The effect of novel biotechnological vermicompost on tea yield, plant nutrient content, antioxidants, amino acids, and organic acids as an alternative to chemical fertilizers for sustainability.

In this study, the performance of a novel organic tea compost developed for the first time in the world from raw tea waste from tea processing factories and enriched with worms, beneficial microorganisms, and enzymes was tested in comparison to chemical fertilizers in tea plantations in Rize and Artvin provinces, where the most intensive tea cultivation is carried out in Turkey. In the field trials, the developed organic tea vermicompost was incorporated into the root zones of the plants in the tea plantations in amounts of 1000 (OVT1), 2000 (OVT2) and 4000 (OVT4) (kg ha-1). The experimental design included a control group without OVT applications and positive controls with chemical fertilizers (N: P: K 25:5:10, (CF) 1200 kg ha-1) commonly used by local growers. The evaluation included field trials over two years. The average yields obtained in two-year field trials in five different areas were: Control (6326), OVT1 (7082), OVT2 (7408), OVT4 (7910), and CF (8028) kg ha-1. Notably, there was no significant statistical difference in yields between the organic (at 4000 kg ha-1 ) and chemical fertilizers (at 1200 kg ha-1). The highest nutrient contents were obtained when CF and OVT4 were applied. According to the average values across all regions, the application of OVT4 increased the uptake of 63% N, 18% K, 75% P, 21% Mg, 19% Na, 29% Ca, 28% Zn, 11% Cu and 24% Mn compared to the control group. The application of chemical fertilizers increased the uptake of 75% N, 21% K, 75% P, 21% Mg, 28% Na, 27% Ca, 30% Zn, 18% Cu and 31% Mn compared to the control group. The organic fertilizer treatment had the lowest levels of antioxidants compared to the control groups and the chemical fertilizers. It was also found that the organic fertilizer increased the levels of amino acids, organic acids and chlorophyll in the tea plant. Its low antioxidant activity and proline content prepared them for or protected them from stress conditions. With these properties, the biotechnologically developed organic tea compost fertilizer has proven to be very promising for tea cultivation and organic plant production.

The relationship of extent of initial radiological involvement with the need of intensive care, mortality rates, and laboratory parameters in Covid-19

Background/aim: It is very important for the efficient use of limited capacity and the success of treatment to predict patients who may need ICU with high mortality rate in the Covid-19 outbreak. In our study, it was aimed to investigate the value of the radiological involvement on initial CT in demonstrating the ICU transfer and mortality rate of patients. Materials and methods: All PCR-positive patients were included in the study, whose CT, PCR, and laboratory values were obtained simultaneously at the time of first admission. Patients were divided into 4 groups in terms of the extent of radiological lesions. These groups were compared in terms of intensive care transfer needs and Covid-related mortality rates. Results: A total of 477 patients were included in the study. Ninety of them were group 0 (no lung involvement), 162 were group 1 (mild lesion), 89 were group 2 (moderate lesion), and 136 were group 3 (severe lung involvement). A significant relationship was found between the extensiveness of the radiological lesion on CT and admission to intensive care and mortality rate. As the initial radiological involvement amounts increased, the rate of ICU transfer and mortality increased. The mortality rates of the groups were 0%, 3%, 12.3%, and 12.5%, respectively, and the difference was significant (p < 0.001). Similarly, the ICU transfer rates of the groups were 2.2%, 5.6%, 13.5%, and 17.7%, respectively, and the difference was significant (p < 0.001). Conclusion: In conclusion, in our study, the strong relationship between the initial radiological extent assessment and the need for intensive care and mortality rates has been demonstrated, and we believe that our results will make a significant contribution to increase the success of the health system in predicting patients who may progress, helping clinicians and managing pandemics.

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

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

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

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

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

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

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

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

The carbapenem-resistant Enterobacteriaceae threat is growing: NDM-1 epidemic at a training hospital in Turkey.

BACKGROUND: Recently, new carbapenemases in Enterobacteriaceae strains and non-fermentative gram-negative bacilli have been reported. The New Delhi metallo-ß-lactamase-1 (NDM-1) is a major problem around the world. The purpose of this article is to address the NDM-1 Klebsiella pneumoniae epidemic detected in eight cases in our hospital. METHODS: Bacteria identified in this epidemic were from patients already admitted to the intensive care unit of the Sakarya University Training and Research Hospital during efforts toward establishment of infection surveillance and control program. Antimicrobial susceptibility testing of strains was performed using the VITEK 2 system (bioMérieux, France), E-test gradient strips (bioMérieux, France), and the disc diffusion test. For the metallo-beta-lactamase activity, the combined disc diffusion test and modified Hodge test as phenotypic tests were performed. To identify the resistance gene, the Xpert Carba-R kit (Cepheid Inc., USA) and an in-house multiplex polymerase chain reaction (PCR) method designed for five common carbapenemase genes (IMP, VIM, KPC, NDM-1, and OXA-48) were employed. The clonal relationship of these strains was explored by the repetitive PCR (rep-PCR, DiversiLab System, bioMérieux, France) method. RESULTS: During the December 2014 to March 2015 period, NDM-1 positive K. pneumoniae strains were detected in eight patients. All of these strains were found to produce NDM-1, while two of them also revealed the presence of OXA-48. The rep-PCR results reveal a clonal proximity of 95 % for six of the eight strains. CONCLUSIONS: Our findings suggest the tendency of NDM-1-producing strains to spread in our country as well. A carbapenem-resistant K. pneumoniae threat may pose a great risk to our country. It is clear that more comprehensive infection control precautions should be implemented in our hospitals.

The role of multiplex PCR test in identification of bacterial pathogens in lower respiratory tract infections.

OBJECTIVES: Lower respiratory tract infection is one of the most important causes of morbidity and mortality. However establishing a microbial diagnosis for patients with lower respiratory tract infection is still challenging and is often achieved in only half of cases by conventional methods. This study was designed to compare the fast responsive PCR method with the culture method in lower respiratory tract infections and to evaluate the reliability of multiplex PCR method. METHODS: One hundred ninety seven patients with the symptoms of acute lower respiratory tract infection, and diagnosed with community-acquired pneumonia, acute exacerbation of chronic obstructive pulmonary disease and exacerbations of bronchiectasis were included in the study. Both culture and PCR methods was performed for the isolation of most commonly seen bacteria, from sputum, nasopharyngeal swabs and bronchoalveolar lavage fluid samples. RESULTS: While at least one bacterial isolation was determined in 62 (31.5%) of all patients with culture method, this number increased to 125 (63.5%) with multiplex PCR. The bacteria most commonly identified by PCR were S. pneumoniae (32%) and H. influenzae (31%). There was a significant difference between PCR and culture in terms of multi-factor detection rates (p<0.005). Multiple bacteria were detected in only two cases in cultures; however, multiple pathogens were detected in 47 cases with PCR. CONCLUSIONS: Conventional methods, such as culture and serology are not always adequate to detect the pathogens in lower respiratory tract. Real-time PCR assays proved highly sensitive and rapid. The prevalence of bacteria and multiple agent detected by real-time PCR compared with culture was substantially higher. Widespread use of PCR methods, by providing the immediate and appropriate ''agent specific antibiotic treatment'' of LRTI, will help reduce failure and contributes to a reduction in antibiotic resistance.

Comparison of time-to-detection of Mindray TDR and BacT/ALERT®3D blood culture systems using simulated blood cultures.

PURPOSE: Blood culture (BC) is the standard for diagnosing bloodstream infections. Available blood culture (BC) systems have been developed to shorten the time to detection (TTD) of positive BCs. This study aimed to evaluate the performance of the Mindray TDR automatic BC system by comparing it with the BacT/ALERT®3D system. METHODS: Sixteen reference strains and 14 clinical isolates were used. Serial dilutions were prepared from all bacterial and yeast colonies with a final concentration of 100 CFU/ml and 10 CFU/ml. The prepared solutions were simultaneously inoculated into the bottles of both systems and placed in blood culture devices. RESULTS: Three hundred and fifty-two (176 BacT/ALERT®3D and 176 Mindray TDR-X060) blood culture bottles were evaluated, 336 aerobic and 16 anaerobic. At both 10 CFU/ml and 100 CFU/ml dilution, there was no significant difference between the two systems in terms of mean detection times for all isolates (p = 0.965, p = 0.245). When evaluated according to the type of organism, the detection time of gram-positive bacteria at 10 CFU/ml dilution was significantly shorter in the BacT/ALERT system (p = 0.019), whereas detection time for yeasts was significantly shorter with the Mindray system (p = 0.047). The number of anaerobic bacteria was too small to draw statistical conclusions, but we observed a trend of shorter detection times in the Mindray TDR-X060 system. CONCLUSION: Two systems with similar operating principles showed different concentrations-dependent performances in terms of positivity detection times depending on the type of microorganism. Mindray TDR-X060 system has been found to be safe to use at high concentrations with this at lower concentrations further comparative studies are needed on the newly introduced Mindray system.

Investigation of the in-vitro lethal effect of spilanthol on demodex and finding the most effective dose.

Demodex species are associated with many dermatological diseases, so an acaricidal agent that is effective against them and safe for skin applications may benefit many diseases. This study aims to investigate the anti-demodex potential of spilanthol, a product obtained from the Spilanthes Acmella plant, by determining the minimal effective dose for the first time in the literature. Demodex mites were obtained from 70 patients with standard superficial skin biopsy. Spilanthol extract was used at 1%, 2%, 3%, 4%, and 5%. Standard immersion oil was used for the negative control, and permethrin 5% was used for the positive control group. The dependent variable is the survival time of the mite. Comparisons with the negative control group, the anti-demodex effect demonstrated itself in all groups, creating a statistically significant difference (p < 0.001). The positive control group, had 3%, 4%, and 5% spilanthol rates which were very similar to the results with 5% permethrin (p > 0.05). Higher concentrations than 3% did not make any additional contribution to survival times. This is the first attempt to show the dose-dependent acaricidal effect of spilanthol on demodex mites. Even the 3% dose shows similar results to 5% permethrin, and no additional effect increase was observed at higher doses. Therefore, in vivo, studies may be planned with a 3% spilanthol dose for further studies.

Investigation of in vitro efficacy of quercetin-meropenem combination in carbapenemase-producing Klebsiella pneumoniae isolates.

INTRODUCTION: In recent years, the rapid spread of carbapenem-resistant K. pneumoniae, their higher mortality rates, and limited treatment alternatives cause difficulties in the treatment of these infections. New treatment alternatives are needed to cope with resistant strains. In recent years, natural products such as Quercetin have started to be preferred in combination studies due to their antimicrobial effects and low side-effect profiles. The aim of this study was to investigate the in vitro efficacy of the combination of Quercetin and Meropenem on carbapenemase-producing (blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP), carbapenem-resistant K.pneumoniae isolates using the checkerboard method. METHODOLOGY: Thirty Carbapenem-resistant K.pneumoniae strains in the culture collection of our laboratory were included in our study. Carbapenemase genes were determined using the Xpert® Carba-R (Cepheid, USA). Synergism with meropenem was assessed by checkerboard analysis, followed by FIC index, and combination index calculation. RESULTS: Twenty (66.6%) strains had OXA-48, 6 (20%) NDM, 1 (3.3%) KPC, 1 (3.3%) OXA-48+NDM genes, and 2 strains (6.6%) gene could not be detected. In the Quercetin and Meropenem combination study, synergy was found in 24 (80%) of the strains; an additive effect was found in 5 (16.6%) and an antagonist effect in 1 (3.3%). In 19 (63.3%) of the strains, meropenem MIC values were below the sensitive limit (MIC ≤ 2 µg/mL). CONCLUSIONS: Although the combination of quercetin and meropenem has a high synergistic effect in carbapenem-resistant K. pneumoniae isolates, it seems that the carbapenemase species affects this situation. however, more work is needed on this subject.

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.

Secondary bacterial infections in patients with coronavirus disease 2019-associated pneumonia.

OBJECTIVE: The vast majority of patients who hospitalized with coronavirus disease 2019 are given empirical antibiotic therapy. However, information on the frequency, microorganism species, and resistance rates of secondary bacterial infections in coronavirus disease 2019 patients are insufficient. We aimed to show the frequency of secondary infections and resistance conditions in patients with coronavirus disease 2019 hospitalized in the intensive care unit. METHODS: The results of tracheal aspirate culture, blood culture, and urine culture obtained from coronavirus disease 2019 patients - at least 2 days after their admission to the intensive care unit - were examined microbiologically. RESULTS: A total of 514 patients hospitalized in intensive care unit were included in our study. Tracheal aspirate, blood, or urine cultures were collected from 369 patients (71.8%). Bacterial reproduction was detected in at least one sample in 171 (33.3%) of all patients. The rate of respiratory tract infection and/or bloodstream infection was found to be 21%. Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa in tracheal aspirate culture; Coagulase-negative staphylococci, K. pneumoniae, and A. baumannii in blood culture; and Escherichia coli, K. pneumoniae, and Enterococcus faecalis in urine culture were the most common microorganisms. A. baumannii was resistant to most antibiotics except colistin and P. aeruginosa strains were resistant to most antibiotics except amikacin, colistin, cefepime, and imipenem. In K. pneumoniae, the highest meropenem sensitivity (73%) was observed; there was a strong resistance to most of the remaining antibiotics. CONCLUSIONS: We think that our study can be useful in choosing empirical antibiotic therapy in the coronavirus disease 2019 pandemic and reducing the mortality that may occur with secondary infection.

Comparison of oxidant/antioxidant balance in COPD and non-COPD smokers.

BACKGROUND/AIM: Oxidative stress plays an important role in the pathogenesis of chronic obstructive pulmonary disease (COPD). Smoking is the leading source of oxidants in lungs. However, it is currently unknown why some individuals are more resistant to the detrimental effects of smoking and do not develop COPD. The aim in this study is to measure and compare the oxidant/antioxidant balance between in non-COPD individuals who smoke and COPD patients who smoke. MATERIALS AND METHODS: Included in the study were 137 patients with COPD and 102 healthy individuals. Participants were divided into groups as COPD patients (former and current smokers), non-COPD individuals who smoke and non-smokers healthy persons. In the following stage, the total antioxidant status (TAS), total oxidant status (TOS) and oxidative stress index (OSI) levels were measured in serum for all participants. RESULTS: In the current-smoker COPD group, the level of oxidant status were significantly higher than the former-smoker COPD group (p < 0.001). Similarly, oxidant levels were significantly high in current-smoker healthy group than never smoker healthy group. According to these results TOS was associated with especially smoking status rather than COPD. Antioxidant status were similar between former-smoker COPD group and current-smoker COPD group. The antioxidant levels were found significantly low in current-smoker COPD patients, compared to the current-smoker non-COPD individuals (p = 0.007). Nevertheless, no significant difference was found in OSI levels between two groups. Briefly, high TOS and OSI values were correlated with only smoking, independently from COPD. CONCLUSION: It was concluded that there are complex pathogenetic mechanisms, including genetic and individual variations other than oxidant/antioxidant balance, involved in the development of smoking-related COPD. TOS and OSI values are not predictive parameters for the development of COPD, but high level of TAS in non-COPD smokers is promising for future studies.

Value of multiplex PCR to determine the bacterial and viral aetiology of pneumonia in school-age children.

BACKGROUND: Conventional methods for the aetiological diagnosis of community-acquired pneumonia (CAP) are often insufficient owing to low sensitivity and the long wait for the results of culture and particularly serology, and it often these methods establish a diagnosis in only half of cases. AIM: To evaluate the most common bacterial and viral agents in CAP using a fast responsive PCR method and investigate the relationship between clinical/laboratory features and aetiology, thereby contributing to empirical antibiotic selection and reduction of treatment failure. METHODS: In children aged 4-15 years consecutively admitted with a diagnosis of CAP, the 10 most commonly detected bacterial and 12 most commonly detected viral agents were investigated by induced sputum using bacterial culture and multiplex PCR methods. Clinical and laboratory features were compared between bacterial and viral pneumonia. RESULTS: In 78 patients, at least one virus was detected in 38 (48.7%) and at least one bacterium in 32 (41%). In addition, both bacteria and viruses were detected in 16 (20.5%) patients. Overall, the agent detection rate was 69.2%. The most common viruses were respiratory syncytial virus and influenza and the most frequently detected bacteria were S. pneumoniae and H. influenzae. PCR was superior to culture for bacterial isolation (41% vs 13%, respectively). Fever, wheezing and radiological features were not helpful in differentiating between bacterial and viral CAP. White blood cell count, CRP and ESR values were significantly higher in the bacterial/mixed aetiology group than in the viral aetiology group. CONCLUSION: In CAP, multiplex PCR is highly reliable, superior in detecting multiple pathogens and rapidly identifies aetiological agents. Clinical features are poor for differentiation between bacterial and viral infections. The use of PCR methods allow physicians to provide more appropriate antimicrobial therapy, resulting in a better response to treatment, and it may be possible for use as a routine service if costs can be reduced.

Secondary bacterial infections in patients with coronavirus disease 2019-associated pneumonia

SUMMARY OBJECTIVE: The vast majority of patients who hospitalized with coronavirus disease 2019 are given empirical antibiotic therapy. However, information on the frequency, microorganism species, and resistance rates of secondary bacterial infections in coronavirus disease 2019 patients are insufficient. We aimed to show the frequency of secondary infections and resistance conditions in patients with coronavirus disease 2019 hospitalized in the intensive care unit. METHODS: The results of tracheal aspirate culture, blood culture, and urine culture obtained from coronavirus disease 2019 patients - at least 2 days after their admission to the intensive care unit - were examined microbiologically. RESULTS: A total of 514 patients hospitalized in intensive care unit were included in our study. Tracheal aspirate, blood, or urine cultures were collected from 369 patients (71.8%). Bacterial reproduction was detected in at least one sample in 171 (33.3%) of all patients. The rate of respiratory tract infection and/or bloodstream infection was found to be 21%. Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa in tracheal aspirate culture; Coagulase-negative staphylococci, K. pneumoniae, and A. baumannii in blood culture; and Escherichia coli, K. pneumoniae, and Enterococcus faecalis in urine culture were the most common microorganisms. A. baumannii was resistant to most antibiotics except colistin and P. aeruginosa strains were resistant to most antibiotics except amikacin, colistin, cefepime, and imipenem. In K. pneumoniae, the highest meropenem sensitivity (73%) was observed; there was a strong resistance to most of the remaining antibiotics. CONCLUSIONS: We think that our study can be useful in choosing empirical antibiotic therapy in the coronavirus disease 2019 pandemic and reducing the mortality that may occur with secondary infection.

A severe Morganella morganii endophthalmitis; followed by bacteremia.

Morganella morganii is rarely isolated from nosocomial infections. However, postoperative infections due to Morganella spp. were documented in literature and eye involvements of the infections usually result in severe sequels. We present a severe case infection, which was caused by M. morganii subsp. morganii, firstly appearing as conjunctivitis and complicated by bacteremia. The infectious agent isolated from both conjunctival and consecutive blood cultures. Identification and antimicrobial susceptibility tests were performed with the Vitek 2(®) automated system. The isolate was resistant to cephalosporins and carbapenems and it had ability to produce extended spectrum beta-lactamases. Patient was successfully treated with intravenous ciprofloxacin according to susceptibility test results. This is the first report of M. morganii infection detected as a local infection then complicated by bacteremia.

Relationship between the GOLD combined COPD assessment staging system and bacterial isolation.

BACKGROUND: Acute exacerbations, which are a significant cause of mortality and morbidity, adversely affect chronic obstructive pulmonary disease (COPD) prognosis by accelerating loss of lung function. It is important to know the microorganisms that commonly cause exacerbations in the patient groups classified according to clinical and functional characteristics for fast and accurate treatment of acute exacerbations. OBJECTIVES: The last Global Initiative for Chronic Obstructive Lung Disease (GOLD) publication recommended a new staging system containing obstruction degree, frequency of exacerbations, and quality of life questionnaires. This study is designed to analyze the relationship between the bacteria isolated in acute exacerbations and new GOLD stages. METHODS: Potentially pathogenic bacteria (PPB) isolation with culture and polymerase chain reaction methods were obtained from 114 acute exacerbation COPD patients, classified into A, B, C, and D groups by analyzing the forced expiratory volume in 1 second (FEV1) value, COPD Assessment Test (CAT) score, and exacerbation frequency according to the new GOLD staging system. RESULTS: There was a significant correlation between exacerbation frequency and PPB isolation (P=0.002). There was no relationship between GOLD stage, FEV1, and CAT score with PPB isolation. The isolated bacteria diversity and mixed infection frequency were higher in the GOLD stage D group. Pseudomonas aeruginosa, Escherichia coli, and Acinetobacter baumannii were isolated only from D group patients. CONCLUSION: Bacterial infection may cause an acute exacerbation equally in each stage for COPD. The difference in bacterial etiology is more related to exacerbation frequency than FEV1 and CAT scores for an acute exacerbation. Determining exacerbation frequency is significant for treatment success in empirical antibiotic selection.