[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.

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

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

[Direct identification and determination of antimicrobial susceptibility of gram negative bacilli using the PhoenixTM FX system in blood cultures flagging positive]. / Gram negatif basillerin PhoenixTM FX sistemi ile pozitif sinyal veren kan kültürü siselerinden direkt tanimlanmasi ve antimikrobiyal duyarliliklarinin belirlenmesi.

Bloodstream infections are one of the main causes of morbidity and mortality worldwide. Shortening the turnover time of microbiological analysis leads to a significant reduction of patient morbidity, mortality and medical care expenses. This study aimed to evaluate the performance of Phoenix 100 Instrument (Becton Dickinson, Sparks, MD, USA) system in bacterial identification and the evaluation of antibiotic susceptibility directly taken from positive blood culture bottles in BD BACTEC™ FX (Becton Dickinson, USA) system in patients with the suspicion of bacterial sepsis. In this study, blood culture bottles with a positive signal in BD BACTEC™ FX (Becton Dickinson, USA) system, and in which gram negative bacilli or coccobacilli was observed in Gram staining were evaluated. In our study, direct inoculation to the Phoenix panel from the blood culture bottles giving positive signal was defined as "direct Phoenix method". The blood culture bottles which were taken from hospitalized patients with a suspicion of sepsis, were analyzed comparatively by using BD Phoenix™ (Becton Dickinson, USA) automated microbiology system and "Bruker Biotyper matrix-associated laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)" (Bruker Daltonics, Germany) in the bottles of patients with the positive signals between August 10, 2015, and December 05, 2015. The effect of the "direct Phoenix method" on the duration of the test and the harmony with conventional methods was demonstrated. A total of 122 gram negative bacteria comprising 95 bacteria in Enterobacteriaceae family, 26 non-fermenting gram negative bacteria (NFGNB) and one Aeromonas spp. were included in the study. In our study, the reporting time of the identification of gram negative bacteria after inoculation with direct Phoenix method ranged from 2.25 hours to 7.84 hours (mean 2.56 hours). When the identification of 122 gram negative bacteria by direct Phoenix method was compared with the identification of Maldi Biotyper (Bruker Daltonics, Germany), an agreement was detected in 96.7% (118/122) of the samples at the genus level and in 86.0% (105/122) of the samples at the species level. Ninety-five bacteria belonging to Enterobacteriaceae family demonstrated an agreement of 95.7% (91/95) and 93.6% (89/95) at the genus and species levels with Maldi Biotyper respectively. Twenty-five NFGNB had an agreement of 96.1% (25/26) and 61.5% (16/26) at genus and species levels with Maldi Biotyper respectively. In our study, the reporting time of antibiotic susceptibility test results of gram negative rods after direct Phoenix method ranged from 7.42 hours to 15.85 hours (mean 12.9 hours). In our study, 2.159 antimicrobial agents were tested for 120 gram negative bacteria (95 strains belonging to Enterobacteriaceae family and 25 NFGNB). Minor error rate was found to be 2.0% with the direct Phoenix method, 1.1% major error rates, and 1.2% very major error rates; making a total of 4.4% (96/2.159). Since error rates in all categories < 10%, very major error rate was < 1.5% and major error rate was < 3%, the direct Phoenix method had an acceptable agreement with the conventional Phoenix method. The direct inoculation of the Phoenix system with culture suspension obtained from positive blood culture bottles decreased reporting time of the identification and determination of the antibiotic susceptibilities for gram negative rods that cause bacteraemia. This result could be important in the clinical benefits for the patients as well as financial savings for the hospital.

[The significance and place of HBsAg neutralization test in the diagnosis and algorithm of hepatitis B infection]. / HBsAg nötralizasyon testinin hepatit B hastaliginin tani algoritmasindaki yeri ve önemi.

The diagnosis of hepatitis B virus infection is evaluated serologically, virologically, biochemically, and with histologic liver indicators. The aim of this study was to investigate the place and significance of the HBsAg neutralization test in the diagnostic algorithm for hepatitis Binfection. From the venous blood samples sent to Ankara Numune Education and Research Hospital Medical Microbiology Laboratory between September 2014 and May 2016 for HBsAg test, serum samples regarded each patient as reactive (≥ 0.9 S\CO) , 9 ≤ S ≤ CO ≤ 30) were studied twice. A total of 105 samples which were reactive in both analyses were included in the study. After the evaluation of these samples by neutralization confirmation test, which is routinely performed in our laboratory, the samples were stored under optimal conditions and studied for HBV DNA with the real-time PCR and for HBeAg, anti-HBeAg, anti-HBc IgM, and anti-HBc total antibody assays by ELISA. The 105 samples, in which HBsAg was detected, were analyzed with the neutralization test. The presence of HBsAg was confirmed by neutralization test in 67 of 105 samples (63.8%), and of these patients, two patients (2.3%) had negative HBV DNA and anti-HBc total antibody test (false positive neutralization test). Of the 105 samples included in the study, the anti-HBc total antibody test was positive in 78 patients (74.3%). However, out of these 78 patients who were positive for the anti-HBc total antibody test, there were 13 patients (16.7%) with negative neutralization and HBV DNA test results (false positive anti-HBc total antibody test). The HBV DNA positivity was detected significantly lower in samples with HBsAg level ≤ 5 S/CO compared to the samples with HBsAg level > 5 S/CO (p= 0.020). Also, if the unit price of the neutralization test used in our study was considered, the cost was 17,00 TL while the unit price of HBV DNA test was 55,00 TL. Utilization of the neutralization test instead of HBV DNA test provides a saving of 38,00 TL per patient. The use of the neutralization test as a validation test when the HBsAg titre was less than or equal to 5S/CO will significantly reduce the cost of the test without the need for HBV DNA test. We suggest that if both the neutralization test and the anti-HBc total antibody test is negative in a sample with an HBsAg titration higher than 5 S/CO, the decision can be made without the need for HBV DNA test. However; if the neutralization test is negative, but the anti-HBc total antibody test is positive, then HBV DNA needs to be determined to eliminate the inconsistency between neutralization and anti-HBc total antibody assays. At the same time, we found that the use of anti-HBc total antibody test along with HBsAg as a screening test did not provide any advantage since the anti-HBc total antibody test was detected to have a high false positivity (16.7%) rate.

[Evaluation of the toxoplasmosis seroprevalence in pregnant women and creating a diagnostic algorithm]. / Gebelerde toksoplazmoz seroprevalansinin degerlendirilmesi ve bir tani algoritmasinin olusturulmasi

Toxoplasma gondii, an obligatory intracellular protozoon is widely distributed around the world and can infect all mammals and birds. While acquired toxoplasmosis is usually asymptomatic in healthy subjects, acute infection during pregnancy may lead to abortion, stillbirth, fetal neurological and ocular damages. For the prevention of congenital toxoplasmosis it is recommended that a screening programme and a diagnostic algorithm in pregnant women should be implemented while considering the cost effectiveness. Thus, it is necessary to determine the seroprevalence of toxoplasmosis in pregnant women and the actual risk of T.gondii transmission during pregnancy in a certain area. The aims of this study were to detect the T.gondii seropositivity in the pregnant women admitted to our hospital and to create a diagnostic algorithm in order to solve the problems arising from interpretation of the serological test results. A total of 6140 women aged 15-49 years who were admitted to our hospital between April 1st, 2010 to July 31st, 2013, were evaluated retrospectively. In the serum samples, T.gondii IgM, IgG and IgG avidity tests were performed by VIDAS automated analyzer using TOXO IgM, TOXO IgG II and TOXO IgG avidity kits (bioMerieux, France). It was noted that, both T.gondii IgM and IgG tests were requested from 4758 (77.5%) of the pregnant women, while only IgM test from 1382 (22.5%) cases. Sole IgM positivity was found as 0.2% (11/6140), IgG as 26.4% (1278/4758) and both IgM + IgG as 0.9% (44/4758). T.gondii IgG avidity tests were requested from 12 of 44 women who were found both IgM and IgG positive and eight of them revealed high avidity and four low avidity. Avidity test was ordered for the 91 (7.1%) of 1278 sole IgG positive cases and four of them were found to have low avidity. IgG avidity test was ordered for 554 (16.2%) of IgM and/or IgG negative subjects, however, the test was not performed according to rejection criteria of the laboratory. It was noticed that no re-testing was requested for none of the seronegative cases (3428/4758; 72%) during their follow-up. In our study, total Toxoplasma seropositivity rate among pregnant women was detected as 28% (1330/4758), showing statistically significant increase (p< 0.05) with age. There was no significant difference (p> 0.05) in the seropositivity rate between the years (2010-2013). Following the evaluation of the test orders, the problems related to test orders and interpretation of the test results were determined and a diagnostic algorithm to be used in our hospital, was established to minimize such problems in toxoplasma serology. It was concluded that a diagnostic algorithm related to toxoplasmosis serology should be implemented for the appropriate evaluation of the risk of acute toxoplasmosis during pregnancy. Such an approach is necessary to support the clinical diagnosis and to minimize the anxiety in pregnant women about congenital toxoplasmosis.

[Evaluation of serum IgG, IgA and IgM levels as indicators of hepatic fibrosis in patients with chronic hepatitis C infection]. / Kronik Hepatit C Enfeksiyonu Olan Hastalarda Karaciger Fibrozu Göstergesi Olarak Serum IgG, IgA ve IgM Düzeylerinin Degerlendirilmesi.

The prediction of development of hepatic fibrosis is of crucial importance in terms of disease monitorization and treatment follow-up of patients with chronic hepatitis C virus (HCV) infections. Liver biopsy which is an invasive and complicated method, still remains as the gold standard method for the diagnosis of liver fibrosis. Recently, non-invasive diagnostic tests to determine the biological markers of liver fibrosis have been developed as a possible alternative to liver biopsy. The aim of this study was to evaluate the levels of serum IgG, IgA and IgM antibodies as possible indicators for hepatic fibrosis among patients with chronic HCV infection. A total of 57 patients (35 female, 22 male; mean age: 51 ± 8.9 years) who were followed-up between January 2007-November 2008, were enrolled in the study. All of the patients were positive for serum anti-HCV and HCV-RNA, while none of them were under antiviral therapy for the last six months. The patients were hospitalized for liver biopsy and biopsy samples were evaluated according to Modified Knodell Histological Activity Index. Forty-nine patients with no liver fibrosis or low to moderate fibrosis were classified as Group 1 (stage 0, 1, 2, 3) and eight patients with high to severe fibrosis were classified as Group 2 (stage 4, 5, 6). Serum IgG, IgA and IgM levels of the patients were determined by a commercial immunonephelometric method (Dade Behring, Germany). Increased antibody levels were detected in a total of 61.4% (35/57) of patients, of which 28 (49.1%) yielded high IgG, 5 (8.8%) yielded high IgM and 2 (3.5%) yielded high IgA levels. The mean IgG levels of patients in Group 1 and 2 were 16.3 ± 4.6 and 21.8 ± 5.2 g/L; mean IgM levels were 1.3 ± 0.6 and 1.6 ± 0.8, and median IgA levels were 2.0 (0.5-5.3) and 3.3 (1.3- 4.3) g/L, respectively. IgG and IgA levels of patients from Group 2 were found significantly higher than those patients from Group 1 (p= 0.003, p= 0.03, respectively), however there was no significant difference between the groups with respect to serum IgM levels (p= 0.311). When the patient groups were also evaluated in terms of other parameters, no statistically significant differences were detected for ALT, AST, HCV-RNA levels and mean ages (p= 0.95, p= 0.21, p= 0.73, p= 0.10, respectively), however, anti-HCV levels were found significantly higher in Group 2 (p= 0.043). The data of this study indicated a significant relationship between the levels of serum IgG, IgA and the severity of hepatic fibrosis among patients with chronic HCV infection. It was concluded that high serum IgG and IgA levels may be helpful indicators together with the other non-invasive markers for the prediction of liver fibrosis in case when liver biopsy could not be performed.

[Seroprevalences of hepatitis B, hepatitis C, and HIV in patients admitted to orthopedic and traumatology department]. / Ortopedi ve travmatoloji hastalarinda hepatit B, hepatit C ve HIV seroprevalansi.

OBJECTIVES: Orthopedic surgeons are at a higher occupational risk for blood-borne infections because of frequent handling of sharp instruments and bone fragments. We investigated the seroprevalences of hepatitis B, hepatitis C, and human immunodeficiency virus (HIV) among patients treated at orthopedic and traumatology department. METHODS: Data on age, sex, diagnoses, and the seroprevalences of HBsAg, anti-HCV and anti-HIV were reviewed in 1,040 patients hospitalized between September 2003 and December 2004. The patients were divided into two groups as orthopedics (n=646; mean age 37.8 years) or trauma (n=394; mean age 38.3 years) according to the initial cause of presentation. The results were compared with those of 28,642 blood donations during the same period. RESULTS: HBsAg positivity was similar in the patients (2.3%) and the controls (2.1%). HBsAg was detected in 16 patients (2.5%) in the orthopedics group and eight patients (2%) in the trauma group (p>0.05), three of whom were younger than one year. Similarly, the prevalences of anti-HCV antibodies were similar in the patient (0.6%) and control (0.3%) groups. Four patients (0.6%) in the orthopedics group and two patients (0.5%) in the trauma group were positive for anti-HCV (p>0.05), and all had a past history of operations. Anti-HIV positivity was not detected in the patient group, whereas it was 0.2% in the control group. CONCLUSION: The similarities between patients admitted to orthopedic and traumatology department and blood donors in the prevalences of HBsAg, and anti-HCV and anti-HIV antibodies suggest that data obtained from blood banks can be used for risk calculations.