Risk analysis of candidemia and its effect on mortality in COVID 19 and non COVID 19 patients.

Background and Objectives: Candidemia is the most common serious fungal infection in critically ill patients in intensive care units (ICU). It series fourth among bloodstream infectious agents. In this study, candidemia risk analysis was examined in COVID 19 and non-COVID 19 patients during the pandemic period. Materials and Methods: COVID 19 and non-COVID 19 cases who were followed up with candidemia in the ICU of our hospital were retrospectively screened. Demographic data, intubation, central venous catheter (CVC), medications, and total parenteral nutrition (TPN) status were evaluated in terms of risk between the two groups. Isolated Candida species and susceptibilty were evaluated. Results: When age, gender, medication, intubation, TPN and CVC were evaluated, no difference was seen in terms of risk. Differences were detected in terms of comorbidities. While the most frequently identified Candida species was C. albicans, the most frequently detected species in the COVID19 patient group was C. parapsilosis. Conclusion: There was no difference in candidemia incidence and risk factors between the two groups. Since candidemias were evaluated in terms of comorbidities, it was determined that Diabetes Mellitus (DM) and chronic obstructive pulmoner disease (COPD) were more common in patients with COVID 19 and less common in coronary artery disease (CAD) and malignancy.

Development of a Molecular Diagnostic Kit for the Sars-Cov-2 Eris Variant.

BACKGROUND: Upon the emergence of the Eris variant in our country, we aimed to develop an RT-qPCR kit to detect the SARS-CoV-2 Eris variant. METHODS: By studying the genome sequences uploaded to GISAID, target regions were designed by focusing on the mutation regions of EG.5 and EG.5.1, which are the main lineage of the Eris variant. When developing the kit, the hydrolysis probe-based detection (e.g., TaqMan®) method was chosen. Target sequences specific to the SARS-CoV-2 EG.5 variant were then specifically amplified, with amplification monitored in real time using fluorescent labeled probes. In the study, 470 samples were used, 109 of which were positive for SARS-CoV-2 RNA, from various Hospitals. RESULTS: Of the 109 samples that were positive for SARS-CoV-2 RNA, 67 (61%) were also detected positive for Eris variant RNA. CONCLUSIONS: It was determined that the developed kit detected the Eris variant and the rate was 61%.

Investigation of respiratory tract coinfections in Coronavirus disease 2019 infected and suspected cases.

OBJECTIVE: The aim of our study is to determine the risk of coinfection with COVID-19 due to the high prevalence of viral agents in Istanbul in autumn (September, October, and November) and winter (December and January) and to investigate the effects of age, gender, season and clinical features on the development of coinfection with COVID-19. METHODS: In the routine studies of our hospital, COVID-19, reverse transcriptase polymerase chain reaction (RTA kit, Turkiye) and Multiplex PCR Bio-Fire (Bio Merieux Company, France) methods were studied from the nasopharyngeal swab sample and the data were recorded. A total of 400 people with a mean age (7.91±17.80) were included in the study by retrospective scanning. RESULTS: Considering the virus distribution, Respiratory syncytial virus (RSV), COVID-19, rhino/entero virus did not show a significant difference in autumn and winter, while H. metapneumovirus, adeno virus, influenza A significantly higher rates were observed in winter months. Parainfluenza (1, 2, 3, 4) and Corona OC43 were detected at a higher rate in autumn compared to other viruses. Double and triple coinfection rates with other viral agents were high for 2 years and younger. CONCLUSION: The risk of coinfection of COVID-19 with influenza A, RSV, parainfluenza, and rhino/entero virus was found to be higher than other viral agents. Especially in winter, the risk of coinfection with influenza A and COVID-19 increases. In terms of treatment management, coinfection should be investigated in risky patients and influenza a vaccine should be offered to risky groups.

COVID-19 PCR test performance on samples stored at ambient temperature.

The WHO-named Coronavirus Disease 2019 (COVID-19) infection had become a pandemic within a short time period since it was detected in Wuhan. The outbreak required the screening of millions of samples daily and overwhelmed diagnostic laboratories worldwide. During this pandemic, the handling of patient specimens according to the universal guidelines was extremely difficult as the WHO, CDC and ECDC required cold chain compliance during transport and storage of the swab samples. The aim of this study was to compare the effects of two different storage conditions on the COVID-19 real-time PCR assay on 30 positive nasopharyngeal and/or oropharyngeal samples stored at both ambient temperature (22 ± 2 °C) and +4 °C. The results revealed that all the samples stored at ambient temperature remain PCR positive for at least six days without any false-negative result. In conclusion, transporting and storing these types of swab samples at ambient temperature for six days under resource-limited conditions during the COVID-19 pandemics are acceptable.

Chest computed tomography findings of 1271 patients with COVID-19 pneumonia and classifications with different age groups: a descriptive study from Istanbul, Turkey.

OBJECTIVE: The objectives of this study were to describe lung computed tomography findings of patients with COVID-19 diagnosed by real-time reverse transcription polymerase chain reaction test, investigate whether the findings differ regarding age and gender, and evaluate the diagnostic performance of chest computed tomography based on the duration of symptoms at the time of presentation to the hospital. METHODS: From March 11 to May 11, 2020, 1271 consecutive patients (733 males and 538 females) were included in this retrospective, cross-sectional study. Based on age, patients were divided into five separate subgroups. Then based on the duration of symptoms, patients were divided into five separate phases. The presence of lung lesion(s) and their characteristics, distribution patterns, and the presence of concomitant pleural thickening/effusion and other findings (malignancy, metastasis, chronic obstructive pulmonary disease, interstitial lung disease, bronchiectasis, bronchiectasis, cardiomegaly, pericardial effusion) were evaluated by five radiologists independently. RESULTS: The "normal lung computed tomography finding" was the most common chest CT finding (37%), followed by ground-glass opacity (31%). Regardless of the shape of the lesion, the distribution features were significant (peripheral, subpleural, and lower lobe distribution) (p<0.05). The presence of pleural thickening posteriorly and adjacent to the lesion was statistically different in groups 1-3 (p<0.05). Other concomitant pathologies, except pulmonary congestion, did not suppress the typical findings of COVID-19. CONCLUSION: Chest computed tomography findings were mostly normal in the early phase (P1). Therefore, it may be appropriate to perform the first computed tomography screening of COVID-19 after 6 days to decrease the radiation exposure.

Chest computed tomography findings of 1271 patients with COVID-19 pneumonia and classifications with different age groups: a descriptive study from Istanbul, Turkey

SUMMARY OBJECTIVE: The objectives of this study were to describe lung computed tomography findings of patients with COVID-19 diagnosed by real-time reverse transcription polymerase chain reaction test, investigate whether the findings differ regarding age and gender, and evaluate the diagnostic performance of chest computed tomography based on the duration of symptoms at the time of presentation to the hospital. METHODS: From March 11 to May 11, 2020, 1271 consecutive patients (733 males and 538 females) were included in this retrospective, cross-sectional study. Based on age, patients were divided into five separate subgroups. Then based on the duration of symptoms, patients were divided into five separate phases. The presence of lung lesion(s) and their characteristics, distribution patterns, and the presence of concomitant pleural thickening/effusion and other findings (malignancy, metastasis, chronic obstructive pulmonary disease, interstitial lung disease, bronchiectasis, bronchiectasis, cardiomegaly, pericardial effusion) were evaluated by five radiologists independently. RESULTS: The "normal lung computed tomography finding" was the most common chest CT finding (37%), followed by ground-glass opacity (31%). Regardless of the shape of the lesion, the distribution features were significant (peripheral, subpleural, and lower lobe distribution) (p<0.05). The presence of pleural thickening posteriorly and adjacent to the lesion was statistically different in groups 1-3 (p<0.05). Other concomitant pathologies, except pulmonary congestion, did not suppress the typical findings of COVID-19. CONCLUSION: Chest computed tomography findings were mostly normal in the early phase (P1). Therefore, it may be appropriate to perform the first computed tomography screening of COVID-19 after 6 days to decrease the radiation exposure.

Seroprevalence of coronavirus disease 2019 (COVID-19) among health care workers from three pandemic hospitals of Turkey.

COVID-19 is a global threat with an increasing number of infections. Research on IgG seroprevalence among health care workers (HCWs) is needed to re-evaluate health policies. This study was performed in three pandemic hospitals in Istanbul and Kocaeli. Different clusters of HCWs were screened for SARS-CoV-2 infection. Seropositivity rate among participants was evaluated by chemiluminescent microparticle immunoassay. We recruited 813 non-infected and 119 PCR-confirmed infected HCWs. Of the previously undiagnosed HCWs, 22 (2.7%) were seropositive. Seropositivity rates were highest for cleaning staff (6%), physicians (4%), nurses (2.2%) and radiology technicians (1%). Non-pandemic clinic (6.4%) and ICU (4.3%) had the highest prevalence. HCWs in "high risk" group had similar seropositivity rate with "no risk" group (2.9 vs 3.5 p = 0.7). These findings might lead to the re-evaluation of infection control and transmission dynamics in hospitals.

Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs.

The gold standard method in the diagnosis of SARS-CoV-2 infection is the detection of viral RNA in the nasopharyngeal sample by RT-PCR. Recently, saliva samples have been suggested as an alternative sample. In the present study, we aimed to compare RT-PCR results in nasopharyngeal, oro-nasopharyngeal and saliva samples of COVID-19 patients. 98 of 200 patients were positive in RT-PCR analysis performed before the hospitalization. On day 0, at least one sample was positive in 67 % of 98 patients. The positivity rate was 83 % for both oro-nasopharyngeal and nasopharyngeal samples, while it was 63 % for saliva samples (p < 0.001). On day 5, RT-PCR was performed in 59 patients, 34 % had at least one positive result. The positivity rate was 55 % for both saliva and nasopharyngeal samples, while it was 60 % for oro-nasopharyngeal samples. Our study shows that the sampling saliva does not increase the sensitivity of RT-PCR tests at the early stages of infection. However, on the 5th day, viral RNA detection rates in saliva were similar to nasopharyngeal and oro-nasopharyngeal samples. In conclusion, we suggest that, in patients receiving treatment, RT-PCR in saliva, in addition to the standard samples, is important to determine the isolation period and control transmission.

The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey.

OBJECTIVE: Turkey is one of the latest countries that COVID-19 disease was reported, with the first case on March 11, 2020, and since then, Istanbul became the epicenter of the pandemic in Turkey. Here, we reveal sequences of the virus isolated from three different patients with various clinical presentations. METHODS: Nasopharyngeal swab specimens of the patients were tested positive for the COVID-19 by qRT-PCR. Viral RNA extraction was performed from the same swab samples. Amplicon based libraries were prepared and sequenced using the Illumina NextSeq platform. Raw sequencing data were processed for variant calling and generating near-complete genome sequences. All three genomes were evaluated and compared with other worldwide isolates. RESULTS: The patients showed various clinics (an asymptomatic patient, patient with mild disease, and with severe pulmonary infiltration). Amplicon-based next-generation sequencing approach successfully applied to generate near-complete genomes with an average depth of 2.616. All three viral genomes carried the D614G variant (G clade according to GISAID classification) with implications for the origin of a spread first through China to Europe then to Istanbul. CONCLUSION: Here, we report the viral genomes circulating in Istanbul for the first time. Further sequencing of the virus isolates may enable us to understand variations in disease presentation and association with viral factors if there is any. In addition, the sequencing of more viral genomes will delineate the spread of disease and will guide and ease the necessary measures taken to stem the spread of the novel coronavirus.

In-vitro activities of imipenem-colistin, imipenem-tigecycline, and tigecycline-colistin combinations against carbapenem-resistant Enterobacteriaceae.

The aim of the study is to determine in-vitro effects of imipenem-tigecycline, imipenem-colistin and tigecycline-colistin against carbapenem-resistant Enterobacteriaceae (CRE) isolates. A total of 25 CRE isolates were included to the study. The minimum inhibition concentrations of imipenem, colistin-sulphate and tigecycline were determined with broth dilution method. Synergistic effects of imipenem-tigecycline, imipenem-colistin and tigecycline-colistin were investigated by microdilution checkerboard technique. All of the isolates were resistant to imipenem, whereas 25% of the isolates were resistant to colistin and tigecycline. Imipenem-colistin, imipenem-tigecycline and tigecycline-colistin combinations were synergistic against 40% (10/25), 24% (6/25), and 36% (9/25) of the isolates, respectively. Antagonism was observed in 8% (2/25) of the isolates in tigecycline-colistin combination. Tigecycline-colistin was the most effective (70% synergy) combination in Klebsiella spp. strains; whereas imipenem-colistin was the most effective (75% synergy) combination in Escherichia coli strains. Synergistic effect was variable and strain-depended against CRE isolates that have been tested.

Efficiency of Direct Microscopy of Stool Samples Using an Antigen-Specific Adhesin Test for Entamoeba Histolytica.

BACKGROUND: E. histolytica is among the common causes of acute gastroenteritis. The pathogenic species E. histolytica and the nonpathogenic species E. dispar cannot be morphologically differentiated, although correct identification of these protozoans is important for treatment and public health. In many laboratories, the screening of leukocytes, erythrocytes, amoebic cysts, trophozoites and parasite eggs is performed using Native-Lugol's iodine for pre-diagnosis. AIMS: In this study, we aimed to investigate the frequency of E. histolytica in stool samples collected from 788 patients residing in the Anatolian region of Istanbul who presented with gastrointestinal complaints. We used the information obtained to evaluate the effectiveness of microscopic examinations when used in combination with the E. histolytica adhesin antigen test. STUDY DESIGN: Retrospective cross-sectional study. METHODS: Preparations of stool samples stained with Native-Lugol's iodine were evaluated using the E. histolytica adhesin test and examined using standard light microscopy at ×40 magnification. Pearson's Chi-square and Fisher's exact tests were used for statistical analysis. Logistic regression analysis was used for multivariate analysis. RESULTS: Of 788 samples, 38 (4.8%) were positive for E. histolytica adhesin antigens. When evaluated together with the presences of erythrocytes, leukocytes, cysts, and trophozoites, respectively, using logistic regression analysis, leukocyte positivity was significantly higher. The odds ratio of leukocyte positivity increased adhesin test-positivity by 2,530-fold (95% CI=1.01-6.330). Adhesin test-positivity was significant (p=0.047). CONCLUSION: In line with these findings, the consistency between the presence of cysts and erythrocytes and adhesin test-positivity was found to be highly significant, but that of higher levels of leukocytes was found to be discordant. It was concluded that leukocytes and trophozoites were easily misjudged using direct microscopy. Although microscopic examination of samples stained with Native-Lugol's iodine is a cheap and simple method, the confusion of trophozoites with leukocytes may direct the clinician toward an incorrect pre-diagnosis. Because trichrome staining is difficult and time consuming, and results may vary depending on the technician, this method is not preferred in most laboratories. Therefore, an enzyme-linked immunosorbent assay method, which is a more advanced method than polymerase chain reaction, should be used to distinguish between E. histolytica and E. dispar in order to achieve an accurate diagnosis.

[Comparison of a new and rapid method, Brucella Coombs gel test with the other methods in the serological diagnosis of brucellosis]. / Brusellozun serolojik tanisinda yeni ve hizli bir yöntem olan Brucella Coombs jel testi ile diger yöntemlerin karsilastirilmasi.

Diagnosis of brucellosis basically depends on blood and/or bone marrow culture and demonstration of high titer specific antibody or seroconversion in serum. In routine serological diagnosis of the disease, after screening with Rose Bengal test, the positive samples are studied with standart tube agglutination (STA) test with serial dilutions. However false negative results can be seen in STA test due to the existence of blocking antibodies, this test should be verified with Coombs anti-Brucella (CAB) or immunocapture agglutination (ICA) tests. In recent years Brucella Coombs gel test (ODAK Brucella Coombs Gel Test, Toprak Medikal, Turkey) developed in our country, was available as a new and rapid agglutination based method. The test is performed in vials that contain Coombs antibodies within gel matrix and results are evaluated visually within two hours.The aim of this study was to compare the efficacy of Brucella Coombs gel test (BCGT) with STA, CAB and ICA methods in serological diagnosis of brucellosis. A total of 100 serum samples with suspected brucellosis sent to our laboratory between January 2012-August 2013 in which 31 high positive (≥ 1/160), 23 low positive (≤ 1/80) and 46 negative samples diagnosed with CAB test (Seromed, Turkey) were included in the study. All the samples were studied using titrations with STA (Seromed, Turkey), ICA (Vircell, Spain) and BCGT (Islab, Turkey) methods. With STA, CAB and BCGT tests ≥ 1/160, with ICA test ≥ 1/320 were accepted as positive titers. The correlation between the tests were evaluated with Cohen's kappa (κ) analysis. In our study, seven of the samples yielded positive results with STA, 30 with ICA, and 32 with BCGT. The number of the sera which yielded positive results with all three methods was 28. Two samples positive with CAB and BCGT resulted low titer/negative with ICA, one sample positive with ICA and BCGT resulted low titer/negative with CAB, and one low titer/negative sample with CAB and BCGT yielded positive with ICA test. STA test was not included in the statistical evaluation due to its very low positivity rate. According to the kappa analysis, almost perfect agreement was detected between the other methods (κ= 0.887 for CAB and ICA, κ= 0.977 for CAB and BCGT, κ= 0.907 for ICA and BCGT). In conclusion, BCGT method showed excellent correlation with both CAB and ICA tests; the application of the test was practical; resulted in a short time such as two hours and visually evaluation was determined to be practical compared to other methods. Although BCGT can be recommended for routine diagnostics, evaluation of specificity and sensitivity with comprehensive studies including a greater number of cases and control samples should be considered.

[Pulmonary nocardiosis with a large solitary cavitary nodule caused by Nocardia cyriacigeorgica in a patient receiving corticosteroid therapy]. / Kortikosteroid tedavisi alan hastada Nocardia cyriacigeorgica'nin neden oldugu soliter kaviter nodül yapan pulmoner nokardiyoz.

Nocardiosis is a rare disease generally caused by members of Nocardia asteroides complex, particularly in immunosupressed patients. Nocardia cyriacigeorgica is a newly described member of this complex. In this article, a case of pulmonary nocardiosis with a large solitary cavitary nodule caused by N. cyriacigeorgica, in a patient receiving corticosteroid therapy was presented. A 29 years old male patient receiving prednisolone for 5 months was admitted to our hospital with fever, cough, right thoracic pain and night sweats. Computed tomography scan of chest demonstrated a large solitary cavitary nodule in the right lower lobe. Gram stained smear of the sputum revealed gram-positive, beaded, branched filamentous bacilli. On the third day of his admission, a catalase positive, oxidase negative and immotile bacilli, compatible with Nocardia spp., were isolated from the sputum sample taken at the day of admission. The isolated bacterium was identified as N. cyriacigeorgica by reference laboratory (Lyon, France). Oral trimethoprim (320 mg/day) and sulfamethoxazole (1600 mg/day) therapy given for three months, resulted in complete cure of the lesion without any sequela. This was the fourth case of pulmonary nocardiosis caused by N. cyriacigeorgica reported from Turkey. Microbiological examination of sputum is the most important tool for the diagnosis. Treatment with appropriate antibiotics may achieve complete cure even in large cavitary lesions. In conclusion, pulmonary nocardiosis should be considered in differential diagnosis of solitary cavitary nodules, especially in immunocompromised patients.

Relevance of autoantibody detection to the rapid diagnosis of brucellosis.

The rose bengal test is often used for rapid diagnosis of human brucellosis in endemic areas. However, autoantibodies have never been investigated as a reason for false-positive or false-negative results. Therefore, the aim of this study was to show the effect of autoantibody detection on the rapid diagnosis of human brucellosis in an endemic area. The study included 2 groups: antinuclear antibody (ANA)-positive and ANA-negative groups. Diagnosis of brucellosis was established by isolation of Brucella spp. from blood culture. The overall sensitivity and specificity of the rose bengal test were 100% and 90.8%, respectively. The specificity (100% versus 89%) and positive predictive value of the test (100% versus 8%) fell markedly from the ANA-negative to the ANA-positive group. As a conclusion, this study verified our suspicion about the effect of autoantibodies on rose bengal test results to the diagnosis of human brucellosis. However, to have definite decisions, extensive studies with larger populations are needed.