[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.

Evaluation of antibody response after COVID-19 vaccination of healthcare workers.

The common goal of all vaccines developed against COVID-19, although they have been designed with different methods, is to develop an effective immunity and antibody response against SARS-CoV-2. However, the postvaccination immune response and antibody levels differ between individuals. This study examined the relationship between postvaccine seropositivity rates, age, gender, smoking, and body mass index (BMI), and antibody titers. A total of 314 healthcare workers (HCW) who were not previously infected with COVID-19 and who had received two doses of CoronaVac inactivated vaccine participated in the study. Seropositivity against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was measured from the participants 4 weeks after the second dose of vaccine using the electrochemiluminescence (ECLIA) method. In addition, the antibody developed against the nucleocapsid protein (NCP) was evaluated and compared using Elecsys Anti-SARS-CoV-2 kit. One hundred and eighty-one of the participants were female (57.6%) with a median age of 39 (interquartile range [IQR], 10) and 133 (42.4%) were male with a median age of 41 (IQR, 11). 99.6% of the volunteers developed seropositivity 4 weeks after the second dose of vaccine. It was also observed that the rate of RBD protein antibody titer was >250 U/ml in smokers, which is quite low compared to nonsmokers (p = 0.032), and that high RBD antibody titers were proportionally lower in obese participants, according to BMI values, compared to those with normal BMI (49.5% and 9.9%). It was observed that seropositivity developed in almost all participants after the CoronaVac vaccine. However, it was determined that the antibody titer measured varied depending on factors such as smoking, BMI, and duration.

[The Identification of Acinetobacter baumannii Blood Isolates by MALDI-TOF MS, ARDRA and blaOXA-51-like Gene-Specific Real-Time PCR]. / Acinetobacter baumannii Kan Izolatlarinin MALDI-TOF MS, ARDRA ve blaOXA-51-benzeri Gene Özgül Gerçek Zamanli Polimeraz Zincir Reaksiyonu ile Tanimlanmasi.

The Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) complex consists of phenotypically very similar nosocomial species; A.baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, Acinetobacter seifertii and Acinetobacter djikshoorniae and one environmental species A.calcoaceticus. The rapid and accurate identification of the members of Acb complex is critical as these nosocomial pathogens can show differences in antimicrobial susceptibility and clinical outcomes. The conventional phenotypic methods are slow, unreliable and less efficient for the differentiation of Acb complex species, including the A.baumannii species within the Acb complex. Although various molecular methods are available, such as amplified ribosomal DNA restriction analysis (ARDRA) and blaOXA-51-like gene specific PCR, they are usually inconvenient for the routine diagnostic laboratories. Recently, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) offers an opportunity for rapid, cost-effective and convenient bacterial identification in routine diagnostic procedures conducted in clinical laboratory. In this study, we aimed to evaluate the diagnosis performance of MALDI-TOF MS system to identify blood isolates of A.baumannii. A total of 180 nonduplicate carbapenem resistant Acb complex (strain numbers; TR1-TR60) and A.baumannii (TR61-TR180) blood isolates were collected from the intensive care units of the three university hospitals in Turkey from January 2016 to December 2016. All isolates were evaluated by using blaOXA-51-like gene specific real time (Rt-PCR) analysis, ARDRA (restriction enzymes-AluI, CfoI, MboI, MspI, RsaI) method and MALDI-TOF MS (VITEK® MS, bioMérieux, France) system. All the strains except TR10, TR31, TR35 and TR52 were identified as A.baumannii by ARDRA method. Out of 177 of all the isolates, presence of blaOXA-51-like gene was found except for TR10, TR31 and TR52 isolates. However, TR31 without the presence of blaOXA-51-like gene was identified as A.pittii using the ARDRA. Totally 176 isolates which were identified as A.baumannii by both of the methods, ARDRA and Rt-PCR- blaOXA-51-like, were accepted as a reference for the evaluation of the diagnosis performance capacity of the MALDI-TOF MS. Overall, for all 176 isolates tested, the sensitivity obtained with the MALDI-TOF MS were 99.4% with 75% specificity. The accuracy value of the method was determined as 98.9% for the identification of A.baumannii to the species level. MALDI-TOF MS is increasingly used in diagnostic microbiology for the routine identification of bacteria to the genus, species or subspecies level with high rates of sensitivity and specificity. In future, by expanding the database, MALDI-TOF MS system would possibly become the ideal method for routine diagnostic laboratories that could potentially identify more species and even determine some characteristics of antimicrobial resistance and virulence determinants.

The correlation of sodium iodide symporter and BRAF(V600E) mutation in classical variant papillary thyroid carcinoma.

BRAF(V600E) mutation was analyzed by real-time polymerase chain reaction in 96 consecutive cases with classical variant papillary thyroid cancer, and immunohistochemical staining of Na+/I- symporter (NIS) protein was evaluated. Localization (intracellular or membranous), density, and the intensity of cytoplasmic staining were characterized semiquantitatively. Extrathyroidal invasion, surgical margin positivity, and lymph node metastasis were compared with BRAF(V600E) mutation and NIS expression. Eighty-eight patients who had at least 24-month follow-up were also included in survival analysis. BRAF(V600E) mutation was determined in 78.1% (75/96) and functional NIS activity in 74% (71/96) of the cases. There were statistically significant differences in mean ages between BRAF(V600E) mutation-positive (48.6) and BRAF(V600E) mutation-negative cases (37.3; Levene test, P=.419; Student t test, P=.001). The surgical margin positivity (46.7%) and extrathyroidal extension percentage (54.7%) in the BRAF(V600E) mutation-positive group were higher than the negative (28.6% and 33.3%, respectively) group, without statistical significance (P=.138 and P=.084, respectively). Functional NIS activity was higher in BRAF(V600E) mutation-positive cases (78.1%) than mutation-negative ones (57.1%; P=.047). The possibility of moderate and intense cytoplasmic staining in BRAF(V600E) mutation-positive cases (72%) was 6.3 times higher than the possibility of weak staining (28%) in the mutation-positive cases (95% confidence interval, 2.2-18.8; P=.001). Functional NIS expression is higher in patients with classical variant papillary thyroid cancer with BRAF(V600E) mutation. However, the clinical features were not found to be associated with NIS expression. There may be different mechanisms determining the outcome of therapy.

[Serological evaluation of Bordetella pertussis infection in adults with prolonged cough]. / Uzamis öksürügü olan eriskinlerde Bordetella pertussis enfeksiyonunun serolojik olarak degerlendirilmesi.

Pertussis is a vaccine-preventable disease that is transmitted from infected to susceptible individuals by respiratory route. Bordetella pertussis infection may occur at any age as neither vaccine nor natural infection induced immunity lasts life-long. This study was planned to demonstrate the serological evidence of infection among adults, to raise awareness among clinicians and to provide data for the development of strategies to protect vulnerable infants. A total of 538 patients (345 female, 193 male) ages between 18-87 years who had a complain of prolonged cough for more than two weeks were included in the study. Anti-pertussis toxin (PT) IgG and anti-filamentous hemagglutinin (FH) IgG levels from single serum samples were measured by an in-house ELISA test which was standardized and shown to be efficient previously. Anti-PT IgG antibody levels of ≥ 100 EU/ml were considered as acute/recent infection with B.pertussis. In our study, 9.7% (52/538) of the patients had high levels of anti-PT IgG (≥ 100 EU/ml) and among those patients 43 (43/52; 82.7%) also had high (≥ 100 EU/ml) anti-FHA IgG levels. There were no statistically significant differences in terms of age, gender, education level, DPT (diphtheria-pertussis-tetanus) vaccination history, smoking history or average daily cigarette consumption (p> 0.05) between the cases with high antibody levels (n= 52). When the symptoms and the presence of cases with high antibody levels were evaluated, it was detected that no one parameter was significantly different from others, except that 24.1% of the cases with inspiratory whooping had high anti-PT levels. There was also no statistically significant difference between high anti-PT levels ≥ 100 EU/ml and the patients with risk factors [smoking (21/200; 10.5%), presence of disease that cause chronic cough and/or drug usage (19/171; %11.1), and whole factors which cause chronic cough (32/306; %10.5)] and without risk factors (p= 0.581; p= 0.357; p= 0.249, respectively). The distribution of anti-PT IgG geometric mean titer (GMT) according to the age groups, was as follows; 32.41 in 18-30 years; 36.28 in 31-50 years; 36.82 in 51-70 years and 31.15 in ≥ 71 years. Our results indicated that B.pertussis infections are also present among adult population with a frequency not to be underestimated (9.7%) and the results also emphasized that since typical whooping cough symptoms may not be seen in adults, pertussis infection should be considered as a differential diagnosis in adults with prolonged cough, even if there are some other underlying factors of cough. The data obtained from this study was also considered to be helpful in the development of adult vaccination policies for the protection of infants who have not completed the vaccination schedule yet.

[Extended-spectrum beta-lactamase production by Enterobacteriaceae isolates from urine cultures of outpatients: results of a 7-year follow-up]. / Ayaktan basvuran hastalarin idrar kültürlerinde üretilen Enterobacteriaceae izolatlarinda genislemis spektrumlu beta-laktamaz üretimi: 7 yillik izlem sonuçlari.

The aim of the study was to evaluate the change of the frequency of extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae isolates from urine samples of outpatients in years and to analyse the antibiotic resistance profiles for a rational drug use. The urine samples cultured in our laboratory from the patients who were admitted to outpatient clinics of our hospital between years 2007-2013 were included in this study. Enterobacteriaceae strains were isolated and identified by conventional methods and API 20E system (BioMérieux, France). The standard antimicrobial susceptibility tests were performed by Kirby Bauer disk diffusion method. ESBL production were screened by double-disk synergy method according to CLSI guidelines. E-test method (BioMérieux, France) were used for the verification of suspicious ESBL production. The identification and antimicrobial susceptibility testing were performed for a total of 12.535 isolates. Of the isolates 8716 were identified as Escherichia coli (69.3%), 1514 were Klebsiella pneumoniae/oxytoca (12.1%), 257 were Proteus mirabilis (2.1%), 345 were other Enterobacteriae members (8%), 411 were various non-fermentative gram-negative bacteria (3.3%) and 1292 were various gram-positive bacteria (10.3%). The total positivity rate of ESBL was found as 21.8% (2.283/10.487), and the ESBL positive rates for E.coli, K.pneumoniae/oxytoca and P.mirabilis were 21.2%, 28.2% and 4.7%, respectively. Other Enterobacteriaceae isolates were not evaluated because of the absence of standardized methods and breakpoint values. There was no statistically significant difference among ESBL producing isolates within seven years (p= 0.364). The antibiotic resistance rates of the ESBL-positive isolates were statistically higher than ESBL-negative isolates [amoxicillin-clavulanate (73.1%/11.3%), trimethoprim-sulfamethoxazole (63.1%/31.0%), nitrofurantoin (17.3%/8.6%), gentamicin (42.2%/10.1%), amikacin (3.5%/0.9%), tobramisin (56.8%/10.5%), imipenem (0.3%/0.1%), ofloxacin (66.8%/19.8%), ticarcillin-clavulanate (73.5%/19.8%), piperacillin-tazobactam (28.8%/5.0%)] (p< 0.05). Statistically significant variations were detected within the years for the resistance rates of amoxicillin-clavulanate (p= 0.001), tobramycin (p=0.003), ofloxacin (p= 0.001), ticarcillin-clavulanate (p= 0.001) and piperacillin-tazobactam (p= 0.001) were detected within the years. Although a quite high percentage of ESBL positivity in Enterobacteriaceae isolates was determined, there was a slight but not statistically significant increase of this value during the seven-year period. The stability of the percentage of ESBL positivity may indicate a positive change in the habit of the usage of beta-lactam antibiotics. According to the results of our study, the most effective drugs for ESBL-producing isolates were piperacillin-tazobactam among inhibitor combinations, amikacin among aminoglycosides and nitrofurantoin among orally-used drugs.

Dobrava-Belgrade virus in Apodemus flavicollis and A. uralensis mice, Turkey.

In 2009, human Dobrava-Belgrade virus (DOBV) infections were reported on the Black Sea coast of Turkey. Serologic and molecular studies of potential rodent reservoirs demonstrated DOBV infections in Apodemus flavicollis and A. uralensis mice. Phylogenetic analysis of DOBV strains showed their similarity to A. flavicollis mice-borne DOBV in Greece, Slovenia, and Slovakia.

West Nile virus seropositivity in Alanya, a coastal city in the Mediterranean region of Turkey.

BACKGROUND: West Nile virus (WNV)-related illness is a global health problem. Understanding the seropositivity rates and identifying the risk factors related to WNV in various animal species including humans is crucial for the implementation of effective prevention strategies. OBJECTIVES: Assess the rate of seropositivity and the risk factors associated with WNV seropositivity. DESIGN: Descriptive, cross-sectional. SETTING: Microbiology and virology departments in a veterinary college. PATIENTS AND METHODS: In a sample of healthy human participants in Alanya, located close to regions where WNV activity has been detected, anti-WNV IgG antibody detection was performed using enzyme-linked immunosorbent assays. The positive results were confirmed by virus neutralization tests (VNTs). The sample was compared with a second group of age- and gender-matched healthy subjects selected from a previous cross-sectional study. MAIN OUTCOME MEASURES: Determination of the seropositivity and risk factors that were associated with WNV in healthy humans. SAMPLE SIZE: 87 in current study; 356 in previous study. RESULTS: The first group of 87, which had a high risk of encountering vector mosquitoes, had a positivity rate of 8% (7/87), whereas positivity in the second group was 4.5% (16/356; P=.181). In the entire sample, the anti-WNV IgG antibody was positive in 23 out of 443 (5.2%) samples by the ELISA test. Among these 23 samples, ten were confirmed as positive using VNTs. Therefore, the WNV IgG seropositivity was 2.3% (10/442). Confirmed IgG seropositivity rates were higher among male (3.8%) than female participants (0.9%; P=.054) and among adults aged ≥45 years (4%) than those aged 18-44 years (0.8%; P=.048). CONCLUSION: This study highlights the presence of WNV infection in the research region. More comprehensive and multidisciplinary studies are required to increase our knowledge about this zoonotic infection including risk factors in line with the One Health approach. LIMITATIONS: Small sample size.

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.

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.

[Seroprevalence of Borrelia burgdorferi and tick-borne encephalitis virus in a rural area of Samsun, Turkey]. / Samsun Kirsalinda Borrelia burgdorferi ve Kene Ensefaliti Virusu Seroprevalansinin Arastirilmasi

Lyme disease or lyme borreliosis is a zoonosis caused by Borrelia burgdorferi transmitted by ticks, especially Ixodes species. Lyme borreliosis is a multi-systemic disease that invades the skin, musculoskeletal, cardiovascular and central nervous systems. Tick-borne encephalitis (TBE) is an important arboviral infection caused by tick-borne encephalitis virus (TBEV). The central nervous system is affected and the disease most often manifests as meningitis, encephalitis or meningoencephalitis. Previous studies have shown that B.burgdorferi and TBEV can be transmitted by the same tick species (Ixodes ricinus). Although the geographic location and climate is similar to some south-eastern European countries where lyme borreliosis and TBE have been reported, the incidence and prevalence of these diseases in Turkey still remain unclear. The aim of this study was to determine the seroprevelance of B.burgdorferi and TBEV in healthy population in Tekkeköy (41° 8-13' North; 36° 24-31' East), a district of Samsun province, Turkey with evidence of tick-borne disease and to explore the possible correlations of life styles of healthy individuals and prevelance. The cross-sectional study population included 419 people selected using a random proportional sampling method. All participants were asked at interview to complete a questionnaire and peripheral blood samples were collected. From the blood samples, B.burgdorferi IgG and IgM antibodies were evaluated using commercial ELISA (Euroimmun, Germany) and confirmed with Western blot (WB, Euroimmun, Germany). ELISA method was also used to asses IgM and IgG antibodies against TBEV, and neutralization test was used for confirmation. Of the 419 samples, 17 (4%) were positive for B.burgdorferi IgG by ELISA, however 14 (14/419; 3.3%) of them were confirmed by WB. B.burgdorferi seropositivity was higher among people living in rural areas, at an altitude of ≥ 400 meters and in locations ecologically suitable for wild boar and rabbits; seropositivity was also seen to be higher among dog owners (p= 0.001, p= 0.001, p= 0.001, p= 0.001, p= 0.018, respectively). For TBEV, two samples yielded IgG positive, and one IgM positive results by ELISA, however none of them were confirmed by neutralization assay. Nevertheless, one of those three TBEV ELISA positive samples, was found positive for West Nile virus specific antibodies with neutralization test. The results of this study emphasized the presence of tick-borne diseases in that specific region, and in this regard the need for public health interventions has been demonstrated.

Sensitivity Affected by Disease Severity and Serum Sampling Time: a Performance Evaluation of Six SARS-CoV-2 Antibody Immunoassays.

Comparative validation and clinical performance data are essential for the reliable interpretation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antibody test results. This study aimed to assess the performance of six SARS-CoV-2 IgG immunoassays in the context of different disease severities. Four automated chemiluminescence immunoassays (Access [Beckman Coulter], Architect [Abbott], Atellica-IM [Siemens], and Elecsys [Roche]) as well as two ELISA assays (SARS-CoV-2 IgG-S1-based and NCP IgG [Euroimmun]) were evaluated using samples from 143 patients as well as 50 pre-pandemic control serum samples. Accuracy and precision tests were performed for validation purposes. Overall sensitivity ranged between 73.38-88.65% and was higher in spike protein-based assays, while the specificity was ≥98% in all immunoassays. The clinical performance of the immunoassays differed depending on disease severity and target antigen. For instance, the IgG response was lower for samples taken <20 days post-symptom onset (87.30%) compared with those taken ≥20 days post-symptom onset (94.80%). Moreover, moderate disease levels led to the highest levels of IgG. Higher levels of antibodies were detected in the clinically moderate disease group. In asymptomatic and mild groups, more antibody positivity was detected with spike protein-based assays. All the assays tested could be used to detect SARS-CoV-2 IgG. However, spike-based assays revealed relatively higher sensitivity rates than nucleoprotein-based assays, particularly in cases of asymptomatic and mild disease.

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.

[Pandemic influenza A (H1N1)v vaccination status and factors affecting vaccination: Ankara and Diyarbakir 2009 data from Turkey]. / Pandemik Influenza A (H1N1)v Asilanma Durumu ve Asilanmaya Etki Eden Faktörler: Ankara ve Diyarbakir 2009 Verileri.

In this study, it was aimed to determine the frequency of the symptoms of influenza-like illness during influenza A (H1N1)v pandemic in two provinces where sentinel influenza surveillance was conducted and also to obtain opinions about H1N1 influenza and vaccination, H1N1 vaccination status and factors affecting vaccination. This cross-sectional study was conducted in the provinces of Ankara (capital city, located at Central Anatolia) and Diyarbakir (located at southeastern Anatolia). It was planned to include 455 houses in Ankara and 276 houses in Diyarbakir. The household participation rate in the study was 78.9% and 53.6% for Ankara and Diyarbakir, respectively. Our study was carried out between January-February 2010, with 1164 participants from Ankara and 804 from Diyarbakir, including every household subjects except for infants younger than 11 months and patients with primary/secondary immunodeficiency diseases. Data was collected by site teams consisting of a physician and a healthcare staff with informed consent. Of the participants 45.5% from Ankara and 35.3% from Diyarbakir stated that they had gone through an influenza-like illness. The most frequently indicated clinical symptoms were fatigue/weakness, rhinitis, sore throat and cough. The rates of admission to a physician with influenza like illness complaints were 50.6% and 58.7%; rates of hospitalization due to influenza-like illness were 1% and 1.5%, and rates of antiviral drug use were 3.8% and 1.9%, in Ankara ve Diyarbakir participants, respectively. The rate of personal precautions taken by the subjects for prevention from pandemic influenza were 59% and 53.3%, in Ankara and Diyarbakir, respectively. These precautions most frequently were "hand washing" and "avoiding crowded public areas". H1N1 influenza vaccine was applied in 9.3% of the participants in Ankara and in 3.7% of the participants in Diyarbakir. Vaccination rate was higher in both of the provinces in adults over 25 years old than children and adolescents and in patients with chronic underlying disease. None of the 25 pregnant participants were vaccinated against pandemic influenza. The educational background, employment status and quality of the job have been detected as factors affecting the status of being vaccinated with H1N1 influenza vaccine in both provinces. In addition, the percentage of having H1N1 influenza vaccination was found to be higher in subjects who had seasonal influenza vaccination previously and in 2009, than those who had not, and this difference was statistically significant in both provinces (Ankara p< 0.001, Diyarbakir p< 0.001). The mostly indicated post-vaccination adverse reactions reported by vaccinated participants were local sensitivity, muscle and joint pains, headache and malaise. The most frequent rationale for not being vaccinated against H1N1 were "I do not consider it necessary/I do not want" (Ankara 33.4%, Diyarbakir 27.4%) and "I do not believe/trust its efficacy" (Ankara 25.6%, Diyarbakir 22.6%). Those data emphasized the insufficient awareness of our population about the importance of pandemic influenza and vaccine. It is also believed that possible case definition in H1N1 case management scheme should be revised. In conclusion an important part of pandemic preparation plans is risk communication with the public to increase awareness and to prevent the missed opportunities.

Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii Blood Culture Isolates from Three Hospitals in Turkey.

We aimed to investigate the clonal relationships, common sequence types, and carbapenemase genes in 177 non-repetitive blood culture isolates of Acinetobacter baumannii collected from patients at three university hospitals in Turkey in 2016. Molecular epidemiological characteristics of the isolates were examined using pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) (Pasteur scheme-cpn60, fusA, gltA, pyrG, recA, rplB, and rpoB). Multiplex PCR was used to investigate the carbapenemase genes, including blaOXA-23-like, blaOXA-24-like, blaOXA-48-like, blaOXA-58-like, blaIMP, blaVIM, and blaNDM. PFGE genotyping yielded 92 pulsotypes with a clustering ratio of 69.7%. As per a ≥85% similarity coefficient, 159 (90.9%) isolates were found to be clonally related. The blaOXA-23-like and blaOXA-58-like genes were identified in 100% and 28.2% of the isolates, respectively. The blaNDM gene was identified in two isolates. The MLST analysis included 54 isolates with different pulsotypes, and 29 sequence types (STs). Most of the isolates (n = 36) belonged to the clonal complex (CC)2, one isolate belonged to CC1, and one isolate belonged to CC164. Sixteen new STs (ST1235-ST1250) were identified. Identifying both global ST2 and a large number of new STs, revealed high genetic diversity in A. baumannii isolates in the study population.

[Establishment of an algorithm for serological testing of syphilis identification]. / Sifiliz tanisinda kullanilan serolojik testler için akis semasinin olusturulmasi.

Serological methods are widely used for the laboratory diagnosis of syphilis or for screening purposes. The aim of this study was to determine an algorithm for the application of laboratory tests that will provide accurate diagnosis of syphilis in a cheap, fast and practical way. A total of 162 serum samples were evaluated by the following tests: VDRL (Venereal Disease Research Laboratory; Omega Diagnostic, UK), TPHA (Treponema pallidum Hemagglutination Test; Omega Diagnostic, UK), ELISA IgG + IgM (Enzyme Linked Immunosorbent Assay; DiaPro Diagnostic Bioprobes, Italy), FTA-ABS (Fluorescent Treponemal Antibody-Absorption; IgG, Euroimmun, Germany) and WB (Western Blot; IgG Euroimmun, Germany). When the gold standard was considered as FTA-ABS test, the sensitivity, specificity, positive and negative predictive values for VDRL were 77.1%, 100% 100% an 80.6%; for TPHA were 92.8%, 98.7%, 98.7% and 92.9%, for ELISA 98.8%, 98.7%, 98.8% and 98.7%, and for WB 98.8%, 100%, 100% and 98.7%, respectively. When the results of screening with VDRL together with TPHA were compared with FTA-ABS, it was observed that if both VDRL and TPHA results were positive, then there was 100% concordance between the tests. However, when both of the test results were negative, 1.3% of them yielded positive result with FTA-ABS. If either one of VDRL or TPHA results were positive (n = 24), 95.8% (n = 23) was positive with FTA-ABS. Therefore, inconsistent results obtained by VDRL and TPHA requires verification by another method. When ELISA or WB tests were used, the borderline results need verification, however, positive or negative results would be reported. The determination of an algorithm for laboratory tests also depend on the number of patients, cost, cost per positive patient and workload of the laboratory. Thus, ELISA could be selected when the number of cases is high and the results should be reported unless they are suspicious. When the number of cases is low, VDRL/TPHA should be selected, and the results should be verified if they are inconsistent. However, the demographic characteristics of patient groups are also important in test selection and work flow. False positive results are troublesome in case of marriage pre-screening and false negative results in sex workers. When all these factors are taken into consideration it may be suggested that either ELISA or VDRL together with TPHA should be performed and the results should be confirmed by a reference test in case of borderline results in ELISA or inconsistency between VDRL and TPHA results. Although screening for syphilis in the setting of blood banking is a matter of debate, if it is to be performed, then ELISA would be better since the work load is high. In case of pregnancy inconsistent VDRL and TPHA results should be verified since no risk could be afforded.

The presence of tick-borne encephalitis in an endemic area for tick-borne diseases, Turkey.

The aim of this study was to indicate the presence of tick-borne encephalitis (TBE) in an endemic area for Crimean-Congo haemorrhagic fever (CCHF) in Turkey. Of 39 CCHF suspected cases, one was found to be TBE virus immunoglobulin M positive and seven were TBE virus immunoglobulin G positive. It is important to report this first appearance of the TBE virus in Turkey since 1967.

[Pertussis seroprevalence and vaccination status in three selected provinces of Turkey]. / Seçilmis üç ilde bogmaca seroprevalansi ve asilanma durumu.

The aim of this community-based seroepidemiological survey was to assess the immune status against pertussis among the healthy population in three selected provinces with different geographical and socioeconomical status (Antalya, Diyarbakir and Samsun, located at Mediterrenean, Southeast Anatolia and Black Sea regions of Turkey, respectively) in relation with DwPT (whole cell pertussis vaccine combined with diphtheria and tetanus toxoids) vaccination status. A total of randomly selected 2085 subjects ages between 6 months to > 50 years were included to the study. Serum samples have been screened for the presence of pertussis antibodies by an in house ELISA method with the use of pertussis toxin (PT) and filamentous hemagglutinin (FHA) antigens. The levels of > or = 10 EU/mL was accepted as positive for anti-PT and anti-FHA. Vaccination rate with 3-4 doses among children under 15 years old was significantly lower in Diyarbakir compared to the other two provinces (p< 0.05). The antibody positivity was increased with age up to the 10-14 year group and was maintained among older groups. There was no statistically significant relationship between the vaccination rate and antibody prevalence (p> 0.05). Adult females showed a significantly higher antibody-positivity rate for anti-PT than the males (p< 0.05). Our study pointed out a high prevalence of pertussis infection in those selected provinces, suggesting that the adults play a role as potential reservoirs for B. pertussis. It can be concluded that adult immunization, especially of those who are likely to have close contact with infants, should be considered.

Tetanus immunization status among women of childbearing age in Turkey.

In order to assess the effect of the neonatal tetanus elimination program in Turkey, tetanus antibody prevalence among women of childbearing age from three selected provinces was evaluated in relation to vaccination doses of the single-type tetanus vaccine. A combined method of in-house enzyme-linked immunosorbent assay and particle agglutination test was used to determine tetanus antibody titers. Among 205 women aged 20-39 years, the tetanus antibody level was higher in women with 1-3 children than those without children. The geometric mean of the log antibody titer was increased proportionally with a slope of 0.405 +/- 0.174 per dose between 0 and 3 doses (P > 0.05). However, the proportion of 20-39-year-old women with the protective antibody in the provinces ranged from 54.8 to 86.6%. Diyarbakir had the lowest immunity with a larger number of children in the household, and a lower educational level. The results of our serological study demonstrated that the neonatal tetanus elimination program in Turkey is effectively promoting immunity against tetanus in pregnant women. However, the study also revealed that the tetanus immunity among women of childbearing age was still insufficient. Intensive implementation of the supplemental immunization activities and encouraging vaccinations through neonatal care services will improve the situation.

Comparison of in-house biotin-avidin tetanus IgG enzyme-linked-immunosorbent assay (ELISA) with gold standard in vivo mouse neutralization test for the detection of low level antibodies.

BACKGROUND: Detection of anti-tetanus antibody levels is necessary for both determination of the immune status of individuals and also for planning preventive measures. ELISA is the preferred test among in vitro tests however it can be affected by the cross reacting antibodies. A previously developed in-house ELISA test was found not reliable for the antibody levels ≤1.0IU/ml. A new method was developed to detect low antibody levels correctly. The aim of the present study was to compare the results of the newly developed in-house biotin-avidin tetanus IgG ELISA test with the in vivo mouse neutralization test, for the antibody levels ≤1.0IU/ml. METHODS: A total of 54 serum samples with the antibody levels of three different levels, =0.01IU/ml, 0.01-0.1IU/ml, 0.1-1IU/ml, which were detected by in vivo mouse neutralization test were studied by the newly developed in-house biotin-avidin tetanus IgG ELISA test. Test was validated by using five different concentrations (0.01IU/ml, 0.06IU/ml, 0.2IU/ml, 0.5IU/ml, 1.0IU/ml). RESULTS: A statistically significant correlation (r2=0.9967 p=0,001) between in vivo mouse neutralization test and in-house biotin-avidin tetanus IgG ELISA test, was observed. For the tested concentrations intra-assay, inter-assay, accuracy, sensitivity, specificity and coefficients of variations were determined as ≤15%. CONCLUSION: In-house biotin-avidin tetanus IgG ELISA test can be an alternative method to in vivo mouse neutralization method for the detection of levels ≤1.0IU/ml. By using in-house biotin-avidin tetanus IgG ELISA test, individuals with non protective levels, will be reliably detected.