (n = 10 (33.33% of all positive results), p < 0.001); the second most common microorganism was Enterococcus faecalis (n = 5 (16.67% of all positive results), p < 0.001). In vitro susceptibility testing showed E. coli, ESBL (ESBL strain with extended-spectrum beta-lactamase) (n = 2 (6.67% of all positive results), p = 0.055) and Klebsiella pneumoniae, ESBL (n = 3 (10% of all positive results), p = 0.005). Urinary tract infection (UTI) was an extremely common problem. [ABSTRACT FROM AUTHOR]

Introduction: Antibiotic use during endourological procedures is often discordant from the reported guidelines, despite the potential risks of antibiotic resistance, adverse effects, and health-care costs. A nationwide audit was conducted, with the support of the Urological Society of India, to ascertain the current antibiotic prescription practices for the endourological procedures and the reasons associated with them. Methods: A multi-institutional, national-level, cross-sectional audit analyzing elective endourological procedures was performed. The data regarding the disease profile; risk factors for infectious complications; urine culture; pre-, per-, and post-operative antibiotic use; additional antibiotic use; and patient demographics were collected in a standardized pro forma. Reasons for prescribing antibiotics divergent from the guideline recommendations were also noted. Any infectious complication that necessitated the antibiotic use was also noted prospectively up to 1 month. All the data were entered into a single centralized and customized online portal on a real-time basis. Results: One thousand five hundred and thirty-eight cases were recruited from 20 hospitals. A single-dose prophylaxis was prescribed in only 319 (20.7%) of the cases, and the majority received a multi-day prophylaxis. A combination of two or more antibiotics was prescribed as the prophylaxis in 51% of the cases. One thousand three hundred and fifty-six (88.2%) cases were continued on a long-duration prophylaxis after the discharge, with 1191 (77.4%) receiving it for > 3 days. One thousand one hundred and sixty (75.4%) cases received a guideline-discordant prophylaxis solely on the basis of the surgeon's or institution's protocol, rather than any specific case based need. Ninety eight (6.4%) cases developed postoperative urinary tract infection. Conclusions: Multi-dose, combination and post-discharge antibiotic prophylaxis for endourological surgeries is highly prevalent in India. This audit highlights the huge potential to reduce such guideline-discordant overuse of antibiotics during the endourological procedures. [ABSTRACT FROM AUTHOR]

Simple Summary: Prostate cancer (PCa) is the most common cancer diagnosed among men aged 50 years and older. There is gaining interest in the genitourinary microbiome in developing ways to control this disease. In this work, an analysis of the bacterial microbiota was performed from urine samples, glans secretions, and prostate biopsies from patients with PCa, and the results were investigated and compared with non-PCa patients. Our results showed a distinct clustering of genera associated with urine samples and prostate biopsies of PCa and non-PCa patients. Observed microbial dysbiosis may increase chronic inflammation and ultimately prostate carcinogenesis. Future research on the biological functions of the uropathogens found is needed to understand their impact on the pathogenesis of PCa. Prostate cancer (PCa) is the most common malignant neoplasm with the highest worldwide incidence in men aged 50 years and older. Emerging evidence suggests that the microbial dysbiosis may promote chronic inflammation linked to the development of PCa. Therefore, this study aims to compare the microbiota composition and diversity in urine, glans swabs, and prostate biopsies between men with PCa and non-PCa men. Microbial communities profiling was assessed through 16S rRNA sequencing. The results indicated that α-diversity (number and abundance of genera) was lower in prostate and glans, and higher in urine from patients with PCa, compared to non-PCa patients. The different genera of the bacterial community found in urine was significantly different in PCa patients compared to non-PCa patients, but they did not differ in glans and prostate. Moreover, comparing the bacterial communities present in the three different samples, urine and glans show a similar genus composition. Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed significantly higher levels of the genera Streptococcus, Prevotella, Peptoniphilus, Negativicoccus, Actinomyces, Propionimicrobium, and Facklamia in urine of PCa patients, whereas Methylobacterium/Methylorubrum, Faecalibacterium, and Blautia were more abundant in the non-PCa patients. In glans, the genus Stenotrophomonas was enriched in PCa subjects, while Peptococcus was more abundant in non-PCa subjects. In prostate, Alishewanella, Paracoccus, Klebsiella, and Rothia were the overrepresented genera in the PCa group, while Actinomyces, Parabacteroides, Muribaculaceae sp., and Prevotella were overrepresented in the non-PCa group. These findings provide a strong background for the development of potential biomarkers with clinical interest. [ABSTRACT FROM AUTHOR]

BACKGROUND: Microbiome dysbiosis plays a role in the pathogenesis of many urological diseases, including bladder cancer (BC). The aim of the study was to compare the urinary and gut microbiota of patients with BC with a healthy control (HC) group. METHODS: The study group included patients hospitalized in 2020 to 2021 with diagnosed BC and HC. Prior to the transurethral resection of bladder tumor, patients collected their urine and stool which was then subjected to 16S rRNA gene sequencing. RESULTS: Overall, 25 patients were enrolled in the study: 18 in the BC group and 7 in the HC group. Analysis of the urine and stool microbiome showed no statistically significant differences between patients with BC and HC in alpha diversity, beta diversity, and difference in taxa relative abundance. Detailed analysis of urine and stool microbiome depending on patient- and tumor-related characteristics also showed no statistically significant differences in alpha diversity and beta diversity. Differences in abundance (ANCOM) were noted in both types of samples in patients with BC. In the urine test, genus Lactobacillus was more common in patients with a positive history of Bacillus Calmette--Guérin (BCG) therapy, while genus Howardella and the strain Streptococcus anginosus were more common in women. In stool samples, abundance of phylum Desulfobacterota was most abundant in Grade G1 and least in G2. Class Alphaproteobacteria, order Rhodospirillales, order Flavobacteriales, and family Flavobacteriaceae were more common in women. CONCLUSIONS: The microbiome of urine and stool of patients with BC does not differ significantly from that of HC; however, its composition in patients with BC varies according to the patient's sex. [ABSTRACT FROM AUTHOR]

Introduction: We aimed to identify the molecular diagnostic techniques available for urinary tract infection (UTI) diagnosis and their accuracy compared to traditional urinary culture. Methods: A systematic search was performed in MEDLINE (OVID), EMBASE, LILACS, and the Cochrane Central Register of Controlled Trials (CENTRAL). The populations were adult and pediatric patients with confirmed UTI by reference standard urine culture. The index test for the diagnosis of UTI was any molecular diagnostic technique. The primary outcome was the diagnosis of UTI with measures of sensitivity, specificity, positive and negative predictive values (PPV and NPV, respectively), positive likelihood ratio (LR+), negative likelihood ratio (LR-), diagnostic odds ratio (DOR), and area under the curve (AUC). The operative characteristics were determined, and a meta-analysis was performed. The evaluation of each included study was performed with the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool. Results: We identified 1230 studies with the search strategies. Ultimately, 13 studies met the inclusion criteria for qualitative analysis, and seven were included for the meta-analysis. Four molecular techniques were identified; however, it was only possible to synthesize the information from two of them. In multiplex polymerase chain reaction (PCR) meta-analysis, overall sensitivity was 0.80 (95% confidence interval [CI] 0.73-0.86) and specificity was 0.83 (95% CI 0.52-0.95). For the DOR, the overall result was 21 (95% CI 4.8-95). For reverse transcription (RT)-PCR, sensitivity was 0.94 (95% CI 0.73-0.99) and specificity was 0.59 (95% CI 0.063-0.96). For the DOR, the overall result was 23 (95% CI 1.1-467). Conclusions: Multiplex PCR and RT-PCR are molecular techniques that might be comparable to standard urine culture for UTI diagnosis. Refinement of these new diagnostic tools will avoid unnecessary antimicrobial therapy and the consequent development of drug-resistant resistant pathogens, as well as improve the ability to identify patients at risk and prevent or minimize sequelae derived from the infection. [ABSTRACT FROM AUTHOR]

Introduction: To understand the role of the urinary microbiome in disease states and interpret non-culture-based diagnostic urine testing of midstream urine specimens, we must have a better understanding of the urinary microbiome in asymptomatic, healthy individuals. We examined the impact of gender, age, and menopausal status on the healthy human urinary microbiome in asymptomatic control subjects enrolled in the multi-institution National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Multidisciplinary Approach to the Study of Chronic Pelvic Pain Network (MAPP) study. Methods: Asymptomatic, healthy controls, recruited to be ageand sex-matched to patients in the Trans-MAPP Epidemiology and Phenotyping Study, provided midstream urine collection for polymerase chain reaction (PCR)-electrospray ionization mass spectrometry identification of urinary microbiota. The microbiomes of male and female participants were described and analyzed for differences in composition and diversity at the species and genus level by sex, age, and, in females, by menopausal status. Results: Sixty-six total species were detected with a mean of 1.2 species (standard deviation [SD] 1.1) per male (n=97; mean age=43) and 2.3 (SD 1.3) per female (n=110, mean age=38) in asymptomatic, healthy controls. Species and genera diversity analyses showed significantly greater richness and diversity in females. With regard to species, Bifidobacterium subtile, Lactobacillus crispatus, and Lactobacillus johnsonii were more predominant in females. The genera Bifidobacterium, Staphylococcus, Lactobacillus, and Corynebacterium were more predominant in females, while for males the most prevalent organisms included Staphylococcus and Propionibacterium; only Propionibacterium approached a significant difference between genders. No significant difference in the presence and/or diversity of micro-organisms with menopausal status could be observed. Sex-specific age trends, particularly diversity, were larger for females than males. Conclusions: These results suggest the urinary microbiome of healthy, asymptomatic subjects differed between genders and age in females, but not menopausal status. Gender differences may be attributable to the detection of urethral/vaginal organisms in females and prostate organisms in males. These findings will better allow us to interpret the results of microbiome reports in the midstream urine specimens of patients with urinary symptoms. [ABSTRACT FROM AUTHOR]

Phosphorus is essential for food production and its supply is limited. Urine is an excellent source of phosphorus and one way to produce fertilizer is through conversion of urine to struvite (MgNH 3 PO 4 .6H 2 O). The present study aimed to understand the bacterial portion of the microbial community composition and dynamics of plasmid-mediated antimicrobial resistant genes during the optimized process of struvite production from composite human urine. Samples for DNA extraction was collected from fresh urine, stored urine and struvite during the process of struvite production. Shotgun metagenomic analysis was employed to understand the bacterial community. The most dominant phyla in the fresh and stored urine samples were Pseudomonadata, which comprised of 60% and 43% respectively, followed by Bacillota, comprised of 25% and 39% respectively. The struvite sample was dominated by the phylum Bacilliota (61%), Pseudomonadota (18%) and bacteroidota (12%). Members of the above phyla persisted in dominating each sample accordingly. Member of the family Morganellaceae was dominant in the fresh sample while the stored urine and struvite samples were dominated by the family Clostridiaceae. A decrease of members of the class Gammaproteobacteria was observed from the fresh to the struvite sample though not statistically significant. The genus Pseudomonas remained to be the most dominant member of Gammaproteobacteria in the fresh and stored urine sample with OTU count of 12,116 and 6,155 with a marked decrease by half in the stored sample. On the other hand, members of the genera Clostridium, Enterococcus, Bacteroides in the stored samples and Clostridium, Alkaliphilus and Pseudomonas in the struvite samples were dominant. 96% of the identified genera were shared in all the samples and the antimicrobial resistance genes (ARGs) identified in the fresh urine were shared by the struvite but not by the stored urine (e.g. sul, cat, aph and aac members). The presence of high abundance of ARGs in struvite needs attention in the persistence and transmissibility of the ARGs before application for agriculture., (© 2024. The Author(s).)

Introduction: Urinary tract infections (UTIs) pose a significant health concern, particularly among pregnant women, for whom accurate diagnosis is essential. However, the use of Urine flow cytometry (UF) for detecting UTIs in this demographic often results in misdiagnosis. The objective of this study was to explore the reasons behind these diagnostic errors and to develop a strategy to minimize the rate of UTI misdiagnosis in pregnant women., Material and Methods: The study enrolled 1,200 women aged 18 to 40 years, categorized into pregnant and non-pregnant groups. UTIs were diagnosed using urine bacterial culture, microscopic examination, and UF, followed by statistical analysis to identify any discrepancies in diagnosis between the groups. Following the calibration of UF analyzer's parameters, the most effective CR(WBC)-CW-FSC-P Gain setting for diagnosing UTIs in pregnant women through UF was ascertained by applying the Youden index., Results: The clinical diagnosis rate of UTIs was significantly higher in pregnant women (40.91%) compared to non-pregnant women (20.26%). However, urine microscopy and bacterial culture showed no significant difference in the rates of UTIs between the two groups, suggesting a potential for misdiagnosis. The false-positive rate for WBCs detected by UF was 30.43%, and adjusting the CR(WBC)-CW-FSC-P Gain value of UF reduced the false-positive rate to 9.45%., Conclusion: The incidence of UTIs in pregnant women may be overestimated because of the limitations inherent to UF. Adjusting the parameters of the UF analyzer, particularly the CR(WBC)-CW-FSC-P Gain value, can significantly reduce the rate of UTI misdiagnosis in pregnant women., Competing Interests: The authors have declared that no competing interests exist, (Copyright: © 2024 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Introduction: While the definitive diagnosis of urinary tract infection (UTI) requires a positive urine culture, the likelihood of UTI can be determined by urinalysis that includes white blood cell (WBC) count. We aimed to determine the optimal urine WBC threshold in urinalysis to predict UTIs in children presenting at the emergency department (ED)., Method: We performed a prospective observational study in the ED at KK Women's and Children's Hospital for children below 18 years old who underwent both urine microscopy and urine cultures, between 10 January and 7 November 2022. We assessed the various urine WBC thresholds associated with culture-proven UTIs using sensitivity, specificity, positive and negative predictive values, positive and negative likelihood ratios, and area under receiver operating characteristic curve., Results: We found a culture-proven UTI rate of 460/1188 (38.7%) among all patients analysed, and 278/998 (27.9%) among those with nitrite-negative urine samples. Among all patients, a urinalysis WBC threshold of 100/μL had a sensitivity of 82.2% (95% confidence interval [CI] 78.4-85.5) and negative predictive value of 86.2% (95% CI 83.6-88.4). Among those who were nitrite-negative, a WBC threshold of ≥100/μL resulted in a potential missed rate of 48/278 (17.3%). By lowering the WBC threshold to ≥10/μL, the potential missed cases reduced to 6/278 (2.2%), with an estimated increase in 419 urine cultures annually., Conclusion: A urine microscopy WBC threshold of ≥100/μL results in a clinically significant number of missed UTIs. Implementation of various thresholds should consider both the potential missed UTI rate and the required resource utilisation.

Small colony variants (SCVs) in Klebsiella pneumoniae are rare and understudied. We report an SCV of Klebsiella pneumoniae isolated from the urine of a prostate cancer patient undergoing prolonged radiotherapy. The strain was non-lactose fermenting, non-mucoid, slow-growing, multi-drug resistant, and showed atypical biochemical reactions and biofilm formation. On whole genome sequencing, it showed low-level virulence, sequence type 231 and gene CTX-M-15. Three major porins OmpK35, OmpK36 and OmpK37 were found. SCVs pose challenges like difficulties in identification, altered metabolism, and increased biofilm formation, which contribute to persistent infections. Radiotherapy and chemotherapy may have led to the formation of the SCV phenotype., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Klebsiella pneumoniae is a global public health concern due to the rising myriad of hypervirulent and multidrug-resistant clones both alarmingly associated with high mortality. The molecular mechanisms underpinning these recalcitrant K. pneumoniae infection, and how virulence is coupled with the emergence of lineages resistant to nearly all present-day clinically important antimicrobials, are unclear. In this study, we performed a genome-wide screen in K. pneumoniae ECL8, a member of the endemic K2-ST375 pathotype most often reported in Asia, to define genes essential for growth in a nutrient-rich laboratory medium (Luria-Bertani [LB] medium), human urine, and serum. Through transposon directed insertion-site sequencing (TraDIS), a total of 427 genes were identified as essential for growth on LB agar, whereas transposon insertions in 11 and 144 genes decreased fitness for growth in either urine or serum, respectively. These studies not only provide further knowledge on the genetics of this pathogen but also provide a strong impetus for discovering new antimicrobial targets to improve current therapeutic options for K. pneumoniae infections., Competing Interests: JG, VT, EG, SM, DS, CC, LW, ZL, JB, MM, KD, CI, JR, TS, PL, AC, JC, IH No competing interests declared, (© 2023, Gray, Torres et al.)

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major human pathogen and a research priority for developing new antimicrobial agents. CRAB is a causative agent of a variety of infections in different body sites. One of the manifestations is catheter-associated urinary tract infection, which exposes the bacteria to the host's urine, creating a particular environment. Exposure of two CRAB clinical isolates, AB5075 and AMA40, to human urine (HU) resulted in the differential expression levels of 264 and 455 genes, respectively, of which 112 were common to both strains. Genes within this group play roles in metabolic pathways such as phenylacetic acid (PAA) catabolism, the Hut system, the tricarboxylic acid (TCA) cycle, and other processes like quorum sensing and biofilm formation. These results indicate that the presence of HU induces numerous adaptive changes in gene expression of the infecting bacteria. These changes presumably help bacteria establish and thrive in the hostile conditions in the urinary tract. These analyses advance our understanding of CRAB's metabolic adaptations to human fluids, as well as expand knowledge on bacterial responses to distinct human fluids containing different concentrations of human serum albumin (HSA)., (© 2024. The Author(s).)

The relationship between urinary system tumors and urothelial microorganisms remains unexplored. This study is aimed at exploring the relationship between urinary flora and urinary tumors and identifying potential biomarkers for urinary tumors and new targets for prevention. We included four healthy adults (control group) and six patients diagnosed with urinary tract tumors (tumor group). In both groups, 10 and 50 ml clean middle urine samples were reserved. The 10 ml samples were analyzed (including pH, specific gravity, and leukocytes) using an automatic urine analyzer, and the 50 ml samples were analyzed by DNA extraction, 16S rRNA gene amplification, and high-throughput sequencing. The correlation between routine urine analysis and sequencing results was also analyzed. Testing using the DESeq2 method showed that, at the order level, there were significant differences in the abundance of Caulobacterales between the urinary flora of the two groups (P < 0.05); family level, Bacteroidaceae, Actinomycetaceae, and Tsukamurellaceae (P < 0.05); genus level, Finegoldia, Varibaculum, Actinobaculum, Propionimicrobium, Bacteroides, Brevundimonas, and Tsukamurella (P < 0.05). LEfSe analysis found specific bacteria at the genus level in the urinary flora of the tumor group, namely, Finegoldia (genus Digestiflora) (P < 0.001) and Varibaculum (P < 0.001). Further correlation analysis showed that both species were positively correlated with the urine pH (P < 0.05). PICRUSt analysis showed significant differences in the two functional pathways of cell transformation and metabolism (P < 0.05). Combined with the results of bioinformatics analysis, some differential bacteria may be new biomarkers for urologic tumors, and there may be a correlation between urine pH and tumor occurrence. However, large-scale prospective studies and in vitro and in vivo experiments are required to further test and verify these findings. [ABSTRACT FROM AUTHOR]

Key content: Bladder pain syndrome (BPS) presents as a spectrum of urological symptoms with poorly understood pathophysiology. Bladder mucosal injury secondary to low grade sub‐clinical infection is a possible trigger, leading to nociceptive upregulation and, subsequently, central sensitisation.Brain abnormalities associated with BPS suggest that neuropathological brain alterations exist, which may contribute to the perceived pain.Central sensitisation plays a role in the disease pathophysiology via an augmentation in the responsiveness of the central pain signalling neurons.The urinary microbiome is implicated as a trigger for the development and maintenance of BPS.Future directions to improve treatment strategies include stratification of patients with BPS into subtypes such as peripheral or central disease and investigation of the urinary microbiome and bladder barrier replacement. Learning objectives: To update clinicians' knowledge of current research into the urinary microbiome and pain sensitisation in BPS pathophysiology.To understand the biodiversity and abundance of urinary microbes and the role of peripheral and central pain sensitisation, which will help identify future management techniques for BPS. Ethical issues: What are the consequences of long‐term antibiotics use for BPS management on bacterial resistance? [ABSTRACT FROM AUTHOR]

Background. Rapid and reliable tests are essential for the diagnostic laboratory confirmation of urinary tract infections (UTIs). Until now, UTI has been confirmed by the microbiology culture of urine, requiring at least 48-hour turnaround time (TAT), with a standardized microscopic method being widely favored. Automated urine flow cytometry, however, has recently been used to improve the rapid TAT by analyzing the urine sediment. This study therefore aimed to compare the diagnostic value of the Shih-Yung conventional microscopic and urine flow cytometry methods in the detection of leukocyte and bacterial parameters of patients with UTIs in an outpatient clinic. Methods. A cross-sectional study was conducted on a total of 100 patients. Seventy urine samples were positive for leukocytes and nitrite chemistry, and 30 were negative for both. The measurements of urine leukocytes and bacteria were compared between Sysmex UF-5000 urine flow cytometry and the Shih-Yung method. The diagnostic value was obtained from ROC analysis of urine flow cytometry and the culture. Results. A leukocyte cutoff value of 87.2/μL had a sensitivity and specificity of 98.33% and 95%, respectively, and 98.33% sensitivity and 75% specificity at a bacterial cutoff of 582.22/μL. Interestingly, our study identified strong and consistent agreement of leukocyte and bacterial parameters between urine flow cytometry and Shih-Yung (k = 0.959, p < 0.001 and k = 0.939, p < 0.001 , respectively). Furthermore, through analyzing the dominance angle of the scattergram, a strong agreement was obtained with the culture result (k = 0.880, p < 0.001). Conclusions. The Shih-Yung method showed consistent agreement with urine flow cytometry for the detection of leukocytes and bacteria. The use of certain cutoffs for bacterial and leukocyte parameters in urine flow cytometry demonstrated very good performance in detecting acquired symptomatic UTIs. [ABSTRACT FROM AUTHOR]

Objectives: Urinalysis by automated urine analyzer, including microscopy and dipstick test, is easy, rapid, and inexpensive. Among these parameters, leukocyte count (WBC) or leukocyte esterase (LE) has relatively sufficient sensitivity in urinary tract infection (UTI) detection. Urine culture is accepted as the gold standard for the diagnosis of UTI. Unnecessary culture requests constitute the majority of the microbiology laboratory workload. This study aimed to evaluate the performance of a multi-criteria algorithm by using urinalysis in predicting negative urine cultures. Methods: During a 2-week period, randomly selected 600 urine samples that reached the microbiology laboratory for urine culture were subjected to chemical and microscopic urinalysis without waiting. Urinalysis was performed using Iris iQ200 (Iris Diagnostics, Chatsworth, USA). LE >25 µL-1, nitrite positive, and WBC >5 per HPF were accepted as abnormal/positive. The sensitivity and specificity were also calculated by Receiver operating characteristic analysis at alternative threshold values for all small particles. A multi-criteria algorithm based on these urine parameters was developed, and its performance was evaluated by determining specificity, sensitivity, negative predictive value (NPV), and positive predictive value. Results: Multi-criteria algorithm based on urinalysis gave false-negative results for only 3 (0.5%) samples. This algorithm had 98.9% NPV and eliminated 47.4% of urine samples from the culture workflow. Conclusion: This algorithm may reduce unnecessary culture requests and more effective use of time and resources. [ABSTRACT FROM AUTHOR]

Copyright of Ahi Evran Medical Journal is the property of Ahi Evran University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Neonatal infections including sepsis and urinary tract infections are considered among the leading causes of mortality in neonatal intensive care units (NICU). Thus, use of empiric antibiotics is very important in infected neonates and the success of this practice is mainly reliant on the availability of an up-to-date antibiogram for currently used antibiotic drugs. In this study, we aim to determine the bacteriological profile and antibiotic susceptibility pattern of bacteria isolated from blood or/and urine cultures belonging to patients at the NICU. A total of 54 urine samples were collected in the period between January 2015 and December 2019. Data of infants with positive urine and blood bacterial isolates were gathered retrospectively. The most commonly isolated bacteria from urine observed were K. pneumoniae (44%) and E. coli (39%), while Acinetobacter baumannii (33%) and K. pneumoniae (22%) predominated in neonatal blood samples. The majority of uropathogens and blood isolates exhibited low resistance to imipenem and tigecycline, respectively. These antibiotics would be recommended for future use as empirical treatment in neonates with urinary tract infections and/or sepsis. This investigation highlights the importance of surveillance studies to manage and ensure the effectiveness of treatment plan for critically ill infants. [ABSTRACT FROM AUTHOR]

Objective. To analyze the potential risk factors that affect the development of urosepsis following uroscopic minimally invasive lithotripsy and to develop a nomogram that predicts the probability of postoperative urosepsis. Methods. We retrospectively analyzed the clinical data from patients that underwent percutaneous nephrolithotripsy (PCNL) or ureteroscopic lithotripsy (URL) between January 2018 and December 2019. The enrolled patients were grouped twice according to systemic inflammatory response syndrome (SIRS) and quick sequential organ failure assessment (qSOFA). After univariate and multivariate logistic regression analyses, we identified the independent predictive factors affecting the development of postoperative SIRS and urosepsis, and built the nomograms. Results. From January 2018 to December 2019, 1959 patients underwent PCNL or URL, of whom 236 patients were accorded with the inclusion criteria. Of all 236 patients, 64 (27.12%) patients developed postoperative SIRS, and 17 (7.20%) patients developed postoperative urosepsis. Multivariate logistic regression analysis showed that positive preoperative urine culture (PUC+) (OR = 2.331 , P = 0.044), procalcitonin (PCT) (OR = 1.093 , P = 0.037), C-reactive protein (CRP) (OR = 1.017 , P < 0.001), and neutrophil ratio (NEUT%) (OR = 1.091 , P = 0.004) of postoperative were independent predictors of SIRS, and PCT (OR = 1.017 , P = 0.003) and CRP (OR = 1.080 , P < 0.001) were independent predictors of urosepsis. Additionally, the nomograms demonstrated good accuracy in predicting SIRS and urosepsis with a C-index of 0.884 (95% CI: 0.835-0.934) and 0.941 (95% CI: 0.885-0.996), respectively. Conclusions. The nomograms achieved the prediction of SIRS and urosepsis after uroscopic minimally invasive lithotripsy. Using this model, the risk of SIRS or urosepsis for an individual patient can be determined, which facilitates early diagnosis and rational treatment. [ABSTRACT FROM AUTHOR]

Aim: Asymptomatic bacteriuria (ASB) and symptomatic bacteriuria with antibiotic-resistant organisms are common in patients with type 2 diabetes. The aim was to study the prevalence, bacterial profile and antibiotic susceptibility pattern in ASB and symptomatic bacteriuria and the factors associated with Escherichia coli bacteriuria in type 2 diabetes. Materials and Methods: This was an observational case-control study done on 400 asymptomatic type 2 diabetes patients, 200 symptomatic urinary tract infection (UTI), and 200 nondiabetic controls. Various clinical, biochemical parameters and urine examination and culture were studied. Results: The prevalence of ASB and symptomatic bacteriuria in type 2 diabetes was 17.5% and 69%, respectively, and were significantly higher as compared to controls (10%). E. coli was present in 52.9% of ASB cases of type 2 diabetes and 70% of nondiabetic control ASB. E. coli (55%) was most commonly isolated in symptomatic bacteriuria. Majority of the Gram-negative bacteria isolates in ASB and symptomatic bacteriuria with type 2 diabetes and controls were sensitive to amikacin, imipenem, piperacillin/tazobactam, and nitrofurantoin. E. coli were more resistant to quinolones in ASB and symptomatic bacteriuria than controls. Most of the Gram-positive bacteria were sensitive to vancomycin, linezolid, and amoxiclav. The factors associated with E. coli bacteriuria in type 2 diabetes were female gender, long duration of diabetes, past history of symptomatic UTI, poor glycemic control, and renal function. Conclusions: E. coli remains the most common isolated microorganism in asymptomatic and symptomatic bacteriuria. E. coli were more resistant to quinolones in patients with type 2 diabetes. [ABSTRACT FROM AUTHOR]

Copyright of Revista Gaucha de Enfermagem is the property of Revista Gaucha de Enfermagem and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: While the urogenital microbiota has recently been characterized in healthy male and female dogs, the influence of sex hormones on the urogenital microbiome of bitches is still unknown. A deeper understanding of the cyclic changes in urinary and vaginal microbiota would allow us to compare the bacterial populations in healthy dogs and assess the impact of the microbiome on various urogenital diseases. Therefore, the aim of this study was to characterize and compare the urogenital microbiota during different phases of the estrous cycle in healthy female dogs. DNA extraction, 16 S rDNA library preparation, sequencing and informatic analysis were performed to determine the vaginal and urinary microbiota in 10 healthy beagle dogs at each phase of the estrous cycle., Results: There were no significant differences in alpha and beta diversity of the urinary microbiota across the different cycle phases. Similarly, alpha diversity, richness and evenness of vaginal bacterial populations were not significantly different across the cycle phases. However, there were significant differences in vaginal beta diversity between the different cycle phases, except for between anestrus and diestrus., Conclusion: This study strongly suggests that estrogen influences the abundance of the vaginal microbiota in healthy female dogs, but does not appear to affect the urinary microbiome. Furthermore, our data facilitate a deeper understanding of the native urinary and vaginal microbiota in healthy female dogs., (© 2024. The Author(s).)

Lactobacillus species are common inhabitants of the 'healthy' female urinary and vaginal communities, often associated with a lack of symptoms in both anatomical sites. Given identification by prior studies of similar bacterial species in both communities, it has been hypothesized that the two microbiotas are in fact connected. Here, we carried out whole-genome sequencing of 49 Lactobacillus strains, including 16 paired urogenital samples from the same participant. These strains represent five different Lactobacillus species: L. crispatus , L. gasseri , L. iners , L. jensenii , and L. paragasseri . Average nucleotide identity (ANI), alignment, single-nucleotide polymorphism (SNP), and CRISPR comparisons between strains from the same participant were performed. We conducted simulations of genome assemblies and ANI comparisons and present a statistical method to distinguish between unrelated, related, and identical strains. We found that 50 % of the paired samples have identical strains, evidence that the urinary and vaginal communities are connected. Additionally, we found evidence of strains sharing a common ancestor. These results establish that microbial sharing between the urinary tract and vagina is not limited to uropathogens. Knowledge that these two anatomical sites can share lactobacilli in females can inform future clinical approaches.

Purpose: To investigate urine microbiome differences among healthy women, women with recurrent uncomplicated cystitis (rUC), and those with sporadic/single uncomplicated cystitis (sUC) to challenge traditional beliefs about origins of these infections., Materials and Methods: Patients who underwent both conventional urine culture and next-generation sequencing (NGS) of urine were retrospectively reviewed. Symptom-free women with normal urinalysis results as a control group were also studied. Samples were collected via transurethral catheterization., Results: In the control group, urine microbiome was detected on NGS in 83.3%, with Lactobacillus and Prevotella being the most abundant genera. The sensitivity of urine NGS was significantly higher than that of conventional urine culture in both the sUC group (91.2% vs. 32.4%) and the rUC group (82.4% vs. 16.4%). In urine NGS results, Enterobacterales , Prevotella , and Escherichia / Shigella were additionally found in the sUC group, while the recurrent urinary tract infection (rUTI)/rUC group exhibited the presence of Lactobacillus , Prevotella , Enterobacterales , Escherichia / Shigella , and Propionibacterium . Moreover, distinct patterns of urine NGS were observed based on menopausal status and ingestion of antibiotics or probiotics prior to NGS test sampling., Conclusions: Urine microbiomes in control, sUC, and rUTI/rUC groups exhibited distinct characteristics. Notably, sUC and rUC might represent entirely separate pathological processes, given their distinct urine microbiomes. Consequently, the use of urine NGS might be essential to enhancing sensitivity compared to conventional urine culture in both sUC and rUTI/rUC groups., Competing Interests: The authors have nothing to disclose., (© The Korean Urological Association.)

Background: Urinary tract infection is one of the most common infections in humans, affecting women in more proportion. The bladder was considered sterile, but it has a urinary microbiome. Moreover, intracellular bacteria (IB) were observed in uroepithelial cells from children and women with urinary tract infections (UTIs). Here, we evaluated the presence of IB in urine from healthy people and patients with UTI symptoms., Methods: Midstream urine was self-collected from 141 donors, 77 females and 64 males; 72 belonged to the asymptomatic group and 69 were symptomatic. IB was characterized by a culture-dependent technique and visualized by confocal microscopy. Urine was also subjected to the classical uroculture and isolated bacteria were identified by MALDI-TOF., Results: One-hundred and fifteen uroculture were positive. A significant association was observed between the presence of symptoms and IB (P = 0.007). Moreover, a significant association between the presence of IB, symptoms and being female was observed (P = 0.03). From the cases with IB, Escherichia coli was the most frequent microorganism identified (34.7%), followed by Stenotrophomonas maltophilia (14.2%), Staphylococcus spp (14.2%), and Enterococcus faecalis (10.7%). Intracellular E. coli was associated with the symptomatic group (P = 0.02). Most of the intracellular Staphylococcus spp. were recovered from the asymptomatic group (P = 0.006)., Conclusions: Intracellular bacteria are present in patients with UTI but also in asymptomatic people. Here, we report for the first time, the presence of S. maltophilia, Staphylococcus spp., and Enterobacter cloacae as intracellular bacteria in uroepithelial cells. These findings open new insights into the comprehension of urinary tract infections, urinary microbiome and future therapies. Uroculture as the gold standard could not be enough for an accurate diagnosis in recurrent or complicated cases., (© 2024. The Author(s).)

Background: Accumulated evidences indicate that dysbiosis of the urinary microbiota is associated with kidney stone formation. In the present study, we aimed to investigate the urinary microbiota composition and functionality of patients with calcium oxalate stones and compare it with those of healthy individuals., Method: We collected bladder urine samples from 68 adult patients with calcium oxalate stones and 54 age-matched healthy controls by transurethral catheterization. 16S rRNA gene and shotgun sequencing were utilized to characterize the urinary microbiota and functionality associated with calcium oxalate stones., Results: After further exclusion, a total of 100 subjects was finally included and analyzed. The diversity of the urinary microbiota in calcium oxalate stone patients was not significantly different from that of healthy controls. However, the urinary microbiota structure of calcium oxalate stone formers significantly differed from that of healthy controls (PERMANOVA, r = 0.026, P = 0.019). Differential representation of bacteria (e.g., Bifidobacterium ) and several enriched functional pathways (e.g., threonine biosynthesis) were identified in the urine of calcium oxalate stone patients., Conclusion: Our results showed significantly different urinary microbiota structure and several enriched functional pathways in calcium oxalate stone patients, which provide new insight into the pathogenesis of calcium oxalate stones., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Xie, Zhang, Guo, Yuan, Xiao and Yuan.)

Bacterial isolates from the human urinary microbiome have been extensively studied for their antibiotic resistance; however, little work has been done on those isolates that are difficult to grow in vitro . This study was designed to qualify a serum-based medium, New York City Broth III (NYCIII), and a broth microdilution method to determine the antibiotic susceptibility of previously underreported or undescribed microbes that have a difficult time growing in standard Mueller-Hinton broth. Here, we demonstrate that NYCIII microbroth dilution can be an effective method for the determination of antibiotic susceptibility of species found in the human urinary microbiome. We show that this method serves well to characterize fastidious and anaerobic urinary microbes that have no Clinical and Laboratory Standards Institute (CLSI) guidelines, including several in the families Aerococcaceae , Lactobacillaceae , or Actinomycetaceae . Previous studies using expanded quantitative urine culture reveal that urine samples from clinical patients are commonly polymicrobial in composition. Thus, we test whether NYCIII can serve as a viable harmonized medium, capable of supporting antibiotic susceptibility testing in a range of fastidious, non-fastidious, and anaerobic urinary microbes. We propose this methodology to be standardized comparable to CLSI standards to allow for resistance testing in uncharacterized urinary bacteria., Importance: Antibiotic susceptibilities of fastidious and anaerobic bacteria of the human urinary microbiome are largely underreported due to difficulty in growing them in the lab environment. The current standard medium, Muller-Hinton broth, has difficulty supporting the growth of many of these species, leaving microbiologists without a standardized method. To address this need, this study offers a methodology to survey susceptibilities in a high-throughput manner of these understudied microbes with a proposed harmonized medium, NYCIII, which is capable of supporting the growth of both fastidious and non-fastidious urinary microbes. Broader standardization of this method can allow for the development of antibiotic-resistant breakpoints of the many uncharacterized urinary microbes., Competing Interests: A.J.W. declares membership on the advisory boards of Pathnostics and Urobiome Therapeutics, and funding from Pathnostics. The other authors declare no conflicts of interest.

Background: The interplay between gut microbiota and metabolites in the early stages of sepsis-induced acute kidney injury (SA-AKI) is not yet clearly understood. This study explores the characteristics and interactions of gut microbiota, and blood and urinary metabolites in patients with SA-AKI., Methods: Utilizing a prospective observational approach, we conducted comparative analyses of gut microbiota and metabolites via metabolomics and metagenomics in individuals diagnosed with SA-AKI compared to those without AKI (NCT06197828). Pearson correlations were used to identify associations between microbiota, metabolites, and clinical indicators. The Comprehensive Antibiotic Resistance Database was employed to detect antibiotic resistance genes (ARGs), while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways informed on metabolic processes and microbial resistance patterns., Results: Our study included analysis of four patients with SA-AKI and five without AKI. Significant disparities in bacterial composition were observed, illustrated by diversity indices (Shannon index: 2.0 ± 0.4 vs. 1.4 ± 0.6, P = 0.230; Simpson index: 0.8 ± 0.1 vs. 0.6 ± 0.2, P = 0.494) between the SA-AKI group and the non-AKI group. N6, N6, N6-Trimethyl-L-lysine was detected in both blood and urine metabolites, and also showed significant correlations with specific gut microbiota (Campylobacter hominis and Bacteroides caccae, R > 0, P < 0.05). Both blood and urine metabolites were enriched in the lysine degradation pathway. We also identified the citrate cycle (TCA cycle) as a KEGG pathway enriched in sets of differentially expressed ARGs in the gut microbiota, which exhibits an association with lysine degradation., Conclusions: Significant differences in gut microbiota and metabolites were observed between the SA-AKI and non-AKI groups, uncovering potential biomarkers and metabolic changes linked to SA-AKI. The lysine degradation pathway may serve as a crucial link connecting gut microbiota and metabolites., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Xu, Xu, Zhu, Mao, Li, Kong, Zhu and Zhang.)

Introduction: Bacterial urinary tract infections (UTI) and some sexually transmitted infections (STI) can have overlapping signs and symptoms or nonspecific findings, such as pyuria on urinalysis. Furthermore, results from the urine culture and the nucleic acid amplification test for an STI may not be available during the clinical encounter. We sought to determine whether gonorrhea, chlamydia, and trichomoniasis are associated with bacteriuria, information that might aid in the differentiation of STIs and UTIs., Methods: We used multinomial logistic regression to analyze 9,650 encounters of female patients who were aged ≥18 years and who underwent testing for STIs. The ED encounters took place from April 18, 2014-March 7, 2017. We used a multivariable regression analysis to account for patient demographics, urinalysis findings, vaginal wet-mount results, and positive or negative (or no) findings from the urine culture and testing for Neisseria gonorrhoeae, Chlamydia trachomatis, or Trichomonas vaginalis., Results: In multivariable analysis, infection with T vaginalis , N gonorrhoeae, or C trachomatis was not associated with having a urine culture yielding 10,000 or more colony-forming units per mililiter (CFU/mL) of bacteria compared with a urine culture yielding less than 10,000 CFU/mL or no urine culture obtained. The diagnosis of a UTI in the ED was not associated with having a urine culture yielding 10,000 or more CFU/mL compared with a urine culture yielding less than 10,000 CFU/mL., Conclusion: After adjusting for covariates, no association was observed between urine culture results and testing positive for trichomoniasis, gonorrhea, or chlamydia. Our results suggest that having a concurrent STI and bacterial UTI is unlikely., Competing Interests: Conflicts of Interest: By the WestJEM article submission agreement, all authors are required to disclose all affiliations, funding sources and financial or management relationships that could be perceived as potential sources of bias. No author has professional or financial relationships with any companies that are relevant to this study. There are no conflicts of interest or sources of funding to declare.

Background: Urinary catheters (UCs) with a closed urinary drainage system have been widely used in patients for many years. However, the frequency of replacing and operating these devices may be associated with catheter-associated urinary tract infection (CAUTI). Purpose: This study was designed to compare the incidence of CAUTI by replacement time (every 14 or ≥ 15 days) of the urinary drainage system. Methods: This 1-year prospective, nonrandomized controlled study was conducted in a major teaching hospital. The Transparent Reporting of Evaluations with Nonrandomized Designs Statement checklist was used. All of the patients with UCs were divided into two groups based on each patient's preference with regard to replacement time of the urinary drainage system. Results: Five hundred sixty-two patients were evaluated, and 341 patients with UCs were enrolled as participants in the study. In the per-protocol analysis, 16 patients (22.2%; 9.3 episodes/ 1,000 catheter-days) in the 14-day group and 15 patients (17.9%; relative risk = 1.24, 95% confidence interval [0.66, 2.34]) in the ≥ 15-day group (7.7 episodes/1,000 catheter-days; incidence density ratio 1.20, 95%confidence interval [0.60, 2.43]) had CAUTIs. A comparison of cleanliness within urinary bags showed no significant intergroup difference (p > .05). In the intention-to-treat analysis, the incidence of CAUTI between the two groups was also not significantly different (p > .05). Conclusions: No statistically significant difference in the incidence of CAUTI was identified between patients who used the 14-day replacement interval and those who used the ≥ 15-day replacement interval for their urinary drainage system. [ABSTRACT FROM AUTHOR]

Background: Immunosuppression in solid organ transplantation is associated with frequent infections. Renal allograft recipients are susceptible to opportunistic infections and can acquire human cytomegalovirus (HCMV) infections even within the allograft. There, HCMV can be found in both the glomerulus and tubular cells, but is mostly restricted to specific and circumscribed sites. Therefore, not all organ infections are identifiable by immunohistology for HCMV proteins in fine needle core biopsies. Thus, we performed a urinalysis study to search for HCMV-specific RNA transcripts in the urine sediment of patients with acute kidney injury.Methods: Urinary sediment of 90 patients with acute kidney injury (AKI), including 48 renal transplant recipients (RTX) and 42 non-transplant recipients (nRTX), was collected from morning urine for RNA extraction and reverse transcription. The copy number of HCMV transcripts was evaluated using a UL132 HCMV-specific probe set and by real-time quantitative polymerase chain reaction (RT-qPCR).Results: Of the 48 RTX patients, ten showed HCMV copies in their urine sediment cells. Within this group, three recipients had negative HCMV serology and received an allograft from an HCMV-seropositive donor. In addition, all three RTX patients on a belatacept-based immunosuppressive regimen had HCMV transcripts in their urine. Of the 42 nRTX patients, only two had detectable HCMV transcripts in urine sediment cells and both were under immunosuppression.Conclusions: Ten immunosuppressed renal allograft recipients and two immunosuppressed non-transplant patients with AKI showed HCMV copies in urine sediment. Thus, HCMV positivity in urinary sediment appears to be associated with immunosuppression. This study describes a novel noninvasive method for detection of HCMV in urinary sediment. Whether all HCMV infections can be detected or only those with viral replication warrants further investigation. [ABSTRACT FROM AUTHOR]

Background. Sepsis is a potentially lethal complication for both flexible ureteroscopy (fURS) and percutaneous nephrolithotomy (PCNL). This study is aimed at comparing the sepsis rate after fURS and PCNL and the risk factors for sepsis in patients with solitary proximal ureteral stone. Methods. We reviewed the data of patients with calculi between 10 mm to 20 mm who underwent fURS or PCNL surgery from Tongji Hospital's database. A total of 910 patients were eligible with 412 fURS cases and 498 PCNL cases. We used univariate analysis and multivariate logistic regression analysis to identify the risk factors for sepsis. Subgroup analysis was performed using logistic regression analysis. Results. In the cohort, 27 (6.6%) and 19 (3.8%) patients developed sepsis after fURS and PCNL, respectively. Multivariate analysis shows that the risk factors for sepsis are fURS (OR = 3.160 , P = 0.004), serum WBC ≥ 10,000 cells/μL (OR = 3.490 , P = 0.008), albumin − globulin ratio < 1.2 (OR = 2.192 , P = 0.029), positive urine culture (OR = 6.145 , P < 0.001), and prolonged operation time (OR = 1.010 , P = 0.046). Subgroup analysis was conducted using potential risk factors: stone size, serum WBC, urine culture, and albumin-globulin ratio (AGR). In subgroup of positive urine culture, patients were more likely to develop sepsis after fURS than PCNL. Conclusions. PCNL may be a better choice than fURS to reduce postoperative sepsis, especially for patients with positive urine culture. [ABSTRACT FROM AUTHOR]

The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA isolation kits result in significantly different DNA yields from urine samples. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. Nevertheless, all five kits provided good quality DNA for high throughput sequencing with non-significant differences in the number of reads recovered, alpha, or beta diversity. [ABSTRACT FROM AUTHOR]

Background: Urinary tract infections are responsible for a significant worldwide disease burden. Performing urine culture is time consuming and labor intensive. Urine flow cytometry might provide a quick and reliable method to screen for urinary tract infection., Methods: We analyzed routinely collected urine samples received between 2020 and 2022 from both inpatients and outpatients. The UF-4000 urine flow cytometer was implemented with an optimal threshold for positivity of ≥100 bacteria/μL. We thereafter validated the prognostic value to detect the presence of urinary tract infection (UTI) based on bacterial (BACT), leukocyte (WBC), and yeast-like cell (YLC) counts combined with the bacterial morphology (UF gram-flag)., Results: In the first phase, in 2019, the UF-4000 was implemented using 970 urine samples. In the second phase, between 2020 and 2022, the validation was performed in 42,958 midstream urine samples. The UF-4000 screen resulted in a 37% (n = 15,895) decrease in performed urine cultures. Uropathogens were identified in 18,673 (69%) positively flagged urine samples. BACT > 10.000/μL combined with a gram-negative flag had a >90% positive predictive value for the presence of gram-negative uropathogens. The absence of gram-positive flag or YLC had high negative predictive values (99% and >99%, respectively) and are, therefore, best used to rule out the presence of gram-positive bacteria or yeast. WBC counts did not add to the prediction of uropathogens., Conclusion: Implementation of the UF-4000 in routine practice decreased the number of cultured urine samples by 37%. Bacterial cell counts were highly predictive for the presence of UTI, especially when combined with the presence of a gram-negative flag., (© 2024 The Authors. Journal of Clinical Laboratory Analysis published by Wiley Periodicals LLC.)

Reactive arthritis is included in the spectrum of seronegative spondyloarthritides, occurring secondary to triggers of genitourinary and gastrointestinal tract infections. We describe two cases of sexually acquired reactive arthritis secondary to genital infection by Chlamydia trachomatis, diagnosed by in-house polymerase chain reaction performed on the first void urine. Both patients were managed with a combined approach of short course antibiotics, immunosuppressive agents, biologicals and surgical intervention., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Objective: Urine culture as a gold standard for the diagnosis of urinary tract infection (UTI) involves a considerable workload in Clinical Microbiology Departments, due to the high number of samples received that will ultimately be negative. Therefore, it is necessary to use screening systems that also reduce the turnaround time for UTI diagnosis. The new flow cytometer UF-5000 (Sysmex Corporation) is able to differentiate between Gram-negative and Gram-positive bacteria using the BACT-info parameter according to manufacturer. The aim of our study was to evaluate the gram discrimination ability of the UF-5000 cytometer., Methods: A prospective study with 449 urine samples collected consecutively was conducted, in the period 7/3/2022-27/5/2022, in which the BACT-info flag was compared with urine culture as the reference method., Results: The sensitivity obtained for both Gram-negative and Gram-positive bacteria was above 95%. However, for Gram-positive bacteria, the moderate Kappa index (0.49) and the low positive predictive value (37.1%) indicated that the correlation between BACT-info flag and urine culture was not acceptable and should not be reported to the requesting clinician., Conclusions: Implementation of the third generation UF-5000 cytometer represents a significant advance in the aetiological orientation of UTIs caused by Gram-negative bacteria. Reporting the Gram morphology in the urine samples reduces the response time in the microbiological diagnosis of UTI, which would have an impact on the reduction and optimisation of empirical treatment, and thus on the generation of antimicrobial resistance., (©The Author 2023. Published by Sociedad Española de Quimioterapia. This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)(https://creativecommons.org/licenses/by-nc/4.0/).)

Purpose: To determine the efficacy and safety of PCNL in patients with positive urine culture without an any other risk factors prior to surgery, and to define an optimal pre-operative antibiotic regimen for these patients.Materials and Methods: The study included 269 consecutive PCNL cases. These cases were divided into 2 groups according pre-operative urine culture results: sterile (group 1, n=166) and positive (group 2, n=103). Patients with risk factors linked to infection complications were excluded from study. All patients underwent PCNL in the prone position. In group 1, the antibiotic regimen included parenteral injection 30 minutes prior to operation and for 3 days after surgery. Group 2 was given antibiotics 24 hours before PCNL as well as 30 minutes before PCNL and then for 3 days following surgery. On the first day after the operation low dose CT and common blood count were performed on all patients to determine residuals, hematomas, blood loss, and inflammatory markers.  Results:  Mean age, stone size, failed ESWL, and prior nephrostomy tube insertion were higher in group 2. Although rate of pre-stented patients was equal in groups. No significant differences were observed between group 1 and 2 in regard to operative time (74,3±26,9 vs 70,2±26,5  min, P=.52), length of stay (3,9±1,2 vs 3,8±1,6 days, P=.24), SIRS (6,0% vs 7,8% patients, P=.07), and leukocyte levels exceeding  10*10*9 (77 (46,4%) vs 49 (47,6%) P=.11). Moreover, there was no sepsis or hemotransfusion in either group. Stone-free rates were also similar (78,9% vs 77,7%, P=.35).Conclusion: 24-hours continuous antibiotic administration before the operation (paying respect to specific resistance bacterial features) can be considered as alternative to 1-week treatment and allow to perform PCNL with sufficient safety in selected patients. Infected urine is not an independent risk factor of post-operative infections complications after PCNL in low risk patients with kidney stones. [ABSTRACT FROM AUTHOR]

Background: This study's purposes were to characterize detection rates of several sexually transmitted infection (STI) agents and describe the effect additional specimen source and analyte screening has on STI detection within a cohort of young men who have sex with men and transgender women.Methods: Within a 16-month interval, 1966 encounters involved dual urine and rectal swab submissions assessed by commercial transcription-mediated amplification-based assays for Chlamydia trachomatis and Neisseria gonorrhoeae and by off-label transcription-mediated amplification-based Trichomonas vaginalis and Mycoplasma genitalium testing. Identification of STI carriers used algorithms involving Food and Drug Administration-cleared screening methods, laboratory-modified testing for extraurogenital C. trachomatis and N. gonorrhoeae, and laboratory-developed tests for T. vaginalis and M. genitalium.Results: Food and Drug Administration-indicated urine C. trachomatis and N. gonorrhoeae screening revealed 39 encounters (2.0%) yielding one or both agents. Via C. trachomatis and N. gonorrhoeae screening that included rectal swab analysis, 264 encounters (13.4%) yielded evidence of either (140 C. trachomatis, 88 N. gonorrhoeae) or both (36 participants) infections. Detection rates for C. trachomatis and N. gonorrhoeae were 1.4% and 0.6% for urine screening and 8.2% and 6.2% for rectal screening, respectively. Off-label screening identified 413 additional encounters with STI (5 T. vaginalis, 396 M. genitalium, 12 with both). Of these identifications, 82.1% were generated from analysis of rectal swabs (4 participants with T. vaginalis, 323 participants with M. genitalium, 12 with both). Overall detection rates of T. vaginalis (0.2% urine, 1.3% rectal) and M. genitalium (9.1% urine, 21.5% rectal) were variable.Conclusions: Additive analyte testing, including extraurogenital collections, contributes to comprehensive STI screening within a high-risk demographic. [ABSTRACT FROM AUTHOR]

Pneumonia is the leading cause of infectious related death costing 12 billion dollars annually in the United States alone. Despite improvements in clinical care, total mortality remains around 4%, with inpatient mortality reaching 5–10%. For unknown reasons, mortality risk remains high even after hospital discharge and there is a need to identify those patients most at risk. Also of importance, clinical symptoms alone do not distinguish viral from bacterial infection which may delay appropriate treatment and may contribute to short-term and long-term mortality. Biomarkers have the potential to provide point of care diagnosis, identify high-risk patients, and increase our understanding of the biology of disease. However, there have been mixed results on the diagnostic performance of many of the analytes tested to date. Urine represents a largely untapped source for biomarker discovery and is highly accessible. To test this hypothesis, we collected urine from hospitalized patients with community-acquired pneumonia (CAP) and performed a comprehensive screen for urinary tract microbiota signatures, metabolite, and cytokine profiles. CAP patients were diagnosed with influenza or bacterial (Streptococcus pneumoniae and Staphylococcus aureus) etiologies and compared with healthy volunteers. Microbiome signatures showed marked shifts in taxonomic levels in patients with bacterial etiology versus influenza and CAP versus normal. Predictive modeling of 291 microbial and metabolite values achieved a + 90% accuracy with LASSO in predicting specific pneumonia etiology. This study demonstrates that urine from patients hospitalized with pneumonia may serve as a reliable and accessible sample to evaluate biomarkers that may diagnose etiology and predict clinical outcomes. [ABSTRACT FROM AUTHOR]

Objective: Since microscopic hematuria and pyuria can be observed in patients with a ureteral double-J (DJ) stent in place, urinalysis findings are not considered significant in terms of predicting stent-related infections. This study evaluates the presence of bacterial colonization and the value/ effectiveness of urine tests in predicting the results of DJ stent cultures. Materials and Methods: In the present prospective study, we analyzed data from patients who were treated with a DJ stent placement following endourological surgery due to ureteral stones. DJ stents were removed only after the urine cultures appeared sterile or after a period of empiric antibiotic use. The relationship between urinalysis results and stent cultures was assessed. Results: A total of 65 patients (mean age, 42.6±13.5 years; 16 females and 43 males) were evaluated. Bacterial colonization was detected in 12 (18%) DJ stent cultures with Enterococcus faecalis (n=4), extended-spectrum beta-lactamase producer (ESBL (+) Escherichia coli (n=4), Corynebacterium urealyticum (n=2), candida (n=1) and methicillin-resistant Staphylococcus aureus (n=1) growth being reported. The antibiogram results of the patients that showed colonization in their cultures demonstrated penicillin (n=4), ampicillin (n=4), tetracycline (n=3), imipenem (n=2), and linezolid (n=1) sensitivity. The rate of leukocyte esterase- and nitrite-positive patients, of those having significant number of leukocytes, and urine culturepositive patients in the groups with and without positive urine culture was 58.5%, 32%, 49%, and 7.5% vs 50%, 16.6%, 50%, and 8.5%, respectively. There were no statistically significant differences between the groups (p=>0.05). None of the study patients applied to our hospital with active infection following DJ stent removal. Conclusion: Urinalysis is insufficient in predicting catheter culture results. Based on the results of this study, we assume that stent culture for removed DJ stents is not a necessity; empirical antibiotic therapy with ampicillin-tetracycline should be started in patients with postoperative infection. [ABSTRACT FROM AUTHOR]

Objective: The objective of this study was to determine the risk factors in community-acquired urinary tract infections (UTIs) caused by extended spectrum p-lactamase (ESBL)-producing Escherichia coli, and antibiotic resistance rates in these strains. Methods: Patients who had been admitted to the Trakya University Health Center for Medical Research and Practice Infectious Diseases and Clinical Microbiology Department with the diagnosis of UTI from January 1, 2008 through January 1, 2018 and had E. coli growth in urine culture were analyzed retrospectively. Patients who had ESBL-positive E. coli growth in their urine cultures were the case group and patients with the ESBL-negative E. coli growth in their urine cultures were the control group. Results: In the study, 379 UTI episodes were detected in 346 patients. There were 117 (30.9%) episodes in the case group and 262 (69.1%) episodes in the control group. In univariate analysis, young age (approximately 62±19.6 years in the case group, 68±19.4 years in the control group), malignancy in a solid organ, urinary pathologies, urinary catheterization, history of uro-logical procedure in the last six months, history of hospitalization in the last three months, history of antibiotic use in the last three months and recurrent UTI were statistically significant for ESBL production (p<0.05). In multivariate analysis, malignancy in a solid organ (OR: 2.267; CI: 1.205-4.266; p=0.011), urinary catheterization (OR: 2.266; CI: 1.186-4.330; p=0.013), and antibiotic use in the last three months (OR: 5.050; CI: 3.038-8.395; p=0.000) were found to be the independent risk factors for ESBL production. Empirical treatment effectiveness rate was lower and hospital stay was longer in the case group. E. coli strains were found to have higher resistance rates to antibiotics other than fosfomycin and nitrofurantoin and they were not suitable for empirical treatment of UTIs. Conclusions: Knowing the risk factors and antibiotic resistance rates in terms of ESBL production in the community patients will both increase the empirical treatment success of UTIs and reduce unnecessary antibiotic use. [ABSTRACT FROM AUTHOR]

Background: Preliminary data suggest that the urinary microbiome may play a role in bladder cancer. Information regarding the most suitable method of collecting urine specimens is needed for the large population studies needed to address this. To compare microbiome metrics resulting from 16S ribosomal RNA gene sequencing between midstream, voided specimens and those obtained at cystoscopy.Methods: Adults, with a history of superficial urothelial cell carcinoma (non-muscle invasive bladder cancer) being followed with periodic surveillance cystoscopy had a urine sample collected by a mid-stream, voided technique and then from the bladder at cystoscopy. Urine samples underwent 16S ribosomal RNA gene sequencing on the Illumina MiSeq platform.Results: 22 subjects (8 female, 14 male) were included. There was no significant difference in beta diversity (diversity between samples) in all samples between collection methods. However, analysis by sex revealed a difference between voided and cystoscopy samples from the same individual in males (p = 0.006, Adonis test) but not in females (p = 0.317, Adonis test). No differences were seen by collection method in any alpha diversity (diversity within a sample) measurement or differential abundance of taxa.Conclusions: Beta diversity of the urine microbiome did differ by collection method for males only. This suggests that the urinary microbiomes of the two collection methods are not equivalent to each other, at least in males, which is the sex that bladder cancer occurs most frequently in. Therefore, the same collection method within a given study should be used. [ABSTRACT FROM AUTHOR]

Fifty eight isolates of Streptococcus agalactiae were obtained from wound and urine specimens among one hundred thirty six from patients with diabetes mellitus and identified through cultural, morphological, and biochemical examinations in addition to VITEK 2 Compact System. All of the isolates were tested regarding their sensitivity to 18 antibiotics and the results showed that all of the isolates were resist to clindamycin, and sensitive to teicoplanin. The current study was carried out to use two methods (i.e. microtiter biofilm and Congo red agar ) so as to provide and extend insight into bacterial colonization and biofilm formation among diabetic patients. The two methods were compared and the results revealed that microtiter was the best method for biofilm detection, and two chemical materials (i.e. silver oxide, and iron oxide) were used as anti-biofilms for all isolates, one of the best concentration and kind of chemical materials was Iron oxide at 75 mg/ml for reducing biofilm formation. PCR system was employed in order to detect the virulence genes (i.e lmb gene), the results that 30(51.72%) were positive for lmb genes. [ABSTRACT FROM AUTHOR]