An alternative method for SARS-CoV-2 detection with use modified fluorescent in situ hybridization.

The real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) tests are the gold standard in detecting SARS-CoV-2 virus infection. However, despite high sensitivity and specificity, they have limitations that in some cases may result in false negative results. Therefore, it is reasonable to search for additional tools that could support microbiological diagnosis of SARS-CoV-2. The aim of the study was to develop a highly specific molecular test capable of detecting and visualizing SARS-CoV-2 infection. A universal probe and a set of 18 specific oligonucleotides with a FLAP sequence attached to them on both sides were designed to visualize SARS-CoV-2 virus infection based on the fluorescence in situ hybridization method (FISH). FISH conditions using the developed kit were standardized on the Vero CCL-81 cell line infected by SARS-CoV-2 virus. The method was tested on 290 nasopharyngeal swabs (collected in a doublet) from patients with clinical symptoms of SARS-CoV-2. Each one swab from the doublet was subjected to RNA isolation and amplification by rRT-PCR. From the second swab, a microscopic preparation was performed for FISH. The use of the rRT-PCR allowed obtaining 200 positive and 90 negative results, while our FISH method allowed for 220 positive results and 70 negative results. The differences obtained using both methods were statistically significant (p = 0.008). The obtained results support the use of FISH as an additional method in microbiological diagnostics of SARS-CoV-2.

Direct oral and fiber-derived butyrate supplementation as an anti-obesity treatment via different targets.

BACKGROUND & AIMS: Butyric (one of the short-chain fatty acids), a major byproduct of the fermentation of non-digestible carbohydrates (e.g. fiber), is supposed to have anti-obesity and anti-inflammatory properties. However, butyrate's potential and mechanism in preventing obesity and the efficient form of administration remain to be clarified. METHODS: Hence, we studied the effect of oral supplementation with 5% (w/w) sodium butyrate and 4% (w/w) ß-glucan (fiber) on young male mice (C57BL/6J) with high-fat diet-induced obesity (HFD: 60 kcal% of fat + 1% of cholesterol). Six weeks old mice were fed diets based on HFD or control (AIN-93G) diet with/without supplements for 4 weeks. The unique, interdisciplinary approach combining several Raman-based techniques (including Raman microscopy and fiber optic Raman spectroscopy) and next-generation sequencing was used to ex vivo analyze various depots of the adipose tissue (white, brown, perivascular) and gut microbiome, respectively. RESULTS: The findings demonstrate that sodium butyrate more effectively prevent the pathological increase in body weight caused by elevated saturated fatty acids influx linked to a HFD in comparison to ß-glucan, thereby entirely inhibiting diet-induced obesity. Moreover, butyrate significantly affects the white adipose tissue (WAT) reducing the epididymal WAT mass in comparison to HFD without supplements, and decreasing lipid saturation in the epididymal WAT and perivascular adipose tissue of the thoracic aorta. Contrarily, ß-glucan significantly changes the composition and diversity of the gut microbiome, reversing the HFD effect, but shows no effect on the epididymal WAT mass and therefore the weight gain inhibition is not as effective as with sodium butyrate. CONCLUSIONS: Here, oral supplementation with sodium butyrate and ß-glucan (fiber) has been proven to have an anti-obesity effect through two different targets. Administration-dependent effects that butyrate imposes on the adipose tissue (oral administration) and microbiome (fiber-derived) make it a promising candidate for the personalized treatment of obesity.

Duodenal microbiota and weight-loss following sleeve gastrectomy and Roux-en-Y gastric bypass - a pilot study.

BACKGROUND: Bariatric surgery is the most effective method of morbid obesity treatment. Microbiota has many functions in human body and many of them remain to be unknown. The aim of this study was to establish if the composition of duodenal microbiota influences success rate of bariatric surgery. METHODS: It was a prospective cohort study. The data concerning demographics and comorbidities was collected perioperatively. The duodenal biopsies were collected prior to surgery with the gastroscope. Then DNA analysis was conducted. The data connected to the operation outcomes was gathered after 6 and 12 months after surgery. RESULTS: Overall, 32 patients were included and divided into two groups (successful - group 1 and unsuccessful - group 0) based on percentage excess weight loss after 6 months were created. The Total Actual Abundance was higher in group 0. In group 0 there was a significantly higher amount of Roseburia and Arthrobacter (p = 0.024, p = 0.027, respectively). Genus LDA effect size analysis showed Prevotella, Megasphaera and Pseudorhodobacter in group 1 to be significant. Whereas abundance of Roseburia and Arthrobacter were significant in group 0. CONCLUSIONS: Duodenal microbiota composition may be a prognostic factor for the success of the bariatric surgery but further research on the larger group is needed.

Changes in the gut mycobiome in pediatric patients in relation to the clinical activity of Crohn's disease.

BACKGROUND: Numerous studies have shown that in Crohn's disease (CD), the gut microbiota is of great importance in the induction and maintenance of inflammation in the gastrointestinal tract. Until recently, studies have focused almost exclusively on bacteria in the gut. Lately, more attention has been paid to the role of intestinal fungi. AIM: To study the gut mycobiome analysis of pediatric patients with CD (in different stages of disease activity) compared to healthy children. METHODS: Fecal samples were collected from patients: With active, newly diagnosed CD (n = 50); active but previously diagnosed and treated CD (n = 16); non-active CD and who were in clinical remission (n = 39) and from healthy volunteers (n = 40). Fungal DNA was isolated from the samples. Next, next generation sequencing (MiSeq, Illumina) was performed. The composition of mycobiota was correlated with clinical and blood parameters. RESULTS: Candida spp. were overrepresented in CD patients, while in the control group, the most abundant genus was Saccharomyces. In CD patients, the percentage of Malassezia was almost twice that of the control (P < 0.05). In active CD patients, we documented a higher abundance of Debaryomyces hansenii (D. hansenii) compared to the non-active CD and control (P < 0.05) groups. Moreover, statistically significant changes in the abundance of Mycosphaerella, Rhodotorula, and Microidium were observed. The analyses at the species level and linear discriminant analysis showed that in each group it was possible to distinguish a specific species characteristic of a given patient population. Moreover, we have documented statistically significant correlations between: D. hansenii and patient age (negative); C. zeylanoides and patient age (positive); C. dubliniensis and calprotectin (positive); C. sake and calprotectin (positive); and C. tropicalis and pediatric CD activity index (PCDAI) (positive). CONCLUSION: Mycobiome changes in CD patients, and the positive correlation of some species with calprotectin or PCDAI, give strong evidence that fungi may be of key importance in the development of CD.

New insights into diversity of the upper respiratory tract microbiota and its relationship with SARS-CoV-2 viral load in the nasopharyngeal epithelial cells in patients with COVID-19.

INTRODUCTION: The effects of SARS­CoV­2 infection on the composition of the upper respiratory tract (URT) microbiota are yet to be established, and more attention to this topic is needed. OBJECTIVES: The study aimed to assess the bacterial profile and the possible association between the URT microbiota composition and the SARS­CoV­2 viral load. PATIENTS AND METHODS: Nasopharyngeal swabs were taken from 60 adult patients with SARS­CoV­2 infection who were divided into 3 groups based on the quantification cycle (Cq) value in the quantitative polymerase chain reaction test: group I (n = 20), Cq lower than or equal to 31 (high replication rate); group II (n = 20), Cq greater than 31 and lower than 38 (low replication rate), and group III (n = 20), Cq higher than or equal to 38 (virus eliminated from the nasopharyngeal epithelial cells). The obtained genetic libraries of 16S rRNA were sequenced and taxonomic diversity profiling was performed to determine the α- and ß­biodiversity in each group. RESULTS: A significantly lower abundance of Prevotella species was noted in group I, as compared with groups II and III. Akkermansia muciniphila, Faecalibacterium prausnitzii, Fusicatenibacterium saccharivorans, and Bacteroides dorei abundance was characteristic of and significantly greater in group I than in groups II and III. Overall, the microbiota composition was the most diverse in group I, whereas groups II and III were more homogenous in terms of taxonomic diversity. CONCLUSIONS: The arbitrary division of patients according to the SARS­CoV­2 viral load was reflected in diverse composition of their bacterial microbiota, which implies an association between these 2 factors. The patients with a low viral replication rate and those who eliminated the virus from the epithelial cells belonged to a group with a less diverse microbiota community than the patients with a high viral replication rate.

Biocidal Activity of Tannic Acid-Prepared Silver Nanoparticles towards Pathogens Isolated from Patients with Exacerbations of Chronic Rhinosinusitis.

The microbiome's significance in chronic rhinosinusitis (CRS) is unclear. Antimicrobials are recommended in acute exacerbations of the disease (AECRS). Increasing rates of antibiotic resistance have stimulated research on alternative therapeutic options, including silver nanoparticles (AgNPs). However, there are concerns regarding the safety of silver administration. The aim of this study was to assess the biological activity of tannic acid-prepared AgNPs (TA-AgNPs) towards sinonasal pathogens and nasal epithelial cells (HNEpC). The minimal inhibitory concentration (MIC) for pathogens isolated from patients with AECRS was approximated using the well diffusion method. The cytotoxicity of TA-AgNPswas evaluated using an MTT assay and trypan blue exclusion. A total of 48 clinical isolates and 4 reference strains were included in the study (Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Klebsiellaoxytoca, Acinetobacter baumannii, Serratia marcescens, Enterobacter cloacae). The results of the studies revealed that the MIC values differed between isolates, even within the same species. All the isolates were sensitive to TA-AgNPs in concentrations non-toxic to human cells during 24 h exposition. However, 48 h exposure to TA-AgNPs increased toxicity to HNEpC, narrowing their therapeutic window and enabling 19% of pathogens to resist the TA-AgNPs' biocidal action. It was concluded that TA-AgNPs are non-toxic for the investigated eukaryotic cells after short-term exposure and effective against most pathogens isolated from patients with AECRS, but sensitivity testing may be necessary before application.

"Impact of preoperative gastrointestinal microbiota on weight-loss after Roux-en-Y gastric bypass: a pilot study ".

BACKGROUND INFORMATION: In recent years the composition of gut microbiome has been linked to development of several diseases. The goal of the following study was to establish whether it is connected to the outcome of bariatric surgery. The objective was to analyze the oral and gut microbiota of patients suffering from morbid obesity who underwent laparoscopic Roux-en-Y gastric bypass (LRYGB). METHODS: The following is a prospective cohort study that was conducted between November 2018 and June 2019. Participants underwent LRYGB surgery. Patients then were assigned to group 1- success (surgical participants who achieved a percentage of excess weight loss [%EWL] >50%), group 2 (surgical participants who achieved a %EWL <50%). The follow up to establish the %EWL was conducted 6 months after the surgery. Before surgery, oral swabs were obtained, and stool samples were provided. The endpoint was the composition of the gut microbiota. RESULTS: Group 1 consisted of 4 participants; group 2 consisted of 2 participants. No participants were lost to follow-up during the study. Participants in group 1 had an oral microbiota that was enriched in the family Tissirelia of the phylum firmicutes. Gut microbiome of patients in group 1 was enriched with with Tanerella of the Bacteroidetes phylum. Group 2 did not present enriched microbiota by any of the analyzed organisms. Gut microbiota was enriched by deltaprotebacteria class (phylum Proteobacteria), bernesiellaceae of the phylum Bacteroidetes.

Comparison of iSeq and MiSeq as the two platforms for 16S rRNA sequencing in the study of the gut of rat microbiome.

Amplicon-based next-generation sequencing (NGS) of the 16S ribosomal RNA (16S) regions is a culture-free method used to identify and analyze Procaryota occurring within a given sample. The prokaryotic 16S rRNA gene contains conserved regions and nine variable regions (V1-V9) frequently used for phylogenetic classification of genus or species in diverse microbial populations. This work compares the accuracy and efficacy of two platforms, iSeq and MiSeq from Illumina, used in sequencing 16S rRNA. The most important similarities and differences of 16S microbiome sequencing in 20 fecal rat samples were described. Genetic libraries were prepared according to 16S Metagenomic Sequencing Library Preparation (Illumina) for the V3 and V4 regions of the 16S. The species richness obtained using iSeq technology was lower compared to MiSeq. At the second taxonomy level (L2), the abundance of taxa was comparable for both platforms. At the L7, the taxa abundance was significantly different, and the number of taxa was higher for the MiSeq. The alpha diversity was lower for iSeq than for MiSeq, starting from the order to the species level. The beta diversity estimation revealed statistically significant differences in microbiota diversity starting from the class level to the species level in samples sequenced on two investigated platforms. This work disclosed that the iSeq platform could be used to evaluate the bacterial profile of the samples to characterize the overall profile. The MiSeq System seems to be better for a detailed analysis of the differences in the microbiota composition. KEY POINTS: • iSeq platform allows to shorten the sequencing time three times compared to the MiSeq. • iSeq can only be used for an initial and quick microbiome assessment. • MiSeq is better for a detailed analysis of the differences in the microbiota composition.

Changes in the Composition of Oral and Intestinal Microbiota After Sleeve Gastrectomy and Roux-En-Y Gastric Bypass and Their Impact on Outcomes of Bariatric Surgery.

BACKGROUND: We aimed to assess the changes in composition of bacterial microbiota at two levels of the digestive tract: oral cavity and large intestine in patients 6 months after bariatric surgery. METHODS: This was a prospective cohort study including patients undergoing bariatric surgery. Before surgery and 6 months after the procedure, oral swabs were obtained and stool samples were provided. Our endpoint was the analysis of the differences in compositions of oral and fecal microbiota prior and after the surgical treatment of obesity. RESULTS: Bacteria from phylum Bacteroidetes seemed to increase in abundance in both the oral cavity and the large intestine 6 months after surgery among patients undergoing bariatric surgery. The subgroup analysis we conducted based on the volume of weight-loss revealed that patients achieving at least 50% of excess weight loss present similar results to the entire study group. Patients with less favorable outcomes presented an increase in the population of bacteria from phylum Fusobacteria and a decrease of phylum Firmicutes in oral cavity. CONCLUSION: Intestinal microbiota among these patients underwent similar changes in composition to the rest of the study group. Bariatric surgery introduces a significant change in composition of oral and intestinal microbiota.

Effect of poly(tert-butyl methacrylate) stereoregularity on polymer film interactions with peptides, proteins, and bacteria.

The impact of polymer stereoregularity on its interactions with peptides, proteins and bacteria strains was studied for three stereoregular forms of poly(tert-butyl methacrylate) (PtBMA): isotactic (iso), atactic (at) and syndiotactic (syn) PtBMA. Principal component analysis of the time-of-flight secondary ion mass spectrometry data recorded for thin polymer films indicated a different orientation of ester groups, which in the case of iso-PtBMA are exposed away from the surface whereas for at-PtBMA and syn-PtBMA these are located deeper within the film. This arrangement of chemical groups modified the interactions of iso-PtBMA with biomolecules when compared to at-PtBMA and syn-PtBMA. For peptides, the affected interactions were explained by the preferential hydrogen bonding and electrostatic interaction between the exposed polar ester groups of iso-PtBMA and positively charged peptides. In turn, for protein adsorption no impact on the amount of adsorbed proteins was observed. However, the polymer stereoregularity influenced the orientation of immunoglobulin G and induced conformational changes in bovine serum albumin structure. Moreover, the impact of polymer stereoregularity occurred equally for their interactions with Gram-positive bacteria (S. aureus), which absorbed preferentially onto iso-PtBMA films as compared to two other stereoregularities.

Changes in Diet and Anthropometric Parameters in Children and Adolescents with Celiac Disease-One Year of Follow-Up.

Celiac disease (CD) may cause numerous nutrient deficiencies that a proper gluten-free diet (GFD) should compensate for. The study group consists of 40 children, aged 8.43 years (SD 3.5), on average, in whom CD was diagnosed on the basis of clinical symptoms, immunological and histopathological results. The patients' height, weight, diet and biochemical tests were assessed three times: before diagnosis, after six months, and following one year of GFD. After one year, the patients' weight and height increased but nutritional status (body mass index, BMI percentile) did not change significantly. The children's diet before diagnosis was similar to that of the general Polish population: insufficient implementation of the dietary norm for energy, fiber, calcium, iodine, iron as well as folic acid, vitamins D, K, and E was observed. Over the year, the GFD of the children with CD did not change significantly for most of the above nutrients, or the changes were not significant for the overall assessment of the diet. Celiac patients following GFD may have a higher risk of iron, calcium and folate deficiencies. These results confirm the need for personalized nutritional education aimed at excluding gluten from the diet, as well as balancing the diet properly, in patients with CD.

Antibacterial and Antifungal Properties of Silver Nanoparticles-Effect of a Surface-Stabilizing Agent.

The biocidal properties of silver nanoparticles (AgNPs) prepared with the use of biologically active compounds seem to be especially significant for biological and medical application. Therefore, the aim of this research was to determine and compare the antibacterial and fungicidal properties of fifteen types of AgNPs. The main hypothesis was that the biological activity of AgNPs characterized by comparable size distributions, shapes, and ion release profiles is dependent on the properties of stabilizing agent molecules adsorbed on their surfaces. Escherichia coli and Staphylococcus aureus were selected as models of two types of bacterial cells. Candida albicans was selected for the research as a representative type of eukaryotic microorganism. The conducted studies reveal that larger AgNPs can be more biocidal than smaller ones. It was found that positively charged arginine-stabilized AgNPs (ARGSBAgNPs) were the most biocidal among all studied nanoparticles. The strongest fungicidal properties were detected for negatively charged EGCGAgNPs obtained using (-)-epigallocatechin gallate (EGCG). It was concluded that, by applying a specific stabilizing agent, one can tune the selectivity of AgNP toxicity towards desired pathogens. It was established that E. coli was more sensitive to AgNP exposure than S. aureus regardless of AgNP size and surface properties.

Association of Fungi and Archaea of the Gut Microbiota with Crohn's Disease in Pediatric Patients-Pilot Study.

The composition of bacteria is often altered in Crohn's disease (CD), but its connection to the disease is not fully understood. Gut archaea and fungi have recently been suggested to play a role as well. In our study, the presence and number of selected species of fungi and archaea in pediatric patients with CD and healthy controls were evaluated. Stool samples were collected from children with active CD (n = 54), non-active CD (n = 37) and control subjects (n = 33). The prevalence and the number of selected microorganisms were assessed by real-time PCR. The prevalence of Candida tropicalis was significantly increased in active CD compared to non-active CD and the control group (p = 0.011 and p = 0.036, respectively). The number of Malassezia spp. cells was significantly lower in patients with active CD compared to the control group, but in non-active CD, a significant increase was observed (p = 0.005 and p = 0.020, respectively). There were no statistically significant differences in the colonization by archaea. The obtained results indicate possible correlations with the course of the CD; however, further studies of the entire archeobiome and the mycobiome are necessary in order to receive a complete picture.

Differences in Compositions of Oral and Fecal Microbiota between Patients with Obesity and Controls.

Background and Objectives: The aim of this study was to compare the differences in compositions of oral and fecal bacterial microbiota between patients with morbid obesity and normal-weight controls. Material and Methods: This was a prospective cohort study. The study included group 1 (patients with BMI ≥ 40 kg/m2) and group 2 (patients with BMI from 18.5 to 24.9 kg/m2). Our endpoint was the analysis of the differences in compositions of oral and fecal microbiota between the groups. Oral swabs and fecal samples were collected from the patients. The analysis of microbiota was conducted using next-generation sequencing. Results: Overall, the study included 96 patients; 52 (54.2%) were included in group 1, 44 (39.8%)-in group 2. In group 1, oral microbiota included significantly more bacteria from genera Veillonella, Oribacterium and Soonwooa, whereas, in group 2, Streptobacillus, Parvimonas and Rothia were more common. Fecal microbiota in group 1 included more Bacteroides, Odoribacter and Blautia and group 2 was more abundant in Ruminococcus, Christensenella and Faecalibacterium. Conclusions: Both oral and fecal gastrointestinal microbiota differs significantly among patients with severe obesity and lean individuals.

Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study.

The studies on microbiome in the human digestive tract indicate that fungi could also be one of the external factors affecting development of diabetes. The aim of this study was to evaluate the quantitative and qualitative mycobiome composition in the colon of the adults with type 1 (T1D), n = 26 and type 2 (T2D) diabetes, n = 24 compared to the control group, n = 26. The gut mycobiome was characterized in the stool samples using the analysis of the whole internal transcribed spacer (ITS) region of the fungal rDNA gene cluster by next-generation sequencing (NGS) with increased sensitivity. At the L2 (phylum) level, Basidiomycota fungi were predominant in all 3 study groups. Group T1D presented significantly lower number of Ascomycota compared to the T2D group, and at the L6 (genus) level, the T1D group presented significantly lower number of Saccharomyces genus compared to control and T2D groups. In the T1D group, a significant positive correlation between total cholesterol and low-density lipoprotein cholesterol (LDL-C) levels and fungi of the genus Saccharomyces, and in the T2D group, a negative correlation between the total cholesterol level and Malassezia genus was found. The obtained results seem to be a good foundation to extend the analysis of the relationship between individual genera and species of fungi and the parameters determining the metabolism of carbohydrates and lipids in the human body.

Challenging the gold standard: methods of sampling for microbial culture in patients with chronic rhinosinusitis.

PURPOSE: Chronic rhinosinusitis (CRS) is a highly prevalent multifactorial disorder. Culture-directed antibiotics are frequently prescribed to patients with CRS and the middle nasal meatus (MM) is traditionally believed to be a representative sampling site of the sinuses as a whole. The purpose of our study was to reevaluate the reliability of the MM as a sampling site in patients with CRS who suffer from impaired drainage from the sinuses to the MM. METHODS: Swabs and tissue biopsies were collected from the MM, maxillary sinus and frontal sinus from 50 patients with CRS. The results of bacterial culture were compared between sampling methods and sites in relation to the patency of the sinus ostia. RESULTS: 782 bacterial isolates were cultured from the samples. Concordant results between the MM and the sinus cavity were noted in 80% of patients for the maxillary sinus, but only 66% for the frontal sinus and 76% for the sinuses a whole. The differences were similarly prevalent in patients with open and occluded sinus ostia. Notably, swabs from all three sites provided representative information in 92% of patients and tissue biopsies did not provide additional information compared to multiple swabs. CONCLUSION: The traditional method of sampling from the middle meatus provides inadequate information in 24% of patients with CRS, which may result in inadequate antibiotic therapy and contribute to increasing antibiotic resistance. Additional sampling from the sinuses should be recommended whenever possible, while invasive sampling is not necessary.

Relationship between bariatric surgery outcomes and the preoperative gastrointestinal microbiota: a cohort study.

BACKGROUND: The composition of the gastrointestinal microbiota is associated with obesity. We hypothesized that the gut microbiota influences the outcomes of bariatric surgery. OBJECTIVES: We aimed to analyze using oral swabs and stool samples the microbiota of patients with morbid obesity who were undergoing laparoscopic sleeve gastrectomy (SG). SETTING: A university hospital in Poland. METHODS: This prospective cohort study was conducted between November 2018 and June 2019. Participants underwent SG or no surgery (controls). Results were then analyzed as a group 1 (surgical participants who achieved a percentage of excess weight loss [%EWL] >50%), group 2 (surgical participants who achieved a %EWL <50%), and group 3 (nonsurgical controls). %EWL was measured 6 months following surgery. Before surgery, oral swabs were obtained and stool samples were provided. The endpoint was the composition of the gut microbiota. RESULTS: Group 1 comprised 19 participants, group 2 comprised 11 participants, and group 3 comprised 16 participants. No participants were lost to follow-up during the study. Participants in group 1 had an oral microbiota that was enriched in the phyla Proteobacteria, and Bacteroidetes. Their intestinal microbiota was enriched in the Proteobacteria. In contrast, the oral microbiota of group 2 was enriched in the Actinobacteria and the intestinal microbiota was enriched in the phyla Bacteroidetes and Firmicutes. CONCLUSIONS: The compositions of the microbiota of the oral cavity and large intestine are related to the weight loss achieved following SG.

The Gut Microbiota Profile According to Glycemic Control in Type 1 Diabetes Patients Treated with Personal Insulin Pumps.

Recently, several studies explored associations between type 1 diabetes (T1DM) and microbiota. The aim of our study was to assess the colonic microbiota structure according to the metabolic control in T1DM patients treated with insulin pumps. We studied 89 T1DM patients (50.6% women) at the median age of 25 (IQR, 22-29) years. Pielou's evenness (p = 0.02), and Shannon's (p = 0.04) and Simpson's diversity indexes (p = 0.01), were higher in patients with glycosylated hemoglobin (HbA1c) ≥ 53 mmol/mol (7%). There were no differences in beta diversity between groups. A linear discriminant analysis effect size (LEfSe) algorithm showed that one family (Ruminococcaceae) was enriched in patients with HbA1c < 53 mmol/mol, whereas one family (Streptococcaceae) and four species (Ruminococcus torques, unclassified species of Lactococcus, Eubacteroim dolichum, and Coprobacillus cateniformis) were enriched in patients with HbA1c ≥ 53 mmol/mol. We found that at class level, the following pathways according to Kyoto Encyclopedia of Genes and Genomes were enriched in patients with HbA1c < 53 mmol/mol: bacterial motility proteins, secretion system, bacterial secretion system, ribosome biogenesis, translation proteins, and lipid biosynthesis, whereas in patients with HbA1c ≥ 53 mmol/mol, the galactose metabolism, oxidative phosphorylation, phosphotransferase system, fructose, and mannose metabolism were enriched. Observed differences in alpha diversity, metabolic pathways, and associations between bacteria and HbA1c in colonic flora need further investigation.

Comparison of Antigen Tests and qPCR in Rapid Diagnostics of Infections Caused by SARS-CoV-2 Virus.

Diagnostics of the coronavirus disease 2019 (COVID-19) using molecular techniques from the collected respiratory swab specimens requires well-equipped laboratory and qualified personnel, also it needs several hours of waiting for results and is expensive. Antigen tests appear to be faster and cheaper but their sensitivity and specificity are debatable. The aim of this study was to compare a selected antigen test with quantitative polymerase chain reaction (qPCR) tests results. Nasopharyngeal swabs were collected from 192 patients with COVID-19 symptoms. All samples were tested using Vitassay qPCR SARS-CoV-2 kit and the Humasis COVID-19 Ag Test (MedSun) antigen immunochromatographic test simultaneously. Ultimately, 189 samples were tested; 3 samples were excluded due to errors in taking swabs. The qPCR and antigen test results were as follows: 47 positive and 142 negative, and 45 positive and 144 negative, respectively. Calculated sensitivity of 91.5% and specificity of 98.6% for the antigen test shows differences which are not statistically significant in comparison to qPCR. Our study showed that effectiveness of the antigen tests in rapid laboratory diagnostics is high enough to be an alternative and support for nucleic acid amplification tests (NAAT) in the virus replication phase in the course of COVID-19.