Managing Viral Emerging Infectious Diseases via Current and Future Molecular Diagnostics.

Emerging viral infectious diseases have been a constant threat to global public health in recent times. In managing these diseases, molecular diagnostics has played a critical role. Molecular diagnostics involves the use of various technologies to detect the genetic material of various pathogens, including viruses, in clinical samples. One of the most commonly used molecular diagnostics technologies for detecting viruses is polymerase chain reaction (PCR). PCR amplifies specific regions of the viral genetic material in a sample, making it easier to detect and identify viruses. PCR is particularly useful for detecting viruses that are present in low concentrations in clinical samples, such as blood or saliva. Another technology that is becoming increasingly popular for viral diagnostics is next-generation sequencing (NGS). NGS can sequence the entire genome of a virus present in a clinical sample, providing a wealth of information about the virus, including its genetic makeup, virulence factors, and potential to cause an outbreak. NGS can also help identify mutations and discover new pathogens that could affect the efficacy of antiviral drugs and vaccines. In addition to PCR and NGS, there are other molecular diagnostics technologies that are being developed to manage emerging viral infectious diseases. One of these is CRISPR-Cas, a genome editing technology that can be used to detect and cut specific regions of viral genetic material. CRISPR-Cas can be used to develop highly specific and sensitive viral diagnostic tests, as well as to develop new antiviral therapies. In conclusion, molecular diagnostics tools are critical for managing emerging viral infectious diseases. PCR and NGS are currently the most commonly used technologies for viral diagnostics, but new technologies such as CRISPR-Cas are emerging. These technologies can help identify viral outbreaks early, track the spread of viruses, and develop effective antiviral therapies and vaccines.

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).

Diagnosis of monkeypox virus - An overview.

Monkeypox is an emerging zoonotic disease caused by monkeypox virus which is a DNA virus. The virus is transmitted to humans as a result of close contact with infected animals, infected humans or contaminated inanimate objects. The disease has a incubation period usually 7-14 days and it causes fever, headache, fatigue, myalgia, widespread body aches, swelling in lymph nodes and skin lesions. It may be difficult to distinguish monkeypox on the basis of clinical presentation alone, especially for cases with an atypical appearance, because of the various conditions that cause skin rashes. Testing should be offered to anyone who falls under the suspected case definition for monkeypox infection. Suitable samples are surface lesion and/or skin materials such as exudates swabs and crusts. Laboratory confirmation of specimens from suspected case is done using nucleic acid amplification testing, such as real-time or conventional polymerase chain reaction. Confirmation of MPXV infection should consider clinical and epidemiological information. Positive detection using an OPXV PCR assay followed by confirmation of MPXV via PCR and/or sequencing, or positive detection using MPXV PCR assay in suspected cases indicates confirmation of MPXV infection. Genetic sequence data (GSD) provide information on the origin and epidemic and characteristics of cases. There is a need to develop a more global and effective laboratory network for this emerging zoonosis, as well as to strengthen laboratory capacity, and international specimens referral capacities.

[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.

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.

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.

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.

Vaccine hesitancy and refusal among parents: An international ID-IRI survey.

INTRODUCTION: Although vaccines are the safest and most effective means to prevent and control infectious diseases, the increasing rate of vaccine hesitancy and refusal (VHR) has become a worldwide concern. We aimed to find opinions of parents on vaccinating their children and contribute to available literature in order to support the fight against vaccine refusal by investigating the reasons for VHR on a global scale. METHODOLOGY: In this international cross-sectional multicenter study conducted by the Infectious Diseases International Research Initiative (ID-IRI), a questionnaire consisting of 20 questions was used to determine parents' attitudes towards vaccination of their children. RESULTS: Four thousand and twenty-nine (4,029) parents were included in the study and 2,863 (78.1%) were females. The overall VHR rate of the parents was found to be 13.7%. Nineteen-point three percent (19.3%) of the parents did not fully comply with the vaccination programs. The VHR rate was higher in high-income (HI) countries. Our study has shown that parents with disabled children and immunocompromised children, with low education levels, and those who use social media networks as sources of information for childhood immunizations had higher VHR rates (p < 0.05 for all). CONCLUSIONS: Seemingly all factors leading to VHR are related to training of the community and the sources of training. Thus, it is necessary to develop strategies at a global level and provide reliable knowledge to combat VHR.

Investigation of intestinal microbiome in chronic spontaneous urticaria patients.

BACKGROUND: Chronic urticaria is a disorder characterized by itchy erythematous plaques with edema lasting 6 weeks or more. The prevalence is 1%, and two thirds of these cases are "chronic spontaneous urticaria (CSU)." Drugs, food, infections, and systemic diseases may be etiologic factors for CSU, although it may be idiopathic. OBJECTIVES: The aim of this study was to compare the diversity and distribution of the intestinal microbiome in CSU patients with that of healthy individuals. The hypothesis was to determine the probable association of intestinal microbiome with CSU. METHODS: This study was conducted in Sakarya University Training and Research Hospital, Department of Dermatology. In this study, 20 CSU patients and 10 healthy volunteers were included. Stool samples were collected from all participants. 16S RNA sequencing and bioinformatic analysis were performed after isolation of DNA isolation from all samples. RESULTS: Diversity in microorganisms, stool pH averages, Bristol scores, and the ratio of Firmicutes/Bacteroidetes were the significant changes between the two groups. LIMITATIONS: Due to high cost involved in microbiota studies, only a limited number of patients and volunteers participated. CONCLUSION: The alteration in the intestinal microbiota (dysbiosis) may be an essential factor for CSU development and may explain idiopathic cases.

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.

Investigation of In-vitro Efficacy of Intravenous Fosfomycin in Extensively Drug-Resistant Klebsiella pneumoniae Isolates and Effect of Glucose 6-Phosphate on Sensitivity Results.

BACKGROUND: The aim of this study was to determine the in vitro efficacy of intravenous (IV) fosfomycin against extensively drug-resistant Enterobacterales strains and the effect of glucose 6-phosphate (G6-P) on sensitivity results. MATERIAL METHOD: Thirty-two extensively drug-resistant Klebsiella pneumonia strains were included in the study. Detection of the carbapenemase genes was performed using the Gene-Xpert® System Carba R® kit. Susceptibility of IV fosfomycin was assessed using the agar dilution method. The agar dilution method was repeated using Muller-Hinton Agar medium without G6-P to assess the effect of G6-P on sensitivity results. RESULTS: All strains in the study produced carbapenemases and were resistant to all drugs tested, including carbapenems, piperacillin-tazobactam, ceftriaxone, and ceftazidime. Fosfomycin resistance was detected in 3 (9.3%) strains. When the sensitivity test was repeated without G6-P, fosfomycin resistance was detected in 82.7% of the fosfomycin-susceptible strains. The Gene-Xpert® System showed NDM-1 in 46.8%, OXA-48 in 18.7%, KPC in 3.1%, and NDM-1 + OXA-48 in 21.8% of the strains. OXA-48 was detected in one of the resistant strains, and none of the viable genes were detected in two of the resistant strains. CONCLUSION: This study shows that IV fosfomycin is a potentially important treatment alternative for infections caused by common resistant strains. Accurate results may not be obtained unless G6-P is used in the agar dilution method for in vitro susceptibility studies of fosfomycin.

Major and minor subgroup profile of blood in patients receiving multiple transfusions and donors.

OBJECTIVE: It was aimed to profile the blood subgroups of our region and to reveal the prevalence of auto/alloimmune sensitization in patients who had to undergo multiple erythrocyte transfusions and to establish the sensitization profile by screening major and minor subgroups. MATERIALS AND METHODS: In this study, the distribution of ABO and Rh system major subgroups was studied in 100 donor blood. As the patient group, 50 patients who received three or more red blood cell transfusions were included. In addition to this group, Kell, Lewis, Duffy blood group systems were studied. RESULTS: According to the ABO system, 35% of the donors were in O, 33% in A, 17% in AB, and 15% in B. According to the Rh system, 75% is Dvi positive. Rh system is 99% e positive and 33% E positive in major subgroups and Kell1 positivity is 8%. In the patient group, 22% D(-) was determined compared to Rh blood group. Among the major subgroups of Rh, C was 68%, E was 14%, c was 76%, and e positivity was found to be 100%. The Kell1 negativity rate is 96%. The highest negativity was found in 86% Lea antigen in Lewis system, in 36% S antigen in MNS system, 34% Fyb antigen in Duffy system, and 24% Jka antigen in Kidd system. When inappropriate blood is given for any antigen, a double population is formed. The double negativities we detected in our study occurred as follows according to blood group systems: E 18%, C 12%, c 8%, Cw 2%, Kell 1 2%, M 8%, N 4%, S 18%, s 6%, Fya 8%, Jka 6%, Jkb 22%. Indirect Agglutination Test (IAT) was negative in all patients. CONCLUSION: IAT negativity in all patient groups suggests that we do not develop alloimmunization, but the high rates of double population suggest a high risk of alloimmunization.

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.

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.

Evaluation of the presence of SARS-COV-2 in the vaginal fluid of reproductive-aged women.

OBJECTIVES: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is mainly transmitted through respiration and direct contact. The status of the infection in the female genital system is still unknown. The study aimed to evaluate whether SARS-CoV-2 is present in the vaginal fluid of women with COVID-19 infection in reproductive period. MATERIAL AND METHODS: Women who were between the ages of 18-50 years and clinically confirmed to have COVID-19 infection at our hospital between 20 April-31 May 2020 were included in the study. Women who were in their menstrual cycle during the study and who had a known cervical intraepithelial lesion and/or cancer, sexually transmitted disease and history and/or symptoms of vaginitis were excluded from the study. In patients in whom no pathology was detected during the examination, a sample was taken from the vaginal fluid for PCR by using Dacron tip swab. Analysis was performed with Genesig Real-Time PCR COVID-19 kit (Primer Design, England). RESULTS: Eighteen women who were in reproductive period and diagnosed with severe COVID-19 pneumonia were included in the study. The mean age of the patients was 38.16 ± 8.54. None of the patients were in their menopause period. The clinical symptoms of these women were similar to those of confirmed severe COVID-19 cases. SARS-CoV-2 was found to be negative in the samples taken from the vaginal fluid in all patients. CONCLUSIONS: SARS-CoV-2 virus was not detected in the vaginal fluid of the patients who tested positive for COVID-19 in reproductive period.

Managing adult patients with infectious diseases in emergency departments: international ID-IRI study.

We aimed to explore factors for optimizing antimicrobial treatment in emergency departments. A single-day point prevalence survey was conducted on January 18, 2020, in 53 referral/tertiary hospitals in 22 countries. 1957 (17%) of 11557 patients presenting to EDs had infections. The mean qSOFA score was 0.37 ± 0.74. Sepsis (qSOFA ≥ 2) was recorded in 218 (11.1%) patients. The mean qSOFA score was significantly higher in low-middle (1.48 ± 0.963) compared to upper-middle (0.17 ± 0.482) and high-income (0.36 ± 0.714) countries (P < 0.001). Eight (3.7%) patients with sepsis were treated as outpatients. The most common diagnoses were upper-respiratory (n = 877, 43.3%), lower-respiratory (n = 316, 16.1%), and lower-urinary (n = 201, 10.3%) infections. 1085 (55.4%) patients received antibiotics. The most-commonly used antibiotics were beta-lactam (BL) and BL inhibitors (n = 307, 15.7%), third-generation cephalosporins (n = 251, 12.8%), and quinolones (n = 204, 10.5%). Irrational antibiotic use and inappropriate hospitalization decisions seemed possible. Patients were more septic in countries with limited resources. Hence, a better organizational scheme is required.

[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.

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.

Investigation of the In Vitro Effectiveness of Aztreonam/Avibactam, Colistin/Apramycin, and Meropenem/Apramycin Combinations Against Carbapenemase-Producing, Extensively Drug-Resistant Klebsiella pneumoniae Strains.

This study aimed at investigating the in vitro effectiveness of aztreonam/avibactam, colistin/avibactam, colistin/apramycin, and meropenem/apramycin combinations against carbapenemase-producing, extensively drug-resistant (XDR) Klebsiella pneumoniae strains. This study evaluated 38 carbapenem-resistant, carbapenemase-producing, and XDR K. pneumoniae strains. The checkerboard method was used to examine the efficacy of aztreonam/avibactam, and meropenem/apramycin combinations in all strains and the colistin/apramycin combination in colistin-resistant strains (n = 26). It was found that when used alone, aztreonam and avibactam had high minimum inhibitory concentration values in all strains and that all strains were resistant to aztreonam. Nevertheless, the aztreonam/avibactam combination was found to have a synergistic effect against all strains. Apramycin alone was effective against 30 K. pneumoniae strains (79%); however, 8 strains (21%) were found to be resistant. In the synergy testing of 26 colistin-resistant strains with the checkerboard method, the colistin/apramycin combination was found to have a synergistic effect against 4 strains (15.3%), an antagonistic effect against 8 strains (30.7%), and an additive effect against 14 strains (54%). By comparison, the meropenem/apramycin combination had a synergistic effect against 20 strains (52%) and an additive effect against 12 strains (31%). The aztreonam/avibactam combination showed a high in vitro synergistic effect on carbapenemase-producing and XDR K. pneumoniae strains, such as Metallo-ß-lactamase, and provided good prospects for the successful treatment. The meropenem/apramycin combination was also highly synergistic. The synergistic effects were low for the colistin/apramycin combination that was tested on colistin-resistant strains. However, it is promising that apramycin has low minimal inhibitory concentration values.