Stool Samples Of Patients Research Articles

Phage-antibiotic synergism against Salmonella typhi isolated from stool samples of typhoid patients.

Typhoid fever is a fatal disease in humans that is caused by Salmonella typhi. S. typhi infections need immediate antibiotic therapy, and their extensive use has led to multidrug-resistant (MDR) pathogens. The use of bacteriophages is becoming a new way to treat these resistant bacteria. This research was directed to bacteriophage isolation against S. typhi and to determine phage-antibiotic synergism. To isolate bacteriophages targeting S. typhi, the causative agent of typhoid fever, and investigate their potential synergistic effects when combined with antibiotics. A cross-sectional study. The Widal test was positive; twenty diarrheal stool samples were taken, and for confirmation of S. typhi, different biochemical tests were performed. The disc-diffusion technique was used to determine antimicrobial resistance, and the double agar overlay method was used for bacteriophage isolation from sewage water against S. typhi. To test antibiotic-phage synergism, the S. typhi bacteria was treated by phages together with varying antibiotic concentrations. Eleven samples were positive for S. typhi with black colonies on SS-agar. These were catalase and MR positive with alkali butt on TSI. Clear plaques were observed after the agar overlay. Isolated phages were stable at various pH and temperature levels. Synergism was observed on agar plate. The zone was enlarged when phages were combined with bacterial lawn culture and ciprofloxacin disk. Bacterial growth inhibition had a significant p-value of 0.03 in titration plates, with the phage-ciprofloxacin combination being more effective than the phage and antibiotic alone. The study highlights the synergistic effects of isolated bacteriophages with antibiotics, which are not only effective against S. typhi infection but also decrease antibiotic resistance.

Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis

Early detection of human disease is associated with improved clinical outcomes. However, many diseases are often detected at an advanced, symptomatic stage where patients are past efficacious treatment periods and can result in less favorable outcomes. Therefore, methods that can accurately detect human disease at a presymptomatic stage are urgently needed. Here, we introduce “frequentmers”; short sequences that are specific and recurrently observed in either patient or healthy control samples, but not in both. We showcase the utility of frequentmers for the detection of liver cirrhosis using metagenomic Next Generation Sequencing data from stool samples of patients and controls. We develop classification models for the detection of liver cirrhosis and achieve an AUC score of 0.91 using ten-fold cross-validation. A small subset of 200 frequentmers can achieve comparable results in detecting liver cirrhosis. Finally, we identify the microbial organisms in liver cirrhosis samples, which are associated with the most predictive frequentmer biomarkers.

Comparison of methods investigating Giardia intestinalis, Entamoeba histolytica, and Cryptosporidium spp. in stool samples of patients with diarrhea

Comparison of methods investigating Giardia intestinalis, Entamoeba histolytica, and Cryptosporidium spp. in stool samples of patients with diarrhea

Microbial Regulation of Vitamin D Linked to Colorectal Cancer: A Sex Bias.

In a recent issue of Cancer Cell, Li and colleagues revealed that Carnobacterium maltaromaticum (C. maltaromaticum) was significantly depleted in the stool samples of patients with colorectal cancer in a female-specific manner. C. maltaromaticum actively participated in the generation of vitamin D intermediary metabolites, which together with Faecalibacterium prausnitzii and Lachnispiraceae bacterium produce an active metabolite of vitamin D that protects against colorectal cancer development. C. maltaromaticum supplementation induced in a female-specific manner an increase in vitamin D levels that would activate its receptor in the colonic epithelium, protecting against the development of colorectal cancer.

An Investigation on the Prevalence of Escherichia Albertii in Urine and Stool Samples of Patients in Kermanshah, Iran

An Investigation on the Prevalence of Escherichia Albertii in Urine and Stool Samples of Patients in Kermanshah, Iran

Molecular prevalence of Pneumocystis jirovecii and Cryptosporidium in patients with asthma

Asthma is characterized by chronic airway inflammation. In addition to allergens, microorganisms can affect the clinical course of asthma. It has been shown that some fungi play an important role in the progression of asthma. However, the effects of Pneumocystis jirovecii and Cryptosporidium spp., on the disease are little known.We investigated P. jirovecii and Cryptosporidium spp. in the sputum and stool sample of patients with asthma (n = 40) by microscopy and PCR compared to the healthy group (n = 40).P. jirovecii (12.5 %), and Cryptosporidium spp. (12.5 %) were detected in the sputum samples of only asthmatic patients (p = 0.029 and 0.029 respectively). However, Crpytosporidium spp. was detected equally in stool samples of both groups (p = 0.682).Our results indicate that P. jirovecii and Cryptosporidium spp. should be considered in patients with asthma and molecular screening of these neglected eukaryotes in respiratory tract samples may be beneficial in the clinical management of the disease.

Genotyping of cryptosporidium species in cases of irritable bowel syndrome: A case control study from a tertiary care center

Irritable bowel syndrome (IBS) is functional bowel disorder characterized by abdominal pain or discomfort and altered bowel habits in the absence of detectable structural abnormalities. Protozoan cysts are commonly found in the stool samples of patients with IBS and a rising body of evidence suggests a direct causal relationship. Cryptosporidium infection can be a potential candidate for IBS. We studied prevalence, association, and genotype of cryptosporidium at a tertiary care centre. Using a case-control design, a total of 100 cases and 100 controls were selected between 2016 and 2017. Fresh stool samples were collected and processed for microscopic examination. Positive samples were subjected to PCR RFLP for speciation and results analysed for Odd’s ratio, relative risk and relationship between variables. There was a high male preponderance (m: f=9:1). Most patients belonged to the middle age group (34.8-42.4 years). Amongst the clinical subtype IBS with diarrhoea (IBS-D) was the most common subtype (63%). Odd’s ratio for having IBS was 57.5 with cryptosporidium with a relative risk of 2.09. Adjusted Odd’s ratio for age was 1.014 suggesting a linear correlation (r value=0.07) with age. Our study shows a significant risk of developing IBS with cryptosporidium infection. The authors recommend studies with larger population samples both within the northern regions of India and across the country to determine prevalence, speciation of cryptosporidium and its relationship to IBS.

The Role of Gut Microbiome Supplementation in COVID-19 Management.

COVID-19, which is caused by the RNA virus, SARS-CoV-2, mainly affects the respiratory system and has a varied clinical presentation. However, several studies have shown that COVID-19 can also affect the gastrointestinal (GI) system. Patients can experience various GI symptoms, such as vomiting and diarrhea, and the virus has been detected in the stool samples of patients hospitalized with COVID-19. There have also been rare reports of COVID-19 presenting with isolated GI symptoms and lack of respiratory symptoms, and the virus has also been detected for prolonged periods in the fecal samples of COVID-19 patients. Major alterations in the gut microbiome in the form of depletion of beneficial organisms and an abundance of pathogenic organisms have been reported in the fecal samples of hospitalized COVID-19 patients. Although the US FDA has approved several drugs to manage COVID-19, their efficacy remains modest. So, there is a constant ongoing effort to investigate novel treatment options for COVID-19. Health supplements like probiotics, prebiotics, postbiotics, and synbiotics have been popularly known for their various health benefits. In this review, we have summarized the current literature, which shows the potential benefit of these health supplements to mitigate and/or prevent the clinical presentation of COVID-19.

Fecal short chain fatty acids and urinary 3-indoxyl sulfate do not discriminate between patients with Crohn´s disease and ulcerative colitis and are not of diagnostic utility for predicting disease severity

BackgroundUrinary 3-indoxyl sulfate levels as well as fecal short chain fatty acid (SCFA) concentrations are surrogate markers for gut microbiota diversity. Patients with inflammatory bowel diseases (IBDs) and patients with primary sclerosing cholangitis (PSC), a disease closely associated with IBD, have decreased microbiome diversity. In this paper, the fecal SCFAs propionate, acetate, butyrate and isobutyrate of patients with IBD and patients with PSC-IBD and urinary 3-indoxyl sulfate of IBD patients were determined to study associations with disease etiology and severity.MethodsSCFA levels in feces of 64 IBD patients and 20 PSC-IBD patients were quantified by liquid chromatography with tandem mass spectrometry (LC–MS/MS). Urinary 3-indoxyl sulfate levels of 45 of these IBD patients were analysed by means of reversed-phase liquid chromatography-electrospray ionization-tandem mass spectrometry. Feces of 17 healthy controls and urine of 13 of these controls were analyzed in parallel. These cohorts had comparable sex distribution and age.ResultsUrinary 3-indoxyl sulfate concentrations (normalized to urinary creatinine levels) was increased (P = 0.030) and fecal isobutyrate levels (normalized to dry weight of the stool sample) of IBD patients were decreased (P = 0.035) in comparison to healthy controls. None of the analyzed metabolites differed between patients with Crohn´s disease (CD) and patients with ulcerative colitis (UC). Fecal acetate and butyrate positively correlated with fecal calprotectin (P = 0.040 and P = 0.005, respectively) and serum C-reactive protein (P = 0.024 and P = 0.025, respectively) in UC but not CD patients. UC patients with fecal calprotectin levels above 150 µg/g, indicating intestinal inflammatory activity, had higher fecal acetate (P = 0.016), butyrate (P = 0.007) and propionate (P = 0.046) in comparison to patients with fecal calprotectin levels < 50 µg/g. Fecal SCFA levels of PSC-IBD and IBD patients were comparable.ConclusionsCurrent findings suggest that analysis of urinary 3-indoxyl-sulfate as well as fecal SCFAs has no diagnostic value for IBD and PSC-IBD diagnosis or monitoring of disease severity.

Frequency of Rotavirus and Adenovirus in Children with Diarrhea

ABSTRACT Aim: The aim of this study is retrospective evaluation of the frequency of rotavirus and adenovirus in stool, and their distribution according to gender, age and seasons in children with diarrhea admitted at outpatients or hospitalized in our hospital. Material and Methods: Stool samples of patients aged between 0-18 years received at the Medical Microbiology Laboratory between 2021–2022 were evaluated for rotavirus–adenovirus. Rotavirus and adenovirus antigens were determined qualitatively by immunochromatographic cassette test method. Chi-square test was used in the statistical analysis. Results: A total of 1148 stool samples of pediatric patients were received by our laboratory during these two years for rotavirus and adenovirus antigen test. Of 1148 patients, 8.6% were positive for rotavirus, 5.1% for adenovirus, and 0.6% for both rotavirus and adenovirus antigens. Rotavirus and adenovirus was positive in 7.2% and 5.6% of males, respectively, and 10.6% and 4.5% of females, and there were no statistically significant differences. Rotavirus was most frequently found in the age group 3-5 years (11.6%) and adenovirus was most frequently found in the age group 6-9 years (8.4%), with no significant difference. Rotavirus was most frequently detected in spring (12.9%) while adenovirus was found most frequently in winter (8.1%), without significant differences. Antigen positivity was 4.1% and 4.9% in outpatients for rotavirus and adenovirus, respectively, and 15.1% and 5.5% in hospitalized patients. Rotavirus positivity was significantly higher in hospitalized patients than outpatients, and adenovirus positivity did not show a significant difference. Conclusion: We found that rotavirus and adenovirus were significant agents causing diarrhea in children, especially those younger than 5 years old, and that its frequency increased in winter and spring, and as rotavirus is a cause of hospitalization, implementation of rotavirus vaccine into routine vaccination programs seem to be beneficial for patients.

Analysis of Fecal Microbiota in Patients with Hypertension Complicated with Ischemic Stroke.

Ischemic stroke is a disease with a very high incidence in the clinic, and hypertension is the most important variable risk factor of ischemic stroke. Studies have shown that intestinal microbes are involved in the occurrence and development of various diseases. This study aims to explore whether intestinal microbes play an important role in the pathogenesis of ischemic stroke in a hypertensive population. In this study, the inpatients in the Department of Neurology and Cardiology of the Second Affiliated Hospital of Shandong First Medical University in April 2021 were selected, including seven patients with hypertension complicated with ischemic stroke and only seven patients with hypertension. After collecting the stool samples of patients, the gene sequence of the samples was detected by 16S rRNA sequencing technology, and the double-ended 2 × 150bp sequencing was carried out. After sequencing, the results were analyzed by diversity analysis, species difference analysis, species function difference analysis, and other bioinformatics tests. According to the test results, serum proteomics and biochemical blood tests were carried out to verify. There was no significant difference in α diversity and β diversity between hypertension complicated with the cerebral infarction and hypertension groups. LEfSe analysis showed that at the genus level, compared with the hypertension group, Bacteroides, UCG_009, and Eisenbergiella had significantly increased relative abundance. The genera with relatively significantly reduced abundance are Ruminococcus_gnavus_group, Sutterellaceae, Burkholderia, and Prevotella and the LDA score of Prevotella is < - 4, which indicates that there are significant differences. Compared with the blood biochemical indexes, the results showed that the level of APOA1 in hypertensive patients with ischemic stroke was significantly higher than that in hypertensive patients (p < 0.05), but there was no significant difference in total cholesterol (CHOL), triglyceride (TG), high-density lipoprotein (HDL), low-density lipoprotein (LDL), apolipoprotein B (APOB), and free fatty acid (NEFA). Proteomic analysis showed that there were 89 up-regulated genes and 51 down-regulated genes in the serum of the two groups, and the expression of APOC2 and APOC3 in the cerebral infarction group with hypertension was significantly higher than that in the hypertension group (p < 0.05). The intestinal diversity of patients with hypertension complicated with stroke is similar to that of patients with hypertension, but there are differences in microbiota, among which Prevotella is the most significant. Prevotella could affect lipid metabolism so that APOC2 and APOC3 in the blood are significantly increased, leading to cerebral artery atherosclerosis and, finally, ischemic stroke. This provides a new idea for preventing and treating ischemic stroke in patients with hypertension, but the mechanism of Prevotella acting on apolipoprotein needs further verification by basic medical research.

Investigating the Significance of Non-jejuni/coli Campylobacter Strains in Patients with Diarrhea.

Campylobacter is one of the most commonly reported foodborne bacteria worldwide. Although Campylobacter jejuni and Campylobacter coli have been reported to be responsible for the great majority of campylobacteriosis, the burden of infections by species other than C. jejuni and C. coli have been increasing as a result of a transition to diagnostic test methods that enable the isolation of emerging species. The aim of the present study was to recover C. jejuni, C. coli, and emerging species from the stool samples of 500 patients with gastroenteritis and 100 healthy subjects via the use of a filtration method and culture techniques using Butzler agar and mCCDA under a microaerobic or hydrogen-enriched atmosphere, identify the species by multiplex PCR methods and assess the significance of emerging species in enteric diseases. Thirty-one (6.2%) Campylobacter spp. were isolated from the stool samples of diarrheic patients but none from healthy individuals. Of 31 isolates, 21 (67.8%), nine (29%), and one (3.2%) were identified as C. jejuni, C. coli, and Campylobacter concisus by multiplex PCR, respectively. The filtration method was superior to the culture technique using mCCDA under a microaerobic atmosphere. C. concisus was evaluated as the etiology of gastroenteritis as a result of laboratory and clinical evaluations. The present study was the first to indicate that emerging Campylobacter species are rarely detected and C. concisus is linked to acute gastroenteritis in Turkey where additional studies are warranted to clarify the significance of emerging species in gastroenteritis.

Etiological Survey and Traceability Analysis of a Foodborne Disease Outbreak of Salmonella Senftenberg in Guizhou Province.

To conduct a study that examined the molecular epidemiology and pathogenesis of Salmonella Senftenberg isolates associated with an outbreak of foodborne disease in Guizhou Province and to provide a reference basis for the traceability of foodborne salmonellosis outbreaks and clinical diagnosis and treatment in the province. Fourteen strains of suspected Salmonella isolated from patient stool and food samples were used for pathogenic identification and serotyping by biochemical and mass spectrometry methods. Fourteen types of antibiotics were tested for drug sensitivity by the microbroth dilution method, and molecular typing was performed by pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). After the sequencing data were spliced by SPAdes, the gene protein sequences were compared with the Comprehensive Antibiotic Research Database and Virulence Factor Database, drug resistance and virulence genes were predicted, and whole genome multilocus sequence typing (wgMLST) was performed. The results were compared with those for Salmonella strains of the same serotype from the past 5 years in China detailed on the TraNet website. All 14 strains were identified as Salmonella Senftenberg (with the antigenic formula 1,3,19:g,s,t:-), and in the PFGE cluster tree, the strains were divided into two band types, with a similarity of 88.9%. The 14 strains were sensitive to the 14 antibiotics. WGS analysis showed that the 14 strains carried the same drug resistance and virulence genes and that all strains carried 3 aminoglycoside and lipopeptide drug resistance genes, including 114 virulence genes. The wgMLST results showed that the strains were distributed on the same small branch as those obtained from previous outbreaks of infection in Tianjin and Jilin. Salmonella Senftenberg, which caused the outbreak, carries a variety of virulence genes, which suggests that the strain is highly pathogenic. These pathogenic bacteria may be associated with the Salmonella strain in Tianjin, Jilin, and other places and have caused foodborne disease outbreaks as a result of imported contamination.

Engineered calprotectin-sensing probiotics for IBD surveillance in humans

Inflammatory bowel disease (IBD) is a spectrum of autoimmune diseases affecting the gastrointestinal tract characterized by a relapsing and remitting course of gut mucosal inflammation. Disease flares can be difficult to predict, and the current practice of IBD disease activity surveillance through endoscopy is invasive and requires medical expertise. Recent advancements in synthetic biology raise the possibility that symbiotic microbes can be engineered to selectively detect disease biomarkers used in current clinical practice. Here, we introduce an engineered probiotic capable of detecting the clinical gold standard IBD biomarker, calprotectin, with sensitivity and specificity in IBD patients. Specifically, we identified a bacterial promoter in the probiotic strain Escherichia coli Nissle 1917 (EcN) which exhibits a specific expression increase in the presence of calprotectin. Using murine models of colitis, we show that the reporter signal is activated in vivo during transit of the GI tract following oral delivery. Furthermore, our engineered probiotic can successfully discriminate human patients with active IBD from those in remission and without IBD using patient stool samples, where the intensity of reporter signal quantitatively tracks with clinical laboratory-measured levels of calprotectin. Our pilot study sets the stage for probiotics that can be engineered to detect fecal calprotectin for precise noninvasive disease activity monitoring in IBD patients.

Characteristics of Clostridioides difficile isolates circulating in the Slovak hospitals

Clostridioides difficile is a frequent cause of hospital-acquired diarrhea associated with antibiotics. Hypervirulent strains of Clostridioides difficile are associated with a severe course of Clostridioides difficile infection and a higher mortality. We have confirmed 322 non-duplicate Clostridioides difficile isolates in stool samples of patients hospitalized in three Slovak hospitals providing primary health care between January and December 2021 and determined genes encoding toxins, ribotypes and susceptibility to antimicrobials. 93.7% of them were toxigenic and co-occurrence of genes tcdA, tcdB, cdtA, cdtB, which encode toxins, was detected in 71.4% isolates. Nosocomially associated ribotypes 176, 001, and 027 were confirmed in 61.1%, 10.2%, and 5.2% of isolates, respectively, and found to be the most frequent. Although ribotype 176 predominated in all three hospitals, the highest incidence was recorded in Košice (73.5%). Results of antimicrobial susceptibility testing revealed 65.8% resistance rate for rifampicin, 5.2% for vancomycin, 1.5% for metronidazole, 1.2% for teicoplanin and 0.6% for doxycycline. The correlation of frequent ribotypes and results of antimicrobial susceptibility testing points to the predominance of rifampicin resistance in isolates belonging to ribotypes 176 and 027. The above results reflect the problematic situation in our hospitals during the COVID-19 pandemic, that was related to the misuse of broad-spectrum antibiotics and impossibility to follow epidemiological measures to prevent the spread of hypervilulent isolates.

Evaluation of Gut Microbiota in Healthy Persons and Type 1 Diabetes Mellitus Patients in North-Western Russia.

Bacterial microbiota in stool may vary over a wide range, depending on age, nutrition, etc. The purpose of our work was to discriminate phyla and genera of intestinal bacteria and their biodiversity within a healthy population (North-Western Russia) compared to the patients with type 1 diabetes mellitus (T1DM). The study group included 183 healthy persons 2 to 53 years old (a mean of 26.5±1.0 years old), and 41 T1DM patients (mean age 18.2±1.8 years old). The disease onset was at 11±1.5 years, with a T1DM experience of 7±1.5 years. Total DNA was isolated from the stool samples, and sequencing libraries were prepared by amplifying the V3-V4 region of the 16S rRNA gene sequenced by Illumina MiSeq. Bioinformatic processing of NGS databases was adapted for microbiota evalutaion. Despite the broad scatter, the biological diversity for bacterial microbiota expressed as the Shannon index was significantly increased from younger to older ages in the comparison group, higher in adult healthy persons, with a trend for decrease in the Actinomycetota phylum which includes Bifidobacterium longum species. Similar but non-significant age trends were noted in the T1DM group. Concordant with the Bacillota prevalence in stool samples of diabetic patients, some anaerobic bacteria (Faecalibacteria, Lachnospira and Ruminococcae, Roseburia) were enriched in the T1DM microbiome against controls. Hence, correction of microbiota for Ruminococcus and Lachnospiraceae requires future search for new probiotics. Lower abundance of Actinomycetota and Bifidobacter in T1DM suggests potential usage of Bifidobacter-based probiotics in this cohort.

Prevalence of parasitic infections in Al-Kindy Teaching Hospital and Medical City Teaching Hospital

Background: Intestinal parasitic infections including amoebiasis, blastocystosis, giardiasis, are all worldwide distribution with harmful effects, it is an important cause of morbidity and death rate in the poor countries. Objective: This study was done to collect information of the frequency of these diseases in some regions of Baghdad. Our objectives are to detect the frequency of human pathogenic parasites in some regions of Baghdad in stool samples of patients who would attend to AL-Kindy Teaching Hospital, Medical City Teaching Hospital and to determine the most common age group affected. Materials and Methods: Data were collected from Al-Kindy Teaching Hospital and Medical City Teaching Hospital, in the lab of parasitology from June 2021 to February 2022. The present study included (200) sample, which were collected from patients at different ages of both genders, samples of the study were selected randomly. Results: The results of epidemiological study showed that the total number infected with Entamoeba histolytica parasite was (129) positive samples with total percentage of (64.5%) in both of Al-Kindy Teaching Hospital and Medical City Teaching Hospital, Percentage of infective cases with this parasite in the two hospitals, were (93%, and 36%) respectively, followed by Blastocystis hominis with total number of (59) positive samples and a percentage of (29.5%). The percentage of infective cases with this parasite in the two hospitals, were (5%, and 54%) respectively, and then Giardia lamblia with total number of (12) positive samples, and a percentage of (6%). The percentage of infective cases with this parasite in the two hospitals, were (2%, and 10%) respectively. Males showed higher number and percentage of infection with E. histolytica, (85) case with percentage of (42.5%), while females were (44) case with percentage of (22%), while number and percentage of infection with B. hominis in males were (34) case with percentage of (17%), and females were (25) case with percentage of (12.5%), finally number and percentage of infection with G. lamblia in males (6) cases with percentage of (3%), equal females were (6) case with percentage of (3%). Infection highest percentage happened among age group (20-29) years with percentage of (28%), while the lowest percentage of infection occurred among age group (1-9) years, with percentage (1%), were detected in Medical City Teaching Hospital. In conclusions: Entamoeba histolytica was the most frequent parasite in our study, followed by Blastocystis hominis, while Giardia lambilia was the least frequent one. Also males were more affected than females to parasitic infections, and the most common age group affected was (20-29) years.Health education, safety of food and water must get higher to increase the knowledge of community about diseases caused by intestinal parasites.Using permanent stains, culture, molecular methods, and serological methods for detection of parasites, also making more studies including increasing in number of samples.

Evaluation of droplet digital qRT-PCR (dd qRT-PCR) for quantification of SARS CoV-2 RNA in stool and urine specimens of COVID-19 patients.

There have been a few reports of viral load detection in stool and urine samples of patients with coronavirus disease 2019 (COVID-19), and the transmission of the virus through faecal oral route. For clinical diagnosis and treatment, the widely used reverse transcription-polymerase chain reaction (qRT-PCR) method has some limitations. The aim of our study to assess the presence and concentration of SARS CoV-2 RNA in stool and urine samples from COVID-19 patients with mild, moderate, and severe disease, we compared a traditional qRT-PCR approach with a ddPCR. ddPCR and qRT-PCR-based target gene analysis were performed on 107 COVID-19-confirmed patients paired samples (N1 and N2). The MagMax magnetic beads base method was used to isolate RNA. Real-time qRT-PCR and dd PCR were performed on all patients. The average cycle threshold (Ct) of qRT-PCR was highly correlated with the average copy number of 327.10 copies/l analyzed in ddPCR. In ddPCR, urine samples showed 27.1% positivity while for stool it was 100%. This study's findings not only show that SARS CoV-2 is present in urine and faeces, but also suggest that low concentrations of the viral target ddPCR make it easier to identify positive samples and help resolve for cases of inconclusive diagnosis.

Microbiome alteration via fecal microbiota transplantation is effective for refractory immune checkpoint inhibitor-induced colitis.

Immune checkpoint inhibitors (ICIs) target advanced malignancies with high efficacy but also predispose patients to immune-related adverse events like immune-mediated colitis (IMC). Given the association between gut bacteria with response to ICI therapy and subsequent IMC, fecal microbiota transplantation (FMT) represents a feasible way to manipulate microbial composition in patients, with a potential benefit for IMC. Here, we present a large case series of 12 patients with refractory IMC who underwent FMT from healthy donors as salvage therapy. All 12 patients had grade 3 or 4 ICI-related diarrhea or colitis that failed to respond to standard first-line (corticosteroids) and second-line immunosuppression (infliximab or vedolizumab). Ten patients (83%) achieved symptom improvement after FMT, and three patients (25%) required repeat FMT, two of whom had no subsequent response. At the end of the study, 92% achieved IMC clinical remission. 16S rRNA sequencing of patient stool samples revealed that compositional differences between FMT donors and patients with IMC before FMT were associated with a complete response after FMT. Comparison of pre- and post-FMT stool samples in patients with complete responses showed significant increases in alpha diversity and increases in the abundances of Collinsella and Bifidobacterium, which were depleted in FMT responders before FMT. Histologically evaluable complete response patients also had decreases in select immune cells , including CD8+ T cells, in the colon after FMT when compared with non-complete response patients (n = 4). This study validates FMT as an effective treatment strategy for IMC and gives insights into the microbial signatures that may play a critical role in FMT response.

Aptamer-Based Electrochemical Microfluidic Biosensor for the Detection of Cryptosporidium parvum.

Cryptosporidium parvum is a high-risk and opportunistic waterborne parasitic pathogen with highly infectious oocysts that can survive harsh environmental conditions for long periods. Current state-of-the-art methods are limited to lengthy imaging and antibody-based detection techniques that are slow, labor-intensive, and demand trained personnel. Therefore, the development of new sensing platforms for rapid and accurate identification at the point-of-care (POC) is essential to improve public health. Herein, we propose a novel electrochemical microfluidic aptasensor based on hierarchical 3D gold nano-/microislands (NMIs), functionalized with aptamers specific to C. parvum. We used aptamers as robust synthetic biorecognition elements with a remarkable ability to bind and discriminate among molecules to develop a highly selective biosensor. Also, the 3D gold NMIs feature a large active surface area that provides high sensitivity and a low limit of detection (LOD), especially when they are combined with aptamers,. The performance of the NMI aptasensor was assessed by testing the biosensor's ability to detect different concentrations of C. parvum oocysts spiked in different sample matrices, i.e., buffer, tap water, and stool, within 40 min detection time. The electrochemical measurements showed an acceptable LOD of 5 oocysts mL-1 in buffer medium, as well as 10 oocysts mL-1 in stool and tap water media, over a wide linear range of 10-100,000 oocysts mL-1. Moreover, the NMI aptasensor recognized C. parvum oocysts with high selectivity while exhibiting no significant cross-reactivity to other related coccidian parasites. The specific feasibility of the aptasensor was further demonstrated by the detection of the target C. parvum in patient stool samples. Our assay showed coherent results with microscopy and real-time quantitative polymerase chain reaction, achieving high sensitivity and specificity with a significant signal difference (p < 0.001). Therefore, the proposed microfluidic electrochemical biosensor platform could be a stepping stone for the development of rapid and accurate detection of parasites at the POC.