Elevated levels of anti-Golgi antibodies: An early sign of seronegative rheumatoid arthritis.

Anti-Golgi antibodies are uncommon antibodies that exhibit specific, polarized cytoplasmic staining on the Hep-2 substrate. The objective of our study was to identify the clinical and laboratory features associated with anti-Golgi antibodies. We examined 4.5 years of data from a Turkish tertiary hospital in this retrospective cohort analysis. The indirect immunofluorescence staining patterns, antinuclear antibody (ANA) titres and clinical data of all patients were obtained from the hospital record system. A total of 146,055 ANAs were detected, of which 224 patients (0.15%) exhibited anti-Golgi antibody staining. In total, 39.4% of diagnosed patients had autoimmune diseases (AIDs). Of the AIDs, 26 (46.4%) were rheumatoid arthritis (RA). This is a very high rate and another remarkable point is that 17 (65.3%) of these patients had seronegative RA. High-titre results (1 ≥ 1/320) were more common in patients with AID. Anti-Ro52 was prevalent in 50% of extractable nuclear antigen (ENA)-positive patients, making it a remarkable finding. The majority of individuals with high-titre anti-Golgi antibodies had AID, particularly RA. The majority of these patients also tested negative for anti-cyclic citrullinated peptide (anti-CCP) and rheumatoid factor (RF). Finally, high-titre anti-Golgi antibodies may be an important serologic marker for seronegative RA in the Turkish population.

Molecular characterization of the multi-drug resistant Myroides odoratimimus isolates: a whole genome sequence-based study to confirm carbapenem resistance.

The bacteria belonging to the Myroides genus are opportunistic pathogens causing community or hospital-acquired infections that result in treatment failure due to antibiotic resistance. This study aimed to investigate molecular mechanisms of antibiotic resistance, clonal relatedness, and the biofilm forming capacity of the 51 multi-drug resistant Myroides odoratimimus. All isolates were screened for blaKPC, blaOXA, blaVIM, blaIMP, blaMUS, blaTUS, blaNDM, and blaB genes by using PCR amplification. Whole genome sequencing (WGS) was applied on three randomly selected isolates for further investigation of antibiotic resistance mechanisms. Clonal relatedness was analyzed by Pulsed-field gel electrophoresis (PFGE) and the microtiter plate method was used to demonstrate biofilm formation. All isolates were positive for biofilm formation. PCR analysis resulted in a positive for only the blaMUS-1 gene. WGS identified blaMUS-1, erm(F), ere(D), tet(X), and sul2 genes in all strains tested. Moreover, the genomic analyses of three strains revealed that genomes contained a large number of virulence factors (VFs). PFGE yielded a clustering rate of 96%. High clonal relatedness, biofilm formation, and multi-drug resistance properties may lead to the predominance of these opportunistic pathogens in hospital environments and make them cause nosocomial infections.

Investigation of intestinal parasites by conventional and molecular methods in children with gastrointestinal system complaints.

Intestinal parasitic infections are a global health problem that causes morbidity and mortality, especially in children living in rural areas. In this study, stool samples of pediatric patients with gastrointestinal complaints were examined by conventional and molecular methods to determine the prevalence of intestinal parasites. A total of 100 pediatric patients with gastrointestinal complaints and 50 healthy children were included in the study. Stool samples were collected from each child and examined by direct microscopic examination (native-Lugol method), formol-ethyl acetate concentration technique, Kinyoun's acid-fast staining, and Wheatley trichrome staining methods. Real-time PCR was used for the detection of Blastocystis spp. and D. fragilis in the stool samples. Sanger sequencing was used to identify Blastocystis spp. subtypes. One or more intestinal parasites were found in 12% (n = 100) of the patient group and 1% (n = 50) of the control group using conventional techniques. By using real-time PCR, Blastocystis spp. was discovered in 14% (14/100) of the patient group and 8% (4/50) of the control group. There was no significant difference in the frequency of Blastocystis spp. between the two groups. The most prevalent Blastocystis subtype was ST1 and the most frequent allele was a2 among the samples successfully amplified and sequenced. D. fragilis was detected in 17% (17/100) of the patient group and 8% (4/50) of the control group by real-time PCR. The prevalence of D. fragilis was not significantly different between the patient and control groups, as well. Blastocystis spp. and D. fragilis were found in high prevalence in pediatric patients with gastrointestinal complaints in this study. Although the role of these protists as a pathogen in humans is still controversial, it is supposed to the presence of the parasites are associated with gastrointestinal disorders such as diarrhea, abdominal pain, nausea, and vomiting. More case-control studies are needed to understand the pathogenic or commensal role of these parasites on the intestinal microbiota, especially in both patients with gastrointestinal disorders and healthy individuals.

[Evaluation of Antibiotic Susceptibility, Biofilm Production and Clonal Analysis of Corynebacterium striatum Isolates]. / Corynebacterium striatum Izolatlarinin Antibiyotik Duyarliliklari, Biyofilm Üretimi ve Klonal Analizlerinin Degerlendirilmesi.

In this study, it was aimed to determine the possible factors affecting the clinical importance of Corynebacterium striatum isolates, which were accepted as infectious or contamination/colonization agents, by comparing their clinical and microbiological characteristics, antimicrobial susceptibility results, biofilm forming abilities and genotypic characteristics. The patients with C.striatum growth in the clinical samples sent to the laboratory were evaluated as infection or contamination/colonization with the evaluation of the examination findings and other laboratory parameters by the relevant physician. This study included 58 isolates, 29 of which were considered as infection and 29 as contamination/colonization. Length of hospital stay, presence of underlying disease [diabetes mellitus (DM), neurological disease, ischemic heart disease, chronic kidney disease, solid tumor], surgical operation status in the last month, and antibiotic use in the last three months of the patients were examined. Identification of the bacterial type was made with MALDI-TOF MS (Bruker/Germany) system. Antimicrobial susceptibility tests were performed by disc diffusion and gradient diffusion method and evaluated according to EUCAST standards. Biofilm production was determined in 96-well microtiter plates on negatively charged polystyrene surfaces. Clonal analyzes were performed by PFGE method using Xba1 enzyme. It was observed that there was no difference in terms of demographic characteristics in the two patient groups included in the study. It was observed that C.striatum strains isolated from outpatients were mostly found in the contamination/ colonization group. The presence of diabetes mellitus, ischemic heart disease, chronic kidney disease and solid tumor was not statistically different in the two patient groups. It was observed that C.striatum strains grown in the samples of patients with neurological disease were mostly found in the infectious agent group (p= 0.025). It has been observed that C.striatum strains grown purely in culture were mostly found in the infectious agent group (p= 0.001). Biofilm production was found to be significantly higher in the infectious agent group (p= 0.015). In antimicrobial susceptibility tests, it was observed that there was widespread multidrug resistance (MDR) in both groups and there was no significant difference between the groups in terms of antimicrobial susceptibility. In our study, it was determined that the strains showed very different PFGE patterns and were not clonally related to each other. In this study, it was determined that the demographic characteristics and comorbidities of the patients were not helpful in evaluating the clinical significance of C.striatum. Biofilm production was observed to be a common virulence factor in C.striatum strains. It was thought that there may be difficulties in the treatment of C.striatum in the future due to the widespread MDR detection among this bacterium strains. Our study contributes to draw attention to the increase in C.striatum infections, resistance and virulence factors.

[Viral Respiratory Tract Infection Agents Detected Between Years 2019-2021, COVID-19, and Co-Infections]. / 2019-2021 Yillari Arasinda Saptanan Viral Solunum Yolu Enfeksiyonu Etkenleri, COVID-19 ve Ko-Enfeksiyonlar.

Respiratory tract infections are a major cause of morbidity and mortality at all ages and are seen as a very important public health problem all over the world. In this study, we aimed to evaluate the effect of the pandemic on the epidemiological and seasonal characteristics of the agents by analyzing the respiratory viral infection agents, viral co-infections and associations with Coronavirus diseases-2019 (COVID-19) studied by multiplex polymerase chain reaction (PCR) test in the molecular microbiology laboratory in a three-year period, including the one-year period before the pandemic. Between March 2019 and December 2021, 8825 respiratory tract specimens accepted to the molecular microbiology laboratory with respiratory tract multiplex PCR test requests were included in the study. In addition, severe acute respiratory syndrome (SARS-CoV-2) PCR test results of the patients with positive results with respiratory tract multiplex PCR test, which were studied within ± 3 days, were evaluated retrospectively. Respiratory viral pathogens were detected using FTD Respiratory Pathogens 21 kit (Fast Tract Diagnostics, Siemens Healthineers Company). Two different kits based on real-time reverse transcription PCR were used for SARS-CoV-2 RNA detection in different periods. According to our results, at least one viral agent was detected in 2156 (24.4%) of a total of 8825 samples and a single agent was detected in 1843 (85.5%) of these. The distribution of viruses in the samples with a single agent was determined as RV, RSV A/B, HCoVs, AdV, flu A virus, MPV A/B, PIV 1-4, flu B virus, EV, BoV and PeV, in order of frequency. Multiple agents were found in 313 (14.5%) of these 2156 samples. They were found to be two agents in 291 samples, three in 21 samples and four in one sample. When the SARS-CoV-2 PCR test results of the patients who had positive results with respiratory tract multiplex PCR and who were studied within ± 3 days were evaluated retrospectively, SARS-CoV-2 RNA was detected in 45 (3.5%) of 1277 samples in which at least one agent was detected. In four of these patients, SARS-CoV-2 was found together with multiple agents. Consequently, there was a sharp decrease in the prevalence of all viral agents during the pandemic period. It was evaluated that besides the COVID-19 infection, the restrictions applied during the pandemic period were also effective in this situation.

Management of pregnant women with COVID-19: A tertiary pandemic center experience on 1416 cases.

The aim of this study is to share the comprehensive experience of a tertiary pandemic center on pregnant women with COVID-19 and to compare clinical outcomes between pregnancy trimesters. The present prospective cohort study consisted of pregnant women with COVID-19 who were followed up at Ankara City Hospital between March 11, 2020 and February 20, 2021. Clinical characteristics and perinatal outcomes were compared between the pregnancy trimesters. A total of 1416 pregnant women (1400 singletons and 16 twins) with COVID-19 were evaluated. Twenty-six (1.8%) patients were admitted to the intensive care unit (ICU) and maternal mortality was observed in six (0.4%) cases. Pregnancy complications were present in 227 (16.1%) cases and preterm labor was the most common one (n = 42, 2.9%). There were 311, 433, and 672 patients in the first, second, and third trimesters of pregnancy, respectively. Rates of mild and severe/critic COVID-19 were highest in the first and second trimesters, respectively. The hospitalization rate was highest in the third trimester. Pregnancy complications, maternal mortality, and NICU admission rates were similar between the groups. The course of the disease and obstetric outcomes may be different among pregnancy trimesters. A worse course of the disease may be observed even in pregnant women without any coexisting health problems.

[Comparision of Colistin Broth Disc Elution, Rapid Resapolymyxin NP and Broth Microdilution Methods in Determining Colistin Sensitivity in Acinetobacter, Pseudomonas and Enterobacterales species]. / Acinetobacter, Pseudomonas ve Enterobacterales Türlerinde Kolistin Duyarliliginin Belirlenmesinde Kolistin Sivi Disk Elüsyon, Hizli Resapolimiksin NP ve Sivi Mikrodilüsyon Yöntemlerinin Karsilastirilmasi.

In recent years, with the increase of carbapenem resistance in Acinetobacter, Pseudomonas, Enterobacterales species, the use of colistin in treatment has gradually increased. Since the broth microdilution method which is recommended as a reference method in colistin susceptibility tests, is laborious and expensive and other susceptibility tests do not give reliable results, all these cause laboratories to search for new methods for the determination of colistin susceptibility testing. In this study, it was aimed to compare the broth microdilution method which is the reference method with the colistin broth disc elution and rapid resapolymyxin NP tests for the determination of the susceptibility of colistin in Acinetobacter, Pseudomonas, Enterobacterales species which are common healthcare-associated infection agents.Colistin susceptibility of a total of 157 isolates isolated from patients hospitalized in Ankara City Hospital [Klebsiella pneumoniae (n= 74), Acinetobacter spp. (n= 33), Escherichia coli (n= 26), Pseudomonas aeruginosa (n= 24)] were tested by broth microdilution, colistin broth disc elution and rapid resapolymixin NP methods. The categorical and basic agreement was evaluated by comparing the broth microdilution results with the rapid resapolymyxin NP results and the colistin broth disc elution. When compared with broth microdilution, the categorical agreement of colistin broth disc elution test for Enterobacterales, Acinetobacter, Pseudomonas species was found to be 93%, 48%, 100%, respectively. When the essential agreement was evaluated the values of 95%, 45%, 100% were found, respectively. Very major error rates were found to be 10%, 70% and 0%, respectively. The categorical agreement of the rapid resapolymyxin test for Enterobacterales, Acinetobacter, Pseudomonas species was 85%, 36%, 100%, while very major error rates were found to be 10%, 88% and 0%, respectively. When compared with the reference method, both tests showed high categorical and essential agreements for P.aeruginosa. Accepted level of categorical and essential agreement was found in colistin broth disc elution method for Enterobacterales species, and low categorical agreement was found in rapid resapolymyxin NP test. For Acinetobacter species, both tests detected low categorical agreement and high rate of very major error. In addition, compared to the broth microdilution method, both colistin broth disc elution and rapid resapolymyxin NP tests were found to be cost-effective and easy to prepare. It was considered to be an additional advantage to have the results in rapid polymyxin NP test in four hours. In conclusion, in our study, it was shown that both colistin broth disc elution and rapid resapolymyxin NP test methods can be used in determining the susceptibility of colistin for P.aeruginosa and Enterobacterales species but both methods were found to be unsuccessful for Acinetobacter species.

SARS-CoV-2 Detection with De Novo-Designed Synthetic Riboregulators.

SARS-CoV-2 is a human pathogen and the main cause of COVID-19 disease, announced as a global pandemic by the World Health Organization. COVID-19 is characterized by severe conditions, and early diagnosis can make dramatic changes for both personal and public health. Low-cost, easy-to-use diagnostic capabilities can have a very critical role in controlling the transmission of the disease. Here, we are reporting a state-of-the-art diagnostic tool developed with an in vitro synthetic biology approach by employing engineered de novo riboregulators. Our design coupled with a home-made point-of-care device can detect and report the presence of SARS-CoV-2-specific genes. The presence of SARS-CoV-2-related genes triggers the translation of sfGFP mRNAs, resulting in a green fluorescence output. The approach proposed here has the potential of being a game changer in SARS-CoV-2 diagnostics by providing an easy-to-run, low-cost diagnostic capability.

Vertical transmission of SARS-CoV-2: A prospective cross-sectional study from a tertiary center.

The aim was to investigate the association of the delivery mode and vertical transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) through the samples of vaginal secretions, placenta, cord blood, or amniotic fluid as well as the neonatal outcomes. This cross-sectional study presents an analysis of prospectively gathered data collected at a single tertiary hospital. Sixty-three pregnant women with confirmed coronavirus disease 2019 (COVID-19) participated in the study. Vertical transmission of SARS-CoV-2 was analyzed with reverse transcriptase-polymerase chain reaction (RT-PCR) tests and blood tests for immunoglobulin G (IgG)-immunoglobulin M (IgM) antibodies. All patients were in the mild or moderate category for COVID-19. Only one placental sample and two of the vaginal secretion samples were positive for SARS-CoV-2. Except for one, all positive samples were obtained from patients who gave birth by cesarean. All cord blood and amniotic fluid samples were negative for SARS-CoV-2. Two newborns were screened positive for COVID-19 IgG-IgM within 24 h after delivery, but the RT-PCR tests were negative. A positive RT-PCR result was detected in a neof a mother whose placenta, cord blood, amniotic fluid, and vaginal secretions samples were negative. He died due to pulmonary hemorrhage on the 11th day of life. In conclusion, we demonstrated that SARS-CoV-2 can be detectable in the placenta or vaginal secretions of pregnant women. Detection of the virus in the placenta or vaginal secretions may not be associated with neonatal infection. Vaginal delivery may not increase the incidence of neonatal infection, and cesarean may not prevent vertical transmission. The decision regarding the mode of delivery should be based on obstetric indications and COVID-19 severity.

Development and validation of nomogram to predict severe illness requiring intensive care follow up in hospitalized COVID-19 cases.

BACKGROUND: Early identification of severe COVID-19 patients who will need intensive care unit (ICU) follow-up and providing rapid, aggressive supportive care may reduce mortality and provide optimal use of medical resources. We aimed to develop and validate a nomogram to predict severe COVID-19 cases that would need ICU follow-up based on available and accessible patient values. METHODS: Patients hospitalized with laboratory-confirmed COVID-19 between March 15, 2020, and June 15, 2020, were enrolled in this retrospective study with 35 variables obtained upon admission considered. Univariate and multivariable logistic regression models were constructed to select potential predictive parameters using 1000 bootstrap samples. Afterward, a nomogram was developed with 5 variables selected from multivariable analysis. The nomogram model was evaluated by Area Under the Curve (AUC) and bias-corrected Harrell's C-index with 95% confidence interval, Hosmer-Lemeshow Goodness-of-fit test, and calibration curve analysis. RESULTS: Out of a total of 1022 patients, 686 cases without missing data were used to construct the nomogram. Of the 686, 104 needed ICU follow-up. The final model includes oxygen saturation, CRP, PCT, LDH, troponin as independent factors for the prediction of need for ICU admission. The model has good predictive power with an AUC of 0.93 (0.902-0.950) and a bias-corrected Harrell's C-index of 0.91 (0.899-0.947). Hosmer-Lemeshow test p-value was 0.826 and the model is well-calibrated (p = 0.1703). CONCLUSION: We developed a simple, accessible, easy-to-use nomogram with good distinctive power for severe illness requiring ICU follow-up. Clinicians can easily predict the course of COVID-19 and decide the procedure and facility of further follow-up by using clinical and laboratory values of patients available upon admission.

Immunogenicity and safety of the CoronaVac vaccine in patients with cancer receiving active systemic therapy.

Aim: To evaluate the immunogenicity and safety of the CoronaVac vaccine in patients with cancer receiving active systemic therapy. Methods: This multicenter, prospective, observational study was conducted with 47 patients receiving active systemic therapy for cancer. CoronaVac was administered as two doses (3 µg/day) on days 0 and 28. Antibody level higher than 1 IU/ml was defined as 'immunogenicity.' Results: The immunogenicity rate was 63.8% (30/47) in the entire patient group, 59.5% (25/42) in those receiving at least one cytotoxic drug and 100% (five of five) in those receiving monoclonal antibody or immunotherapy alone. Age was an independent predictive factor for immunogenicity (odds ratio: 0.830; p = 0.043). Conclusion: More than half of cancer patients receiving active systemic therapy developed immunogenicity.

[A case of Peritonitis Caused by Wickerhamomyces anomalus (Candida pelliculosa) Related to Peritoneal Dialysis]. / Wickerhamomyces anomalus (Candida pelliculosa)'un Etken Oldugu Periton Diyalizi Iliskili Bir Peritonit Olgusu.

Fungal peritonitis is less commonly seen than bacterial peritonitis in patients undergoing peritoneal dialysis (PD), but it is a serious complication with high morbidity and mortality. It often results in catheter loss and modifying therapy from PD to hemodialysis. The causative organisms are often Candida species. In this report, a PD-associated peritonitis caused by Wickerhamomyces anomalus (Candida pelliculosa), a rare fungal infection agent with increasing clinical importance by causing different clinical pictures was presented. An outpatient peritoneal fluid culture was sent from a 48-yearold male patient, who had been undergoing continuous peritoneal dialysis (CAPD) for 9 years, due to abdominal pain and blur in peritoneal fluid during dialysis. The patient admitted to the emergency department four days later due to the persistence of his complaints. A sample of peritoneal fluid was taken in the emergency department and sent to the laboratory for microbiological analysis. In the direct microscopical examination of the peritoneal fluid; cell number was determined as 210/mm3, and no microorganisms were seen in the Gram and methylene blue staining. The patient was admitted to the nephrology service with a pre-diagnosis of PD-associated peritonitis. Enterobacter aerogenes was grown in the peritoneal fluid culture which was sent from the dialysis outpatient clinic four days ago. The peritoneal fluid sample sent from the emergency department was inoculated on 5% sheep blood , EMB and chocolate agars and no growth was detected. As the patient's complaints and peritoneal fluid leukocyte count continued to increase, peritoneal fluid cultures were repeated and recurrent growth of yeast was detected in cultures. The yeast was identified as Candida pelliculosa by matrix assisted laser desorption ionization time-of-flight mass spectrofotometry (MALDI-TOF) VITEK®MS (bioMerieux, France). The species identification was confirmed by sequencing the target ITS gene regions on the rRNA and the isolate was identified as 100% Wickerhamomyces anomalus (sexual reproduction form of Candida pelliculosa, teleomorph). The reference microdilution method was performed according to the recommendations of the Clinical and Laboratory Standards Institute (CLSI) in order to test the antifungal susceptibility. After 24 hour incubation, the minimal inhibitory concentrations (MIC) were determined as 0.03 µg/ml for amphotericin B, 0.125 µg/ml for caspofungin 0.125 µg/ml for voriconazole, 0.03 µg/ ml for itraconazole and 4 µg/ml for fluconazole. Fluconazole and anidulafungin were started for the treatment of fungal peritonitis. The patient's peritoneal dialysis catheter was removed and hemodialysis was applied to the patient. Clinical and laboratory symptoms regressed with antifungal therapy and the patient's anidulafungin treatment was discontinued for 14 days after the catheter removal. In conclusion, in patients undergoing CAPD, as in our case, fungal pathogens should also be considered although it is rare, when there is no laboratory and clinical improvement, and the response to treatment is not complete in PD-associated peritonitis to prevent delays in diagnosis and treatment.

[Investigation of the Relationship of Systemic Immune-Inflammation Index, C-Reactive Protein and Interleukin-6 with Viral Dynamics in Patients with COVID-19]. / COVID-19 Tanili Hastalarda Sistemik Immün-Enflamasyon Indeksi, C-Reaktif Protein ve Interlökin-6'nin Viral Dinamik ile Iliskisinin Arastirilmasi.

Coronaviruses are enveloped, positivepolarity, single-stranded RNA viruses that can cause respiratory and gastrointestinal tract infections, less likely to cause infections with hepatic, neurological and nephrotic involvement. A novel coronavirus termed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in the city of Wuhan, China, and caused an outbreak of unusual viral pneumonia at the end of 2019. This study aimed to reveal the relationship between systemic immune-inflammation index (SII), C-reactive protein (CRP) and interleukin-6 (IL-6) and viral dynamics in COVID-19 patients. This retrospective, single-center study was conducted in Ankara City Hospital from April 1 to May 31, 2020. A total of 338 hospitalized patients who had positive results in SARS-CoV-2 reverse transcrytase polymerase chain reaction (RT-PCR) test from nasopharyngeal and oropharyngeal samples during their hospital admission were included in this study. Patients were divided into three groups according to their ward/intensive care unit, intubation and mortality situation and their clinical data were evaluated. Correlation analysis was performed to determine the relationship between viral dynamics and laboratory parameters such as SII, the neutrophil-to-lymphocyte ratio (NLR), the lymphocyte-to-CRP ratio (LCR), the lymphocyte-to-monocyte ratio (LMR), the platelet-to-lymphocyte ratio (PLR), CRP, IL-6 ferritin, albumin levels and lymphocyte count. Advanced age, low Ct value, increase in IL-6, increase in SII, decrease in albumin, increase in ferritin, decrease in lymphocyte count, increase in NLR, decrease in LCR, decrease in LMR, increase in PLR and increase in CRP levels were found statistically significantly different in all three groups (p<0.001; p= 0.02; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001, respectively). Statistical analysis revealed a significant negative correlation between serum IL-6, NLR, LCR and CRP values with Ct values (p<0.01, r= -0.233; p= 0.021, r= -0.126; p=0.004, r= -0.156 and p= 0.011, r= -0.138, respectively) and a significant positive correlation between Ct values and lymphocyte count and albumin levels (p= 0.005; r= 0.151 and p= 0.050; r= 0.106, respectively). Severe progression was observed in patients with advanced age, low Ct value, high IL-6 levels, high SII, hypoalbuminemia, high ferritin levels, lymphopenia, high NLR, low LCR, low LMR, high PLR and high CRP. In these patients hospitalization in intensive care unit, intubation and mortality were found to be higher. High levels of IL-6, NLR, LCR and CRP, lymphopenia and hypoalbuminemia were associated with low PCR Ct values.

Detection of HPV DNA in Esophageal Lesions: a Cross-Sectional Study.

BACKGROUND: Several studies have documented human papillomavirus (HPV) in extra-cervical tumors. We aimed to detect HPV type 16 and HPV other than type 16 (OT-16) DNA in esophageal papilloma and esophagus squamous cell carcinoma (ESCC) samples and to compare clinicopathological features of HPV positive and negative patients. METHODS: Materials were obtained from a tertiary care public hospital and studied in an university hospital for this cross-sectional study. Seventy-six tissue samples (50 papilloma and 26 ESCC) were included. After deparaffinization by xylene and DNA extraction by phenol chloroform-isoamyl-alcohol, 76 samples were studied with a G6PDH control kit. Forty-four papilloma and 21 ESCC samples with enough tissues were studied for HPV DNA. HPV OT-16 DNA and HPV type 16 were detected by real time-polymerase chain reaction. RESULTS: Twelve (27.3%) and one (2.3%) of the papilloma samples were HPV type 16 and other than type 16 positive, respectively. Eleven (52.4%) and one (4.8%) of ESCC samples were HPV type 16 and mixed type positive, respectively. CONCLUSIONS: We suggest that HPV infection is common in esophageal papilloma and ESCC. Due to the wellknown association of HPV with premalignant and malignant conditions, follow-up of these patients accompanied by HPV should be implemented.

COVID-19 experience of the major pandemic response center in the capital: results of the pandemic's first month in Turkey

Background/aim: The aim of this study is to evaluate the epidemiological and clinical characteristics and parameters that determined the clinical course and prognosis of the COVID-19 patients admitted to Ankara City Hospital during the first month of the pandemic in Turkey. Materials and methods: SARS-CoV-2 PCR positive patients who were hospitalized between March 10 and April 10, 2020 were included. Results: Among 222 patients, mean age was higher in severe acute respiratory illness (SARI)/critical disease group (P < 0.001). Median time from illness onset to admission and presence of comorbidity, especially coronary artery disease and chronic obstructive pulmonary disease, were significantly higher in the SARI/critical disease group (P < 0.05). Cough and fever were the most common symptoms, while anosmia and loss of taste were observed in 8.6% and 7.7% patients, respectively. The mortality rate was 5.4%. A high neutrophil/lymphocyte ratio; low lymphocyte, monocyte, and platelet count; elevated liver enzymes; low GFR; and high levels of muscle enzymes, ferritin, and IL-6 on admission were found to be associated with SARI/critical disease (P < 0.05). Bilateral ground-glass opacity and patchy infiltration were more frequently seen in the SARI/critical disease group (P < 0.001). Patients older than 65 years had an 8-fold increased risk for development of SARI/critical disease. Conclusion: This cohort study regarding COVID-19 cases in Turkey reveals that older age, presence of comorbidity, bilateral infiltration on CT, high neutrophil/lymphocyte ratio, low monocyte and platelet count, elevated liver enzymes, low GFR, high levels of muscle enzymes, and high levels of ferritin and IL-6 on admission are predictors of SARI and severe disease.

The Role of Human Parvovirus B19 in the Pediatric Patients with Pancytopenia?

BACKGROUND: Parvoviruses are small DNA viruses causing erythema infectiosum, which is known as the fifth disease. The aim of this study was to investigate the presence of Parvovirus B19 DNA by Real-Time-PCR retrospectively in clinical samples of children diagnosed as acute leukemia and aplastic anemia when investigating the cause of pancytopenia and to investigate its relationship with the clinical manifestations. METHODS: The study samples were collected between March 2014 and March 2018 in Gazi University, Faculty of Medicine, Department of Pediatric Hematology. Sixty pediatric patients; 37 males and 23 females, were included in the study. Nucleic acid isolation was performed by using MagNA-Pure Compact Nucleic Acid Isolation Kit (Roche, Germany). Extracted DNA was studied with LightCycler® 2.0 using the Real-Time PCR method and LightCycler® Parvovirus B19 Quantification Kit (Roche, Germany), and the results were evaluated quantitatively. Parvovirus B19 DNA detection interval of the kit was 101 - 106 copies/mL. RESULTS: Sixty serum samples were investigated and 8.3% (5/60) Parvovirus B19 DNA positivity was determined. Of the five patients with Parvovirus B19 DNA positivity, three had acute lymphoblastic leukemia and two were diagnosed as aplastic anemia. Regarding viral load; 2/5, 1/5, 1/5, and 1/5 of the samples had a viral load of 102, 103, 104, and 105 copies/mL, respectively. Parvovirus B19 DNA positivity was detected in samples from March (2/5), April (2/5), and August (1/5). CONCLUSIONS: Patients with acute leukemia and aplastic anemia in childhood using immunosuppressive drugs, blood, and blood products during chemotherapy, encounter Parvovirus B19 infections in the follow-up period and are diagnosed by serological and molecular methods. As a result of the study, we suggest that the detection of Parvovirus B19 DNA by Real-Time PCR method in children being admitted with pancytopenia and diagnosed as acute leukemia and aplastic anemia is useful in the follow-up and treatment.

Is Human Papillomavirus and Helicobacter pylori Related in Gastric Lesions?

BACKGROUND: Human papillomavirus (HPV), the causative agent of cervical cancer, is also suggested as a risk factor for gastric adenocarcinoma. Many infectious agents besides Helicobacter pylori have been associated with gastritis. The aim of this study was to investigate HPV DNA and genotyping HPV type 16 DNA in gastric adenocarcinoma and Helicobacter pylori gastritis cases. METHODS: A hundred and six gastric adenocarcinoma and Helicobacter pylori gastritis samples and 26 controls were included. After deparaffinization by xylene, DNA extraction was performed by the phenol-chloroform-isoamyl alcohol method and 106 samples were studied with a G6PDH control kit (Eurogentec, Seraing, Belgium). Fifty-three adenocarcinoma and 43 Helicobacter pylori samples were thought to have enough tissue and were studied for HPV DNA. HPV types other than 16 and HPV type 16 DNA were detected by Real Time PCR using the L1 region. Amplifications of MY09/11 products were done by GP5+/GP6+ primers and Cyanine-5 labeled HPV DNA and HPV 16 DNA specific probe in Light Cycler 2.0 (Roche Diagnostics, Germany) device. RESULTS: Among gastric adenocarcinoma and Helicobacter pylori gastritis samples, 20/53 (38%) and 18/43 (41.8%) were HPV DNA positive, respectively. Five (19.2%) of 26 controls were HPV DNA positive. CONCLUSIONS: Our 38% positive result in the gastric carcinoma group is in concordance with previous reports. This is the first study revealing the HPV-H. pylori relationship in gastritis cases and we concluded that with regard to the nearly three-fold higher HPV DNA (41.8%) in gastritis cases compared to controls, Helicobacter pylori positive cases should also be evaluated in favor of HPV in the gastritis group.

Re-emergence of genotype G9 during a five-and-a-half-year period in Turkish children with rotavirus diarrhea.

This study was done to understand the dynamics of rotavirus genotype distribution in Turkish children. Samples were collected from January 2006 through August 2011 from children at a hospital in Ankara. Rotavirus was detected in 28 % (241/889) of the samples. Genotype G9P[8] was predominant (28 %), followed by G1P[8] (16.3 %) and G2P[8] (15.9 %). G9 was absent in the samples from 2006 and 2007 and then re-emerged in 2008 and increased gradually. Phylogenetic analysis showed that Turkish G9 rotaviruses of the present study formed a sublineage with strains from Italy and Ethiopia, possibly indicating spread of a clone in these countries.

Candidemia in critically ill COVID-19 patients: Risk factors and impact on mortality.

Background: Risk factors of candidemia are well-described in intensive care units (ICUs) before the Coronavirus disease 2019 (COVID-19) pandemic. The increased rates of admission to ICUs have appeared during the pandemic. Methods: Patient characteristics and laboratory data of 80 candidemia with COVID-19, 101 candidemia without COVID-19, and 100 non-candidemia with COVID-19 patients were evaluated, in this study. Results: Systemic inflammatory response syndrome (SIRS) ≥ 2, solid malignancy, total parenteral nutrition (TPN), central venous catheterization (CVC), hypotension, fever, urea, alanine aminotransferase (ALT), D-dimer, procalcitonin, ferritin, and delta neutrophil index (DNI) was found to be associated with candidemia in COVID-19 patients. TPN, hypotension, and fever were identified as independent predictors of candidemia in COVID-19, and candidemia in COVID-19 is characterized by significantly high mortality rates. Urea, lactate, and procalcitonin were defined as independent predictors of hospital mortality in candidemia patients with COVID-19. Conclusion: The presence of candidemia increases mortality in COVID-19. TPN, fever, and hypotension werefound to be the most powerful predictors of candidemia in COVID-19. Overall, these data show that candidemia in COVID-19 is characterized by significantly high mortality rates. Determination of distinctive features can prevent candidemia and mortality.

Detection of Blastocystis sp. and Dientamoeba fragilis using conventional and molecular methods in patients with celiac disease.

Blastocystis sp. and Dientamoeba fragilis are intestinal protists, which are common worldwide, but the pathogenic role of these organisms in gastrointestinal diseases is still controversial. This study aimed to investigate the frequency of Blastocystis sp. and D. fragilis in stool samples from adult patients with celiac disease (CD) by using conventional and molecular methods. A total of 75 patients with CD and 75 healthy individuals were included in this study. Fresh stool specimens collected from each individual were analyzed by conventional and molecular methods. The overall prevalence of Blastocystis sp. and D. fragilis was 41.3% (31/75) and 24% (18/75) in patients with CD, and 46.7% (35/75) and 13.3% (10/75) in healthy controls, respectively. There was no statistically significant difference in the prevalence of Blastocystis sp. and D. fragilis between CD patients and healthy individuals. Blastocystis sp. subtypes were identified in 20 CD and 16 control patients and the overall subtype distribution was observed as ST1 13.9%, ST2 30.6%, and ST3 55.6%. The prevalence of Blastocystis sp. and D. fragilis in adults with CD is similar to the prevalence of protozoa in healthy adults. In this study, the most prevalent Blastocystis subtype was ST3 and the most frequent allele was a34 in both CD patients and healthy individuals. No significant difference was found between the two groups in terms of the detection rates of Blastocystis sp. and D. fragilis, and it is thought that both protists may be colonisers of the intestinal microbiome.