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.

Catheter-related Infections in Pediatric Patients Due to a Rare Pathogen: Herbaspirillum huttiense.

BACKGROUND: Herbaspirillum species are nonfermenting, aerobic, helical or curved, Gram-negative bacteria belonging to the class Betaproteobacteria, order Burkholderiales. To date, only a few studies have reported on the epidemiology, clinical symptoms, antibiotic susceptibility profiles, treatment and outcomes of Herbaspirillum huttiense -related infections in pediatric patients. METHODS: The aim of this study was to present 3 years of H.huntiense data, antibiotic susceptibility profiles, systemic antibiotics and antibiotic lock therapy (ALT) options and clinical outcomes. RESULTS: Fourteen episodes of infection in 12 patients were included in this retrospective study. The patients had a male/female ratio of 1:1 and a median age of 160.5 months (range, 3-198 months). Catheter-related bloodstream infection (CRBSI) was detected in 11 patients. Only 1 patient developed catheter-related infective endocarditis. The patient's catheter was removed, and she was successfully treated with systemic antibiotics for 4 weeks. Systemic antibiotics were used in all infections related to H. huttiense . In septic, critically ill patients, the catheter was removed, and systemic antibiotics were started. Port catheters were removed in 5 patients. ALT was performed in clinically stable patients. ALT using amikacin was administered to 6 patients through the port catheter. Two patients had a 2nd attack. After the 2nd ALT treatment, 1 patient cured, and the catheter of the other patient was removed due to persistent microbial growth in cultures. Antimicrobial susceptibility testing of the reported isolates showed susceptibility to meropenem (90%), ceftazidime (87%) and piperacillin/tazobactam (65%), with 92% resistance to colistin. CONCLUSION: H. huttiense is an emerging pathogen in CRBSI. Piperacillin/tazobactam, ceftazidime and meropenem appear to be good therapeutic options for the treatment of H. huttiense infections. ALT and systemic antibiotics can be used in H. huttiense -CRBSI to sterilize and preserve the central venous catheter.

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.

Is SARS-CoV-2 Now More Like the Seasonal Coronaviruses Following Its Evolution?

BACKGROUND: SARS-CoV-2 has evolved significantly since the beginning of the COVID-19 pandemic. COVID-19 mortality has decreased due to increased population immunity and possibly the reduced intrinsic severity of the new variants. SARS-CoV-2 is now considered an endemic virus, but the extent to which its clinical findings resemble those of seasonal coronaviruses (sCoV) is not fully understood. METHODS: Pediatric patients under 18 years of age who were sent for SARS-CoV-2 polymerase chain reaction real-time reverse transcription polymerase chain reaction between January 1, 2022 and January 14, 2023 and whose results were positive were included in this study. To include only symptomatic COVID-19 patients in the study, asymptomatic patients who were positive in their screening tests were excluded. For the sCoV patients' group, patients who had a respiratory viral polymerase chain reaction assay between January 10, 2022 and January 11, 2023 and were positive for any type of sCoV were included in the study. The 2 groups were compared for clinical and laboratory characteristics. RESULTS: The study included 213 patients with COVID-19 and 194 patients with sCoV infection. Fever was a more common symptom in patients with COVID-19. sCoV was associated with lower respiratory involvement while increasing age was protective. The likelihood of hospitalization was decreased by increasing age but increased by the presence of comorbid conditions and lower respiratory tract involvement. The type of virus had no effect on the likelihood of hospitalization. CONCLUSIONS: In conclusion, sCoV infections carry a higher risk for lower respiratory involvement than COVID-19, and COVID-19 has a milder course than sCoV infections in children.

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.

Radiographic findings of adenoviral pneumonia in children.

OBJECTIVE: Adenovirus pneumonia is a common cause of community-acquired pneumonia in children and can mimic bacterial pneumonia, but there are few publications on its radiographic features. This study has evaluated the chest radiography findings of community-acquired adenovirus pneumonia in children. The frequency of radiological findings mimicking bacterial pneumonia was investigated. The clinical features of patients with adenovirus pneumonia possessing radiological findings mimicking bacterial pneumonia were also evaluated. MATERIALS AND METHODS: The chest radiographs of patients diagnosed with adenovirus pneumonia were retrospectively reviewed. The chest radiographs were interpreted independently by a pediatric infectious disease specialist and a pediatric radiologist. Chest radiography findings mimicking bacterial pneumonia (bacterial-like) were specified as consolidation +/- pleural effusion. Other findings on chest radiography or a completely normal chest X-ray were specified as findings that were compatible with "typical viral pneumonia". RESULTS: A total of 1407 patients were positive for adenovirus with respiratory multiplex PCR. The 219 patients who met the study criteria were included in the study. Chest radiographs were normal in 58 (26.5 %) patients. The chest radiograph findings mimicked bacterial pneumonia in 41 (18.7 %) patients. CONCLUSION: Adenovirus pneumonia occurs predominantly in children aged five years and younger, as with other viral pneumonias. The radiographic findings in adenovirus pneumonia are predominantly those seen in viral pneumonia. Increasing age and positivity for only adenovirus without other viruses on respiratory multiplex PCR were associated with the chest radiograph being more likely to be "bacterial-like". Adenovirus may lead to lobar/segmental consolidation at a rate that is not very rare.

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.

Three Cases of Catheter-related Bloodstream Infection Caused by Phialemonium curvata : A Case Report and Literature Review.

BACKGROUND: With recent developments in the field of microbiology, an increasing number of yeasts and molds with the potential to cause infections in humans are identified every year. In addition to the challenges in identifying clinical isolates, there is limited antifungal susceptibility data available for Phialemonium species, leading to uncertainty in optimal treatment recommendations. METHODS: In this article, catheter-related bloodstream infections caused by Phialemonium curvata (previously Phialemonium curvatum ) in 3 immunosuppressed patients are presented. Furthermore, the literature was reviewed to identify the clinical spectrum and treatment approaches for the reported infections. RESULTS: The cases presented here were analyzed along with 24 cases reported in the literature. Among all cases, 21 (77.7%) patients had an underlying condition. Nine (33.3%) patients had hematological/oncological malignancies and solid organ transplants. Twenty-two (81.4%) patients had a history of device or invasive interventions. Surgical procedures, removal of contaminated devices or tissue were found to reduce the risk of death by 86.7%. Correspondence analysis revealed a significant association between antifungal treatment and outcome ( P < 0.001). The correspondence analysis could explain 53.9% of this relationship. Monotherapy and combination therapy were associated with survival. While salvage treatment or no antifungal therapy was associated with mortality, intravitreal injection or topical application of voriconazole was associated with sequelae. CONCLUSIONS: Surgical intervention and removal of contaminated devices or tissue should be considered at an early stage.

[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.

Impact of non-pharmaceutical interventions on circulating respiratory viruses during the COVID-19 pandemic in Turkey.

BACKGROUND: Non-pharmaceutical interventions (NPIs) applied to limit the SARS-CoV-2 pandemic also affect the circulation and seasonal characteristics of other respiratory viruses. OBJECTIVES: Assess the impact of NPIs on the spread and seasonal characteristics of non-SARS-CoV-2 respiratory viruses and examine viral respiratory co-infections. DESIGN: Retrospective cohort SETTING: Single center in Turkey. PATIENTS AND METHODS: Syndromic multiplex viral polymerase chain reaction (mPCR) panel results of patients admitted to the Ankara Bilkent City Hospital with symptoms of acute respiratory tract infection between April 1, 2020 and October 30, 2022 were evaluated. Two study periods before and after 1 July 2021, when the restrictions were discontinued, were statistically analyzed and compared to determine the effect of NPIs on circulating respiratory viruses. MAIN OUTCOME MEASURES: Prevalence of respiratory viruses as determined by syndromic mPCR panel. SAMPLE SIZE: 11300 patient samples were evaluated. RESULTS: At least one respiratory tract virus was detected in 6250 (55.3%) patients. Of these, at least one respiratory virus was detected in 5% in the first period (between April 1, 2020 and June 30, 2021, when NPIs were applied), and in 95% in the second period (between July 1, 2021 and October 30, 2022, when NPIs were relaxed). After the removal of NPIs, there was a statistically significant increase in hRV/EV, RSV-A/B, Flu A/H3, hBoV, hMPV, PIV-1, PIV-4, hCoV-OC43, PIV-2 and hCoV-NL63 (P<.05). In the 2020-2021 season, when strict NPIs were applied, all respiratory viruses evaluated did not have the usual seasonal peak and there were no seasonal influenza epidemics during this period. CONCLUSIONS: NPIs resulted in a dramatic decrease in the prevalence of respiratory viruses and notable disruption of seasonal characteristics. LIMITATIONS: Single-center study and retrospective. CONFLICT OF INTEREST: None.

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.

Investigation of SARS-CoV-2 using RT-PCR in vaginal swab samples of female patients with a diagnosis of severe COVID-19.

OBJECTIVE: It is important to determine the presence of SARS-CoV-2 in the vaginal fluid samples of reproductive-aged women with severe disease during the acute stage of the disease and to determine the risks of transmission by sexual or vertical transmission. MATERIAL AND METHODS: Adult women with confirmed severe COVID-19 who were admitted to Ankara City Hospital intensive care unit (ICU) between December 1st, 2020, and January 1st, 2021, were enrolled in the study. Vaginal swab samples were collected within 48 h in the ICU using Dacron or rayon swabs and tested for SARS-CoV-2 using reverse transcription real-time polymerase chain reaction (RT PCR). RESULTS: Thirty women of reproductive age were included in the study, five (16.7%) of whom were pregnant. The mean age was 44.9 (±10.5) years. The most common symptoms were headache (100%), muscle soreness (86.7%), cough (76.7%), fever (60%), and nausea and vomiting (20%). Nineteen (63.3%) patients had underlying medical conditions. The time interval from obtaining vaginal swab samples to admission to the ICU was 48 h. The time between vaginal sampling and PCR positivity ranged from 2 to 18 days. SARS-CoV-2 was not detected in any vaginal samples. CONCLUSION: Our study showed that women with severe COVID-19 did not have SARS-CoV-2 in their vaginal fluids. Investigation of the presence of SARS-CoV-2 in vaginal secretions may help in determining the risks of sexual transmission and vertical transmission from mother to baby. Information on this subject is still limited. Larger studies on comprehensive biological samples are needed.

Molecular epidemiology and antifungal susceptibilities of Aspergillus species isolated from patients with invasive aspergillosis.

OBJECTIVE: The aim of this study was to evaluate the demographic data, molecular epidemiology, and in vitro antifungal susceptibility results of patients with Aspergillus isolated from various clinical specimens. METHODS: A total of 44 Aspergillus strains were studied. The definition of invasive aspergillosis in patients was made according to European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) criteria. Strains were phenotypically and molecularly identified. Demographic characteristics of patients and genotypes of strains were evaluated. Phylogenetic analysis was done by the The Unweighted Pair-Group Method with Arithmetic Mean (UPGMA). Antifungal susceptibility of strains was determined according to The Clinical and Laboratory Standards Institute (CLSI)-M61-Ed2 and The European Committee on Antimicrobial Susceptibility Testing (EUCAST). RESULTS: A total of 11 patients were classified as proven and 33 as probable invasive aspergillosis. There was a statistically significant difference in age groups, subdisease, neutropenic, and receiving chemotherapy between groups. A total of 23 strains were identified as Aspergillus fumigatus, 12 as Aspergillus niger, 6 as Aspergillus flavus, and 3 as Aspergillus terreus. Phylogenetic analysis revealed five different genotypes. No statistical difference was found in the comparisons between patients groups and genotype groups. There was a statistically significant difference between genotype groups and voriconazole, posaconazole, and itraconazole Minimum Inhibition Concentration (MIC). CONCLUSION: Accurate identification of strains and antifungal susceptibility studies should be performed due to azole and amphotericin B resistance. Genotyping studies are important in infection control due to identifying sources of infection and transmission routes.

[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.

Molecular epidemiology and antifungal susceptibilities of Aspergillus species isolated from patients with invasive aspergillosis

SUMMARY OBJECTIVE: The aim of this study was to evaluate the demographic data, molecular epidemiology, and in vitro antifungal susceptibility results of patients with Aspergillus isolated from various clinical specimens. METHODS: A total of 44 Aspergillus strains were studied. The definition of invasive aspergillosis in patients was made according to European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) criteria. Strains were phenotypically and molecularly identified. Demographic characteristics of patients and genotypes of strains were evaluated. Phylogenetic analysis was done by the The Unweighted Pair-Group Method with Arithmetic Mean (UPGMA). Antifungal susceptibility of strains was determined according to The Clinical and Laboratory Standards Institute (CLSI)-M61-Ed2 and The European Committee on Antimicrobial Susceptibility Testing (EUCAST). RESULTS: A total of 11 patients were classified as proven and 33 as probable invasive aspergillosis. There was a statistically significant difference in age groups, subdisease, neutropenic, and receiving chemotherapy between groups. A total of 23 strains were identified as Aspergillus fumigatus, 12 as Aspergillus niger, 6 as Aspergillus flavus, and 3 as Aspergillus terreus. Phylogenetic analysis revealed five different genotypes. No statistical difference was found in the comparisons between patients groups and genotype groups. There was a statistically significant difference between genotype groups and voriconazole, posaconazole, and itraconazole Minimum Inhibition Concentration (MIC). CONCLUSION: Accurate identification of strains and antifungal susceptibility studies should be performed due to azole and amphotericin B resistance. Genotyping studies are important in infection control due to identifying sources of infection and transmission routes.

Comparison of clinical characteristics of wild-type SARS-CoV-2 and Omicron.

OBJECTIVE: This study aimed to investigate the effect of mutations by comparing wild-type SARS-CoV-2 and Omicron regarding clinical features in patients with COVID-19. It also aimed to assess whether SARS-CoV-2 cycle threshold value could predict COVID-19 severity. METHODS: A total of 960 wild-type and 411 Omicron variant patients with positive results in SARS-CoV-2 real-time reverse transcriptase polymerase chain reaction test from oropharyngeal and/or nasopharyngeal samples during their hospital admissions were included in this retrospective study. The reference symptoms of the patients were obtained from the hospital database. The correlation between chest computed tomography findings and the "cycle threshold" of patients with wild-type SARS-CoV-2 was assessed. RESULTS: Cough, fever, shortness of breath, loss of taste and smell, and diarrhea were found to be statistically significantly higher (p=0.001; 0.001; 0.001; 0.001; and 0.006; respectively) in the wild-type cohort, while in the Omicron cohort, sore throat and headache were found to be statistically significantly higher (p=0.001 and 0.003, respectively). An inverse relationship was found between chest computed tomography findings and viral load. CONCLUSION: This study revealed that the Omicron variant tended to infect predominantly the upper respiratory tract and showed decreased lung infectivity, and the disease progressed with a milder clinical course. Therefore, the study showed that the tropism of the virus was changed and the viral phenotype was affected. It was also found that SARS-CoV-2 viral load did not predict COVID-19 severity in patients with wild-type SARS-CoV-2.

The influence of COVID-19 pandemic on intrauterine fetal demise and possible vertical transmission of SARS-CoV-2.

OBJECTIVE: The impact of COVID-19 on intrauterine fetal demise (IUFD) and vertical transmission of the SARS-CoV-2 from the mother to the fetus are crucial issues of the COVID-19 pandemic. In the current study, we aimed to detect the pandemic's influence on the IUFD and evaluate the vertical transmission of the SARS-CoV-2 through analysis of placental tissues collected from PCR positive women with IUFD above 20 weeks of gestation. MATERIALS AND METHODS: The pregnant women above 20 weeks of gestation and had a fetus intrauterine demised during pandemic were included in the study. The pregnant women screened for COVID-19. Vertical transmission searched from placental tissues of COVID-19 positive women by RT-PCR tests for the presence of SARS-CoV-2 RNA. The number of IUFD before the pandemic and during the pandemic compared to assess the influence of the COVID-19 pandemic on the IUFD ratio. RESULTS: Among 138 pregnant women with IUFD, 100 of them could screen for COVID-19 status. RT-PCR test results of 6 of the screened pregnant women were positive for SARS-CoV-2. Placental tissues of these six women were analyzed, and one test result was positive for SARS-CoV-2 RNA. The IUFD ratio was significantly increased during the pandemic. CONCLUSION: It is clear that COVID-19 increases the IUFD ratio. Previous data for vertical transmission of SARS-CoV-2 during the second trimester is limited. We present the third case of literature that has positive placental results for SARS-CoV-2 RNA in the second trimester of pregnancy.

A Genetically Engineered Biofilm Material for SARS-CoV-2 Capturing and Isolation.

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously infecting people all around the world since its outbreak in 2019. Studies for numerous infection detection strategies are continuing. The sensitivity of detection methods is crucial to separate people with mild infections from people who are asymptomatic. In this sense, a strategy that would help to capture and isolate the SARS-CoV-2 virus prior to tests can be effective and beneficial. To this extent, genetically engineered biomaterials grounding from the biofilm protein of Escherichia coli are beneficial due to their robustness and adaptability to various application areas. Through functionalizing the E. coli biofilm protein, diverse properties can be attained such as enzyme display, nanoparticle production, and medical implant structures. Here, E. coli species are employed to express major curli protein CsgA and Griffithsin (GRFT) as fusion proteins, through a complex formation using SpyTag and SpyCatcher domains. In this study, a complex system with a CsgA scaffold harboring the affinity of GRFT against Spike protein to capture and isolate SARS-CoV-2 virus is successfully developed. It is shown that the hybrid recombinant protein can dramatically increase the sensitivity of currently available lateral flow assays for Sars-CoV-2 diagnostics.