Coronaviruses (CoVs) cause a broad spectrum of diseases in domestic and wild animals, poultry, and rodents, ranging from mild to severe enteric, respiratory, and systemic disease, and also cause the common cold or pneumonia in humans. Seven coronavirus species are known to cause human infection, 4 of which, HCoV 229E, HCoV NL63, HCoV HKU1 and HCoV OC43, typically cause cold symptoms in immunocompetent individuals. The others namely SARS-CoV (severe acute respiratory syndrome coronavirus), MERS-CoV (Middle East respiratory syndrome coronavirus) were zoonotic in origin and cause severe respiratory illness and fatalities. On 31 December 2019, the existence of patients with pneumonia of an unknown aetiology was reported to WHO by the national authorities in China. This virus was officially identified by the coronavirus study group as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the present outbreak of a coronavirus-associated acute respiratory disease was labelled coronavirus disease 19 (COVID-19). COVID-19’s first cases were seen in Turkey on March 10, 2020 and was number 47,029 cases and 1006 deaths after 1 month. Infections with SARS-CoV-2 are now widespread, and as of 10 April 2020, 1,727,602 cases have been confirmed in more than 210 countries, with 105,728 deaths.

Antibiotic resistance is one of the most important public health problem and one of the most critical steps in preventing resistance is the monitorization of the resistance. Local, regional and global monitoring enables the spread of antibiotic resistance to be understood more clearly. In this study, it was aimed to evaluate the results of the pilot study for the establishment of molecular-based carbapenem surveillance system in Escherichia coli and Klebsiella pneumoniae isolates and to investigate the carbapenemase epidemiology in Turkey. Hospitals (n= 28) from 26 different statistical level II regions from Turkey were included in the study. The hospitals participated in the study submitted ten carbapenem susceptible and ten carbapenem resistant E.coli and K.pneumoniae isolates to our laboratory that were isolated in two different periiods of six-month either between 1 March-31 August or 1 April-30 September 2019. A total of 509 isolates were collected from 26 of the 28 participating hospitals in the study. Isolates were identified by matrix assisted laser desorptionization-time of flight mass spectrophotometry (MALDI TOF MS) (Bruker Daltonics, Germany) method and antibiotic susceptibility tests for imipenem, meropenem and colistin were studied by broth microdilution. Moreover, susceptibilities to amikacin, amoxicillin-clavulanic acid, ampicillin, aztreonam, cefepime, cefotaxime, ceftazidime, ciprofloxacin, ertapenem, gentamicin, piperacillin-tazobactam, tobramycin and trimethoprim-sulfamethoxazole were determined by disc diffusion method. The resistance genes were investigated in isolates which were found to be phenotypically resistant to carbapenem and colistin, in house method was used to investigate carbapenemase genes and a commercial colistin resistant real-time PCR kit (Biospeedy, Turkey) was used for colistin resistance genes. In total, 493 of the 509 isolates collected from hospitals were identified as E.coli (25.7%, n= 127) and K.pneumoniae (74.3%, n= 366) and included in the study. It was determined that 31% of the isolates evaluated were from community-acquired infections and 69% were either from healthcare-associated infections or from colonization sites. Among the tested isolates, 248 (50.3%) were susceptible to carbapenems and 245 (49.7%) were resistant. The types of carbapenemases in carbapenemase-producing isolates were OXA-48 (52.2%), KPC (16.1%), NDM-1 (15%), OXA-48 + NDM-1 (12.6%), KPC + NDM-1 (2.8%) and VIM (0.5%) and OXA-48+VIM (0.5%). Resistance to colistin was detected in 23.3% of the isolates but mcr1-8 genes were not detected. It was found that all colistin resistant isolates are resistant to at least one of the carbapenems. The importance of a molecular-based antimicrobial resistance surveillance system in our country was demonstrated with this pilot study. It is thought that continuous monitoring of these epidemiological features will contribute to the management of infections due to carbapenemase-producing organisms.

Background: Brucellosis is a worldwide zoonotic disease that causes serious public health problems. This study aimed to identify Brucella strains isolated from various clinical samples by conventional and molecular methods and to determine antimicrobial susceptibilities against doxycycline (DOX), streptomycin (STR), ciprofloxacin (CIP) and rifampicin (RIF) by the gradient strip (E test) test method. Methods: A total of 87 Brucella strains isolated from various clinical specimens between 2004 and 2018 were included in this study. While four of the 87 strains included in the study were identified only at the genus level, the remaining 83 strains were identified at the species level by the Real-Time Multiplex PCR (M-RT-PCR) method and conventional methods were used for biotyping. Results: According to molecular identification results, 83 strains were identified as B. melitensis by the M-RT-PCR method, with 82 strains identified as Brucella melitensis biovar (bv) 3 and one as B. melitensis bv 1 according to the conventional biotyping method. Among the antibiotics studied, CIP was found to be the most active agent according to the minimum inhibitory concentrations (MIC)₉₀ values. This was followed by DOX and STR, respectively. While all of the isolates were sensitive to CIP, DOX and STR, 18 (20.7%) strains were found to be moderately susceptible to RIF, with the highest values of MIC₅₀ and MIC₉₀. Conclusions: In our study, all strains were identified as B. melitensis. DOX, STR, CIP and RIF used in the treatment of brucellosis were found to be effective.

Background and Aims: Sickle cell disease (SCD) is a chronic hemolytic anemia that may be life-threatening due to multisystemic effects. Identification of the factors which affect the pathophysiology of the disease is important in reducing mortality and morbidity. This study aimed to determine gut microbial diversity in children and adolescents with SCA compared with healthy volunteers and to evaluate the clinical impact of microbiota. Materials and Methods: The study included 34 children and young adolescents with SCD and 41 healthy volunteer participants. The microbiome was assessed by 16S rRNA sequencing in stool samples. Laboratory parameters of all participants, such as complete blood count and C-reactive protein values and clinical characteristics of SCD patients, were determined and compared, as well as clinical conditions of the patients, such as vascular occlusive crisis and/or acute chest syndrome, frequency of transfusions, intake of penicillin, hydroxyurea, and chelation therapy were recorded. Results: White blood cell count, hemoglobin, immature granulocyte and C-reactive protein levels were significantly higher in the patient group (P<0.05). Microbiota analysis revealed 3 different clusters among subjects; controls and 2 clusters in the SCD patients (patient G1 and G2 groups). Bacteroides spp. were more prevalent, while Dialester spp. and Prevotella spp. were less prevalent in SCD compared with controls (t=2.142, P<0.05). Patient G2 (n=9) had a higher prevalence of Bacteroides and a lower prevalence of Prevotella than patient G1 (n=25). Conclusion: In our study, there was a difference between SCD patients and the control group, while 2 different microbiota profiles were encountered in SCD patients. This difference between the microbiota of the patients was not found to affect the clinical picture (such as vascular occlusive crisis, acute chest syndrome).

Toxoplasmosis caused by Toxoplasma gondii (T. gondii), which is an obligatory intracellular parasite, is a worldwide zoonotic parasitic disease. In this study, results of T. gondii test conducted between January 2009 and May 2019 were analysed. This study aimed to evaluate the results of T. gondii test of patients who were admitted to the General Directorate of Public Health, National Parasitology Reference Laboratory between 2009 and 2019. The results of anti-T. gondii IgG, IgM, IgG avidity and Sabin-Feldman dye tests (SFDT), which are used to detect the presence of T. gondii, were examined. ELISA was used for anti-T. gondii IgG, IgM and IgG avidity tests. SFDT, which is the reference test in the diagnosis of T. gondii, is still the gold standard. In addition to laboratory analyses, information on gender, age, city of origin, year distribution of all cases and type of sample sent was also collected. Of the 2.778 patients evaluated, 25.4% were males and 74.6% were females. Moreover, 47.1% and 10.2% of the patients were positive for anti-T. gondii IgG and anti-T. gondii IgM antibodies, respectively. In SFDT, 1.228 (52%) patients were found to be positive, including 319 (59.4%) of 537 men and 909 (49.8%) of 1.824 women. In this 10-year study, the most common seropositivity titre of SFDT was at the level of 1/64. In our study, IgG levels were found to be positive in all cases in which IgG avidity was studied when all the cases in which all three of the anti-T. gondii IgG, IgM and IgG avidity tests were studied together in one patient were evaluated. In addition, of the 293 patients with positive anti-T. gondii IgG, 62.8% had high avidity, 24.2% had a limit value and 13% had a low avidity. In cases involving both mother and baby, anti-T. gondii IgG and IgM seropositivity rates were 80% and 5% for both, respectively. These high rates support the transfer of antibodies from the mother to the baby. Regarding the distribution of provinces from which the samples originated, the highest number of cases came from Ankara (80.7%). Blood is the most predominant sample, followed by cerebrospinal fluid. T. gondii maintains its importance in public health, owing to its high positivity rates. This study, in which 10-year data were collected, showed that despite an increase in awareness, high seropositivity still continues. Therefore, systematic collection and evaluation of laboratory analysis results for toxoplasmosis diagnosis will contribute in taking control measures.