Q-Scoring System for the Evaluation of the Superficial Wound Swab Samples: A Clinical Microbiological Aspect.

Purpose: Wound swab cultures are frequently requested from patients suspected of having a wound infection. The quality of the sample should also be evaluated by performing a Gram-stained microscopic examination. "Q-scoring system" is not widely used and the literature on the subject is limited. Methods: A total of 4648 wound swab samples were evaluated. Samples with a Q-score of "0" were considered as "poor quality samples", and those with a score of " ≥ 1" were classified as "good quality samples". Microorganisms grown in the culture of samples that scored above one were identified by mass spectrometry, and antimicrobial susceptibility testing was performed. Results: Gram stain results were found to be consistent with the culture result in 57.10% (n = 1078) of and inconsistent with the culture result in 42.90% (n = 813) of the samples. The number of samples with Q-scores one, two, and three among the 813 samples was 62, 29, and 722, respectively. The value observed in Q3 was found to be statistically significantly higher than the values observed in Q1 and Q2 (p < 0.05). Samples sent from surgical departments (61.92%) with a Q-score of ≥ 1, were statistically significant compared to internal medicine departments (p < 0.0001). There was no significant difference between samples sent from intensive care units and those sent from other inpatient services. For both groups with Q-scores ≥ 1 and "0" similar microorganisms were identified. Conclusion: As a conclusion, the Q-scoring system will provide a common language between the laboratory and the clinic, especially by standardizing the evaluation of wound swab samples.

Investigation of the presence of Capnophilic bacteria in routine urine cultures.

Capnophilic Escherichia coli (CEC) strains are rarely isolated from urinary tract infections (UTIs). The purpose of this research was to look into the incidence and traits of the CEC strains that cause UTIs. Nine (0.11%) epidemiologically unrelated CEC isolates with varying antibiotic susceptibility patterns were identified from patients with various co-morbidities after the evaluation of 8500 urine samples. Three of these strains belonged to the O25b-ST131 clone, and none of them possessed the yadF gene. Due to adverse incubation conditions, CEC isolation is difficult. Although rare, capnophilic incubation of urine cultures may be considered particularly for patients with underlying predisposing conditions.

Comparison of a novel antigen detection test with reverse transcription polymerase chain reaction assay for laboratory diagnosis of SARS-CoV-2 infection.

Molecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR) in respiratory specimens is considered the gold standard method. This method is highly sensitive and specific but it has some limitations such as being expensive and requiring special laboratory equipment and skilled personnel. RapidFor™ Antigen Rapid Test Kit is a commercially available Ag-RDT which is produced in Turkey and designed to detect the nucleocapsid antigen of SARS-CoV-2 in nasopharyngeal swab samples. The aim of this study was to evaluate the performance of this novel SARS-CoV-2 antigen detection considering the RT-PCR method as the gold standard. Four hundred forty-four nasopharyngeal swab samples which were collected from the patients who met clinical criteria of COVID-19 from ten centers in Turkey between September 2020 and February 2021 were included in the study. All the nasopharyngeal swab samples were tested for SARS-CoV-2 RNA using commercial RT-PCR kits (Bioeksen and A1 Lifesciences, Istanbul, Turkey) according to the manufacturer's instructions. Viral loads were assessed according to the cycle threshold (Ct) values. RapidFor™ SARS-CoV-2 antigen test (Vitrosens Biotechnology, Istanbul, Turkey) was used to investigate the presence of SARS-CoV-2 antigen in all samples following the manufacturer's instructions. Out of 444 nasopharyngeal swab samples tested, 346 (77.9%) were positive and 98 (22.1%) were negative for SARS-CoV-2 RNA by RTPCR. Overall sensitivity of the RapidFor™. Antigen Rapid Test Kit was 80.3% whereas specificity was found to be 87.8%. Positivity rate of rapid antigen test in samples with Ct values over 25 and below 30 was 82.7%, while it increased to 95.7% in samples 20 ≤ Ct < 25 and reached 100% in samples with Ct values below 20. RapidFor™ SARS-CoV-2 Ag test might be a good choice in the screening of symptomatic and asymptomatic patients and their contacts for taking isolation measures early, with advantages over RT-PCR as being rapid, easy and being applicable in every laboratory and even at point of care.

[Evaluation of the Epidemiological, Clinical and Radiological Features of Pneumonia Cases Caused by Mycoplasma pneumoniae in Childhood]. / Çocukluk Çaginda Mycoplasma pneumoniae'nin Etken Olarak Saptandigi Pnömoni Olgularinin Epidemiyolojik, Klinik ve Radyolojik Özelliklerinin Degerlendirilmesi.

The current study aimed to investigate the clinical, laboratory and radiological findings of the pneumonia cases in children that were confirmed as M.pneumoniae by polymerase chain reaction (PCR) testing and to reveal the factors that can be decisive in the diagnosis. Seventy-seven children were included in this study. The median age of the patients was 31 months (1 month-17 years 4 months). The 63.6% of the patients were younger than five years of age, 53.2% were girls and 46.8% were boys. During the eight-year research period, the frequency of M.pneumoniae in the patients hospitalized with the diagnosis of pneumonia was found to be 3.1%. The rate of M.pneumoniae as the underlying factor of pneumonia was found to be statistically significantly lower in patients aged 0-60 months compared to the patients aged 61-216 months. In patients with M.pneumoniae accompanied by viruses, the age group was more likely to between 0-60 months. The most common symptoms were cough (96.1%) and fever (74%). Physical examinations revealed that 70.1% of the patients had rales, 63.6% had tachypnea, 45.5% had oropharyngeal hyperaemia, 35.1% had subcostal-intercostal retraction, 31.2% had long expiration period, 26% had rhonchus, 24.7% had decrease in breath sounds, 15.6% had cervical lymphadenopathy, 13% had tachycardia, 3.9% had otitis media, 3.9% had tonsil hypertrophy and 2.6% had a maculopapular rash. The rate of hypoxemia was found to be 42.2%. When the physical examination findings of patients with only M.pneumoniae detected in multiplex PCR analysis and those with accompanying viruses in M.pneumoniae were compared, tachypnea, oropharyngeal hyperemia and decreased breath sounds were found to be statistically significantly higher in patients with M.pneumoniae only. Retraction was detected more frequently in patients with accompanying viruses. When the laboratory results of the patients were evaluated according to age, leukocytosis was detected in only 18.2% of the patients, while the erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) were found to be high in 75% and 85.7% of the patients, respectively. In the multiplex PCR analysis, the CRP values of the patients with only M.pneumoniae were found to be higher than the patients with accompanying viruses. M.pneumoniae was accompanied by viruses at the rate of 40.3%. The most common accompanying viruses were rhinovirus, adenovirus, bocavirus and metapneumovirus. The 55.8% of the patients had lobar-segmental consolidation, 46.8% had parahilar-peribronchial thickening, 18.2% had atelectasis, 11.7% had pleural effusion, 9.1% had increase in reticulonodular density, 6.5% had lymphadenopathy whereas no abnormality was observed in 5.2% of them. No diffuse interstitial involvement was recorded. The CRP value of the patients who had lobar segmental consolidation which was detected through chest X-rays were statistically higher than those without consolidation. In multiplex PCR analysis, the rate of parahilar-peribronchial thickening detected in chest X-ray findings was found to be higher in patients with M.pneumoniae accompanied by viruses compared to those with only M.pneumoniae. The rate of the patients who were given empirical antibiotics against atypical agents was 45.5%. The rate of empirically administered antibiotic treatment for atypical agents after being hospitalization was higher in patients diagnosed with only M.pneumoniae compared to patients with M.pneumoniae and viruses. One patient (1.3%) died. As there are no typical clinical, laboratory or radiological findings specific to M.pneumoniae pneumonia, all of the findings should be assessed as a whole to establish a diagnosis. Besides, for the detection of M.pneumoniae, diagnostic tests which are cost effective, with rapid results and are capable of distinguishing colonisation from active infection should be developed.

[Interferon Gamma Release Assay Request Indications: From Laboratory to Clinical Perspective]. / Interferon Gama Salinim Test Istemi Endikasyonlari: Laboratuvardan Klinige Bakis Açisi.

Tuberculosis is a re-emerging infectious disease that causes high morbidity and mortality worldwide and remains a major health threat in many parts of the world. With the increase in the incidence of HIV-positive/AIDS patients and immunocompromised individuals, accurate and timely diagnosis of latent TB (LTB) and active TB (ATB) has gained great importance. The aim of this study was to investigate the rationale lying behind interferon gamma release assay (IGRA) requests for patients applying to various clinics of a tertiary care hospital. In the study, 2905 IGRA tests requested in two years period were analyzed retrospectively. The IGRA test positivity rates were recorded and analyzed by linking with the requesting departments and indications. IGRA test positivity was determined in 503 cases (17.31%). IGRA test positivity rates were above 20% in samples sent from general surgery, pulmonology, nephrology, and transplantation departments, respectively. At all, 54.17% of the cases from whom IGRA requests were made constituted the first group of "pre-treatment investigation", and the positivity rate in this group was 12.96%. The positivity rate was highest [163 (28.69%)] in the patient group from whom the test was requested with the suspicion of TB. As a conclusion, until today, there is no study in which IGRA test requests are evaluated in terms of clinics. In this respect, this study is thought to be important. It is also desired to highlight that it is important for each country to develop its specific guidelines, country specific indications for IGRA test requests. Multi-centered studies are also essential for a global suggestion.

Medically important Candida spp. identification: an era beyond traditional methods.

BACKGROUND: Candida infections are gaining more attention for the last few decades so diagnostic tools are very important for early diagnosis. Conventional identification of yeasts is time-consuming, molecular methods are more complicated and relatively expensive gold-standard methods. Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) was put into the market due to its speed and high accuracy. The aim of this study was to evaluate the performance of corn meal tween-80 agar (CMTA), CHROMagar Candida medium, and MALDI-TOF MS and to compare the obtained results with DNA sequencing. METHODS: The CHROMagar Candida medium, CMTA, and MALDI-TOF MS Biotyper System were used to test 416 isolates. The isolates with discrepant results by at least one of the three methods were subjected to sequence analysis. RESULTS: The identification results of the 351 (%84.4) were compatible with all three methods. When compared to the sequencing results, the most accurate results were obtained by the MALDI-TOF MS, especially for rare Candida species. DISCUSSION: MALDI-TOF MS is found to be the most accurate identification tool for clinically important Candida strains. CMTA alone should not be used for the final identification of Candida species and the chromogenic medium should always be considered presumptive.

Antibody response to two doses of inactivated SARS-CoV-2 vaccine (CoronaVac) in kidney transplant recipients.

BACKGROUND: Coronavirus Disease-19 (COVID-19) has high mortality in kidney transplant recipients (KTR), and vaccination against severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is vital for this population. Although the humoral response to messenger RNA vaccines was shown to be impaired in KTR, there is a lack of data regarding the antibody response to inactivated vaccines. We investigated the antibody response to two consequent doses of the inactivated SARS-CoV-2 vaccine (CoronaVac; Sinovac Biotech, China). METHODS: A total of 118 patients from two centers were included. The levels of anti-SARS-CoV-2 immunoglobulin-G antibodies against the nucleocapsid and spike antigens were determined with enzyme immunoassay (DIA.PRO; Milano, Italy) before the vaccine and one month after the second dose of the vaccine. Thirty-three patients were excluded due to antibody positivity in the serum samples obtained before vaccination. RESULTS: Eighty-five patients, 47 of whom were female, with a mean age of 46 ± 12, were included in the statistical analysis. The maintenance immunosuppressive therapy comprised tacrolimus (88.2%), mycophenolate (63.6%), and low-dose steroids (95.3%) in the majority of the patients. After a median of 31 days following the second dose of the vaccine, only 16 (18.8%) patients developed an antibody response. The median (IQR) antibody level was 52.5 IU/ml (21.5-96). Age (48 vs. 38, p = .005) and serum creatinine levels (1.14 vs. 0.91, p = .04) were higher in non-responders and were also found to be independently associated with the antibody response (odds ratio (OR): 0.93, p = 0.012 and 0.15, p = 0.045, respectively) in multivariate analysis. CONCLUSION: In this study, we found the antibody response to the inactivated vaccine to be considerably low (18.8%) in KTR. Increased age and impaired renal function were associated with worse antibody response. Based on the knowledge that mRNA vaccines yield better humoral responses, this special population might be considered for additional doses of mRNA vaccination.

An unusual course of SARS-CoV-2 infection: Challenging diagnosis of Guillain-Barré Syndrome.

COVID-19, caused by severe acute respiratory syndrome coronavirus-2, typically presents with respiratory symptoms and fever, but still a variety of clinical presentations have been reported. In this study, it was aimed to report a case of COVID-19 with an atypical presentation and an atypical course. As well, the recovery phase was complicated with GBS and consequently cytomegalovirus infection. It should be kept in mind that patients with COVID-19 severe disease need to be followed for neurological and other complications which may arise during the course of critical illness.

High mobility group box-1 levels may be associated with disease activity of Behcet's disease

BACKGROUND: High mobility group box- 1 (HMGB- 1) is a nuclear protein acting as a proinflammatory molecule. The serum HMGB- 1 levels were found elevated in chronic inflammatory diseases. In this cross-sectional study, serum HMGB- 1 levels in Behcet's disease (BD) patients and healthy controls (HC) were studied. Also, its association with disease activity scores and clinical findings were evaluated. METHODS: Ninety BD patients and 50 age-sex matched HC were included in the study. Disease activity scores were assessed by Behcet Disease Current Activity Form (BDCAF) and Behcet Syndrome Activity Score (BSAS). Serum HMGB- 1 levels were measured using a commercial ELISA kit. A p value of < 0.05 was considered to be statistically significant. RESULTS: Serum HMGB- 1 levels were significantly higher in BD than in HC (43.26 pg/mL and 16.73 pg/mL; p < 0.001, respectively). Serum HMGB- 1 levels were statistically significantly associated with presence of erythema nodosum (EN) and genital ulcers in the last one month prior to recruitment (p = 0.041 and p < 0.001, respectively). BDCAF and BSAS scores were positively correlated with serum HMGB- 1 level ( p = 0.03 and p = 0.02, respectively). DISCUSSION: HMGB - 1 may play a role in the development of BD. Also, due to its positive correlation with disease activity indices, it can be used as a novel disease activity parameter in BD.

[Direct Identification of Microorganisms from Positive Blood Cultures by MALDI-TOF MS Using an in-House Tween® 80 Method: Experimental and Clinical Study]. / "In-House" Tween® 80 Yöntemi ile Pozitif Kan Kültürlerinden Mikroorganizmalarin MALDI-TOF MS Yöntemi ile Dogrudan Tanimlanmasi: Deneysel ve Klinik Çalisma.

It has been reported that direct identification from blood culture bottles with positive signals and reporting the results to the clinics earlier has positive effects on mortality and morbidity. Extraction methods especially using detergents are used for the direct identification from the bottles which give positive signal. For this purpose, in-house methods developed based on the usage of saponin are widely available in the literature. In this study, it was aimed to develop a simple, easy-to-apply and reliable protocol for identifying the agent directly from the blood culture bottle that gives positive signal with the use of detergent Tween® 80, and to study the obtained protocol in clinical samples in a routine microbiology laboratory and to evaluate the results. The study was carried out in two stages, the experimental stage where the method was developed and the clinical stage where the method was applied. In the experimental stage, blood culture bottles were created with standard strains and isolates previously diagnosed with the 16S rRNA method. 10% solution of Tween® 80 was prepared with distilled water. 1 ml sample was transferred from the bottle that gave positive signal to the microcentrifuge tube, 100 µl of 10% solution of Tween® 80 was added, vortexed for 10 seconds and then incubated for 5 minutes at room temperature. The tubes were centrifuged for 5 min at 14.000 rpm, the supernatant was discarded and the pellet was washed with 1 ml of distilled water and centrifuged at 14.000 rpm for 5 minutes in three times. Samples taken from the pellets were rubbed on the slide and dried on air. Firstly, 1 µl of 70% formic acid, then 1 µl, of matrix solution was added and it was used after drying. In the second stage of the study, the method was applied to the 502 vials giving positive signal in the Microbiology Laboratory of Ankara University Faculty of Medicine Ibni Sina Hospital between 17 April 2018-31 August 2018 and the results were compared with the subculture results. The results obtained at the end of extraction in the experimental stage were compared with the subculture results and no statistical difference was found. In 383 (82.9%) bottles among 462 (92.1%) bottles with monomicrobial positive cultures, compatible results with the subculture results were obtained. Of the microorganisms correctly identified, 350 (91.3%) were bacteria and 33 (8.7%) were fungi. On the other hand, 216 (56.4%) of the bacteria were gram positive and 134 (34.9%) of them were gram negative bacteria. At least one microorganism was correctly identified in 19 (47.5%) of 40 (7.9%) bottles with polymicrobial blood cultures. Their distribution was gram negative (n= 10) and gram positive (n= 8) and yeast (n= 1). No microorganisms were identified in six bottles with polymicrobial cultures. According to the results, we believe that this in-house method developed using Tween® 80 will be a routinely applicable method for blood culture bottles that give positive signal in microbiology laboratories and it will contribute to the early diagnosis.

Successful treatment of COVID-19 infection in a patient with tracheostomy.

Coronavirus disease 2019 (COVID-19) has been demonstrated to be the cause of emerging atypical pneumonia. In patients with tracheostomy, coronavirus hypothetically coexists with well-known bacterial agents. A 61-year-old male patient with tracheostomy was admitted to the hospital with dyspnea, fever and increased tracheal secretions. Laboratory findings revealed lymphopenia and elevated C-reactive protein and procalcitonin levels. Chest computed tomography showed consolidation areas and ground-glass opacities more prominent in subpleural areas. Although; two consecutive RT-PCR analyses of combined nasopharengeal/oropharengeal swabs were found to be negative for SARS-CoV-2 RNA, positivity was reported for endotracheal aspirate (ETA) sample. Significant growth of Pseudomonas aeruginosa and Stenotrophomonas maltophilia was detected in the bacterial culture of ETA sample. In conclusion, clinical samples for SARS-CoV-2 should be obtained through the lower respiratory tract, if possible and if upper airway samples are negative. To the best our knowledge, our paper is the first report of the patient with tracheostomy who was treated successfully for COVID-19.

[Evaluation of blood culture practices: Use of system (Epicenter) data]. / Kan kültürü uygulamalarinin degerlendirilmesi: Isletim sistemi (Epicenter) verilerinin kullanimi.

Sepsis is a serious clinical problem and estimated to be responsible for 18 million annual deaths worldwide. Therefore, the use and the rapid processing of blood cultures are important for the transition from empiric therapy to directed therapy. The aim of this study was to assess the best blood culture practices in Turkey. We have examined the collection practices and techniques at four different hospitals, and a total of 165.443 blood culture bottles were evaluated (2013-2015). At the preanalytical phase most of the data which were important and which could support hospital quality systems/practices were not entered into the HIS and EpiCenter system. At the analytical phase loading of the bottles and removal of positive bottles primarily occurred between 6:00 and 9:00 AM but the positivity rate of the bottles showed a homogeneous distribution throughout the day. In other words, there were significant delays at processing positive blood culture bottles related to laboratory workers. The effect of education regarding best practices, transition from single bottle to two bottle cultures was successful in all hospitals. Single bottle usage decreased below 10% in all hospitals. Significantly more positive cultures were detected at multiple cultures when compared with the single bottle collection practice. In retrospective patient records, it was seen that all the laboratories reported the results of Gram staining to the clinics. However, these data were not recorded to the EpiCenter. The contamination rates of Ankara Numune Hospital and Akdeniz University Faculty of Medicine Hospital are 6.2% and 5.4% respectively, contamination rates were not reported in other hospitals. The most common isolates detected in blood cultures were Escherichia coli, Klebsiella pneumoniae, Enterococcus faecium, Staphylococcus aureus, and Acinetobacter baumannii. The mean time for the detection of these organisms were less than 20 hours in the aerobic bottle and anaerobic bottles. A total of 79.6% of facultative anaerobic isolates were detected in both bottles; 9.8% were detected only in the aerobic bottles; 10.6% of the isolates were detected only in the anaerobic bottles. As a result, the educational efforts in Turkey have met with success for transition from collecting single bottle blood culture sets to two bottle blood cultures. However, further efforts are needed to increase the number of blood culture sets collected during a 24 hours' period. In addition, errors at the preanalytical, analytical and postanalytical periods (taking samples, loading bottles into the system and processing positive blood cultures) should be eliminated.

[Antimicrobial susceptibilities and molecular characterization of toxin-positive Clostridium difficile isolates: the first report on the presence of hypervirulent strains from Turkey]. / Toksin Pozitif Clostridium difficile Izolatlarinin Antimikrobiyal Duyarliliklari ve Moleküler Karakterizasyonu: Türkiye'den Hipervirülan Suslarin Varligi ile Iliskili Ilk Bildirim.

Clostridium difficile infection is one of the most important hospital-acquired infections. Infections caused by hypervirulent C.difficile strains which produce toxins at high levels, have higher morbidity and mortality rates, more complications and relapses. They are characterized by higher sporulation ratios and resistance rates for fluoroquinolones. In order to prevent serious morbidities, mortalities and remarkable increase in health costs, highly pathogenic C.difficile strains must be identified before causing severe outbreaks. The aim of this study was to determine the antimicrobial susceptibilities and molecular characteristics of 61 C.difficile strains isolated by culture from toxin-positive fecal samples of patients who were admitted to three different laboratories in Ankara, between September 2012 and November 2014. Antimicrobial susceptibilities were determined by using gradient test strips and results were interpreted according to the current CLSI and EUCAST criteria. The presence of toxin genes was investigated by polymerase chain reaction (PCR), and mutations in the tcdC gene were determined by sequence analysis following PCR amplification. Genetic characterization of one hypervirulent strain was performed by Public Health Institution of Turkey using the GenoType CDiff (Hain Lifescience, Germany) test. All strains were susceptible to vancomycin and metronidazole. Three (4.9%) isolates were resistant to moxifloxacin with a minimum inhibitory concentration (MIC) of > 8 µg/ml. The MIC50 and MIC90 values for erythromycin and clindamycin were 1.5-3 µg/ml, and 2-4 µg/ml, respectively. All strains carried the tcdA and tcdB genes, and 1 (1.6%) was positive for the binary-toxin (cdtA and cdtB) genes. The binary-toxin positive strain carried a 54 bp deletion as well as a single nucleotide change in the tcdC gene. Various single nucleotide changes were found in the tcdC gene of 12 strains (19.6%). Our results have shown that, hypervirulent strains exist in our country, but we have no evidence for the presence of ribotype 027 yet. On the other hand, when the increasing incidence of these strains through out the world is taken into consideration, it would be of great importance to perform surveillance studies and characterize the isolated strains.

[Investigation of cytokine responses and variations in the expression of beta-defensin-3 of Caco-2 human colon epidermal adenocarsinoma and THP-1 human leukemia monocyte cell lines in response to Toxoplasma gondii under various conditions]. / Caco-2 insan kolon epidermal adenokarsinom ve THP-1 insan lösemi monosit hücre dizilerinin çesitli kosullarda Toxoplasma gondii'ye karsi sitokin yanitlarinin ve insan beta-defensin-3 ekspresyon degisikliklerinin arastirilmasi.

Mononuclear phogocytic cells and epithelial cells are effective during the initiation and regulation of the innate immune response. They have an active role in mucosal immune response both mechanically and by interaction with other cells with cytokine release. Defensins are microbicidal peptides that are expressed in various cells and are thought to be effective in the first line defense against pathogens. IL-12 and IL-10, showing proinflamatory and antiinflamatory activities, respectively, are actors of the cellular immunity and limit the infection of the host without causing immunopathology. The aim of this study was to observe the differences in the release of IL-12 and IL-10 and the expression of human beta-defensin-3 (hBD-3) inCaco-2 (human colon epidermal adenocarcinoma cell) and THP-1 (human leukemia monocytic cell) cell lines cultured alone or in co-culture, by the stimulation of Toxoplasma gondii tachyzoites either in direct contact with the cells or separated by an insert filter from the cells. Twenty-four hours after the addition of RH strain tachyzoites to the cells, the supernatants were collected from the experiment wells, and commercial ELISA kits (Invitrogen) were used according to the manufacturers instructions to measure IL-12 and IL-10 levels. HBD-3 expression of cells collected from the experiment wells afterfour and 24 hourswere analyzed by using real time PCR. For this procedure, complementary c-DNA was obtained (Transcriptor High Fidelity cDNA Synthesis Kit, Roche Diagnostics, Germany)after the extraction of RNA with a commercial kit (High pure RNA isolation kit, Roche Diagnostics, Germany). IL-12 was higher than IL-10 in all experiment wells. IL-12 was induced more in the co-culture wells where Caco-2 and THP-1 cells were challenged together, than the wells in which the cells infected with T.gondii tachyzoites alone. No differences in respect to cytokine response were observed between the cells with which tachyzoites were in contact and the cells which were separated from the parasites with an insert. In hBD-3 experiments, Caco-2 and THP-1 cells interacted in co-culture wells when infected with tachyzoites and displayed a higher level of hBD-3 expression than the condition when they were infected alone. This study showed that, IL-12 release and hBD-3 expression, which play a role in innate immunity, are greater when various antigens of T.gondii interacted with stimulated mononuclear cell and epithelial cells.

[Investigation of biofilm formation properties of staphylococcus isolates]. / Stafilokok izolatlarinin biyofilm olusturma özelliklerinin arastirilmasi.

Biofilm production is an important virulence factor which allows staphylococci to adhere to medical devices. The principal component of biofilm is a "polysaccharide intercellular adhesin (PIA)" which is composed of a beta-1,6-N-acetylglucosamine polymer synthesized by an enzyme (N-acetylglucosamine transferase) encoded by the ica operon found on the bacterial chromosome. This operon is composed of four genes (A, B, C, and D), and a transposable element IS256. In this study, we aimed to determine the biofilm production characteristics of invasive/non-invasive staphylococcus isolates and different staphylococcus species. Biofilm production of 166 staphylococci was phenotypically investigated on Congo Red Agar (CRA); the presence of icaA, icaD and IS256 genes were investigated by polymerase chain reaction (PCR). 74 of the isolates (44.6%) were identified as methicillin resistant Staphylococcus aureus (MRSA), 25 (15.1%) as methicillin sensitive S.aureus (MSSA), 25 (37.3%) as Staphylococcus hominis, 20 (12%) as S.epidermidis, ten (15%) as Staphylococcus haemolyticus, nine (13.4%) as Staphylococcus capitis, two (3%) Staphylococcus saprophyticus and one (1.5%) as Staphylococcus warnerii. Of the MRSA strains, 52 were isolated from blood and 22 from nose; all MSSA strains were isolated from nose cultures. Coagulase-negative staphylococci (CoNS) strains were composed of invasive and non-invasive strains isolated from nose, catheter tip and blood cultures from patients with catheter. Production with CRA method was found to be statistically significant in invasive isolates (p< 0.001). It is concluded that; as the biofilm formation capacity of invasive isolates can cause refractory infections and the importance of carriage and hospital infections of these bacteria, it is important to prevent the spread of these isolates. A combination of phenotypic and genotypic tests is recommended for the investigation of biofilm formation in staphylococci. 40.3% of the CoNS isolates, and 85.8% of S.aureus isolates produced biofilm on CRA (p< 0.001) and with PCR method the ratio of carrying three genes was found to be statistically important in S.aureus when compared with CoNS. Carriage of three genes and biofilm formation capacity of invasive isolates can cause refractory infections and the importance of carriage and hospital infections of these bacteria, it is important to prevent the spread of these isolates. A combination of phenotypic and genotypic tests is recommended for the investigation of biofilm formation in staphylococci.

Detecting Gram-positive anaerobic cocci directly from the clinical samples by multiplex polymerase chain reaction in odontogenic infections.

PURPOSE: Gram-positive anaerobic cocci (GPAC) can be isolated as pathogens from odontogenic infections. Culturing GPAC is time consuming and labor intensive. The objectives of the present study were to examine the utility of polymerase chain reaction (PCR) in directly detecting the presence of GPAC in clinical samples obtained from patients with odontogenic infections and to compare the distribution of GPAC in infected and healthy tissue. MATERIALS AND METHODS: In the present case-control study, the infected tissue from patients and oral mucosal swabs from healthy control subjects were subjected to anaerobic culture and direct PCR analysis for the presence of GPAC. The McNemar, chi-square, and Fisher exact tests and kappa analysis were used for the statistical analyses. P < .05 was regarded as significant. RESULTS: The patient group included 13 men and 14 women, including 9 patients diagnosed with granulation of tooth extraction, 6 with impacted tooth follicles, 4 with peri-implantitis, 3 with abscesses, 2 with epithelial cysts, 2 with infected cysts, and 1 with an oroantral fistula. The control group included 14 men and 12 women. All the patient and control samples contained at least 1 GPAC. The groups did not differ by method of determining GPAC presence, but more microorganisms were detected when clinical samples were directly used for PCR analysis than when cultured bacteria were used (P = .001). CONCLUSIONS: The presence of GPAC in infected tissue cannot be directly related to the development of odontogenic infections. PCR performed directly on clinical material is a sensitive and specific method that can detect GPAC and save time.

The effect of temperature and contact time of sodium hypochlorite on human roots infected with Enterococcus faecalis and Candida albicans.

The aim of this study was to evaluate the effectiveness of 2.5 % NaOCl at different temperature and time intervals on Enterococcus faecalis and Candida albicans-infected human roots. A total of 112 root cylinders prepared from extracted single-rooted humans were infected by E. faecalis (Group A, n = 56) or C. albicans (Group B, n = 56); 3 root cylinders served as negative controls. Both groups were further divided into 6 subgroups according to three contact times (30 s, 1 min, 5 min) with NaOCl at two different temperatures (25 or 37 °C). Microorganism growth was controlled at the 24th and 48th hours. Statistical analysis was performed using the Chi-square test. While NaOCl at 25 °C for 5 min was the most effective irrigation regimen to eliminate E. faecalis (p < 0.001), NaOCl at 37 °C for 5 min exhibited significantly superior antifungal properties (p < 0.05). At the same contact times, difference in the temperature of NaOCl did not affect the growth of either E. faecalis or C. albicans. As a result, the irrigation time of NaOCl was more effective than the temperature to eliminate E. faecalis, while pre-heating of NaOCl to 37 °C increased its effectiveness on C. albicans at 5 min contact time.

A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society.

EXECUTIVE SUMMARY: Microbes are all pervasive in their distribution and influence on the functioning and well-being of humans, life in general and the planet. Microbially-based technologies contribute hugely to the supply of important goods and services we depend upon, such as the provision of food, medicines and clean water. They also offer mechanisms and strategies to mitigate and solve a wide range of problems and crises facing humanity at all levels, including those encapsulated in the sustainable development goals (SDGs) formulated by the United Nations. For example, microbial technologies can contribute in multiple ways to decarbonisation and hence confronting global warming, provide sanitation and clean water to the billions of people lacking them, improve soil fertility and hence food production and develop vaccines and other medicines to reduce and in some cases eliminate deadly infections. They are the foundation of biotechnology, an increasingly important and growing business sector and source of employment, and the centre of the bioeconomy, Green Deal, etc. But, because microbes are largely invisible, they are not familiar to most people, so opportunities they offer to effectively prevent and solve problems are often missed by decision-makers, with the negative consequences this entrains. To correct this lack of vital knowledge, the International Microbiology Literacy Initiative-the IMiLI-is recruiting from the global microbiology community and making freely available, teaching resources for a curriculum in societally relevant microbiology that can be used at all levels of learning. Its goal is the development of a society that is literate in relevant microbiology and, as a consequence, able to take full advantage of the potential of microbes and minimise the consequences of their negative activities. In addition to teaching about microbes, almost every lesson discusses the influence they have on sustainability and the SDGs and their ability to solve pressing problems of societal inequalities. The curriculum thus teaches about sustainability, societal needs and global citizenship. The lessons also reveal the impacts microbes and their activities have on our daily lives at the personal, family, community, national and global levels and their relevance for decisions at all levels. And, because effective, evidence-based decisions require not only relevant information but also critical and systems thinking, the resources also teach about these key generic aspects of deliberation. The IMiLI teaching resources are learner-centric, not academic microbiology-centric and deal with the microbiology of everyday issues. These span topics as diverse as owning and caring for a companion animal, the vast range of everyday foods that are produced via microbial processes, impressive geological formations created by microbes, childhood illnesses and how they are managed and how to reduce waste and pollution. They also leverage the exceptional excitement of exploration and discovery that typifies much progress in microbiology to capture the interest, inspire and motivate educators and learners alike. The IMiLI is establishing Regional Centres to translate the teaching resources into regional languages and adapt them to regional cultures, and to promote their use and assist educators employing them. Two of these are now operational. The Regional Centres constitute the interface between resource creators and educators-learners. As such, they will collect and analyse feedback from the end-users and transmit this to the resource creators so that teaching materials can be improved and refined, and new resources added in response to demand: educators and learners will thereby be directly involved in evolution of the teaching resources. The interactions between educators-learners and resource creators mediated by the Regional Centres will establish dynamic and synergistic relationships-a global societally relevant microbiology education ecosystem-in which creators also become learners, teaching resources are optimised and all players/stakeholders are empowered and their motivation increased. The IMiLI concept thus embraces the principle of teaching societally relevant microbiology embedded in the wider context of societal, biosphere and planetary needs, inequalities, the range of crises that confront us and the need for improved decisioning, which should ultimately lead to better citizenship and a humanity that is more sustainable and resilient. ABSTRACT: The biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us-individuals/communities/nations/the human world-and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI. HERE, WE PRESENT: our concept of how microbiology literacy may be achieved and the rationale underpinning it; the type of teaching resources being created to realise the concept and the framing of microbial activities treated in these resources in the context of sustainability, societal needs and responsibilities and decision-making; and the key role of Regional Centres that will translate the teaching resources into local languages, adapt them according to local cultural needs, interface with regional educators and develop and serve as hubs of microbiology literacy education networks. The topics featuring in teaching resources are learner-centric and have been selected for their inherent relevance, interest and ability to excite and engage. Importantly, the resources coherently integrate and emphasise the overarching issues of sustainability, stewardship and critical thinking and the pervasive interdependencies of processes. More broadly, the concept emphasises how the multifarious applications of microbial activities can be leveraged to promote human/animal, plant, environmental and planetary health, improve social equity, alleviate humanitarian deficits and causes of conflicts among peoples and increase understanding between peoples (Microbial Biotechnology, 2023, 16(6), 1091-1111). Importantly, although the primary target of the freely available (CC BY-NC 4.0) IMiLI teaching resources is schoolchildren and their educators, they and the teaching philosophy are intended for all ages, abilities and cultural spectra of learners worldwide: in university education, lifelong learning, curiosity-driven, web-based knowledge acquisition and public outreach. The IMiLI teaching resources aim to promote development of a global microbiology education ecosystem that democratises microbiology knowledge.