Urine Samples Of Patients Research Articles

Specific molecular peak analysis by ion mobility spectrometry of volatile organic compounds in urine of COVID-19 patients: A novel diagnostic approach

IntroductionSARS-CoV-2 is usually diagnosed from naso-/oropharyngeal swabs which are uncomfortable and prone to false results. This study investigated a novel diagnostic approach to Covid-19 measuring volatile organic compounds (VOC) from patients’ urine. MethodsBetween June 2020 and February 2021, 84 patients with positive RT-PCR for SARS-CoV-2 were recruited as well as 54 symptomatic individuals with negative RT-PCR. Midstream urine samples were obtained for VOC analysis using ion mobility spectrometry (IMS) which detects individual molecular components of a gas sample based on their size, configuration, and charge after ionization. ResultsPeak analysis of the 84 Covid and 54 control samples showed good group separation. In total, 37 individual specific peaks were identified, 5 of which (P134, 198, 135, 75, 136) accounted for significant differences between groups, resulting in sensitivities of 89–94% and specificities of 82–94%. A decision tree was generated from the relevant peaks, leading to a combined sensitivity and specificity of 98% each. DiscussionVOC-based diagnosis can establish a reliable separation between urine samples of Covid-19 patients and negative controls. Molecular peaks which apparently are disease-specific were identified. IMS is an additional non-invasive and cheap device for the diagnosis of this ongoing endemic infection. Further studies are needed to validate sensitivity and specificity.

Application of High-Resolution Terahertz Gas Spectroscopy for Studying the Composition of Thermal Decomposition Products in Human Urine of Prostate Cancer Patients

The results of using nonstationary high-resolution THz spectroscopy for detecting a characteristic set of metabolites of thermal decomposition products of urine from prostate cancer patients, aimed at identifying specific markers, are presented. Studies of the composition of biological fluid in prostate cancer were carried out using 12 urine samples from cancer patients and 4 samples from conditionally healthy volunteers. Differences in the composition and content of substances in the urine samples of cancer patients compared to the urine of conditionally healthy volunteers were identified, which allows preliminary conclusions to be drawn about substances promising for use as markers of prostate cancer in urine. The presented approach is promising for developing a method for noninvasive study of the composition of biological fluids, which makes it possible to identify metabolite markers of various pathologies and diseases.

Vagococcus fluvialis isolation from the urine of a bladder cancer patient: a case report

Vagococcus fluvialis infection is rare in humans, and there is limited research on the clinical manifestations and antimicrobial susceptibility testing of Vagococcus fluvialis infection. Here, We isolated Vagococcus fluvialis from the urine samples of bladder cancer patients at Hunan Provincial People’s Hospital, and it is the first reported case of Vagococcus fluvialis isolated from the urine. The fully automated microbial identification system and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identified the bacterium as Vagococcus fluvialis with a confidence level of 99.9%. The VITEK-2Compact fully automated microbial susceptibility analysis system indicated that it was most sensitive to tigecycline, vancomycin, quinupristin/dalfopristin, linezolid, and showed moderate sensitivity to erythromycin, levofloxacin, ciprofloxacin, ampicillin/sulbactam, and tetracycline. Additionally, it exhibited synergy when combined with high-level gentamicin and vancomycin, showing sensitivity. However, it displayed poor activity against penicillin and furanth. According to our knowledge, this is the first study to isolate and identify Vagococcus fluvialis from the urine of bladder cancer patients and the systematically reviewed other reported Vagococcus infections on human, which provide an experimental basis for guiding the rational use of drugs in the clinical treatment and diagnose of Vagococcus fluvialis infection and related pathogenic mechanism research. Meanwhile, we have systematically reviewed other reported.

A new methodology to reveal potential nucleic acid modifications associated with the risk of endometrial cancer through dispersive solid-phase extraction coupled with UHPLC-QE-Orbitrap-MS/MS and HPLC-UV.

Nucleic acid modifications have attracted increasing attention in recent years since they have been found to be related to a number of diseases including cancer. Previous studies have shown that the early development of endometrial cancer (EC) is often accompanied by changes in methylation levels of related genes, and the expression of related proteins that regulate reactive oxygen species (ROS) shows significant differences in EC cells and tissues. However, it has not been reported whether nucleic acid modifications related to methylation or ROS can serve as biomarkers for EC. Accurate quantification of these nucleic acid modifications still has challenges because their amounts in urine are very low and the interferences in urine are complicated. In this study, a novel dispersive solid-phase extraction (DSPE) method based on chitosan-carbon nanotube-Al2O3 (CS-CNT-Al2O3) has been established for the analysis of 5-hydroxymethyluracil (5mU), 5-methyl-2'-deoxycytidine (5-mdC), 5-hydroxymethyl-2'-deoxycytidine (5-hmdC), 5-formyl-2'-deoxycytidine (5-fdC), and 8-hydroxy-2'-deoxyguanosine (8-OHdG) in EC patient urine samples coupled with UHPLC-QE-Orbitrap-MS/MS and HPLC-UV. Firstly, the synthesis of the CS-CNT-Al2O3 nanocomposite was conducted by a sono-coprecipitation method and was characterized by scanning electron microscope (SEM), energy dispersive spectrometer (EDS), and Fourier transform infrared (FTIR). Under the optimal extraction conditions of DSPE, we successfully quantified 5mU, 5-mdC, 5-hmdC, 5-fdC, and 8-OHdG in urine samples from 37 EC patients and 39 healthy controls. The results showed that there were significant differences in the levels of 5-mdC, 5-hmdC, 5-fdC, and 8-OHdG in EC patients compared to the healthy control group. The receiver operator characteristic (ROC) curve analysis was carried out to evaluate the potential of 5-mdC, 5-hmdC, 5-fdC, and 8-OHdG to distinguish EC patients from healthy volunteers. The area under the curve (AUC) for 5-mdC, 5-hmdC, 5-fdC, and 8-OHdG was 0.7412, 0.667, 0.8438, and 0.7981, respectively. It indicated that 5-mdC, 5-hmdC, 5-fdC, and 8-OHdG had certain potential in distinguishing between EC patients and healthy volunteers and they could act as potential non-invasive biomarkers for early diagnosis of EC. Moreover, the present study would stimulate investigations of the effects of nucleic acid modifications on the initiation and progression of EC.

Antimicrobial Activity of Four Different Commercially Available Antibiotics against Selected Bacteria Isolated from Urine Samples of UTI Patients

More than thirty percent of the global population suffers from urinary tract infections. While many infections are currently treated empirically, appropriate standards for the prudent use of antibiotics should be concentrated on preventing the emergence of bacterial resistance and the elevated risk of infections that are challenging to treat. The article includes and discusses pertinent information about risk factors, severity levels, and the proper microbiological interpretation of pathogens. Research was done to compare the in vitro antibacterial activity of commercial antibiotics that are frequently used to treat urinary tract infections (UTIs) to clinical isolates that were obtained from urine samples of patients who were suffering from UTIs. A total of 5 isolates were identified as Escherichia coli, Staphylococcus aureus, Salmonella typhi, Staphylococcus epidermidis and Pseudomonas aeruginosa, following different morphological, physiological and biochemical tests. Antibiotic sensitivity of four commercial antibiotics viz., cefpodoxime, cefuroxime, amoxicillin, and ciprofloxacin was screened by disc diffusion assay. Among the four antibiotic discs tested 40% of isolates were resistant to cefuroxime followed by 20% to cefpodoxime, amoxicillin and ciprofloxacin. 40% of the isolates were found to be resistant to multiple antibiotics and termed as multi-drug resistant (MDR) isolates. Cefpodoxime shows smallest zone of inhibition against Staphylococcus epidermidis and Staphylococcus aureus of about 7 mm and 8 mm, respectively. Hence, further research should be carried out to identify the active biomolecules or Phyto-molecules from the plants and determine the effects of them in vitro as well as in vivo.

Targeting cancer-derived extracellular vesicles by combining CD147 inhibition with tissue factor pathway inhibitor for the management of urothelial cancer cells

BackgroundExtracellular vesicles (EVs), including microvesicles, hold promise for the management of bladder urothelial carcinoma (BLCA), particularly because of their utility in identifying therapeutic targets and their diagnostic potential using easily accessible urine samples. Among the transmembrane glycoproteins highly enriched in cancer-derived EVs, tissue factor (TF) and CD147 have been implicated in promoting tumor progression. In this in vitro study, we explored a novel approach to impede cancer cell migration and metastasis by simultaneously targeting these molecules on urothelial cancer-derived EVs.MethodsCell culture supernatants from invasive and non-invasive bladder cancer cell lines and urine samples from patients with BLCA were collected. Large, microvesicle-like EVs were isolated using sequential centrifugation and characterized by electron microscopy, nanoparticle tracking analysis, and flow cytometry. The impact of urinary or cell supernatant-derived EVs on cellular phenotypes was evaluated using cell-based assays following combined treatment with a specific CD147 inhibitor alone or in combination with a tissue factor pathway inhibitor (TFPI), an endogenous anticoagulant protein that can be released by low-molecular-weight heparins.ResultsWe observed that EVs obtained from the urine samples of patients with muscle-invasive BLCA and from the aggressive bladder cancer cell line J82 exhibited higher TF activity and CD147 expression levels than did their non-invasive counterparts. The shedding of GFP-tagged CD147 into isolated vesicles demonstrated that the vesicles originated from plasma cell membranes. EVs originating from invasive cancer cells were found to trigger migration, secretion of matrix metalloproteinases (MMPs), and invasion. The same induction of MMP activity was replicated using EVs obtained from urine samples of patients with invasive BLCA. EVs derived from cancer cell clones overexpressing TF and CD147 were produced in higher quantities and exhibited a higher invasive potential than those from control cancer cells. TFPI interfered with the effect when used in conjunction with the CD147 inhibitor, further suppressing homotypic EV-induced migration, MMP production, and invasion.ConclusionsOur findings suggest that combining a CD147 inhibitor with low molecular weight heparins to induce TFPI release may be a promising therapeutic approach for urothelial cancer management. This combination can potentially suppress the tumor-promoting actions of cancer-derived microvesicle-like EVs, including collective matrix invasion.Graphical

Co-transfer of IncFII/IncFIB and IncFII plasmids mediated by IS26 facilitates the transmission of mcr-8.1 and tmexCD1-toprJ1

PurposeThis study aimed to characterise the whole-genome structure of two clinical Klebsiella pneumoniae strains co-harbouring mcr-8.1 and tmexCD1-toprJ1, both resistant to colistin and tigecycline.MethodsK. pneumoniae strains TGC-02 (ST656) and TGC-05 (ST273) were isolated from urine samples of different patients hospitalised at separate times in 2021. Characterisation involved antimicrobial susceptibility testing (AST), conjugation assays, whole-genome sequencing (WGS), and bioinformatics analysis. Comparative genomic analysis was conducted on mcr-8.1-carrying and tmexCD1-toprJ1-carrying plasmids.ResultsBoth K. pneumoniae isolates displayed a multidrug-resistant phenotype, exhibiting resistance or reduced susceptibility to ampicillin, ampicillin/sulbactam, cefazolin, aztreonam, amikacin, gentamicin, tobramycin, ciprofloxacin, levofloxacin, nitrofurantoin, trimethoprim/sulfamethoxazole, apramycin, tigecycline and colistin. WGS analysis revealed that clinical strain TGC-02 carried the TmexCD1-toprJ1 gene on a 200-Kb IncFII/IncFIB-type plasmid, while mcr-8 was situated on a 146-Kb IncFII-type plasmid. In clinical strain TGC-05, TmexCD1-toprJ1 was found on a 300-Kb IncFIB/IncHI1B/IncR-type plasmid, and mcr-8 was identified on a 137-Kb IncFII/IncFIA-type plasmid. Conjugation experiments assessed the transferability of these plasmids. While transconjugants were not obtained for TGC-05 despite multiple screening with tigecycline or colistin, pTGC-02-tmex and pTGC-02-mcr8 from clinical K. pneumoniae TGC-02 demonstrated self-transferability through conjugation. Notably, the rearrangement of pTGC-02-tmex and pTGC-02-mcr8 via IS26-based homologous recombination was observed. Moreover, the conjugative and fusion plasmids of the transconjugant co-harboured the tmexCD1-toprJ1 gene cluster and mcr-8.1, potentially resulting from IS26-based homologous recombination.ConclusionThe emergence of colistin- and tigecycline-resistant K. pneumoniae strains is concerning, and effective surveillance measures should be implemented to prevent further dissemination.

Enterobacter cloacae from urinary tract infections: frequency, protein analysis, and antimicrobial resistance

The genus Enterobacter belongs to the ESKAPE group, which includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. This group is characterized by the development of resistance to various antibiotics. In recent years, Enterobacter cloacae (E. cloacae) has emerged as a clinically important pathogen responsible for a wide range of healthcare-associated illnesses. Identifying Enterobacter species can be challenging due to their similar phenotypic characteristics. The emergence of multidrug-resistant E. cloacae is also a significant problem in healthcare settings. Therefore, our study aimed to identify and differentiate E. cloacae using Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as a fast and precise proteomic analytical technique. We also tested hospital-acquired E. cloacae isolates that produce Extended-spectrum beta-lactamases (ESBL) against commonly used antibiotics for treating urinary tract infections (UTIs). We used a total of 189 E. cloacae isolates from 2300 urine samples of patients with UTIs in our investigation. We employed culturing techniques, as well as the BD Phoenix™ automated identification system (Becton, Dickinson) and Analytical Profile Index (API) system for the biochemical identification of E. cloacae isolates. We used the MALDI Biotyper (MBT) device for peptide mass fingerprinting analysis of all isolates. We utilized the single peak intensities and Principal Component Analysis (PCA) created by MBT Compass software to discriminate and cluster the E. cloacae isolates. Additionally, we evaluated the sensitivity and resistance of ESBL-E. cloacae isolates using the Kirby Bauer method. Out of the 189 E. cloacae isolates, the BD Phoenix system correctly identified 180 (95.24%) isolates, while the API system correctly identified 165 (87.30%) isolates. However, the MBT accurately identified 185 (98.95%) isolates with a score of 2.00 or higher. PCA positively discriminated the identified E. cloacae isolates into one group, and prominent peaks were noticed between 4230 mass-to-charge ratio (m/z) and 8500 m/z. The ESBL-E. cloacae isolates exhibited a higher degree of resistance to ampicillin, amoxicillin-clavulanate, cephalothin, cefuroxime, and cefoxitin. Several isolates were susceptible to carbapenems (meropenem, imipenem, and ertapenem); however, potential future resistance against carbapenems should be taken into consideration. In conclusion, MALDI-TOF MS is a powerful and precise technology that can be routinely used to recognize and differentiate various pathogens in clinical samples. Additionally, the growing antimicrobial resistance of this bacterium may pose a significant risk to human health.

Surface-enhanced Raman Spectroscopy in urinalysis of hypertension patients with kidney disease

Arterial hypertension (AH) is a multifactorial and asymptomatic disease that affects vital organs such as the kidneys and heart. Considering its prevalence and the associated severe health repercussions, hypertension has become a disease of great relevance for public health across the globe. Conventionally, the classification of an individual as hypertensive or non-hypertensive is conducted through ambulatory blood pressure monitoring over a 24-h period. Although this method provides a reliable diagnosis, it has notable limitations, such as additional costs, intolerance experienced by some patients, and interferences derived from physical activities. Moreover, some patients with significant renal impairment may not present proteinuria. Accordingly, alternative methodologies are applied for the classification of individuals as hypertensive or non-hypertensive, such as the detection of metabolites in urine samples through liquid chromatography or mass spectrometry. However, the high cost of these techniques limits their applicability for clinical use. Consequently, an alternative methodology was developed for the detection of molecular patterns in urine collected from hypertension patients. This study generated a direct discrimination model for hypertensive and non-hypertensive individuals through the amplification of Raman signals in urine samples based on gold nanoparticles and supported by chemometric techniques such as partial least squares-discriminant analysis (PLS-DA). Specifically, 162 patient urine samples were used to create a PLS-DA model. These samples included 87 urine samples from patients diagnosed with hypertension and 75 samples from non-hypertensive volunteers. In the AH group, 35 patients were diagnosed with kidney damage and were further classified into a subgroup termed (RAH). The PLS-DA model with 4 latent variables (LV) was used to classify the hypertensive patients with external validation prediction (P) sensitivity of 86.4%, P specificity of 77.8%, and P accuracy of 82.5%. This study demonstrates the ability of surface-enhanced Raman spectroscopy to differentiate between hypertensive and non-hypertensive patients through urine samples, representing a significant advance in the detection and management of AH. Additionally, the same model was then used to discriminate only patients diagnosed with renal damage and controls with a P sensitivity of 100%, P specificity of 77.8%, and P accuracy of 82.5%.

Alginate microspheres encapsulating hox transcript antisense RNA siRNA regulate the Hedgehog-Gli1 pathway to alleviate epidermal growth factor receptor tyrosine kinase inhibitors resistance.

The long non-coding RNA HOTAIR and the Hedgehog-Gli1 signaling pathway are closely associated with tumor occurrence and drug resistance in various cancers. However, their specific roles in the development of EGFR-TKIs resistance in non-small cell carcinoma remain unclear. To address the issue of EGFR-TKIs resistance, this study utilized the electrospray method to prepare sodium alginate microspheres encapsulating HOTAIR siRNA (SA/HOTAIR siRNA) and investigated its effects on RNA interference (RNAi) in the gefitinib-resistant cell line PC9/GR. Furthermore, the study explored whether HOTAIR could modulate EGFR-TKIs resistance through the Hedgehog-GLi1 signaling pathway. The experimental results showed that sodium alginate (SA) microspheres demonstrated excellent biocompatibility with high encapsulation efficiency and drug-loading capacity, effectively enhancing the silencing efficiency of siRNA. HOTAIR siRNA significantly inhibited the proliferation, migration, and invasion abilities of PC9/GR cells while promoting apoptosis. Additionally, HOTAIR siRNA effectively suppressed tumor growth and downregulated the Hedgehog-GLi1 pathway and anti-apoptotic proteins, which were confirmed in animal experiments. Moreover, SA/HOTAIR siRNA exhibited superior inhibition of cellular and tumor functions compared to using HOTAIR siRNA alone. Clinical research findings indicated that monitoring the expression level of HOTAIR in the serum and urine samples of NSCLC patients before and after receiving EGFR-TKIs treatment can predict the efficacy of EGFR-TKIs to a certain extent. This study provided evidence that HOTAIR siRNA effectively mitigated the development of acquired resistance to EGFR-TKIs by inhibiting the Hedgehog-GLi1 pathway. Furthermore, it introduced a reliable and long-lasting drug delivery system for combating acquired resistance to EGFR-TKIs.

Two novel phages, Klebsiella phage GADU21 and Escherichia phage GADU22, from the urine samples of patients with urinary tract infection.

Phages are found in a wide variety of places where bacteria exist including body fluids. The aim of the present study was to isolate phages from the urine samples of patients with urinary tract infection. The 10 urine samples were cultured to isolate bacteria and also used as phage sources against the isolated bacteria. From 10 urine samples with positive cultures, 3 phages were isolated (33%) and two of them were further studied. The Klebsiella phage GADU21 and Escherichia phage GADU22 phages infected Klebsiella pneumonia and Escherichia coli, respectively. Among the tested 14 species for host range analysis, the Klebsiella phage GADU21 was able to infect two species which are Klebsiella pneumonia and Proteus mirabilis, and Escherichia phage GADU22 was able to infect four species which are Shigella flexneri, Shigella sonnei and Escherichia coli. Among different isolates of the indicator bacteria for each phage, GADU21 infected half of the tested 20 Klebsiella pneumonia isolates while GADU22 infected 85% of the tested 20 E. coli isolates. The genome sizes and GC ratios were 75,968bp and 44.4%, and 168,023bp and 35.3% for GADU21 and GADU22, respectively. GADU21 and GADU22 were both lytic and had no antibiotic resistance and virulence genes. GADU21 was homologue with Klebsiella phage vB_KpP_FBKp27 but only 88% of the genome was covered by this phage. The non-covered parts of the GADU21 genome included genes for tail-fiber-proteins and HNH-endonuclease. GADU22 had 94.8% homology with Escherichia phage vB_Eco_OMNI12 and had genes for immunity proteins. Phylogenetic analysis showed GADU21 and GADU22 were members of Schitoviridae family and Efbeekayvirus genus and Straboviridae family and Tevenvirinae genus, respectively. VIRIDIC analysis classified these phages in new species clusters. Our study demonstrated the possibility to use infected body fluids as phage sources to isolate novel phages. GADU21 is the first reported Klebsiella phage isolated from human body fluid. The absence of virulence and antibiotic resistance genes in their genomes makes the phages a potential therapeutic tool against infections.

Pterin Profiling in Serum, Dried Blood Spot, and Urine Samples Using LC-MS/MS in Patients with Inherited Hyperphenylalaninemia

Background: Hyperphenylalaninemia (HPA) is defined as blood phenylalanine (Phe) levels exceeding the normal values (>120 μmol/L or >2 mg/dL) and is caused by a deficiency in the enzyme phenylalanine hydroxylase (PAH). The widespread screening of Phe levels in newborn screening programs has led to a very high number of patients with HPA. Methods: The samples were collected at various ages, not at the point of diagnosis. Nine pterin derivatives, including isoxanthopterin, sepiapterin, xanthopterin, primapterin, biopterin, neopterin, 7,8-dihydrobiopterin, 7,8-dihydroneopterin, and tetrahydrobiopterin (BH4), were analyzed in different HPA classes in serum, dried blood spots (DBS), and urine samples. A total of 18 patients, including six classical phenylketonuria (PKU), eight BH4-responsive PKU, and four mild HPA patients, were included in the study. Results: Among the nine pterin derivatives measured, a significant increase was observed in the levels of isoxanthopterin, biopterin, and 7,8-dihydrobiopterin in serum, dried blood spots (DBS), and urine samples of patients with HPA compared to the control group. However, elevations in isoxanthopterin, biopterin, and 7,8-dihydrobiopterin were observed in all HPA groups, although the extent of elevation varied among the different disease groups. There were also significant differences between HPA subgroups among these high values. Conclusion: In this study, it might be suggested that pterin profiling shows promising potential for its effective utilization in the differential diagnosis of HPA. Pterin profiling demonstrated its efficacy in accurately categorizing patients into distinct subtypes. This approach offers several notable advantages, including the ability to simultaneously screen multiple HPA subtypes through a single test, establish disease decision limits for pterins, shorten the time required for HPA differential diagnosis, reduce the risk of misdiagnosis, and increase overall diagnostic accuracy. This study is the most comprehensive study examining the association between HPA pterin in the literature. In our study, samples obtained from BH4-responsive PKU patients were on treatment. This may have affected the results. Preliminary findings on pterin profiles may need to be replicated in a prospective cohort of samples collected at the time of diagnosis to confirm the results.

Antimicrobial Resistance of Bacteria Isolated from Urine Samples of Patients Above 15 Years at Rimt Multispeciality Hospital, Punjab, India

Antimicrobial Resistance of Bacteria Isolated from Urine Samples of Patients Above 15 Years at Rimt Multispeciality Hospital, Punjab, India

Prevalence and antimicrobial resistance profile of pathogens isolated from patients with urine tract infections admitted to a university hospital in a medium-sized Brazilian city.

This study aimed to determine the antibiotic profile of microorganisms isolated from urine samples of patients with community urine tract infections (UTI) admitted to the University Hospital of the Federal University of Sao Carlos to support an appropriate local empirical treatment. A retrospective cross-sectional study was conducted from October 2018 to October 2020. Data from 1,528 positive urine cultures for bacterial pathogens and antibiograms were tabulated. Bacterial species prevalence and their resistance profile were analyzed and compared by sex and age. For Gram-negative fermenting bacteria, resistance rates were compared between patients with previous hospitalization and the total of infections caused by this group. For comparisons, the Chi-square test was performed, using Fisher's exact test when necessary (BioEstat program, adopting p ≤ 0.05). A multivariate analysis was applied to assess the effect of the studied variables in predicting multidrug resistance. Infections were more prevalent in women and older adults. Gram-negative bacteria represented 90.44% of total cultures. In both sexes, E. coli prevalence was significantly higher in adults compared with older adults (p < 0.0001). For several antibiotics, resistance rates were higher in the older adults compared with other ages and in patients with Gram-negative fermenting infections and previous hospitalization compared with the total of infections by this group of bacteria. The closer to the hospitalization, the higher the number of antibiotics with superior resistance rates. Resistance rates for aminoglycosides, carbapenems, ceftazidime, nitrofurantoin, piperacillin+tazobactam, and fosfomycin were less than 20%, considered adequate for empirical treatment. Only hospitalization in the previous 90 days was statistically significant in predicting infections by multidrug-resistant bacteria.

Pediatric Uropathogens and their Antimicrobial Susceptibility Pattern: Experience from an Impoverished District of Karachi, Pakistan.

Urinary tract infection (UTI) is the most common infection of the pediatric age group. Several factors linked to higher prevalence include poor personal hygiene, improper sanitation, lower socioeconomic status, and malnourishment. In addition to having a worse quality of life, the 1.8 million children who live in Karachi's Korangi district are routinely exposed to such factors. The study aims to evaluate the frequency of UTI and distribution of uropathogens along with their antimicrobial susceptibility pattern in patients presenting to a pediatric tertiary care center in the Korangi district of Karachi, Pakistan. The study employed an observational cross-sectional design. The study was conducted at the Microbiology laboratory of Sindh Institute of Child Health and Neonatology, Karachi, Pakistan from 1st January to 15th August 2023. Urine samples of patients 1 to 16 years of age were collected via midstream clean catch method and of patients from birth up to 1 year were collected in urine collection bags. The samples were cultured on Cystine Lactose Electrolyte Deficient (CLED) agar and antibiotic susceptibility testing was performed using the Kirby-Bauer Disc Diffusion method. A total of 457 urine samples were collected, of which 90 (19.7%) were positive for significant uropathogens. With a mean age of 4.6 years, majority of the culture-positive patients were female (n = 72; 80%). Enterobacterales were the most frequently isolated (n = 88; 95.6%), of which Escherichia coli was the most common (73.9%; n = 68). Citrobacter (n = 7; 7.6%), Klebsiella (n = 6; 6.5%), Serratia (n = 4; 4.3%), Proteus (n = 2; 2.2%), Salmonella (n = 2; 2.2%), and Enterobacter (n = 1; 1.1%) were among the other Enterobacterales isolated. Meropenem and imipenem were the most effective in isolates from Enterobacterales (n = 88) followed by amikacin (n = 84), ciprofloxacin (n = 75), and piperacillin-tazobactam (n = 70). Ceftriaxone and cefixime exhibited moderate susceptibility (n = 69 and 52) whereas, amoxicillin-clavulanate was the least susceptible (n = 3). We report high frequency of UTI in our pediatric population with uropathogens and associated antimicrobial susceptibility pattern confirming to the existing trends of pediatric UTIs in Pakistan. In addition to valuable insights for treating patients under similar conditions, our study serves as a catalyst for further multi-center research in this area.

Prevalence of SARS-CoV-2 virus in saliva, stool, and urine samples of COVID-19 patients in Bihar, India.

Introduction. The coronavirus illness caused by SARS-CoV-2 can cause multiple organ involvement, with varying degrees of severity. Besides inhalation as a route for transmission, feco-oral has also been proposed. Its transmission to sewage systems is a growing public health issue. Objective. To detect SARS-CoV-2 RNA in non-respiratory samples (saliva, urine, and stool) collected from COVID-19 cases, in Bihar. Methods. This cross-sectional observational study was conducted from January 2021 to March 2022 on human non-respiratory samples. A total of 345 samples including saliva (116), stool (97), and urine (132) were collected from 143 COVID-19 cases. Samples were analysed for SARS-CoV-2 by multiplex RT-PCR targeted against E, ORF 1ab, and RdRp genes. Results. In this study, out of 143 cases, a total of 107 (74.8 %) were positive for SARS-CoV-2 RNA in at least one of the non-respiratory samples. Conclusion. There is a high prevalence of SARS-CoV-2 virus in non-respiratory samples.

Fluorescence spectroscopic profiling of urine samples for predicting kidney transplant rejection

Rejection is the primary factor affecting the functionality of a kidney post-transplant, where its prompt prediction of risk significantly influences therapeutic strategies and clinical outcomes. Current graft health assessment methods, including serum creatinine measurements and transplant kidney puncture biopsies, possess considerable limitations. In contrast, urine serves as a direct indicator of the graft's degenerative stage and provides a more accurate measure than peripheral blood analysis, given its non-invasive collection of kidney-specific metabolite. This research entailed collecting fluorescent fingerprint data from 120 urine samples of post-renal transplant patients using hyperspectral imaging, followed by the development of a learning model to detect various forms of immunological rejection. The model successfully identified multiple rejection types with an average diagnostic accuracy of 95.56 %.Beyond proposing an innovative approach for predicting the risk of complications post-kidney transplantation, this study heralds the potential introduction of a non-invasive, rapid, and accurate supplementary method for risk assessment in clinical practice.

A comprehensive proteomic profiling of urinary exosomes and the identification of early non-invasive biomarker in patients with coronary artery disease

Urinary small extracellular vesicles or exosomes (uEVs) source could be an emerging trove of biomarkers in coronary artery disease (CAD). It is a chronic inflammatory disease having a long asymptomatic phase of fatty-fibrous development in arteries leading to angina, myocardial infarction, and death. Our study was aimed at identifying differential protein expression profiling of uEVs in CAD. We collected urine samples of CAD patients (n = 41) age 18–65 years and gender matched healthy controls (n = 41). We isolated uEVs using differential ultracentrifugation. Further, uEV samples were characterized by western blotting exosome markers (Flotillin, TSG, CD63, and CD9), nano tracking analysis, and transmission and scanning electron microscopy. A total of 508 proteins were identified by iTRAQ-based mass spectrometry. We observed protein expression levels of AZGP1, SEMG1/2, ORM1, IGL, SERPINA5, HSPG2, prosaposin, gelsolin, and CD59 were upregulated, and UMOD, KNG1, AMBP, prothrombin, and TF were downregulated. Protein-protein interactions, gene ontology and pathway analysis were performed to functionally annotate identified uEVs proteins. A novel uEVs differential protein signature is shown. On validating UMOD protein by ELISA in two clinically different CAD, stable-CAD patients had lower levels than healthy controls whereas recent myocardial infarction patients had lowest. Our findings suggest UMOD importance as early diagnostic biomarker. SignificanceCoronary artery disease is a chronic inflammatory disease caused by gradual deposition of cholesterol and fat along with other proteins to develop plaque inside arteries. This further leads to blockage of artery, heart attack and death. There are no identifiable early biomarkers to diagnose this. For the first time, we have identified the differentially expressed proteins isolated from non-invasive uEV of CAD patients compared to healthy controls by using MS Orbitrap and iTRAQ labelling of peptides. We have identified decreased levels of UMOD protein in CAD. These findings have been confirmed by ELISA. Furthermore, the levels of UMOD were observed as more highly decreased in recent myocardial infarction CAD patients, indicating the importance of this protein as an early diagnostic biomarker. Conclusively, our study represents a non-invasive urinary EVs trove of differentially expressed proteins in CAD. This will form a groundwork for understanding the pathophysiology of CAD and will help in future translational research utilizing uEVs.

Microbiome Profiling in Bladder Cancer Patients Using the First-morning Urine Sample

BackgroundSeveral studies support the interplay between the urinary microbiome (ie, urobiome) and bladder cancer (BCa). Specific urinary bacteria may be responsible for chronic inflammation, which in turn promotes carcinogenesis. Different signatures of urobiome in BCa patients were identified depending on tumor type, geographical area, age, and sex. ObjectiveWe explored the urobiome in BCa patients undergoing transurethral resection of bladder tumor (TURBT), to identify possible predictive biomarkers of cancer. Design, setting, and participantsThe urobiome analysis was conducted in 48 patients (13 females) undergoing TURBT, of whom 30 with BCa (five females) and 18 with benign bladder tumor, analyzing bacterial 16S rRNA by next-generation sequencing in first-morning (FM) urine samples. Forty-three cancer-free individuals and 17 prostate cancer patients were used as controls. Outcome measurements and statistical analysisFirst, we identified the better urine collection procedure to perform the urobiome analysis, comparing bacterial composition between catheterized (CAT) and FM urine samples in TURBT patients. Successively, we observed a specific urobiome in BCa patients rather than controls. A combined pipeline including the DESeq2 and linear discriminant analysis effect size tests was used to identify differential urinary taxa, strictly associated with BCa patients. Results and limitationsThe bacterial composition of CAT and FM urine samples was comparable, so the latter was used for the following analyses. An increased abundance of Porphyromonas and Porphyromonas somerae was found in BCa patients compared with controls. This signature seems to be more related (p <0.05) to male BCa patients over 50 yr old. Owing to the low biomass of urinary microbiota, several samples were excluded from the study, reducing the number of BCa patients considered. ConclusionsFM urine samples represent a manageable specimen for a urobiome analysis; P. somerae is a specific biomarker of BCa risk. Patient summaryOur study showed an increased abundance of Porphyromonas and Porphyromonas somerae in male bladder cancer (BCa) patients, supporting the use of a first-morning urine sample, a less invasive and low-cost collection method, for the urobiome analysis of patients at risk of BCa.

Characterization of VIM, VEB and CTX-M Beta-lactamase Gene in Escherichia coli and Pseudomonas aeruginosa Isolated from Urine Samples of Patients Visiting a Tertiary Hospital in Abakaliki

The spread and convergence of multiple beta-lactamase genes across distinct resistant bacterial populations from various hosts and settings demonstrates increased risk of morbidity and mortality in humans. This study was undertaken to characterize blaVIM, blaVEB and blaCTX-M beta-lactamase gene in Escherichia coli and P. aeruginosa isolates from patients visiting a tertiary hospital in Abakaliki. A total of three hundred (300) urine samples were collected from patients and were subjected to bacteriological examination using culture, Gram staining and biochemical technique, for routine microbiological identification and further confirmed using the VITEK-2 Automated System (Biomerieux, France). Antimicrobial susceptibility studies were determined using the Kirby–Bauer disk diffusion method. All isolate were further screen for various beta-lactamase resistant gene by PCR using specific primer. Of the 300 urine samples collected, prevalence rate of 187 (62.3%) and 91 (30.3 %) E. coli and P. aeruginosa were recorded. The isolates exhibited 50.0-100% percentage of resistance to Amoxycillin-Clavulanic acid, Azetronam, Cefoxitin, Ceftriaxone and Piperacillin/tazobactam. The proportion of beta-lactamase gene in E. coli were as follows (VEB 143/76.5 %; CTX-M 175/93.5 %; VIM 77/41.2 %) while beta-lactamase gene in P. aeruginosa were as follows (VEB 91/100 %; CTX-M 63/69.2%; VIM 48/52.7 %). The presence of these gene in our study indicates the possibility of therapeutic failure, serious consequences for infection control and increased risk of morbidity and mortality in patients. Hence, continuous effort in hospital surveillance, infection control, and clinical audits must be conducted to fight against the rapid development and spread of antibiotic-resistant bacteria pathogens. Keywords: Beta-lactamase, Escherichia coli, Pseudomonas aeruginosa, VIM, VEB, CTX-M