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Objective: biofilm formation is one of the most important virulence factors of Candida species which leads to permanent infection foci by adhering to foreign materials and which are difficult to treat. Candida parapsilosis, which is one of the most common causes of candidemia in our country, is frequently isolated as a causative agent in catheterrelated infections. The most commonly used methods for evaluating the biofilm formation of Candida species are measuring cell viability with XTT (2,3-bis (2-methoxy-4-nitro-5- sulfophenyl)-5-[(phenylamino) carbonyl]-2H-tetrazolium hydroxide) and evaluating the total biofilm mass with crystal violet (CV). The aim of this study is to evaluate the biofilm formation ability of C. parapsilosis candidemia isolates by XTT and (CV) methods and compare these methods with each other. Materials and methods: C. parapsilosis isolates sent from various hospitals between 2015 and 2019 were included in the study retrospectively, and the species-level identification was performed using the matrix- assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) The biofilm formation of the isolates was compared based on the optical density (OD) values obtained by crystal violet and XTT methods. The biofilm formation of the isolates was evaluated by categorizing them into low, medium and high biofilm groups as ± 20% according to the median value of all strains. Results: totally, 79 C. parapsilosis candidemia isolates were included in this study and categorical compatibility between CV and XTT methods in low, medium and high biofilm groups was found as 69.6%, 60.6% and 73.9%, respectively. The OD values of the XTT method in the high biofilm group were found statistically significantly higher when compared with the values from the CV method. Conclusion: the compatibility of XTT and crystal violet methods in terms of biofilm measurement in C. parapsilosis isolates was considered acceptable, and no major variations were detected between the categories. According to these results, when evaluating the biofilm levels of C. parapsilosis isolates, high OD values obtained by the XTT method should be confirmed with the CV method., NA

Vaccines have been seen as the most important solution for ending the coronavirus disease 2019 (COVID‐19) pandemic. The aim of this study is to evaluate the antibody levels after inactivated virus vaccination. We included 148 healthcare workers (74 with prior COVID‐19 infection and 74 with not). They received two doses of inactivated virus vaccine (CoronaVac). Serum samples were prospectively collected three times (Days 0, 28, 56). We measured SARS‐CoV‐2 IgGsp antibodies quantitatively and neutralizing antibodies. After the first dose, antibody responses did not develop in 64.8% of the participants without prior COVID‐19 infection. All participants had developed antibody responses after the second dose. We observed that IgGsp antibody titers elicited by a single vaccine dose in participants with prior COVID‐19 infection were higher than after two doses of vaccine in participants without prior infection (geometric mean titer: 898 and 607 AU/ml). IgGsp antibodies, participants with prior COVID‐19 infection had higher antibody levels as geometric mean titers at all time points (p

Soluble ACE2 (sACE2) decoys are promising agents to inhibit SARS-CoV-2, as their efficiency is unlikely to be affected by escape mutations. However, their success is limited by their relatively poor potency. To address this challenge, multimeric sACE2 consisting of SunTag or MoonTag systems is developed. These systems are extremely effective in neutralizing SARS-CoV-2 in pseudoviral systems and in clinical isolates, perform better than the dimeric or trimeric sACE2, and exhibit greater than 100-fold neutralization efficiency, compared to monomeric sACE2. SunTag or MoonTag fused to a more potent sACE2 (v1) achieves a sub-nanomolar IC50, comparable with clinical monoclonal antibodies. Pseudoviruses bearing mutations for variants of concern, including delta and omicron, are also neutralized efficiently with multimeric sACE2. Finally, therapeutic treatment of sACE2(v1)-MoonTag provides protection against SARS-CoV-2 infection in an in vivo mouse model. Therefore, highly potent multimeric sACE2 may offer a promising treatment approach against SARS-CoV-2 infections., Koç University Isbank Center for Infectious Diseases (KUISCID); Koç University Research Center for Transla-tional Medicine (KUTTAM)

Adaptation of Acinetobacter baumannii to colistin use on a disease course of a patient was described. Effects of colistin was mimicked in the laboratory conditions. The colistin resistant isolate was identified from the patient after 25 days of colistin treatment. In the laboratory, the expressions of pmrCAB were the highest at the generation which was corresponded to the duration of therapy. A. baumannii can develop a stable colistin-resistant phenotype after three weeks of colistin exposure.

Background: The maintenance of vaginal microbiota is an important factor to achieve ideal pregnancy outcomes. Coronavirus disease (COVID-19) has been shown to have potential adverse effects on pregnancy and neonatal outcomes. Pregnancy itself is a risk factor for the severity of COVID-19, with an increased risk of intensive care unit (ICU) admission, maternal morbidity, and mortality. the role of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in vaginal microbiome composition in pregnant women with COVID-19 has not yet been investigated. Therefore, we anticipate that COVID-19 may unfavorably affect the composition of the vaginal microbiota, resulting in adverse pregnancy outcomes. We aimed to describe the alterations of the composition of vaginal microbiota in pregnant women with COVID-19.Results: A prospective case-control study was conducted among 19 pregnant women with COVID-19 and 28 healthy controls matched according to the gestational week and age. The vaginal swabs were collected during the active phase of infection and consecutively, within a month after recovering from infection. In three patients, longitudinal samples before, in the course, and after infection were also obtained. The microbiome alterations were examined by 16S rRNA gene sequencing. We indicated that COVID-19 was associated with vaginal dysbiosis during pregnancy, which was indicated by an increased alpha diversity index. There was a significantly decrease in Firmicutes (P=0.007) and Lactobacillus (P=0.019) with an increase in Bacteroidetes (P=0.024) in the COVID-19 group. In the moderate/severe group, increased amounts of Ureaplasma and vanishing of Lactobacillus gasseri were found in women, compared to the asymptomatic or mild group (P=0.001). In longitudinal analysis, elevation of Actinobacteria with reduction of Firmicutes and Bacteroides were indicated during the active phase. Conclusions: The study revealed vaginal dysbiosis with a low abundance of Lactobacillus and an increase in Bacteroidetes in relation to SARS-CoV-2 infection. Vaginal dysbiosis in COVID-19 could be a contributing factor in pregnancy adverse outcomes. Trial registration: clinicaltrials, Registered 15 November 2019, https://www.clinicaltrials.gov/ct2/show/NCT04165252?cond=microbiota&cntry=TR&draw=3&rank=12

Scope: the objective of these guidelines is to identify the most appropriate diagnostic test and/or diagnostic approach for SARS-CoV-2. The recommendations are intended to provide guidance to clinicians, clinical microbiologists, other health care personnel, and decision makers. Methods: an ESCMID COVID-19 guidelines task force was established by the ESCMID Executive Committee. A small group was established, half appointed by the chair and the remaining selected with an open call. Each panel met virtually once a week. For all decisions, a simple majority vote was used. A list of clinical questions using the PICO (population, intervention, comparison, outcome) format was developed at the beginning of the process. For each PICO, two panel members performed a literature search focusing on systematic reviews, with a third panellist involved in case of inconsistent results. Quality of evidence assessment was based on the GRADE-ADOLOPMENT (Grading of Recommendations Assessment, Development and Evaluation - adoption, adaptation, and de novo development of recommendations) approach. Recommendations: a total of 43 PICO questions were selected that involve the following types of populations: (a) patients with signs and symptoms of COVID-19; (b) travellers, healthcare workers, and other individuals at risk for exposure to SARS-CoV-2; (c) asymptomatic individuals, and (d) close contacts of patients infected with SARS-CoV-2. The type of diagnostic test (commercial rapid nucleic acid amplification tests and rapid antigen detection), biomaterial, time since onset of symptoms/contact with an infectious case, age, disease severity, and risk of developing severe disease are also taken into consideration., "Hycor Biomedical; Bencard Allergie; Thermo Fisher Scientific; Mead Johnson Nutrition; Universities Giessen and Marburg Lung Center; German Center for Lung Research; University Hospital Giessen and Marburg; Deutsche Forschungsgemeinschaft-funded SFB 1021; KFO 309 (P10); SK 317/1-1; Foundation for Pathobiochemistry and Molecular Diagnostics; Fundacion Progreso y Salud; Consejería de Salud; Junta de Andalucía; Philipps University Marburg Fundation of the Faculty of Medicine; Deutsche Jose Carreras Leukamie-Stiftung"

Introduction: maternal anti-SARS-CoV-2 Spike antibodies can cross the placenta during pregnancy, and neonates born to infected mothers have acquired antibodies at birth. Few studies reported data on the histopathological changes of the placenta during infection and placental infection. SARS-CoV-2 infection may cause impaired development of the placenta, thus predisposing maternal and fetal unfavorable outcomes. The prospective study aims to evaluate the risk of vertical transmission of SARS-CoV-2 and placental passage of anti-Spike antibodies as well as the impact of clinical severity on placental structures. Methods: this is a prospective cohort study on 30 pregnant women infected by SARS-CoV-2 with their neonates. The demographic features and pregnancy outcomes were collected. Gross and microscopic examinations of the placentas were done. Maternal and umbilical cord sera were obtained at the time of delivery. Nasopharyngeal swabs were collected from neonates immediately after birth. Results: the concentrations of total anti-SARS-CoV-2 Spike antibodies were higher in pregnant women with moderate to severe/critical disease. The maternal total anti-SARS-CoV-2 Spike levels were correlated with those of neonatal levels. The rate of placental abnormalities is high in the mothers with severe disease, and those with positive anti-SARS-CoV-2 IgM. All neonates had negative nasopharyngeal swabs for SARS- CoV-2 infections and all placentas were negative in immunohistochemical staining for Spike protein. Discussion: the maternally derived anti-SARS-CoV-2 Spike antibody can transmit to neonates born to infected mothers regardless of gestational age. Our results indicated that the disease severity is associated with ischemic placental pathology which may result in adverse pregnancy outcomes., NA

Objectives: We aimed to describe the mechanisms of colistin resistance in Acinetobacter baumannii. Materials and Methods: Twenty-nine patients diagnosed with colistin-resistant A. baumannii infecti...

Coronavirus disease 2019 (COVID-19) continues to threaten public health globally. Severe acute respiratory coronavirus type 2 (SARS-CoV-2) infection-dependent alterations in the host cell signaling network may unveil potential target proteins and pathways for therapeutic strategies. In this study, we aim to define early severity biomarkers and monitor altered pathways in the course of SARS-CoV-2 infection.We systematically analyzed plasma proteomes of COVID-19 patients from Turkey by using mass spectrometry. Different severity grades (moderate, severe, and critical) and periods of disease (early, inflammatory, and recovery) are monitored. Significant alterations in protein expressions are used to reconstruct the COVID-19 associated network that was further extended to connect viral and host proteins.Across all COVID-19 patients, 111 differentially expressed proteins were found, of which 28 proteins were unique to our study mainly enriching in immunoglobulin production. By monitoring different severity grades and periods of disease, CLEC3B, MST1, and ITIH2 were identified as potential early predictors of COVID-19 severity. Most importantly, we extended the COVID-19 associated network with viral proteins and showed the connectedness of viral proteins with human proteins. The most connected viral protein ORF8, which has a role in immune evasion, targets many host proteins tightly connected to the deregulated human plasma proteins.Plasma proteomes from critical patients are intrinsically clustered in a distinct group than severe and moderate patients. Importantly, we did not recover any grouping based on the infection period, suggesting their distinct proteome even in the recovery phase. The new potential early severity markers can be further studied for their value in the clinics to monitor COVID-19 prognosis. Beyond the list of plasma proteins, our disease-associated network unravels altered pathways, and the possible therapeutic targets in SARS-CoV-2 infection by connecting human and viral proteins. Follow-up studies on the disease associated network that we propose here will be useful to determine molecular details of viral perturbation and to address how the infection affects human physiology.

This paper describes the elimination of healthcare-associated Acinetobacter baumannii infections in a highly endemic region. A prospective, observational study was performed between October 2012 and October 2017. Acinetobacter baumannii were isolated from 59 patients, and >95% similarity was demonstrated among isolates of seven patients (DiversiLab™, BioMérieux). Carbapenemase activity was detected in 15 of 17 (88%) isolates, and all were OXA-23 type. The control of Acinetobacter baumannii outbreaks can be achieved by close follow-up supported by molecular techniques, strict application of infection control measures, and isolation of transferred patients., NA

COVID-19 is detected using reverse transcription polymerase chain reaction (RT-PCR) of nasal swabs. A very sensitive and rapid detection technique using easily-collected fluids like saliva must be developed for safe and precise mass testing. Here, we introduce a metasurface platform for direct sensing of COVID-19 from unprocessed saliva. We computationally screen gold metasurfaces out of a pattern space of 2100 combinations for strongly-enhanced light-virus interaction with machine learning and use it to investigate the presence and concentration of the SARS-CoV-2. We use machine learning to identify the virus from Raman spectra with 95.2% sensitivity and specificity on 36 PCR positive and 33 negative clinical samples and to distinguish wild-type, alpha, and beta variants. Our results could pave the way for effective, safe and quantitative preventive screening and identification of variants.

Soluble ACE2 (sACE2) decoy receptors are promising agents to inhibit SARS-CoV-2, as their efficiency is less likely to be affected by common escape mutations in viral proteins. However, their success may be limited by their relatively poor potency. To address this challenge, we developed a large decoy library of sACE2 fusion proteins, generated with several protease inhibitors or multimerization tags. Among these decoys, multimeric sACE2 consisting of SunTag or MoonTag systems, which were originally utilized for signal amplification or gene activation systems, were extremely effective in neutralizing SARS-CoV-2 in pseudoviral systems and in clinical isolates. These novel sACE2 fusion proteins exhibited greater than 100-fold SARS-CoV-2 neutralization efficiency, compared to monomeric sACE2. SunTag or MoonTag in combination with a more potent version of sACE2, which has multiple point mutations for greater binding (v1), achieved near complete neutralization at a sub-nanomolar range, comparable with clinical monoclonal antibodies. Pseudoviruses bearing mutant versions of Spike, alpha, beta, gamma or delta variants, were also neutralized efficiently with SunTag or MoonTag fused sACE2(v1). Finally, therapeutic treatment of sACE2(v1)-MoonTag provided protection against SARS-CoV-2 infection in an in vivo mouse model. Overall, we suggest that the superior activity of the sACE2-SunTag or sACE2-MoonTag fusions is due to the greater occupancy of the multimeric sACE2 receptors on Spike protein as compared to monomeric sACE2. Therefore, these highly potent multimeric sACE2 decoy receptors may offer a promising treatment approach against SARS-CoV-2 infections.One Sentence SummaryMultimerization of sACE2 markedly enhanced the neutralization of SARS-CoV-2 by blocking multiple viral spike proteins simultaneously.

Objective: to compare the effectiveness of different mask types in limiting the dispersal of coughed air. Method: the Schlieren method with a single curved mirror was used in this study. Coughed air has a slightly higher temperature than ambient air, which generates a refractive index gradient. A curved mirror with a radius of curvature of 10 m and a diameter of 60 cm was used. The spread of the cough wavefront was investigated among five subjects wearing: (1) no mask; (2) a single surgical mask; (3) a double surgical mask; (4) a cloth mask; (5) a valveless N95 mask; and (6) a valved N95 mask. Results: all mask types reduced the size of the contaminated region significantly. The percentage reduction in the cross-sectional area of the contaminated region for the same mask types on different subjects revealed by normalized data suggests that the fit of a mask plays an important role. Conclusions: no significant difference in the spread of coughed air was found between the use of a single surgical mask or a double surgical mask. Cloth masks may be effective, depending on the quality of the cloth. Valved N95 masks exclusively protect the user. The fit of a mask is an important factor to minimize the contaminated region., 2232 International Fellowship for Outstanding Researchers Program; Scientific and Technological Research Council of Turkey (TÜBİTAK)

We proposed the hypothesis that high-risk clones of colistin-resistant K. pneumoniae (ColR-Kp) possesses a high number of virulence factors and has enhanced survival capacity against the neutrophil activity. We studied virulence genes of ColR-Kp isolates and neutrophil response in 142 patients with invasive ColR-Kp infections. The ST101 and ST395 ColR-Kp infections had higher 30-day mortality (58%, p = 0.005 and 75%, p = 0.003). The presence of yersiniabactin biosynthesis gene (ybtS) and ferric uptake operon associated gene (kfu) were significantly higher in ST101 (99%, p ≤ 0.001) and ST395 (94%, p &lt, 0.012). Being in ICU (OR: 7.9, CI: 1.43–55.98, p = 0.024), kfu (OR:27.0, CI: 5.67–179.65, p &lt, 0.001) and ST101 (OR: 17.2, CI: 2.45–350.40, p = 0.01) were found to be predictors of 30-day mortality. Even the neutrophil uptake of kfu+-ybtS+ ColR-Kp was significantly higher than kfu--ybtS- ColR-Kp (phagocytosis rate: 78% vs. 65%, p &lt, 0.001), and the kfu+-ybtS+ ColR-Kp survived more than kfu--ybtS- ColR-Kp (median survival index: 7.90 vs. 4.22, p = 0.001). The kfu+-ybtS+ ColR-Kp stimulated excessive NET formation. Iron uptake systems in high-risk clones of colistin-resistant K. pneumoniae enhance the success of survival against the neutrophil phagocytic defense and stimulate excessive NET formation. The drugs targeted to iron uptake systems would be a promising approach for the treatment of colistin-resistant high-risk clones of K. pneumoniae infections.

We report infectivity of adult and pediatric COVID-19 patients in presence of viral shedding and anti-SARS-CoV-2 antibody response A total of 408 consequent samples from eleven adult and five pediatric patients with SARS-CoV-2 infection were included. The samples every second day from saliva, nasopharynx, feces, serum, urine, tear were studied by RT-PCR and viral culture. Anti-SARS-CoV-2 antibodies were measured. The median duration of RNA shedding in all specimens was 7(2-15) days in adults and 5(3-19) days in children. The median duration from onset of symptoms to admission was three days.The viral RNA was positive in 44.7 % of the nasopharynx and 37.6% of saliva samples up 16 days in adults and 19 days in chldren. The latest viral culture positivity was detected on day 8 of symptoms in nasopharynx. The viral RNA was found in 6.1% of feces, 4.4% ofserum, 4.3 % of tear, 2.9% of urine. The earliest seroconversion was the 7th day for adults and 8th day for children. Atthe 14th day, total antibody positivity was 78% in adults, and 80% in children. After seroconversion, the viral RNA was still detected in the nasopharynx and saliva of three patients, however, the infectious virus was not present. Earlier hospital admission could be associated with shorter SARS-CoV-2 RNA shedding. The infectivity of patient is very low after 8 days of symptoms. The risk of fecal-oral transmission is very low, and strict hand hygiene measures could be preventive. The positive antibody test result could be used as a discharge criterion.

Here, we presented 11 cases with colistin-resistant Pseudomonas aeruginosa infection and co-existence of OXA-48 and NDM-1 in the ST235 high-risk clone. The molecular analyses were performed by Sanger sequencing and RT–PCR. The eight patients (72.7%) had an invasive infection and three (27.3%) had colonization. The 30-day mortality rate was 87.5% (7/8). Three patients (37.5%, 3/8) received colistin therapy before isolation of P. aeruginosa. In the Multilocus sequence typing (MLST) analysis of 11 isolates, eight (72.7%) isolates belonged to P. aeruginosa ST235 clone. All isolates were NDM-1 positive, and nine isolates (81.8%) were found to be positive for both OXA-48 and NDM-1. Sequences of pmrAB and phoPQ revealed numerous insertions and deletions in all isolates. In 10 isolates pmrAB and phoPQ were found to be upregulated. In conclusion, the co-existence of OXA-48 and NDM-1 genes in colistin-resistant P. aeruginosa ST235 high-risk clone indicates the spread of carbapenemases in clinical isolates and highlights need of continuous surveillance for high-risk clones of P. aeruginosa.

Antimicrobial photodynamic therapy (aPDT) and antimicrobial photothermal therapy (aPTT) are promising local and effective alternative therapies for antibiotic resistant bacterial infections and biofilms. A combination of nanoparticles and organic photosensitizers offers a great opportunity to combine PDT and PTT for effective eradication of both planktonic bacteria and their biofilms. In this work, photo-induced antibacterial activity of indocyanine green (ICG), 3-aminopropylsilane coated superparamagnetic iron oxide nanoparticles (APTMS@SPIONs) and ICG loaded APTMS@SPIONs was evaluated on planktonic cells and biofilms of Gram-negative (E. coli,K. pneumoniae,P. aeruginosa) and Gram-positive (S. epidermis) bacteria. A relatively low dose of ICG (25 mu g mL(-1)) and SPIONs (0.425 mu g mL(-1)nanoparticle) in combination with single, short (10 min) laser irradiation at 808 nm with a power of 1150 mW was used in this study. No dark toxicity of the agents or antibacterial effect of the laser irradiation was observed. The charge of the particles did not provide a significant difference in their penetration to Gram-negativeversusGram-positive bacterial strains or their biofilms. APTMS@SPION/laser treatment completely eliminatedP. aeruginosaand provided 7-log reduction in the colony forming unit (CFU) ofE. Coli, but was not effective on the other two bacteria. This is the first example for antibacterial phototoxicity of this nanoparticle. ICG/laser and ICG-APTMS@SPION/laser treatments provided complete killing of all planktonic cells. Successful eradication of all biofilms was achieved with ICG/laser (3.2-3.7 log reduction in CFUs) or ICG-APTMS@SPION/laser treatment (3.3-4.4 log reduction in CFUs). However, an exceptionally high, 6.5-log reduction as well as a dramatic difference between ICGversusICG/APTMS@SPION treatment was observed inK. pneumoniaebiofilms with ICG-APTMS@SPION/laser treatment. Investigation of the ROS production and increase in the local temperature of the biofilms that were subjected to phototherapy suggested a combination of aPTT and aPDT mechanisms for phototoxicity, exhibiting a synergistic effect when ICG-APTMS@SPION/laser was used. This approach opens an exciting and novel avenue in the fight against drug resistant infections by successfully utilizing the antimicrobial and antibiofilm activity of low dose FDA approved optically traceable ICG and relatively low cost clinically acceptable iron oxide nanoparticles to enable effective aPDT/aPTT combination, inducedviashort-duration laser irradiation at a near-infrared wavelength., Scientific and Technological Research Council of Turkey (TÜBİTAK)

This study aimed to describe the effect of initial antifungal therapy on patient mortality and to detail the current distribution and resistance patterns of Candida spp. among patients with candidaemia. A prospective observational study was performed among consecutive patients with candidaemia from 10 Turkish medical centres between January 2015 and November 2018. The primary outcome was 10-day mortality. Species were identified using MALDI-TOF/MS. A total of 342 patients with candidaemia were included, of which 175 (51.2%) were male and 68 (19.9%) were aged, NA

SummaryHere we proposed the hypothesis that hypervirulent colistin resistant K.pneumoniae (ColR-Kp) exhibit high number of virulence factors and have enhanced survival capacity against neutrophil activity.We studied virulence genes of ColR-Kp isolates and neutrophil response in 142 patients with invasive infections.The patients infected with hypervirulent ST101 and ST395 ColR-Kp had higher 30-day mortality (58%, p=0.005 and 75%, p=0.003, respectively. The yersiniabactin biosynthesis gene (ybtS) and ferric uptake operon associated gene (kfu) were significantly higher in ST101 (99%, p=+-ybtS+ ColR-Kp by neutrophils was significantly higher than kfu--ybtS- ColR-Kp (78% vs 65%, p+-ybtS+ ColR-Kp were more resistant to the killing activity of neutrophils than negative ones (7.90 vs 4.22; p=0.001). The kfu+-ybtS+ ColR-Kp stimulated excessive NET formation while the NET’s against kfu--ybtS- ColR-Kp were weak and rare.Iron uptake systems enhance successful survival of K.pneumoniae against neutrophil phagocytic defense, and stimulate excessive NET formation. The drugs targeted to iron uptake systems would be a promising approach for treatment of hypervirulent K.pneumoniae infections.

Coronavirus disease 2019 (COVID-19) is caused by the SARS-CoV-2 virus and has been affecting the world since the end of 2019. The disease led to significant mortality and morbidity in Turkey, since the first case was reported on March 11th, 2020. Studies suggest a positive association between air pollution and SARS-CoV-2 infection. The aim of the present study was to investigate the role of ambient particulate matters (PM), as potential carriers for SARS-CoV-2. Ambient PM samples in various size ranges were collected from 13 sites including urban and urban-background locations and hospital gardens in 10 cities across Turkey between 13th of May and 14th of June 2020 to investigate the possible presence of SARS-CoV-2 RNA on ambient PM. A total of 203 daily samples (TSP, n = 80; PM2.5, n = 33; PM2.5-10, n = 23; PM10?m, n = 19; and 6 size segregated PM, n = 48) were collected using various samplers. The N1 gene and RdRP gene expressions were analyzed for the presence of SARS-CoV-2, as suggested by the Centers for Disease Control and Prevention (CDC). According to real time (RT)-PCR and three-dimensional (3D) digital (d) PCR analysis, dual RdRP and N1 gene positivity were detected in 20 (9.8%) samples. Ambient PM-bound SARS-CoV-2 was analyzed quantitatively and the air concentrations of the virus ranged from 0.1 copies/m3 to 23 copies/m3. The highest percentages of virus detection on PM samples were from hospital gardens in Tekirdağ, Zonguldak, and Istanbul, especially in PM2.5 mode. Findings of this study have suggested that SARS-CoV-2 may be transported by ambient particles, especially at sites close to the infection hot-spots. However, whether this has an impact on the spread of the virus infection remains to be determined., Koç University Research Center for Translational Medicine (KUTTAM)

Bloodstream infections caused by Escherichia coli ST131 and ST131 H30-Rx subclones have emerged worldwide. This study was carried out to evaluate the prevalence of the ST131-Rx subclone and characterize the virulence properties of the Rx isolates among the bloodstream E. coli isolates. A total of 297 non-duplicated E. coli bloodstream isolates were studied. Antibiotic susceptibilities were tested using the disc diffusion method. PCR amplification and sequencing was used to identify ST131 and H30-Rx, the virulence gene, the β-lactamase and virotype. Quinolone resistance among bacteraemic E. coli strains was 51 %, and it was 98 % among E. coli ST131 isolates. The ST131 isolates accounted for 16 % (49) of all isolates and all ST131 isolates belonged to the extraintestinal pathogenic E. coli. The proportion of H30 subclone among the ST131 isolates was 98 %, and 75 % of H30 isolates belonged to the H30-Rx subclone. The prevalence of ST131 increased from 13 to 23 % in 4 years; however, there was a decrease in the ratio of H30-Rx infections. CTX-M-15 was detected in 85 % of ST131 and all of the H30-Rx isolates. The virulence genes associated with adhesion, cell protection, iron uptake and toxins (papA, iha, kpsMTII, iut and sat) were more common in ST131 than in non-ST131 isolates. Most of the ST131 and H30-Rx isolates were of the C virotype. All papA-positive isolates were in virotype C. The E. coli ST131 clone has increased rapidly among bloodstream isolates. However, a decrease in the proportion of the H30-Rx subclone in the quinolone-resistant population suggests the possibility of dissemination of other virulent and quinolone-resistant subclones in hospital settings.

Background: The aim of this study was to determine the effect of colistin resistance and other predictors on fatality among patients with Klebsiella pneumoniae bloodstream infections (Kp-BSI) and to describe the effect of amikacin and tigecycline on the outcome in an OXA-48 dominant country. Method: This was a retrospective study performed among patients >16 years of age in a tertiary hospital with 465 beds. All cases had ≥1 positive blood culture for K. pneumoniae 48 h after admission. Results: Among 210 patients with Kp-BSI, the 30-day mortality rate after isolation of the microorganism was 58%. The rate of carbapenem resistance was higher (64% vs. 38%, p

Purpose: to investigate the effect of interferon alfa-2a on T regulatory (Treg) cells, T helper 17 (Th17) cells, and expression of Toll-like receptors (TLRs) in Behçet disease (BD) patients with uveitis. Methods: twenty-seven patients who received interferon alfa-2a for active BD uveitis despite conventional immunomodulatory therapies and healthy controls were enrolled. Peripheral blood Treg and Th17 cell frequencies were determined by flow cytometry as gated cells for CD3 + CD4 + Foxp3 + and CD3 + CD4 + IL17A + , respectively. Th17 RAR-related orphan receptor (ROR)γt mRNA expression was verified by real-time PCR (RT-PCR). Treg and Th17 cell cytokines were detected by ELISA in the supernatant of short-term cell cultures. RT-PCR was used to assess expression of TLR-2, TLR-3, TLR-4, TLR-8, and TLR-9 using cDNA prepared from CD4 + T cells and monocytes. Results: Treg and Th17 cell frequencies and Th17 RORγt expression were significantly elevated, and IL-10 concentration in Treg cell supernatants was significantly lower in BD patients than in controls. Th17 IL-17, IL-6, IL-21, IL-22, IL-23, IFN-γ, and TNF-α concentrations were significantly higher and all TLR expressions were significantly elevated in patients. Interferon alfa-2a led to a significant reversal in Treg and Th17 cell frequencies, Th17 RORγt expression, Treg and Th17 cell cytokine production, and TLR expression by CD4 + T cells and monocytes. Conclusions: despite a relative increase in Treg cells, impaired IL-10 production suggests that Treg dysfunction may play a role in induction of BD uveitis. Favorable effects of interferon alfa-2a may be associated with recovery of Treg cell function, suppression of Th17 cells, and reduced expression of TLRs on CD4 + T cells and monocytes., Scientific and Technological Research Council of Turkey (TÜBİTAK)

Type 1 diabetes (T1D) is an autoimmune disease characterized by destruction of pancreatic β cells. One of the promising therapeutic approaches in T1D is the transplantation of islets; however, it has serious limitations. To address these limitations, immunotherapeutic strategies have focused on restoring immunologic tolerance, preventing transplanted cell destruction by patients’ own immune system. Macrophage-derived chemokines such as chemokine-ligand-22 (CCL22) can be utilized for regulatory T cell (Treg) recruitment and graft tolerance. Stellate cells (SCs) have various immunomodulatory functions: recruitment of Tregs and induction of T-cell apoptosis. Here, we designed a unique immune-privileged microenvironment around implantable islets through overexpression of CCL22 proteins by SCs. We prepared pseudoislets with insulin-secreting mouse insulinoma-6 (MIN6) cells and human SCs as a model to mimic naive islet morphology. Our results demonstrated that transduced SCs can secrete CCL22 and recruit Tregs toward ​the implantation site in vivo. This study is promising to provide a fundamental understanding of SC-islet interaction and ligand synthesis and transport from SCs at the graft site for ensuring local immune tolerance. Our results also establish a new paradigm for creating tolerable grafts for other chronic diseases such as diabetes, anemia, and central nervous system (CNS) diseases, and advance the science of graft tolerance., Scientific and Technological Research Council of Turkey (TÜBİTAK)

We aimed to detect the etiological agents of acute diarrhea by a molecular gastrointestinal pathogen test (MGPT) and to assess the impact of MGPT on antimicrobial stewardship programs (ASP). This is a prospective observational study and was conducted between 1 January 2015 and 30 June 2017. We included consequent patients who had acute diarrhea. At the end of 2015, we implemented ASP in acute diarrhea cases and compared the outcomes in the pre-ASP and post-ASP periods. An FDA-cleared multiplexed gastrointestinal PCR panel system, the BioFire FilmArray (Idaho Technology, Salt Lake City, UT), which detects 20 pathogens in stool, was used. In 499 out of 699 patients (71%), at least one pathogen was detected. Among 314 adults with positive MGPT, 101 (32%) enteropathogenic Escherichia coli (EPEC), 71 (23%) enteroaggregative E. coli (EAEC), 68 (22%) enterotoxigenic E. coli (ETEC), 55 (18%) Shiga toxin-producing E. coli (STEC) (17%) Norovirus, 48 (15%) Campylobacter, 21 (7%) Salmonella, and 20 (6%) Clostridium difficile strains were detected. Among 185 children, 55 (30%) EPEC, 37 (20%) C. difficile, 32 (17%) Norovirus, 29 (16%) EAEC, 22 (12%) STEC, 21 (11%) ETEC, 21 (11%) Campylobacter, 20 (11%) Salmonella, and 16 (5%) Rotavirus strains were detected. Inappropriate antibiotic use decreased in the post-ASP period compared with the pre-ASP period among inpatients (42.9% and 25.8%, respectively; P = 0.023). Using MGPT in clinical practice significantly decreased the unnecessary use of antibiotics. Detection of high rates of C. difficile in children and Salmonella spp., as well as relatively high rates of Campylobacter spp., which were hard to isolate by routine stool culture, were remarkable., NA

Escherichia coli ST131 is a cause for global concern because of its high multidrug resistance and several virulence factors. In this study, the contribution of acrAB-TolC efflux system of E. coli ST131 to fluoroquinolone resistance was evaluated. A total of nonrepetitive 111 ciprofloxacin-resistant E. coli isolates were included in the study. Multilocus sequence typing was used for genotyping. Expressions of acrA, acrB, and TolC efflux pump genes were measured by RT-PCR. Mutations in marA, gyrA, parC, and aac(6)-lb-cr positivity were studied by Sanger sequencing. Sixty-four (57.7%) of the isolates were classified as ST131, and 52 (81.3%) of the ST131 isolates belonged to H30-Rx subclone. In ST131, CTX-M 15 positivity (73%) and aac(6)-lb-cr carriage (75%) were significantly higher than those in non-ST131 (12.8% and 51%, respectively) (P, NA