[P323L Mutation in a Case with Prolonged SARS-CoV-2 PCR Positivity]. / Uzamis SARS-CoV-2 PCR Pozitifligi Olan Olguda P323L Mutasyonu.

Coronavirus disease-2019 (COVID-19) emerged in the last months of 2019 and caused a pandemic effecting the whole world. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 has changed by various mutations since the day it was first identified, causing the pandemic to continue. Age, male gender, obesity, and comorbidity, which are general risk factors for COVID-19, can also cause prolonged PCR positivity. In this report, a case of 37-year-old male who is working in the hospital's COVID-19 molecular diagnostics laboratory was presented. He was vaccinated with three doses of inactivated vaccine, CoronaVac (Sinovac Biotech, Beijing-China), within the context of the vaccination program carried out in Türkiye. His first SARS-CoV-2 positivity was detected on 12.01.2021, four months after the last vaccination, and he continued to be detected positive for SARS-CoV-2 throughout a period of 39 days by quantitative reverse transcription polymerase chain reaction (qRT-PCR) tests performed with 2-3-day intervals. The patient has a 20-pack/year smoking history and his body mass index (BMI) was 29.8 kg/m2 at the time of his COVID-19. The case, which was clinically defined as mild COVID-19 with symptoms including back and headache, cough, fever (38.5°C), and loss of taste-smell, and without any additional complications or respiratory distress during the disease process. In the radiological examination, the lung was found within normal ranges. Prophylactic enoxaparin sodium anti-xa IU/0.6 ml was administered to the patient due to his cardiovascular risk, and no additional treatment was given. Whole genome sequencing was performed from nasopharyngeal swab samples of the patient at the beginning and 16th day of the infection to investigate the the specific genomic features and mutation pattern of the virus in the host over time, due to the prolonged SARS-CoV-2 PCR positivity. Library preparation for the whole next-generation sequencing (NGS) was performed by the SARS-CoV-2 Panel, Paragon CleanPlex kit (Paragon Genomics, USA), and indexing of the library was done by Clean-Plex Dual-Indexed PCR Primers for Illumina Set B kit (Paragon Genomics, USA). NGS analysis was performed on the Illumina Miniseq (Illumina, USA) platform. As a result of the bioinformatics evaluation, both samples were determined as SARS-CoV-2 Delta variant (Nextclade; 21J-Delta variant, Pango lineage; AY.43). Remarkably, the SARSCoV-2 sequences in the two samples taken 15 days apart; several identical mutations; such as D614G in the S gene, P323L in the ORF 1b gene region, and P1228L in the Nsp3 gene region, were detected. Besides that, when compared to the first sample, three additional mutations (P383L, P539S, L838I) were observed in the sequence of the second sample, which led to three amino acid changes, the clinical significance of which has not yet been determined in the literature. It is thought that; these mutations that change amino acid expression, as well as the other three mutations detected, may contribute to the improvement of the fitness of the virus and may be one of the factors responsible for the prolonged SARS-CoV-2 PCR positivity. Additional data to be obtained by further epidemiological sequencing studies will shed light on this issue.

[Investigation of Ganciclovir Resistance in Cytomegalovirus Isolates by Phenotypic and Genotypic Methods]. / Sitomegalovirüs Izolatlarinda Gansiklovir Direncinin Fenotipik ve Genotipik Yöntemlerle Arastirilmasi.

Ganciclovir-resistant cytomegalovirus (CMV) strains are reported following long-term antiviral agent use, especially for immune-suppressive patients. In this study, it was aimed to investigate the mutations in the UL97 gene of CMV, which causes ganciclovir (GCV) resistance by genotypic and phenotypic methods in patients who developed CMV infection following hematopoietic cell (HCT) or solid organ transplantation (SOT). Thirty patients who had HCT or SOT in Mediterranean University Hospital and developed CMV infection during routine follow-up with a viral load of CMV over 1000 copies/mL were included in the study. CMV DNA was analyzed by an automated system (Cobas Ampliprep/COBAS TaqMan CMV Test, Roche Diagnostics, Germany) quantitatively. DNA sequence analysis of the regions including codons 420-664 in the UL97 gene region was done by the Sanger sequencing method to detect mutations causing antiviral resistance and compared with defined mutations. In order to investigate antiviral resistance by phenotypic methods, heparinized blood samples of the patients were collected, 'buffy coat (leukocyte layer)' was inoculated into MRC-5 cells by centrifugation method and CMV growth in these cells was controlled with monoclonal antibodies when growth was detected, virus titer was determined and plaque reduction test was applied as recommended. It was determined that 22 of the 30 patients were HCT recipients and eight were SOT (five kidney, three liver) recipients. When the CMV serology pattern of the patients was evaluated before transplantation, 29 (96.7%) patients were found to be seropositive and one (3.3%) patient was found to be seronegative. Totally, nine CMV UL97 mutations were detected in seven (23.3%) pediatric patients who had HCT, including six seropositive and one seronegative case. In addition, one mutation (D605E) not known to cause GCV resistance was detected in a seronegative recipient and three previously unidentified mutations were detected (1474T, F499S, V559A) in a seronegative recipient. Five of the mutations defined were UL97 mutations with a defined clinical resistance against GCV in each of the five recipients (C603W, C592G, H520Q, M460V, A594T). In the plaque reduction test using 3 µM, 12 µM, 48 µM and 96 µM concentrations of GCV in CMV strains, the IC50 value was determined to be ≥ 8 µM for the five CMV strains, and the phenotypic presence of GCV resistance was shown. Clinical resistance associated with CMV UL97 mutation was detected in five (22.7%) of 22 patients who had HCT. GCV resistance was also demonstrated in these patients by phenotypic methods. No UL97 mutation was detected in the patients who had SOT.

Effect of BTN162b2 and CoronaVac boosters on humoral and cellular immunity of individuals previously fully vaccinated with CoronaVac against SARS-CoV-2: A longitudinal study.

BACKGROUND: It is essential to know about immune response levels after booster doses of the two different types of vaccines, mRNA, and the inactivated, currently used against COVID-19. For this purpose, we aimed to determine the effects of BNT162b2 (BNT) and CoronaVac (CV) boosters on the humoral and cellular immunity of individuals who had two doses of CV vaccination. METHODS: The study was conducted in three centers (Koc University Hospital, Istanbul University Cerrahpasa Hospital, and Istanbul University, Istanbul Medical School Hospital) in Istanbul, Turkey. Individuals who had been previously immunized with two doses of CV and no history of COVID-19 were included. The baseline blood samples were collected 3-5 months after the second dose of CV. Follow-up blood samples were taken 1 and 3 months after administration of third doses of CV, or one dose of BNT boosters. Neutralizing antibody titers were measured by plaque reduction assay. The CD4+ T cell, CD8+ T cell, effector CD4+CD38+CD69+ T cell, and effector CD8+CD38+CD69+ T cell ratios were determined by flow cytometry. The intracellular IFN-γ and IL-2 responses were measured by ELISpot assay. RESULTS: We found a 3.38-fold increase in neutralizing antibody geometric mean titers (NA GMT, 78.69) 1 month after BNT booster and maintained at the third month (NA GMT, 80). Nevertheless, in the CV booster group, significantly lower NA GMT than BNT after 1 month and 3 months were observed (21.44 and 28.44, respectively) (p < .001). In the ELISpot assay, IL-2 levels after BNT were higher than baseline and CV booster (p < .001) while IFN-γ levels were significantly higher than baseline (p < .001). The CD8+CD38+CD69+ and CD4+CD38+CD69+ T cells were stimulated predominantly in the third month of the BNT boosters. CONCLUSION: The neutralizing antibody levels after 3 months of the BNT booster were higher than the antibody levels after CV in fully vaccinated individuals. On the contrary, ratio of the effector T cells increased along with greater IFN-γ activation after BNT booster. By considering the waning immunity, we suggest a new booster dose with BNT for the countries that already had two doses of primary CV regimens.

Association of SARS-CoV-2 IgG Antibody Levels with Clinical/Laboratory Characteristics in COVID-19 Patients: Data from a Turkish Study.

BACKGROUND: COVID-19 causes clinical manifestations ranging from asymptomatic infection to multi-organ failure. It is reported that those with severe disease have higher anti-SARS-CoV-2 antibody titers compared to asymptomatic or mild cases. We evaluated the correlation of antibody responses with laboratory and clinical indicators in COVID-19 patients. METHODS: Seventy-nine male and 66 female patients (mean age: 39) with at least one positive SARS-CoV-2 RT-PCR test and SARS-CoV-2 IgG antibody result after acute infection were included. RESULTS: Seventy-six (52%), 45 (31%), and 24 (17%) patients had mild, moderate, and severe clinical findings, respectively. Patients with high body mass index and advanced age had significantly more severe disease (p < 0.001). A significant correlation was found between the increase in lymphopenia, C-reactive protein, ferritin, D-dimer, and lactate dehydrogenase and the severity of clinical findings (p = 0.0001). SARS-CoV-2 IgG antibody test was positive in 128 (88.3%) patients. A significant correlation was found between disease severity and antibody levels in the comparison of all groups (p < 0.001). CONCLUSIONS: Long-term monitoring of immune responses will be required to determine the appropriate time for the administration of new vaccines.

Tocilizumab in COVID-19: The Cerrahpasa-PREDICT score.

BACKGROUND: Cytokine release syndrome (CRS), characterized by overproduction of proinflammatory cytokines in the course of severe coronavirus disease 2019 (COVID-19), has been suggested as the major cause of mortality. Tocilizumab, a recombinant humanized monoclonal antibody against human IL-6 receptor, poses a therapeutic option for the treatment of CRS leading to severe acute respiratory syndrome in coronavirus-2 (SARS-CoV-2) infection. METHODS: We performed a single-center retrospective study to reveal the outcome of COVID-19 patients on tocilizumab and proposed "the Cerrahpasa-PREDICT score", a new clinical scoring system using clinical and laboratory parameters that would help predicting the 28-day mortality of COVID-19 patients receiving tocilizumab. RESULTS: Eighty-seven patients (median age: 59 years) were included of whom 75.8% were male. Tocilizumab use significantly improved clinical and laboratory parameters. The 28-day mortality rate on tocilizumab was 16.1%. The Cerrahpasa-PREDICT score, consisting of platelet counts, procalcitonin, D-dimer levels, SO2R and the time from symptom onset to tocilizumab administration had a positive predictive value of 94.5% and negative predictive value of 92.9% for anticipating 28-day mortality. CONCLUSIONS: Severe COVID-19 should closely be monitored for the signs of hyperinflammation. We showed that administration of tocilizumab early in the course of the disease (prior to ICU admission) resulted in a favorable outcome. Close monitoring usually aids identifying patients who would benefit from tocilizumab. In this regard, the Cerrahpasa-PREDICT score might serve as a practical tool for estimating the 28-day mortality in COVID-19 patients who received tocilizumab and would facilitate timely recognition of fatal cases to be evaluated for other therapeutic options.

[Evaluation of the Diagnostic Performance of Different Principles of SARS-CoV-2 Commercial Antibody Tests in COVID-19 Patients]. / SARS-CoV-2 ile Ilgili Farkli Prensipli Ticari Antikor Testlerinin COVID-19 Hastalarindaki Tanisal Performanslarinin Degerlendirilmesi.

Following the emergence of severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) and using only PCR for diagnosis, antibody tests have been rapidly developed by various commercial companies. There are differences between the sensitivity and specificity of these tests due to the usage of different viral target proteins and antibody subclasses. In order to evaluate the diagnostic use of these tests, we aimed to examine the diagnostic performance, especially sensitivity and specificity, of SARS-CoV-2 IgM, IgA and IgG tests of various companies (Abbott, Roche, Euroimmun, Dia.Pro, Anshlabs, Vircell, UnScience and RedCell), which have different principles (ECLIA/CLIA, EIA, LFA). Current (n= 180) and past (n= 180) COVID-19 patients with clinical and molecular diagnosis of COVID-19 admitted to Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine Hospital, Pandemic Polyclinic with suspected COVID-19 infection, were included in our study. The patients admitted within the first 3 weeks after the onset of symptoms were included in the current patient group, and those admitted at the third and after the third week were included in the past patient group. Serum samples (n= 180) obtained from Istanbul Sisli Hamidiye Etfal Training and Research Hospital, Blood Center between April and June 2018 before the COVID-19 pandemic were included in the study as a control group. All the tests included in our study were studied with the recommendations of the manufacturer companies. Between the IgG detection tests with different principles in patients with past COVID-19, the sensitivity and specificity values of the most effective tests were; 86.7%/99.4% (Abbott), 86.1%/98.9% (Dia.Pro), 91.3%/95% (RedCell). Between the IgM detection tests with different principles in current COVID-19 patients, the sensitivity and specificity values were; 67.8%/99.4% (Abbott), 68.9%/98.6% (Vircell), 50%/97.5% (RedCell). Abbott IgM with a kappa coefficient of 0.67 and Vircell IgM + IgA test with a kappa coefficient of 0.65 showed the best fit in patients with current COVID-19 infection. In patients with past COVID-19, Abbott IgG with 0.86 kappa coefficient and Dia.Pro IgG test with 0.85 kappa coefficient showed the best match. Due to the low sensitivity of IgM detection antibody tests, they should not be preferred instead of real-time reverse transcriptase polymerase chain reaction in routine diagnosis. IgG detection tests may be preferred to detect the antibody response and the titers in people who have had COVID-19 for population seroprevalence and especially therapeutic immune plasma production. However, it is thought that the combined use of both ECLIA/CLIA-based and EIA/ELISA-based tests together may be more effective in routine use for SARS-CoV-2 IgG tests.

Epstein-Barr virus, cytomegalovirus and BK polyomavirus burden in juvenile systemic lupus erythematosus: correlation with clinical and laboratory indices of disease activity.

OBJECTIVES: Clinical and laboratory investigations have revealed that Epstein-Barr virus (EBV) is involved in altered immunological response of systemic lupus erythematosus (SLE). Higher seroprevalence rates of anti-EBV antibodies and increased viral load are demonstrated in adult SLE patients. The prevalence of BK polyomavirus (BKV) reactivation is also suggested to be higher in SLE. Herein, we aimed to evaluate the immune response of children with SLE to EBV antigens in addition to EBV and BKV DNA. We also tried to evaluate whether these serological results differ from another connective tissue disease - juvenile systemic sclerosis (jSS) - and healthy individuals. METHODS: Serum levels of EBV early antigen diffuse (EA-D) IgG, EBV nuclear antigen-1 IgG, EBV viral capsid antigen (VCA), cytomegalovirus (CMV) IgG, EBV DNA, CMV DNA and urinary BKV DNA were evaluated in healthy controls and in patients with a diagnosis of juvenile SLE (jSLE) and jSS. RESULTS: A total of 70 jSLE patients, 14 jSS patients and 44 sex-matched healthy individuals were involved in the study. EBV VCA was positive in 84.2% of jSLE patients, 85.7% of jSS patients and 36.3% of healthy controls. EBV EA-D IgG positivity was significantly higher in jSLE patients compared to jSS patients and healthy controls (20% vs. 7.1% and 0%, p = 0.005). EBV VCA positivity was associated with malar rash and immunological disorder, but there was no statistical significance in other antibody positivity in terms of clinical and haemogram findings and autoantibody positivity. CMV DNA positivity was present in only 2.8% of jSLE patients. None of the jSS patients or the healthy controls had CMV DNA positivity. EBV DNA and BKV DNA were also negative in all three groups. CONCLUSION: The results of our study assume a relationship between SLE and EBV, but we could not demonstrate an association between CMV and BKV. The negative DNA results in contrast to serological positivity can be interpreted as an altered and impaired immune system and increased viral susceptibility. These results suggest that EBV contributes to disease continuity, even if it does not directly cause development.

[Investigation of Ganciclovir Resistance in Cytomegalovirus Strains Obtained from Immunocompromised Patients]. / Immün Yetmezlikli Hastalardan Elde Edilen Sitomegalovirüs Izolatlarindaki Gansiklovir Direncinin Arastirilmasi.

CMV is a virus that is asymptomatic in healthy individuals but can cause serious mortality and morbidity in transplant patients and patients with acquired immunodeficiency syndrome (AIDS). Ganciclovir (GCV) is a nucleoside analog that significantly reduces morbidity and mortality in CMV-related infections and is used as the first choice in treatment. It is the first drug shown to be effective in the treatment of CMV disease in humans, and is also homologous to acyclovir. Long-term antiviral therapy is required to prevent or treat CMV disease, but this can cause antiviral resistance which was reported to be 8-14% in CMV. In CMV strains, GCV resistance is most common in the UL97 kinase gene region. The aim of this study was to investigate GCV resistance in CMV strains obtained from the patients with immune deficiency. A total of 49 patients, including 20 children, 29 adults, who were followed in the department of hematology were included in the study. Fifty-three samples from 49 patients with CMV DNA viral load ≥ 103 copies/ml were examined for GCV resistance. In the study, DNA sequences were determined by Sanger sequence analysis method 3500 Abi Prism Genetic Analyser (Applied Biosystems, Thermo Fisher Scientific, USA) in the 674 bp part of the UL97 gene region. The next generation sequencing (NGS) method was applied to the samples that could not be evaluated with this method. GCV resistance was not detected in 35 (66%) of 53 samples with the Sanger method. C592G, C607S and M460I GCV resistance mutation was detected in three patients. Since the sequences were mixed, resistance analysis could not be evaluated with Sanger in 15 patient samples and the resistance was not detected in these samples studied with NGS. Antiviral resistance mutation was detected in three of 49 patients (6.1%). In 20 patients included in the study, three variant sequences (A442G, C592F, A427V) reported in the literature and determined to be sensitive to drugs by phenotypic tests and 78 variant sequences that were not reported in the literature were detected. As a result, the detection of antiviral resistance is important in the follow-up of the patients and guides the clinician in planning of the treatment. It was concluded that the samples that could not be evaluated with the Sanger method should be studied with NGS and further studies are needed to determine the role of the variant sequences detected for the first time in drug resistance.

The Frequency and Associated Factors for BK Virus Infection in a Center Performing Mainly Living Kidney Transplantations.

PURPOSE: BK virus (BKV) nephropathy has increasingly become an important cause of morbidity in renal transplant recipients. We evaluated the frequency and associated factors for BKV infection in a center performing mainly living donor transplantations over a long time period. METHODS: One hundred consecutive renal transplant patients were included. Quarterly visits were planned to examine urine for decoy cells and to measure the BKV DNA in the blood and urine. Renal biopsy was performed in case of deteriorated allograft function. Serological examinations for BKV immunoglobulin G (IgG) were performed in donors. RESULTS: Throughout the entire follow-up period, the rates of viruria, viremia, and the positivity of decoy cells were 12%, 6%, and 13%, respectively. The negative and positive predictive values of decoy cells were 93.1% and 69.2%, respectively, for viruria, and 99.2% and 45.5%, respectively, for viremia. Biopsy-proven BKV nephropathy was observed in 1 patient. The BKV IgG was positive in all living donors. Viruria and viremia were associated with deceased donor transplantation, acute rejection, and pulse steroid therapy. In addition, viremia was associated with antithymocyte globulin therapy and a short duration of the posttransplant period. CONCLUSIONS: The frequency of BKV infection was lower in our transplant unit compared to previous reports. Reduced doses of immunosuppression seem to be the main factor that may explain the reduced frequency. However, an active screening strategy is still of importance for this patient group.

Relationship of plasma cell-free DNA level with mortality and prognosis in patients with Crimean-Congo hemorrhagic fever.

Crimean-Congo hemorrhagic fever (CCHF) is a viral infection. Circulating plasma cell-free DNA (pcf-DNA) is a novel marker indicating cellular damage. So far, the role of pcf-DNA did not investigate in CCHF patients. In the current study, pcf-DNA levels were investigated in CCHF patients with different clinical severity grades to explore the relationship between circulating pcf-DNA level, virus load, and disease severity. Seventy-two patients were categorized as mild, intermediate, and severe based on severity grading scores. The pcf-DNA level was obtained from all participants on admission and from the survivors on the day of the discharge. The controls consisted of 31 healthy. Although the pcf-DNA level at admission was higher in patients than in the controls, the difference was not statistically significant (P = 0.291). However, at admission and in the convalescent period, the difference between pcf-DNA levels in mild, intermediate, and severe patient groups was significant. The pcf-DNA level in severe patients was higher than in the others. Furthermore, compared to survivors, non-survivors had higher pcf-DNA levels at admission (P = 0.001). A direct relationship was found between the pcf-DNA level and the viral load on the day of discharge in surviving patients. ROC curve analysis identified a pcf-DNA level of 0.42 as the optimal cut-off for prediction of mortality. The positive predictive value, negative predictive value, specificity, and sensitivity for predicting mortality was 100%, 72%, 100%, and 79%, respectively. In summary, our findings revealed that pcf-DNA levels may be used as a biomarker in predicting CHHF prognosis.

[Determination of cytomegalovirus glycoprotein B genotypes in different geographical regions and different patient groups in Turkey]. / Türkiye'de farkli cografi bölgelerde ve farkli hasta gruplarindaki sitomegalovirus izolatlarinin glikoprotein B genotiplerinin belirlenmesi.

Cytomegalovirus (CMV), a common virus found all around the world, usually causes asymptomatic infections in immunocompetent hosts, however it may lead to serious complications in immunodeficient patients and in the fetus. CMV is divided into four genotypes according to the polymorphisms in UL55 gene that encodes for envelope glycoprotein B. Nucleotide polymorphisms of CMV gB gene can affect the cell tropism of the virus and host immune response and believed to have important changes in the pathogenesis of CMV. The aim of this study was to determine the gB genotypes of CMV isolates from different patient groups selected from different regions of Turkey. A total of 136 clinical specimens from patients (66 female, 70 male; age range: 0-65 years, mean age: 24.03 ± 17.17) who were diagnosed to have CMV infection by polymerase chain reaction (PCR) and/or antigenemia tests, between 2001-2014, in the medical school hospitals of Akdeniz, Ege, Istanbul Cerrahpasa and Erciyes Universities (located at Mediterranean, Aegean, northwest and central Anatolia regions, respectively), were included in the study. The patient group consisted of 80 renal transplant (RT) recipients, 35 stem cell transplant (SCT) recipients, 13 newborns, seven heart transplant (HT) recipients and one pregnant woman. CMV gB genotypes were determined by PCR-RFLP (restriction fragment length polymorphism) method, and DNA sequencing and phylogenetic analysis were performed for the randomly selected 15 isolates with different genotypes. Among 136 (135 plasma, 1 amnion fluid) samples, the most frequent genotype was gB1 (n= 44, 32.4%), followed by gB2 (n= 39, 28.6%), gB3 (n= 36, 26.5%) and gB4 (n= 8, 5.9%); however nine (6.6%) samples could not be genotyped. When analysis were interpreted according to the patient groups, it was determined that the genotypes in RT recipients were gB1 32.3%, gB2 28.7%, gB3 26.5% and gB4 5.9%; in SCT recipients gB1 34.3%, gB2 28.6%, gB3 22.9% and gB4 5.7%; in HT recipients gB3 57.1%, gB1 14.3% and gB2 14.3%; in newborns gB1 38.4%, gB3 30.8%, gB2 15.4% and gB4 7.7%, and gB2 genotype in the pregnant woman. As our study was a descriptive study to determine the genotypes of CMV gB, the relationship between the genotypes and the variants such as viral load, symptomatic disease and prognosis were not analyzed. As a result, the isolation of different gB genotypes in various case groups from four distinctive provinces, underlines the diversity of CMV gB genotypes in Turkey.

[Evaluation of 10 cases of Lyme disease presenting with erythema migrans in Istanbul, Turkey]. / Istanbul'da eritema migrans ile basvuran 10 Lyme olgusunun degerlendirilmesi.

Lyme disease (LD) is a tick-borne, multisystemic infection caused by Borrelia burgdorferi. Although variable rates of seropositivity for B.burgdorferi have been reported between 2% to 44% in Turkey, its actual prevalence is not well-understood. The aim of this retrospective study was to evaluate the characteristics of 10 cases of LD presenting as erythema migrans (EM) between 2009 and 2013 from Istanbul which is one of the metropolitan cities of Turkey. Of the patients, five were male and five were female, ages between 9-51 years (mean age: 34.5 years). Five of the patients were admitted in June, three in October, one in November and two in December and all have the history of tick bite in last 1-2 weeks. There were no clinical symptoms for systemic infection among the patients with normal level routine laboratory test (whole blood count and biochemical tests) results. Five of the cases had EM lesions in the trunk, three in the upper extremities, and two in the lower extremities. Four patients presented with annular, three with solitary macular, and three with target-like EM lesions. In all cases, the biopsy specimens were positive for B.burgdorferi sensu lato DNA with polymerase chain reaction and all were also positive in terms of B.burgdorferi IgM antibodies with ELISA. Nine patients were treated with oral doxycycline, 100 mg twice daily and one child patient was treated with oral amoxicillin 500 mg twice daily for 21 days. EM lesions disappeared within 2-4 weeks in all patients. There was no clinical evidence for systemic involvement in any of the patients like neurologic, cardiac, and joint involvement at the follow-ups on the third, sixth and 12(th) months. To our best knowledge, 10 patients in this study are the largest EM series reported from Turkey. The increase in the number of LD cases may be associated with increased tick bite and increased awareness due to the emergence of concurrent Crimean-Congo hemorrhagic fever epidemic in Turkey. As a result, when enlarged erythematous lesions on the skin were observed, LH must also be considered in differential diagnosis, history of tick bite should be questioned and etiological diagnostic test should be performed.

Crimean-Congo hemorrhagic fever among health care workers, Turkey.

We investigated 9 cases of Crimean-Congo hemorrhagic fever (1 fatal, 2 asymptomatic) among health care workers in Turkey. Needlestick injuries were reported for 4 workers. Eight received ribavirin. In addition to standard precautions, airborne infection isolation precautions are essential during aerosol-generating procedures. For postexposure prophylaxis and therapy, ribavirin should be given.

Predictors of fatality in pandemic influenza A (H1N1) virus infection among adults.

BACKGROUND: The fatality attributed to pandemic influenza A H1N1 was not clear in the literature. We described the predictors for fatality related to pandemic influenza A H1N1 infection among hospitalized adult patients. METHODS: This is a multicenter study performed during the pandemic influenza A H1N1 [A(H1N1)pdm09] outbreak which occurred in 2009 and 2010. Analysis was performed among laboratory confirmed patients. Multivariate analysis was performed for the predictors of fatality. RESULTS: In the second wave of the pandemic, 848 adult patients were hospitalized because of suspected influenza, 45 out of 848 (5.3%) died, with 75% of fatalities occurring within the first 2 weeks of hospitalization. Among the 241 laboratory confirmed A(H1N1)pdm09 patients, the case fatality rate was 9%. In a multivariate logistic regression model that was performed for the fatalities within 14 days after admission, early use of neuraminidase inhibitors was found to be protective (Odds ratio: 0.17, confidence interval: 0.03-0.77, p=0.022), nosocomial infections (OR: 5.7, CI: 1.84-18, p=0.013), presence of malignant disease (OR: 3.8, CI: 0.66-22.01, p=0.133) significantly increased the likelihood of fatality. CONCLUSIONS: Early detection of the infection, allowing opportunity for the early use of neuraminidase inhibitors, was found to be important for prevention of fatality. Nosocomial bacterial infections and underlying malignant diseases increased the rate of fatality.

Evaluation of the BD Phoenix system for detection of methicilin resistance in Staphylococcus aureus isolates in comparison to BD GeneOhm MRSA assay.

BACKGROUND: In order to identify methicillin-resistant Staphylococcus aureus isolates quickly, automated and semiautomated systems, commercial media, and identification kits are widely used. The Phoenix system (BD, Sparks, MD, USA) has been available since 2004 in our laboratory. This study evaluated the reliability of the Phoenix system for the detection of methicillin resistance in Staphylococcus aureus isolates in comparison to BD GeneOhm MRSA assay (Becton Dickinson Diagnostics GeneOhm, CA, USA). METHODS: A total of 206 clinically significant Staphylococcus aureus isolates, submitted to the clinical microbiology laboratory between March 2011 and May 2013, were included in the study. Phoenix panels were studied for identification and susceptibility testing according to manufacturers' instructions. The detection of MRSA was performed using the BD GeneOhm MRSA assay (Becton Dickinson Diagnostics GeneOhm, CA, USA). The assay is a qualitative real-time PCR method. RESULTS: The Phoenix system results and mecA gene pozitivity were concordant for 134 methicillin-resistant and 71 methicillin-susceptible strains. One discordant isolate, identified as mecA negative by the PCR method, was methicillin-resistant Staphylococcus aureus positive by the Phoenix system (oxacilline MIC = 2 microg/mL; cefoxitin MIC = 8 microg/mL). In this study, Phoenix automated system's sensitivity, specificity, negative predictive value, and positive predictive value are found as 100%, 100%, 100%, and 100%, respectively. CONCLUSIONS: As a result of our study, use of the Phoenix automated identification method for the detection of methicillin-resistant Staphylococcus aureus isolates is a practical and reliable approach for daily clinical laboratory procedures.

The role of Porphyromonas gingivalis in the development of atherosclerosis and its relationship with fim A genotype.

BACKGROUND: Porphyromonas gingivalis, a major periodontal pathogen, is gaining increasing attention for its possible association with atherosclerosis. Its fimbriae are classified into six genotypes (Types I-V, Ib) based on the diversity of the fim A genes encoding the fimbrial subunits. In this study, fim A genotype's distribution of P. gingivalis was analyzed in atherosclerotic plaque specimens. METHODS: A total of 50 atherosclerotic plaque specimens and 50 non-atherosclerotic, post stenotic aneurysm specimens were collected from patients undergoing cardiovascular surgery. Bacterial DNA was also extracted from each specimen, as real-time PCR was carried out with P. gingivalis-specific primer sets. The positive specimens of P. gingivalis were further analyzed to discriminate the fim A genotype using real-time and nested PCR methods. RESULTS: P. gingivalis was detected only in one atherosclerotic plaque; however, the genotype was nontypable in this specimen. CONCLUSIONS: We state that it is not easy to show a significant relationship between P. gingivalis, its fim A genotype, and atherosclerosis. We suggest that new extended studies based especially upon the quantitave determination of P. gingivalis and its genotype distribution on atherosclerotic specimens are needed to show an evident relationship between atherosclerosis and P. gingivalis.

The effect of CD14 and TLR4 gene polymorphisms on asthma phenotypes in adult Turkish asthma patients: a genetic study.

BACKGROUND: Endotoxins stimulate T helper 1 cell maturation and send a negative signal to T helper 2 polarisation. This causes a decrease IgE levels and prevents atopy (Hygiene hypothesis). It is shown that this response is under genetic control by polymorphisms in CD14 and TLR4 genes in some researchs. We aimed to investigate the effects of genetic variants of CD14 (-) and TLR4 (Asp299Gly, Thr399Ile) genes on asthma phenotypes in adults with asthma. METHODS: Asthma patients (n = 131) and healthy control cases (n = 75) were included in the study. Relations between CD14 C-159 T, TLR4 299 and TLR4 399 genotypes and duration of asthma history of allergic rhinitis-dermatitis, total IgE, eosinophil, skin prick test, forced expiratory volume 1 (FEV1) and severity of disease were evaluated. Real time PCR (RT-PCR) was used for genotyping. RESULTS: For CD14-159, presence of the C allele (CC + CT) was more frequent among those with low median log (logarithm) IgE levels, but no statistically significant difference in all asthma group (p = 0.09). C allele was significantly correlated with low total IgE levels and T allele with high total IgE levels in atopics (p = 0.04). CC + CT genotype was more frequent in moderate and severe asthma group in atopics (p = 0.049). TLR4 299 and TLR4 399 genotypes and asthma phenotypes were not found to be significantly correlated (p > 0.05). CONCLUSIONS: Total IgE levels were found to be low among patients with the CC + CT genotype, and high among patients with the TT genotype contrary to the results of many other studies, which is therefore an important finding. Another important finding was that the C allele is a risk factor for moderate and severe asthma.

Evaluation of the BD Phoenix CPO Detect Test for the detection of carbapenemase-producing Enterobacterales.

Aims: This study aimed to evaluate the performance of the BD Phoenix CPO Detect Test (BD Diagnostic Systems) for the detection and classification of carbapenemase-mediated carbapenem resistance. Methods: A total of 447 Enterobacterales strains were included in the study. All strains were tested with the BD Phoenix CPO Detect Test and the modified carbapenem inactivation method. Results: Carbapenemase production was detected in 157 of 159 carbapenemase producers, including 95.7% of class B and 99.2% of class D isolates using the BD Phoenix CPO Detect Test. BD Phoenix CPO Detect has a sensitivity of 98.7% and a specificity of 95.5% in detecting carbapenemase production. Conclusion: The classification of OXA-48 and class B carbapenemases, the most common carbapenemases circulating in Turkey, was highly accurate.

Enterobacterales are a type of bacteria that usually live harmlessly in the gut of humans. However, if the bacteria get access to the bladder or bloodstream, they can cause infection. Carbapenemase-producing Enterobacterales (CPE) are a type of bacteria that can cause carbapenem antibiotic-resistant infections, a group of powerful antibiotics. The rapid spread of CPE will pose an increasing threat to public health and medical treatment practices; therefore, rapid detection of CPE is crucial. This study assessed the performance of the BD Phoenix CPO Detect Test for the detection of carbapenemase-producing Enterobacterales. The BD Phoenix CPO Detect Test offers both the detection of carbapenemase production and antimicrobial susceptibility testing simultaneously and can be clinically useful for determining possible treatment options.

One-Year Post-Vaccination Longitudinal Follow-Up of Quantitative SARS-CoV-2 Anti-Spike Total Antibodies in Health Care Professionals and Evaluation of Correlation with Surrogate Neutralization Test.

Numerous vaccines have been generated to decrease the morbidity and mortality of COVID-19. This study aims to evaluate the immunogenicity of the heterologous boosts by BioNTech against homologous boosts by CoronaVac at three-month intervals in two health care worker (HCW) cohorts, with or without prior COVID-19, for one year post-vaccination. This is a prospective cohort study in which the humoral responses of 386 HCWs were followed-up longitudinally in six main groups according to their previous COVID-19 exposure and vaccination status. Anti-SARS-CoV-2 spike-RBD total antibody levels were measured and SARS-CoV-2 neutralization antibody (NAbs) responses against the ancestral Wuhan and the Omicron variant were evaluated comparatively using international standard serum for Wuhan and Omicron, as well as with the aid of a conversion tool. The anti-SARS-CoV-2 spike-RBD total Ab and Nab difference between with and without prior COVID-19, three months after two-dose primary vaccination with CoronaVac, was statistically significant (p = 0.001). In the subsequent follow-ups, this difference was not observed between the groups. Those previously infected (PI) and non-previously infected (NPI) groups receiving BioNTech as the third dose had higher anti-SARS-CoV-2 spike total Ab levels (14.2-fold and 17.4-fold, respectively, p = 0.001) and Nab responses (against Wuhan and Omicron) than those receiving CoronaVac. Ab responses after booster vaccination decreased significantly in all groups at the ninth-month follow-up (p < 0.05); however, Abs were still higher in all booster received groups than that in the primary vaccination. Abs were above the protective level at the twelfth-month measurement in the entire of the second BioNTech received group as the fourth dose of vaccination. In the one-year follow-up period, the increased incidence of COVID-19 in the groups vaccinated with two or three doses of CoronaVac compared with the groups vaccinated with BioNTech as a booster suggested that continuing the heterologous CoronaVac/BioNTech vaccination, revised according to current SARS-CoV-2 variants and with at least a six-month interval booster would be an effective and safe strategy for protection against COVID-19, particularly in health care workers.