INTRODUCTION:Helicobacter pylori (H. pylori) is a bacterium that infects half of the world's population, and, unless treated, colonization usually persists throughout the lifespan. Noninvasive tests for the detection of H. pylori infections have indeed been valuable because of their ease of use and reduced discomfort. However, many noninvasive tests primarily focus on identifying the presence of bacteria rather than determining antimicrobial susceptibility. The purpose of this work was to use real-time PCR on stool samples to identify H. pylori infections and the point mutations that resulted in clarithromycin resistance. METHODS:A total of 63 patients attending to Gastroenterology Department of Hacettepe University Hospital were included between January 2021 and July 2022. Gastric biopsy culture, rapid urease test, histopathological analysis, stool antigen test, gastric biopsy and stool real-time PCR (RT-PCR) procedures were performed for the diagnosis of H. pylori. As the study's reference standard, a combination of two positive procedures were used. RESULTS:Among the 63 patients included in the study, 42.9 % tested H. pylori positive, while 57.1 % tested H. pylori negative. When the reference standards were compared to stool RT-PCR; for H. pylori detection, sensitivity, specificity, positive predictive value, negative predictive value and diagnostic accuracy were determined 66.6 %, 100 %, 100 %, 80.0 %, 85.7 % respectively. In the detection of clarithromycin point mutations from stool samples with RT-PCR, the overall agreement was 65 % when compared to the results obtained from gastric biopsy RT-PCR. CONCLUSION:In conclusion, the outcomes of this study indicate that utilizing RT-PCR from stool samples holds potential as a diagnostic tool for detecting H. pylori. This is particularly relevant in circumstances where invasive tests present challenges. However, further studies are recommended to validate and refine the method for clarithromycin resistance detection.

IntroductionAnti-rods and rings (anti-RR) antibodies have recently been described as a cytoplasmic pattern in IIF-based screening of autoantibodies on HEp-2 cells and ICAP has named it as AC-23. It is most frequently related to drug-induced antibody generation. This study aimed to investigate the clinical significance of AC-23 positivity and its relevance to the diagnosis and/or follow-up of the associated diseases and/or drug use.MethodsA multicenter retrospective study was conducted among 10 hospitals from six different provinces in Türkiye from January 2017 to December 2021. The laboratory data and clinical information of 600 patients with positive anti-RR antibodies out of 547.558 HEp-2 IIF ANA samples were analyzed.ResultsThe distribution of AC-23 positive patients by year indicated a steady increase between 2017-2021. Anti-RR prevalence in post-COVID-19 period was significantly higher than that of pre-COVID-19 period (p=0.00). Concomitant ANA positivity was detected in 56.5% of patients, the most common patterns being AC-4 and AC-5 (41.1%). The most frequent pathology among the anti-RR positive patients was an autoimmune disease (19.83%); 28.57% of which had rheumatoid arthritis and 17.65% autoimmune liver disease. Among the 600 patients, 65 (10.83%) were diagnosed as hepatitis C virus (HCV) infection. Available data for 38 of the HCV patients revealed that 71.05% of them had a history of interferon alfa+ribavirin and 28.95% of them had a history of NS3/4/5A/5B polymerase inhibitor or protease inhibitor drug use. Significant increase in the rate of anti-RR positivity was observed in the post-COVID-19 period when compared to pre-COVID-19 period (p:0.00).DiscussionThis is the first multicenter study in Türkiye about the clinical association of anti-RR antibodies which may be ignored during routine HEp-2 IIF testing. Pathologies other than HCV should be taken into consideration in terms of the possible role of anti-RR in autoimmune diseases and other pathologies. The preliminary data obtained in this study suggest that anti-RR antibody development might also be associated to COVID-19, supporting the several previous data related to the potential of viruses triggering the formation of autoantibodies. Large-scale prospective studies should elucidate the clinical significance of RR pattern and determine its role in patient diagnosis and follow-up.

Abstract Background and Aims Recent evidence showed the relationship between gut microbiota with hypertension. Few studies also demonstrated that ambulatory blood pressure monitoring variables such as dipping status and linear variability are associated with fecal microbiota and metabolomics. However, the relationship between gut microbiota and metabolomic composition of white-coat hypertensive patients has not been studied yet. In addition, although the link between gut microbiota, blood pressure variability and high salt intake has been shown, none of the studies addressed these changes simultaneously in the same study population. Here, we aimed to investigate the interplay between the gut microbiome, fecal metabolites and 24-hour urine sodium levels between hypertensive, white-coat hypertensive (WCH) and healthy participants diagnosed with ambulatory blood pressure monitoring. Method The study included 18 newly diagnosed hypertensive, 8 WCH, and 21 healthy participants from our tertiary center. Ambulatory blood pressure (BP) monitoring was performed in all participants and nighttime dipping, morning BP surge (MBPS), pre-wake MBPS and linear BP variability were calculated. 16S rRNA sequencing was performed using Illumina MiSeq sequencer. DeSeq2 and linear discriminant analysis effect size (LEfSe) were performed with R. Fecal metabolite levels were analyzed by GC-MS. A partial least squares-discriminant analysis (PLS-DA) model was constructed for the feature selector and classifier. The variable importance in the projection (VIP) coefficient was calculated based on the PLS-DA model. Results ANOVA and post-hoc Tukey test showed WHC and hypertensive groups had higher blood pressure variability and morning-thorough MBPS than normotensive patients (p = 0.02 and 0.04, respectively), whereas 24-h urine Na levels were statistically similar between WCH and hypertensive groups (p = 0.11). There were no significant differences in α- and β-diversity metrics of gut microbiome between study groups. Select taxa were specific to WHC patients, notably Rikenellaceae family and Mitsuokella were higher in WHC against normotensive patients, whereas Ruminococcus callidus, Roseburia, Clostridium, Lactobacillus ruminis, Sutterall, Lachospiraceae and Muribaculaceae were decreased in WHC against normotensive patients in DeSeq2 analysis. Dialister was increased, whereas Bacteroides genus and Bacteroides fragilis were decreased in WHC against hypertensive patients. LEfSe analysis showed positive enrichment in Proteobacteria phylum and negative enrichment in Mitsuokella genus in WHC against hypertensive group. Enterococcus, Lachnobacterium, Odoribacter and Pseudomonas genera had positive; whereas Lactobacillus and Clostridium had negative correlations with 24-h urine Na levels. Positive correlations were shown between linear BP variability and Bacteroides and Paraprevotella genera. Several genera and species were enriched in Q3-4 against Q1-2 quartiles of pre-wake and sleep-thorough MBPS in LEfSe analyzes (Fig. 1). Normotensive and essential hypertensive groups could also be differentiated based on fecal metabolomic composition. Specifically, metabolites with the highest VIP values discriminating WCH from normotensive and hypertensive groups were methyl-palmitoleate, oxalic acid and phenyl β-D-glucopyranoside, respectively (Fig. 2). Conclusion In conclusion, we performed the first study focusing on the fecal microbiome and metabolomic characteristics of white-coat hypertensive patients. Urine Na levels and ambulatory blood pressure variables of the WCH group are different than those of the normotensive and similar to the hypertensive group. Comparative and correlation analyses revealed novel relationships between ambulatory blood pressure variables and gut microbiome of both WCH and hypertensive patients. Fecal metabolomic differences between study groups imply possible mechanisms underlying the effects of gut microbiome on blood pressure. Gut microbiota and metabolites may become valuable targets for interventions of both white-coat and essential hypertension in the near future.

Background: Blastocystis spp. has been proposed as a possible cause of extraintestinal clinical signs such as urticaria pathogenesis. Objectives: The aim of this study was to investigate the differences between microRNA (miRNA) expression profiles of Chronic spontaneous urticaria (CSU) patients in the presence or absence of Blastocystis spp. as well as healthy controls. Additionally, cellular pathways which are affected in the presence of Blastocystis spp. were identified. Methods: Twenty patients diagnosed with CSU were enrolled in the study and divided into equally two groups according to the presence of Blastocystis spp. Besides, six healthy individuals were included in the study. The expression profiles of 372 human-derived miRNAs have been investigated in serum samples from CSU patients and healthy controls with miScript miRNA PCR Array Human miRBase Profiler.Results: Compared to Blastocystis-negative (BN)-CSU patients, expression of 3 miRNAs (hsa-miR-3183, hsa-miR4469, hsa-miR-5191) were found to be downregulated by at least two-fold (p < 0.05) in Blastocystis-positive (BP)CSU patients. Additionally, the miRNA expression profiles of six healthy individuals (n = 3 Blastocystis-positive, n = 3 Blastocystis-negative) were analyzed and it was determined that the expressions of 7 miRNAs (hsa-miR4661-5p, hsa-miR-4666a-5p, hsa-miR-4803, hsa-miR-5587-5p, hsa-miR-4500, hsa-miR-5680, hsa-miR-382-3p) increased at least 3-fold in the serum of individuals with Blastocystis-positive compared to Blastocystis-negative subjects. Most down-regulated miRNAs, in BP-CSU patients, affect cell adhesion molecules (CAMs), and signaling pathways therefore, Blastocystis spp. presence may influence the clinical presentation of urticaria by leading to unbalanced immunity. In addition, Blastocystis spp. presence may be influenced TGF- beta signaling pathway through altered miRNAs and may be laying the groundwork for the development of CSU in healthy individuals. Conclusions: As a consequence, this is the first report to show that the miRNA expression profile is affected by the presence of Blastocystis spp. Further miRNA-based studies are needed in order to enlighten the exact underlying molecular mechanisms of the relationship between Blastocystis spp. and CSU.

The introduction of sophisticated molecular technologies (16S rRNA gene sequencing, matrix-assisted laser desorption ionization–time of flight [MALDI-TOF], and whole-genome sequencing) into many clinical and diagnostic microbiology laboratories has brought with it enhanced capabilities for the accurate identification of many prokaryotic species not resolvable by common phenotypic or commercially automated methods. Along with this heightened capacity to provide highly accurate bacterial identifications have come some indirect consequences that may not be entirely appreciated by the scientific community. Some examples of these consequences are a transitional approach to training and a different skill set for current laboratorians, a quickly changing bacterial taxonomy, and peer-reviewed literature requiring much closer scrutiny. This article provides an overview of the present situation and challenges to microbiologists as the field moves forward.

Objective:Parasitic infections emerge as a significant health problem, especially in underdeveloped and developing countries. Epidemiological data play an important role in taking effective measures against parasitic diseases.Methods:Clinical samples (stool, blood, bone marrow and tissue samples, etc.) that were sent to Hacettepe University Hospitals Parasitology Laboratory between 2014 and 2019 were analyzed retrospectively.Results:The positivity rates of the parasites detected in this study are as follows; Blastocystis sp. (71.6%), Dientamoeba fragilis (13.3%), Giardia lamblia (4.7%), Echinococcus spp. (1.9%), Enterobius vermicularis (1.8%) and Taenia spp. (0.3%). In this study, four of the patients were found to be positive for Leishmania spp. and two patients for Plasmodium falciparum and four patients for Plasmodium spp. E. histolytica/E. dispar cysts and/or trophozoites examined by Trichrome staining in our study were not detected within six years.Conclusion:According to this data and in the light of the results obtained from different regions of our country, it will be possible to properly direct the necessary strategies for the diagnosis, treatment of parasitic infections and the implementation of preventive measures.

Nocardia species are opportunistic bacteria that are frequently contagious by inhalation. Recently, Nocardia abscessus has been described as a different species. We report a 54-year-old male who presented with acute pleuritic chest pain, mimicking pulmonary thromboembolism on the 5th day of discharge from the hospital. The patient was receiving immunosuppressive therapy for newly diagnosed atypical anti-glomerular basement membrane disease. Thorax computed tomography revealed a 17x19 mm soft tissue lesion in the lateral segment of the middle lobe of the right lung. After further examinations, a biopsy decision was made and Nocardia abscessus was isolated in the aerobic culture of the aspiration material.

Leptotrichia species are fastidious anaerobic, fusiform, pencil-shaped Gram-negative bacilli that reside in microbiota of humans. Leptotrichia species have increasingly been recognized as an opportunistic pathogen in humans, mainly in the immunocompromised patient. Anaerobic organisms have rarely been isolated from blood cultures of pediatric patients. In our study, we isolated Leptotrichia trevisanii from central venous catheter culture of a five-year-old male patient. It was identified with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry and confirmed via 16S rRNA gene sequencing. The early recognition of anaerobic bacteremia and administration of appropriate antimicrobial and play an important role preventing mortality and morbidity in children. In our study we report a rarely diagnosed case of L. trevisanii bacteremia in a pediatric patient.

Robinsoniella peoriensis is a gram-positive, spore-forming, anaerobic rod. In our study, we isolated R. peoriensis from an open fracture of the left distal tibia of a three-year-old male patient. Tissue anaerobic culture was positive for R. peoriensis . It was identified with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry and confirmed via 16S rRNA gene sequencing. The patient responded to ampicillin-sulbactam and amikacin antibiotic therapy. Antimicrobial susceptibility testing should be performed to guide the choice of treatment. To the best of our knowledge, this is the first report of R. peoriensis osteomyelitis in a pediatric patient and first report from Turkey.