Use of flow cytometry method to detect contaminations of platelet suspensions.

In this study, it was aimed to investigate bacterial contamination in apheresis platelet suspensions (APS) by automated blood culture system and flow cytometry method (FCM).33 spiked APS each using 11 bacterial strains (5 standard strains, 6 clinical isolates), were prepared in three different dilutions (1-10, 10-50, 50-100 cfu/mL), incubated in two different temperatures (35-37 °C and 22-24 °C) and different incubation times (18-96 h) evaluated by FCM. This three different dilutions were also inoculated into special platelet culture bottles (BacT/ALERT® BPA) and loaded into the blood culture system. Additionally 80 APSs routinely prepared in the Transfusion Center were evaluated by both FCM and the blood culture system. Platelets were lysed by freeze-thaw method.All spiked samples were positive with BacT/ALERT® BPA in 12-18 h. In 96 h incubation at 22-24 °C, the presence of bacteria was detected by FCM in all other samples (31/33) except low dilutions (1-10 and 10-100 CFU/ml) of K.pneumoniae standard strain. In the 35-37 °C, the presence of bacteria was detected by FCM in all samples (33/33) after 48 h of incubation. In routine APS one sample detected as positive (Bacillus simplex) with BacT/ALERT® BPA and no positivity was detected by FCM.The freeze-thaw method, which we have optimized for the lysis of platelets, is very practical and can be easily applied. The BacT/ALERT® system has been found to be very sensitive in detecting bacterial contamination in PSs. Flow cytometry method has been found to be successful, fast, easy to use and low cost in detecting bacterial contamination in PSs.

Determination of safety status and probiotic properties of Enterococcus strains isolated from traditional cheeses in Turkey.

AIMS: This study aimed to evaluate the probiotic properties of Enterococcus strains isolated from Turkish traditional cheeses. METHODS AND RESULTS: Fifty-two Enterococcus spp. were taxonomically determined as follows: Enterococcus faecium (26), Enterococcus faecalis (18), Enterococcus durans (6), and Enterococcus italicus (2). The ability of isolates/strains to survive the harsh conditions (acidity and in-vitro gastric solution) of the gastrointestinal tract was established. They also showed auto-aggregation, hydrophobicity, and co-aggregation ability. Hydrophobicities of the strains were found between 0.8%-21%, 0.7%-56%, and 2%-63% for xylene, chloroform, and ethyl acetate, respectively. Autoaggregation values of the Enterococcus strains were 4%-20%, 7%-30%, and 36%-98% after 2, 4, and 24-h incubation, respectively. In this study, the Enterococcus strains tested showed co-aggregation ability with the Escherichia coli ATCC 25922, Salmonella Typhimurium ATCC 14028, and Staphylococcus aureus ATCC 25923. The results of PCR amplification revealed that only five strains possess virulence factor genes (gelE,asa1,cyl A,esp). We determined antibiotic resistance, biofilm forming abilities, and hemolytic activity for safety evaluation of strains. CONCLUSIONS: In this large and comprehensive study, we found that only few of Enterococcus strains have promising probiotic potential, among which E. faecalis ES1 and E. faecium EM1 showed the best probiotic properties (are the most promising probiotic candidates).

Investigation of Early Diagnostic Value of Glial Fibrillary Acidic Protein and Ubiquitin C-Terminal Hydrolase Blood Levels in Minor Head Trauma in Turkey.

BACKGROUND: The aim was to investigate the early diagnostic value of serum glial fibrillary acidic protein (GFAP) and ubiquitin C-terminal hydrolase (UCH-L1) levels in adults with minor head trauma (MHT) and whether it could be an alternative diagnostic method to computed tomography (CT). This is the first study with the combination of GFAP and UCH-L1 in the first 3 hours of MHT. METHODS: The study comprised 88 patients, 60 patients and 28 controls, who were evaluated as having MHT, were admitted to the emergency department of our hospital within the first 3 hours of the trauma and met the inclusion criteria. CT was performed on all patients. Serum GFAP and UCH-L1 levels were measured within the first 3 hours of the trauma. RESULTS: The median serum GFAP level was 1.07 ng/mL in the group with pathology on CT and 0.42 ng/mL in the group with no pathology on CT. The median serum UCH-L1 level was 0.40 ng/mL in the group with pathology on CT and 0.39 ng/mL in the group with no pathology on CT. A statistically significant difference was found between the serum GFAP levels of the CT (+) group and the CT (-) group (p = 0.021). GFAP levels were compared according to the CT (+) and CT (-) groups with a cutoff value of ≥ 1.56 ng/mL for GFAP, which had 50% sensitivity and 97.5% specificity. This was statistically significant (p = 0.008). It was found that the UCH-L1 level of the control group was lower than the UCH-L1 levels of the CT (+) and CT (-) groups, and this difference was found to be statistically significant (p = 0.003 and p = 0.018, respectively). CONCLUSIONS: GFAP was found to be more specific than UCH-L1 in demonstrating the presence of intracranial pathology in patients with head trauma who were admitted to the emergency department in the first 3 hours after trauma.

Rapid Molecular Diagnosis of Group A Streptococcus with a Novel Loop Mediated Isothermal Amplification Method.

BACKGROUND: Group A Streptococcus (GAS) is the most common bacterial cause of acute tonsillopharyngitis. In this study, it was aimed to evaluate the performance of a novel Loop Mediated Isothermal Amplification (LAMP) method in the rapid diagnosis of GAS in samples taken from children with a prediagnosis of acute bacterial tonsillopharyngitis by comparing it with culture and rapid antigen test (RAT) methods. METHODS: A total of 100 throat swab samples taken from children at the pediatrics outpatient clinic with suspected tonsillopharyngitis were included in the study. Throat swab samples were analyzed by RAT, throat culture, and LAMP method. GAS suspected colonies were identified with MALDI-TOF MS system. The isothermal amplification reaction for LAMP was conducted by a novel LAMP instrument. RESULTS: According to the results of throat cultures; 53 of them were positive and 47 were negative in terms of GAS. Six (11.32%) of the culture positive samples were found to be negative by the RAT (sensitivity; 88.68%, specificity 100%). While the antigen test was positive, no culture negative sample was detected. One of the culture positive samples was found negative by LAMP. In two samples, while throat culture was negative, it was observed that LAMP was positive (sensitivity; 98.11%, specificity; 95.74%). In one of these samples, the bacteria grown in the culture were identified as Streptococcus dysgalactiae by mass spectrophotometry. CONCLUSIONS: In this study, it was determined that the LAMP method used in the diagnosis of throat infections caused by GAS has high sensitivity and specificity. We believe that the instrument is easy to use, low cost, portable, and adaptable to point of care tests. There are very few studies in the literature regarding the use of the instrument in this field, and it should be evaluated in terms of its usability in daily practice with new studies.

The role of serum salusin alpha and beta levels and atherosclerotic risk factors in idiopathic sudden hearing loss pathogenesis.

PURPOSE: The aim of this study was to investigate the importance of atherosclerosis in the pathogenesis of sudden hearing loss by evaluating the newly discovered markers, serum salusin-α and salusin-ß. We also aimed to evaluate atherosclerosis risk factors, such as lipid profile, smoking, body mass index, waist circumference and mean blood pressure of the patients. METHODS: Fifty-two patients diagnosed with sudden hearing loss (study group) and fifty healthy people (control group) were included in the study. Detailed history was taken from the patients and risk factors for atherosclerosis, such as smoking, body mass index, waist circumference, lipid profile, mean blood pressure and serum salusin-α and salusin-ß levels, were evaluated. The study group was divided into recovery group (subgroup I) and non-recovery group (subgroup II). RESULTS: The salusin-ß median value was found to be significantly higher in the study group compared to the control group (p < 0.05). The salusin-ß median value was found to be significantly higher in subgroup 2 and was found to be a poor prognostic factor (p < 0.05). CONCLUSION: From the results obtained in this study, it is thought that salusin-ß peptide is increased in patients with sudden hearing loss and it can be evaluated as a poor prognostic factor.

Determination of antibiotic susceptibility of bacteria by flow cytometric method.

In this study, it was aimed to determine the antibiotic susceptibility of bacterial strains by using flow cytometry method by comparing them with current standardized methods. Eleven clinical isolates and 6 standard bacterial strains were included in the study. MIC values were determined by broth microdilution method (BMD), VITEK 2® automated system and flow cytometric method (FCM). FCM was performed with the Accuri C6 flow cytometer. For all strains except P. aeuruginosa ATCC 27853 [BMD-FCM:r = 0.557(p = 0.048); VITEK 2-FCM:r = 0.529(p = 0.063)], E. faecalis ATCC 29212 [BMD-FCM:r = 0.393(p = 0.295); BMD-VITEK 2:r = 0.393(p = 0.295)], and vancomycin-resistant E. faecium clinical isolate [BMD-FCM:r = 0.452(p = 0.063)] r values were in the range of 0.802-0.969 for BMD-FCM (p < 0.001), 0.655-0.941 for BMD-VITEK 2 (p < 0.005) and 0.667-0.953 for FCM-VITEK 2 (p < 0.005). Correlation values of antibiotic susceptibility test results between three methods for Gram-negative bacteria were found as follows; r = 0.927(p < 0.001) for BMD-FCM, r = 0.851(p < 0.001) for BMD-VITEK 2, r = 0.807(p < 0.001) for VITEK 2-FCM. Correlation values were found as follows for Gram positive bacteria; r = 0.848(p < 0.001) for BMD-FCM, r = 0.877(p < 0.001) for BMD-VITEK 2, r = 0.800(p < 0.001) for VITEK 2-FCM. When all bacteria included in the study were evaluated as a total; it was r = 0.911(p < 0.001) for BMD-FCM, r = 0.888(p < 0.001) for BMD-VITEK 2, r = 0.835(p < 0.001) for VITEK 2-FCM. The methicillin resistance of the clinical methicillin resistant S. aureus isolate could not be detected by FCM. It was determined that there was a high level of correlation between methods. FCM shortens the duration of antibiotic susceptibility tests by 12-14 h and gives results within the same day. However, it has not been standardized to be widely used in microbiology laboratories and experienced personnel are needed for its implementation.

[Shedding of SARS-CoV-2 Virus in COVID-19 Patients and Neutralizing Antibody Level]. / COVID-19 Hastalarinda SARS-CoV-2 Virüs Saçilimi ve Nötralizan Antikor Düzeyleri.

The coronavirus disease 2019 (COVID-19) turned into a pandemic shortly after emerging in December 2019, in the city of Wuhan, China. In this study, it was aimed to investigate the presence of severe acute respiratory system coronavirus-2 (SARS-CoV-2) RNA in various clinical samples and the scattering profile of the virus and the variation of anti-SARS-CoV-2 IgG and neutralizing antibody levels over time in infected patients during and after the period of COVID-19 disease. The study included COVID-19 patients from the community (CCP) (n= 47) (May-June 2020) and healthcare workers (HCWP) (n= 30) (November-December 2020). To investigate the presence of SARS-CoV-2 in clinical samples, oropharynx (OF), nasopharynx (NF), sputum, stool, blood and urine samples were taken from the CCP group on days 0, 3, 7, 14 and 28. For the detection of anti SARS-CoV-2 IgG and neutralizing antibodies serum samples were taken from the CCP group on days 0, 3, 7, 14, 28, 60, 90 and 120 and on days 14, 28, 60, 90, 120 and 150 from HCWP group. Virus RNA was detected by reverse transcription polymerase chain reaction (RT-PCR), anti SARS-CoV-2 IgG antibody levels by enzyme-linked immunosorbent assay (ELISA), neutralizing antibody levels (NAb) by cell culture neutralization and representative neutralization test (sVNT) methods. With the onset of the vaccination program in our country, 11 of the HCWP group patients had SARS-CoV-2 vaccine after the second month serum samples were taken, the remaining HCWP group patients did not get vaccinated during the study period. SARS-CoV-2 RNA was detected with the highest rates in NF (100%), stool (65.8%), sputum (45.7%), OF (41.3%), blood (5.3%), and urine (2.2%) samples, respectively. It was found that viral shedding continued for 14 days in respiratory tract samples and up to 60 days in stool samples, and no virus was detected in blood samples after the third day. It was observed that the viral load was highest at the time of diagnosis in both upper and lower respiratory tract samples, peaking on the seventh day in stool samples and following an irregular course throughout the disease. Anti-SARS-CoV-2 IgG antibody positivity was found in 41.4% of CCP group patients on the first day of diagnosis, and seroconversion was observed in all patients at the fourth month. During the study period, seropositivity was detected in only 82.1% of the patients in the HCWP group. It was observed that the IgG antibody levels peaked at the 7th day in the CCP group patients and at the third month in the HCWP group patients (S/Co: 9.6 and 2.8, respectively). Anti-SARS-CoV-2 IgG antibody levels detected in the CCP group were found to be significantly higher than the HCWP group (p<0.05). At the end of the first month, NAb was detected in all (100%) patients in the CCP group. It was found that NAb titers peaked (1/256) on the 28th day and showed a decreasing trend from the second month. NAb median titers were observed to peak earlier in the severe HCWP group (14 days in the severe group, 28 days in the mild group, p> 0.05). It was observed that 6 (26.1%) of HCWP group patients had low, 11 (47.8%) moderate, 6 (26.1%) high titers of representative NAb. The distribution of representative NAb levels by vaccine status was examined and no statistically significant difference was found (p= 0.400, p= 0.077 and p= 0.830, respectively). As a result; SARS-CoV-2 RNA was detected in many samples such as sputum, stool, blood and urine, and it was observed that viral shedding in stool samples could continue for months. Anti-SARS-CoV-2 IgG antibody positivity was observed in most of the patients in the fourth month, and it was found that the antibody titers decreased after the third month. It was determined that protective antibody levels continued in the fourth month. These findings are important in vaccination strategies and in the fight against the pandemic. However, considering the emergence of new mutant forms of the virus in today's conditions where the pandemic continues, more detailed and comprehensive studies are needed for viral shedding and antibody titer studies.

A Predictive Test in The Screening of HIV Positive Cases; Interferon Gamma Inducible Protein 10 (IP-10).

BACKGROUND: HIV (human immunodeficiency virus), causing acquired immunodeficiency syndrome (AIDS), is one of the most important health problems in the world. Certain cytokines produced during the cytokine storm in an acute infection can be biomarker candidates. The strong association of IFN-γ inducible protein 10 (IP-10) with low CD4 cell counts suggests that it can be an acute phase biomarker. METHODS: In this study, IP-10 was monitored at routine controls during pre-treatment and/or in subsequent phases of treatment, and its correlation with CD4 cell count and viral load was assessed. Venous blood samples, taken from 30 patients (at 0 - 3 - 6 months), and 20 healthy volunteers, were sent to the Laboratory for flow cytometry, nucleic acid tests (NAT) and ELISA tests. RESULTS: The mean IP-10 concentration of patients was 344 pg/mL, and these values for the untreated, treated and control groups were 422 pg/mL and 210 pg/mL and 68 pg/mL respectively. A statistically significant difference was found between the IP-10 values of the patient and control groups (p = 0.006). There was a significant, positive and moderate relation between IP-10 and viral load values (r = 0.59, p < 0.001), while there was a significant, negative and moderate relation between IP-10 and CD4 cell count (r = -0.51, p < 0.001). CONCLUSIONS: IP-10 levels in early HIV-1 patients, which are shown to be closely related to CD4 cell levels and viral replication, may be an alternative or support marker compared to the more expensive viral load tests in monitor-ing viremia changes and response to antiretroviral treatment.

Can prognostic nutritional index and systemic immune-inflammatory index predict disease severity in COVID-19?

BACKGROUND: Prognostic nutritional index (PNI) and systemic immune-inflammatory index (SII) are inflammation-based novel markers that predict the prognosis in various patient populations. We have investigated the relationship between the disease severity in COVID-19, and the PNI and SII scores in the present study. MATERIALS AND METHODS: This cross-sectional retrospective study included 118 hospitalised patients with a confirmed diagnosis of COVID-19. The patients were divided into two groups as those who were hospitalised at the intensive care unit (ICU) and those who had been internalised at the clinic (non-ICU). RESULTS: Of the 118 patients, 50.8% were male. The mean age was 57.7 ± 17.5 years in non-ICU patients and 70.3 ± 11.7 years in ICU patients and the difference was statistically significant (P < .001). The lymphocyte count and the albumin levels were significantly lower in ICU patients (P < .001, P < .001, respectively). The PNI score was significantly lower in ICU patients compared with non-ICU patients (P < .001). The SII score was found to be significantly higher in ICU patients compared with non-ICU patients (P < .001). The value of PNI and SII scores in prediction of the disease severity in COVID-19 was evaluated with the ROC analysis (PNI: AUC = 0.796, 95%CI: 0.715-0.877, P < .001; SII: AUC =0.689, 95% CI: 0.559-0.819, P=.004). When the cut-off value was taken as ≤36.7 for the PNI score, it was found to have 73.4% sensitivity and 70.8% specificity for predicting of the disease severity and ICU admission probability was 4.4 times higher. When the cut-off value was taken as ≥813.6 for SII score, it was found to have 70.8% sensitivity and 66.0% specificity for predicting of the disease severity and ICU admission probability was six times higher. CONCLUSION: The PNI and the SII scores are independent predictors of the prognosis and the disease severity in COVID-19 patients who require hospitalisation at the ICU.

Investigation of Hepatitis E Seroprevalence in HIV Positive Patients by a Novel Enzyme Linked Fluorescent Assay Test.

BACKGROUND: Hepatitis E virus (HEV) infection is usually an acute self-limiting disease, which causes rapidly progressive cirrhosis and chronic infection in patients with hematological malignancies, patients requiring chemotherapy, and HIV-infected patients. The aim of this study was to investigate the positivity of hepatitis E IgM and IgG in HIV positive patients with the recently introduced Enzyme Linked Fluorescent Assay (ELFA) commercial kits. MATERIALS AND METHODS: The study included 126 patients who were followed up by the Infectious Diseases and Clinical Microbiology Clinic of Sakarya University Training and Research Hospital between October 2017 and December 2018 for HIV positivity. Serum samples of the patients were evaluated for anti-HEV IgG and IgM positivity with a novel commercially available kit using the ELFA method (bioMerieux, France). The study group consisted of 126 patients with HIV infection. Anti-HEV IgG antibodies were studied primarily from plasma samples. Anti-HEV IgM positivity was also investigated in patients with anti-HEV IgG positivity. RESULTS: The study group consisted of 114 (90.5%) males and 12 (9.5%) females with a mean age of 38.11 ± 13.32 (min: 18, max: 80) years. Anti-HEV IgG was positive in 5 (4.0%) HIV-positive patients. One of the anti-HEV IgG positive patients was newly diagnosed with HIV and the other four patients were being followed up for HIV positivity. Anti-HEV IgM was negative in all patients. None of the patients with anti-HEV IgG positivity had anti-HCV and HBsAg positivity. CONCLUSIONS: In the study, anti-HEV IgG positivity was found to be 4% in HIV-positive individuals, and no HCV and HBV co-infection was detected in any patients with HIV and HEV coexistence. HEV infections do not emerge as a priority among HIV-infected people, but HEV should also be investigated in HIV-infected individuals with liver abnormalities of uncertain etiology.

Salivary human beta-defensins and cathelicidin levels in relation to periodontitis and type 2 diabetes mellitus.

Objective: Type 2 diabetes mellitus (T2DM) is a well-defined risk factor of periodontitis and it can affect expression of human beta-defensins (hBDs) and cathelicidin (LL-37) as well. The aim of the present study was to evaluate the impact of periodontitis and T2DM on salivary concentrations of these antimicrobial peptides.Material and methods: Unstimulated saliva samples, together with full-mouth periodontal recordings were collected from 92 individuals with periodontitis (63 with T2DM and 21 smokers) and 86 periodontally healthy controls (58 with T2DM and 21 smokers). Salivary hBD-1, -2, -3, LL-37, and advanced glycalization end products (AGE) concentrations were measured by enzyme-linked immunosorbent assay.Results: Among the periodontitis patients, T2DM group demonstrated lower levels of hBD-1 (p = .006), hBD-2 (p < .001) and hBD-3 (p < .001), and higher levels of LL-37 (p < .001) compared to systemically healthy controls. When only periodontally healthy controls were included into the analysis, higher hBD-1 (p = .002) and LL-37 (p < .001) levels were found in T2DM patients in comparison to systemically healthy controls. Salivary LL-37 levels were associated with HbA1c and periodontitis, while hBD-2, hBD-3 and levels associated only with HbA1c.Conclusion: In the limits of this study, hyperglycaemia can be proposed as a regulator of salivary hBD and cathelicidin levels. Periodontitis, on the other hand, affects only salivary LL-37 levels.

Microbial contamination and infection risks of narghile besides hazards of tobacco.

OBJECTIVE: Water-pipe smoking has become a serious public health threat worldwide. In order to raise awareness of adverse effects and transmission of bacteria via water-pipe smoking, we aimed to identify the bacteria and their antimicrobial resistance profiles that colonize different parts of waterpipes. METHODS: We examined totally 182 water pipes from 7 lounges (in Turkey) used in public places and we collected 728 culture samples in total by microbiological methods. We used disposable sterile swabs to sample the inside and outside of the mouthpiece, and the handling piece and sterile injectors were used to collect 5 mL of water from the water pipe bowl. RESULTS: There was a significant (p < 0.05) difference in microbial contamination (growth/presence of bacteria and fungi) among the parts of the water pipes sampled. There was a significant (p < 0.05) difference in the number of bacteria growing (microbial load) among the parts of the water pipes. Only one narghile lounge out of seven, which had 13 water pipes, had a hygiene procedure. The water jars are often contaminated with Gram-negative bacteria. CONCLUSION: Water pipes, especially the interior and outer part of the mouthpieces and the handle, are colonized by microbes and pose a risk of infection. Procedures for water pipe hygiene should be developed, periods should be defined, and the owners and employees of establishments and water-pipe smokers should be educated in this regard. Water-pipe smoking is a threat to public health and should be regulated by the state.

[Comparison of Antiviral Effect of Olive Leaf Extract and Propolis with Acyclovir on Herpes Simplex Virus Type 1]. / Zeytin Yapragi Ekstresi ve Propolisin Herpes Simpleks Virüsü Tip 1 Üzerine Antiviral Etkisinin Asiklovir ile Karsilastirilmasi.

While acyclovir, a nucleoside analogue, is widely used for herpes simplex virus type 1 (HSV-1), emergence of drug-resistant viruses due to frequent usage of this class of medicines, and their toxic side effects require exploring novel active molecules. Despite the studies on developing synthetic molecules in medical sciences and pharmacology, herbs as a natural source of biologically-active compounds remain popular. In this in vitro study, olive leaf extract (OLE) and propolis alone or in combination with acyclovir were investigated for their antiviral efficacy in HSV-1.Toxic doses of OLE, propolis, and dimethyl sulfoxide, propolis diluent, for Hep-2 (ATCC, CCL-23) cells were determined by conventional cell culture. Using "endpoint" method, the viral dose infecting half of the cell culture (TCID50) was calculated, and viral quantity was determined with Spearman-Karber method. Antiviral effects of OLE and propolis on HSV-1 were investigated by conventional cell culture and real-time cell analysis (RTCA). Combinations of the two extracts with one another and with acyclovir were evaluated by RTCA. Active substances prepared at three different dilutions were added to tubes with HSV-1 of logTCID50: 11.5 in descending order starting from the highest non-toxic concentration, and they were left at room temperature for two different durations (one hour and three hours). The aliquots taken from the tubes were cultured in plates containing Hep-2 cells and evaluated after 72 hours. Combinations of extracts and acyclovir at concentrations at least four times lower than the lowest concentration showing antiviral efficacy against HSV-1 were cultured with Hep-2 cells in the e-plates of the xCELLigence RTCA device, measurements were obtained at 30 minute intervals, and data were recorded in real time. In the test with two different durations and at different concentrations of OLE and propolis, antiviral efficacy was observed both with one-hour and three-hour incubation at a concentration of 10 µg/ ml for propolis and 1.2 mg/ml for OLE with RTCA. The duration and concentration of the greatest decrease in viral quantity were in the first one hour and 10 µg/ml for propolis, and in the first one hour and 1.2 mg/ ml for OLE. Combination of propolis and OLE with acyclovir caused no cytopathic effects, and the combination of extracts led to delayed cytopathic effect. According to these results, propolis and OLE, alone and in combinations with acyclovir, have antiviral efficacy against HSV-1. These agents may reduce the dose and side effects of acyclovir in case of co-administration since they exert their effects through a different mechanism than acyclovir,possibly through direct virucidal activity, inhibition of virus internalization or viral inhibition in early stages of replication (inhibition of adsorption/binding of viral particles to the cell). These extracts that do not require conversion to active form have the potential to reduce infectivity in oral lesions, prevent spread, and be used in the topical treatment of acyclovir-resistant HSV infections, particularly in immunocompromised patients. However, in vivo studies should be conducted to determine their medicinal properties and potential toxicities. These results should be supported by further comprehensive studies and the efficacy against other viruses should also be investigated.

[Employee Safety and Biosafety Applications in Microbiology Laboratories; A Multicenter Evaluation in Turkey]. / Mikrobiyoloji Laboratuvarlarinda Çalisan Güvenligi ve Biyogüvenlik Uygulamalari Açisindan Türkiye'de Çok Merkezli Bir Degerlendirme.

Medical laboratory personnel may be exposed to various hazards, especially biological and chemical, during their routine activities. In this multicenter study, which could reflect the nation wide results, it was aimed to determine the safety and biosecurity practices of the employee working in medical microbiology laboratories and to reveal the current situation. A total of 1072 personnel working in the Medical Microbiology Laboratory of 23 hospitals (14 medical faculty hospitals, seven ministry of health training and research hospitals and two state hospitals) from different provinces were provided with a questionnaire consisting of 33 questions inquiring about the rules, opinions, attitudes and behaviors regarding safety and biosafety practices. Statistical analyses were made with institutions, age groups, gender, educational background, working time and occupational groups in terms of exposure to biological and chemical hazards. It was determined that approximately 50% personnel of the university/ training and research hospitals and 2/3 of the state hospitals personnel consumed food and beverages in the laboratories (p<0.05). Compared with other hospitals, it was determined that in state hospitals; the absence of separate resting room (35%), the personnel finding their own knowledge and practices inadequate (28.9%), laboratory coats washed at home (95%), educational organization and participation rates (90%) and medical waste information levels of the personnel were higher (p< 0.05). It was determined that as the age progresses, the rate of education, food and beverage consumption in the laboratory, not being outside the laboratory with protective equipment (gloves, masks and laboratory coats) and the history of laboratory acquired infections were increased (p< 0.05). It was observed that washing the laboratory coats at home was higher in the younger age group and hospital washing was higher in the elderly group (p< 0.05). There was no significant difference between the genders in terms of food and beverage consumption in the laboratory (p= 0.09). It was determined that periodic health checks were not performed in 1/3 of both sexes, but the use of gloves and compliance with medical waste rules was lower in men. Female employees find themselves inefficient in terms of knowledge and practices (p< 0.05). The rate of those who did not have their periodic checkups at regular intervals was higher in the high school and master of science education groups; While non-compliance with medical waste rules, food and beverage consumption in the laboratory was highest in the primary and high school graduates, the lowest rates were found in the master and doctorate groups (p< 0.05). The rate of those who had regular health checkups was higher in the group of specialist physicians and technicians (p< 0.05). It was observed that the rule of not going out of the laboratory with protective equipment was fully observed in the 35+ years working group, while compliance was 70-85% in other groups (p< 0.05), hepatitis B vaccination rate was highest in specialist doctors and lowest in cleaning and other personnel group (p< 0.05). Highest non-compliance rate with medical waste rules was observed in the cleaning personnel group (p< 0.05). As a result, although advances have been made in employee safety practices in medical microbiology laboratories in our country in recent years, it has been found that it is not yet sufficient. The results indirectly reflected the profile of medical laboratories in our country. In the laboratories, physical space and equipment deficiencies should be eliminated, periodic health checkups and vaccination should be provided, non-staff entrance to the laboratory and food, beverage and cigarette consumption should be prevented, laboratory coats should be washed in the hospital, in-service trainings, including medical waste training, should be conducted and these trainings should be developed through mechanisms that will change the behavior.

Comparison of the GeneXpert® MTB/RIF Test and Conventional Methods in the Diagnosis of Mycobacterium tuberculosis.

BACKGROUND: The objective of this study is to evaluate the performance of the GeneXpert MTB/RIF system in Mycobacterium tuberculosis (MTB) diagnosis and the detection of rifampicin resistance in pulmonary and extrapulmonary clinical samples. METHODS: A total of 849 samples (611 pulmonary and 238 extrapulmonary), which were sent to the laboratory of our hospital on suspicion of MTB, were included in the study. The samples cultured on Lowenstein Jensen medium and Mycobacteria Growth Indicator Tubes. All samples were also tested with the GeneXpert MTB/RIF test. The drug susceptibility test was determined using the Bactec MGIT 960 system. RESULTS: MTB grew in the culture in 84 (9.8%) of all samples, and 78 (9.1%) were found to be positive by the GeneXpert MTB/RIF test, while acid-fast bacillus (AFB), MTB/RIF test, and culture positivity were 41 (6.7%), 74 (12.1%), and 75 (12.3%), respectively, in pulmonary samples, and these values were found to be 2 (0.8%), 4 (1.7%), and 9 (3.8%), respectively, in extrapulmonary samples. In the automated culture and susceptibility system, rifampicin resistance was detected in only one of 84 (2.6%) isolated strains. This resistant strain was also identified by the GeneXpert MTB/RIF test. According to the culture results of all samples examined, the sensitivity of the GeneXpert MTB/RIF test was calculated as 83.3%, specificity as 98.9%, PPV as 89.7%, and NPV as 98.1%. CONCLUSIONS: The GeneXpert MTB/RIF test used in the study was found to be highly successful, very quick, and requiring low workload in pulmonary samples and extrapulmonary samples in terms of sensitivity and specificity. It was observed that it can be used safely due to its high sensitivity, especially in AFB-positive samples.

Comparison of the Xpert CARBA-R Test and Phenotypical Tests for Detection of Carbapenemases Types in Multidrug Resistant K. pneumoniae Isolates.

BACKGROUND: The objective of this study is to evaluate the performance of the Xpert CARBA-R Test and the phenotyping confirmation tests (MHT, CIM, Mastdiscs, and Carba NP) for the detection of carbapenemases in multidrug resistant (MDR) Klebsiella pneumoniae isolates. METHODS: A total of 68 MDR K. pneumoniae isolates isolated from various clinical samples, were included in the study. The identification and antibiotic susceptibility tests of these isolates were performed using the VITEK®2 (BioMérieux, France) automated system. The Xpert CARBA-R test was used as the molecular method. The combined disc method was performed using Mastdiscs Combi-D70C that includes four antibiotic discs with specific in-hibitors. The modified Hodge test was performed on all isolates. Carbapenemase inactivation method (CIM) and Carba NP test was used for carbapenemase enzyme production. RESULTS: Of the 50 isolates detected to produce carbapenemase by the molecular method (Xpert CARBA-R Test), 45 (90%) were detected by MHT, 39 (78%) were detected by CIM, and 42 (84%) were detected by Mastdiscs, while all the 50 isolates were detected by the Carba NP test. When the Xpert CARBA-R Test was taken as a reference, significant differences were found between the Carba NP and Xpert CARBA-R Test. There was no significant difference between the other phenotypic methods and Xpert CARBA-R Test. The sensitivity of the MHT, CIM, combined disc, and Carba NP tests was calculated as 0.90, 0.78, 0.84, and 1 and their specificity was calculated as 0.83, 0.83, 0.83 and 0, respectively. According to the gold standard, the predictive power of MHT, CIM, and MAST methods was found to be statistically significant. CONCLUSIONS: There are various methods of carbapenemase detection, including phenotypic and molecular methods. There is no single detection method that is valid and usable in all conditions. Laboratories should choose a suitable carbapenemase detection and confirmation method in line with their needs, economic conditions, and infrastructures. Although the detection of the presence of carbapenemase by molecular methods is fast and reliable, low-cost phenotypic tests can be used in laboratories that do not have this possibility. It is an important advantage that the combined disc method can also determine the enzyme type.

As a Novel Procalcitonin Assay is Architect B∙R∙A∙H∙M∙S PCT; Comparison of Two Commercial Systems.

BACKGROUND: Procalcitonin (PCT) is the precursor structure of the calcitonin hormone with 116 amino acids. The measurement of serum procalcitonin is currently being safely used in community-acquired pneumonia, bacterial peritonitis and sepsis in the diagnosis, decision on the initiation of treatment, and follow-up of the response to treatment. In this study, it is aimed to compare PCT results obtained by the VIDAS PCT that makes measurements by the enzyme-dependent fluorescence (ELFA) method and Architect PCT method, a chemiluminescent microparticle immunoassay (CMIA) that has just been put into use, both of which are B∙R∙A∙H∙M∙S licensed and have method differences. METHODS: Serum samples of 109 patients from different clinics with a PCT request were included in the study. The sera were divided into two groups and the samples were immediately studied with two methods. Cohen's Kappa (κ) coefficient was used to determine concordance between the two methods. Other parameters were analyzed by the paired t-test, and their concordance was evaluated. RESULTS: In the concordance analysis study carried out by considering the significant cutoff value of 0.5 ng/mL in the clinical diagnosis of bacterial infections, the κ value was found to be 0.930, p < 0.001. Concordance was at an excellent level. Upon pairing and analyzing all the results regardless of the cutoff value, the Concordance Coefficient was found to be 0.958 (p < 0.001). It was observed that concordance was at an excellent level. CONCLUSIONS: Upon comparing the patient results obtained as a result of the study, it was observed that the concordance of the methods with each other was excellent. Larger and more comprehensive studies on this issue will be helpful.

The Prevalence of Mixed Genotype Infections in Turkish Patients with Hepatitis C: a Multicentered Assessment.

BACKGROUND: HCV virus infections are one of the major health problems in the world that can cause cirrhosis and liver cancer at a higher rate than other hepatitis data. The aim of this study was to determine the prevalence of mixed infections with different HCV genotypes in Turkey and also to evaluate the current HCV genotype and sub-type distributions by a multicentered assessment. METHODS: The HCV genotype data of 17,578 hepatitis C patients collected from 23 centers from different geographic regions covering all Turkey were collected. The data included information about the HCV genotypes in the last 10 years (between 2007 and 2016), demographic properties of the patients and the methods/systems used to determine the genotypes. RESULTS: Two hundred twenty-eight of the patients (1.3%) had mixed genotype. The most common mixed genotype combination was 1b + 4 (0.83%) followed by 1a + 1b (0.26%). Genotype distribution varies according to geographical regions. However, genotype 1 (82.92%) was the most common genotype in all regions and all years. This was followed by genotype 3 (7.07%) and genotype 4 (5.43%). A variety of methods were used by the centers including sequencing, pyrosequencing, real-time PCR, in-house RFLP, reverse hybridization (LIPA), and hybridization. CONCLUSIONS: Infection with mixed HCV genotypes in Turkey is uncommon. Genotype distribution varies according to geographic regions; the most common genotype 1 is encountered all over the country, while genotypes 3 and 4 are only in some of the centers. Since there is limited information about mixed HCV infection, further investigations are needed to determine the clinical importance of mixed HCV infection.

[Investigation of blaOXA-48-like genes in carbapenemase producing Klebsiella spp. isolates]. / Karbapenemaz üreten Klebsiella pneumoniae suslarinda blaoxa-48-benzeri genlerin arastirilmasi.

The emergence and spread of multi-drug-resistant (MDR), extended-spectrum beta-lactamase (ESBL) producing carbapenem-resistant members of Enterobacteriaceae family has become a worldwide health problem. Carbapenem resistance caused by blaKPC, blaNDM gene regions are sporadic and blaOXA-48 gene region is endemic in our country. The aim of this study was to determine the presence of blaOXA-232, blaOXA-181, blaOXA-162, blaOXA-204, blaOXA-244, blaOXA-163, blaOXA-245 genes in OXA-48 like carbapenemase producing Klebsiella pneumoniae isolates. The isolates used in this study were provided from the Medical Microbiology Laboratory collection of Sakarya University Sakarya Training and Research Hospital. Identification and antibiotic susceptibility tests were determined by the VITEK 2® automated system (biomerieux, France) and the carbapenemase production of isolates was determined by the modified Hodge test. Minimal inhibitor concentration (MIC) values were determined with broth microdilution method. The isolates containing the blaOXA-48-like gene region were identified by real-time polymerase chain reaction (Rt-PCR) method using consensus primers. In "High Resolution Melting Analysis (HRMA)" method carried out by using "Type-it HRM PCR" (Qiagen, Hilden, Germany) kit, isolates which showed a deviation in melting temperatures (Tm) were selected with the suspicion of OXA-48 variant. The sequence analysis (ABI 3500, Applied Biosystems, USA) was carried out to determine which variants were present in these isolates. Compatibility of MIC values was determined between VITEK 2® and the microdilution method with the rate of 82% for imipenem, 77% for meropenem and 90% for ertapenem in carbapenemase-producing K.pneumoniae isolates. In 45 of 100 K.pneumoniae isolates, the blaOXA-48-like gene region was found to be positive by the Rt-PCR method. For the determination of OXA-48 variants, these 45 isolates were evaluated by HRMA method. The sequence analysis revealed that 41 (91.2%) isolates contained blaOXA-48/blaOXA-245 gene regions, while 2 (4.4%) isolates were found to contain blaOXA-181 gene regions and 2 (4.4%) isolates were found to contain blaOXA-244 gene regions. This is the first study to determine OXA-48 and OXA-244 positivity in blaOXA-48-like gene regions in Turkey. As a result of this study, the OXA-48-like gene region was found to be 45%, of which 4.4% had blaOXA-181 and 4.4% had blaOXA-244 gene regions. The detection of blaOXA-48-like gene regions will guide for the selection of antibiotics in critical patient groups.

Detection and Evaluation of Escherichia coli O157:H7 and Shiga-toxin Genes stx1, stx2 in Cattle Meat Samples.

Background: Screening of transmission routes and routine control of the food for foodborne-pathogens are vital in terms of public health. In this study, we aimed to investigate and evaluate the presence of E. coli O157:H7 strains and toxins in the cattle meat samples collected from different markets and butchers. Methods: We collected 116 raw minced cattle beef samples from the supermarkets and the butcher stores. We used bacterial culture-based conventional isolation methods as recommended by the CDC and FDA determination of STEC in the minced cattle beef samples. Then we used PCR to detect stx genes in sorbitol negative E. coli. This way, we indirectly demonstrated the presence of the stx genes in meat samples. Additionally, we used an agglutination test for the detection of E. coli O157:H7. Results: E. coli O157-suspected isolates were found in 17 (14.6%) out of 116 raw minced meat samples examined with tests. STEC stx toxin gene was found in 14 (12.06%) of the sorbitol-negative E. coli isolates tested with real-time PCR method. There was no statistical difference between samples collected from markets and butchers according to STEC stx toxin gene positivity rate. Latex agglutination method performed very poor results in suspected strains compared the PCR results (p < 0.05). Conclusions: Meat products sold in markets and butchers carry low but similar risks for infections and epidemics in our region. In the studies that evaluate the presence of the STEC, agglutination methods cannot be trusted alone and, therefore, this test should be combined with at least one of the conventional microbiological or molecular methods.