Mikrobiyoloji bulteni最新文献

{"title":"[Viral Respiratory Tract Infection Agents Detected Between Years 2019-2021, COVID-19, and Co-Infections].","authors":"Sibel Aydoğan,&nbsp;Füsun Kırca,&nbsp;Ayşegül Gözalan,&nbsp;Alparslan Toyran,&nbsp;Tuğcan Başyiğit,&nbsp;İpek Omay,&nbsp;Bedia Dinç","doi":"10.5578/mb.20239952","DOIUrl":"10.5578/mb.20239952","url":null,"abstract":"<p><p>Respiratory tract infections are a major cause of morbidity and mortality at all ages and are seen as a very important public health problem all over the world. In this study, we aimed to evaluate the effect of the pandemic on the epidemiological and seasonal characteristics of the agents by analyzing the respiratory viral infection agents, viral co-infections and associations with Coronavirus diseases-2019 (COVID-19) studied by multiplex polymerase chain reaction (PCR) test in the molecular microbiology laboratory in a three-year period, including the one-year period before the pandemic. Between March 2019 and December 2021, 8825 respiratory tract specimens accepted to the molecular microbiology laboratory with respiratory tract multiplex PCR test requests were included in the study. In addition, severe acute respiratory syndrome (SARS-CoV-2) PCR test results of the patients with positive results with respiratory tract multiplex PCR test, which were studied within ± 3 days, were evaluated retrospectively. Respiratory viral pathogens were detected using FTD Respiratory Pathogens 21 kit (Fast Tract Diagnostics, Siemens Healthineers Company). Two different kits based on real-time reverse transcription PCR were used for SARS-CoV-2 RNA detection in different periods. According to our results, at least one viral agent was detected in 2156 (24.4%) of a total of 8825 samples and a single agent was detected in 1843 (85.5%) of these. The distribution of viruses in the samples with a single agent was determined as RV, RSV A/B, HCoVs, AdV, flu A virus, MPV A/B, PIV 1-4, flu B virus, EV, BoV and PeV, in order of frequency. Multiple agents were found in 313 (14.5%) of these 2156 samples. They were found to be two agents in 291 samples, three in 21 samples and four in one sample. When the SARS-CoV-2 PCR test results of the patients who had positive results with respiratory tract multiplex PCR and who were studied within ± 3 days were evaluated retrospectively, SARS-CoV-2 RNA was detected in 45 (3.5%) of 1277 samples in which at least one agent was detected. In four of these patients, SARS-CoV-2 was found together with multiple agents. Consequently, there was a sharp decrease in the prevalence of all viral agents during the pandemic period. It was evaluated that besides the COVID-19 infection, the restrictions applied during the pandemic period were also effective in this situation.</p>","PeriodicalId":18509,"journal":{"name":"Mikrobiyoloji bulteni","volume":"57 4","pages":"650-659"},"PeriodicalIF":1.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54230016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Seasonal Trends and Interactions of Viral Pathogens in Children Presenting with Acute Respiratory Tract Infections in the Advancing Periods of SARS-CoV-2 Pandemic].","authors":"Özlem Türkmen Recen,&nbsp;Hörü Gazi,&nbsp;Semra Bayturan Şen,&nbsp;Alkan Bal,&nbsp;Sinem Akçalı","doi":"10.5578/mb.20239947","DOIUrl":"10.5578/mb.20239947","url":null,"abstract":"<p><p>Although various bacteria and viruses have been identified in the etiology of acute respiratory tract infections (ARI), 90% of acute ARIs that develop in children are of viral origin. The aim of this study was to investigate the seasonal trends and interactions between infectious agents and to determine the risk factors associated with ARI in children aged 1-15 years admitted to the Pediatric Emergency Department of Manisa Celal Bayar University Hospital in the advancing periods of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic. To determine the bacterial and viral agents, samples were taken from 314 patients attending to the hospital with symptoms suggestive for ARI, between 06/01/2021 and 05/31/2022. Viral and bacterial agents were identified by multiplex polymerase chain reaction (PCR) and automated identification system, respectively. Demographic data of the participants and possible risk factors for ARI were recorded in the questionnaires. In the study, viral agents were detected in 77.3% of the children, and the most common infectious agent was rhinovirus/enterovirus (RV/EV) (36.3%), followed by influenza viruses (11.2%), and SARS-CoV-2 (10.5%). While RV/EV positivity was found to be higher in children with moderate and below average (p< 0.001) hand hygiene, influenza positivity was found higher in those attending school/preschool institution (p< 0.001) and whose mothers working full-time (p< 0.001). Respiratory syncytial virus positivity was associated with maternal smoking (p= 0.013) and home overcrowding (p= 0.014). Bacterial colonization was detected in 33 (11.6%) of 284 children whose swabs were taken for both bacterial and viral agents and the most frequently detected agents were Staphylococcus aureus (60.6%) and Pseudomonas aeruginosa (15.2%). Having siblings (p= 0.008) and maternal smoking (p= 0.012) were found to be associated with the detection of bacterial agents. In this study, in the advanced period of the pandemic, the most detected agents and seasonal characteristics were found to be similar to the pre-pandemic period. It is thought that knowing the regional etiology and risk factors will contribute to taking the necessary local control and protective measures.</p>","PeriodicalId":18509,"journal":{"name":"Mikrobiyoloji bulteni","volume":"57 4","pages":"580-596"},"PeriodicalIF":1.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54230014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[The Change in Antimicrobial Resistance During the COVID-19 Pandemic in Türkiye].","authors":"Nisel Yılmaz,&nbsp;Gülşen Altınkanat Gelmez,&nbsp;Güner Söyletir","doi":"10.5578/mb.20239943","DOIUrl":"10.5578/mb.20239943","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Antimicrobial resistance (AMR) is one of the most important problems threatening human health worldwide. The impact of the Coronavirus disease-2019 (COVID-19) pandemic on AMR continues to be discussed. Some researchers argue that the pandemic will increase AMR rates, while others suggest the opposite. The aim of this study was to investigate the change in AMR of Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus strains in three cross-sectional periods in Türkiye, the first one before the COVID-19 pandemic, the second and the third one during the pandemic. The change in antibiotic susceptibility in Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus strains isolated from urine, blood, and lower respiratory tract samples of patients hospitalized in intensive care units and wards of hospitals before (November 2019) and during the COVID-19 pandemic (November 2020 and July 2021) was investigated in this study. A total of 17 voluntary hospitals, members of the Antibiotic Susceptibility Surveillance Study Group (ADSI) of the Society for Clinical Microbiology Specialists (KLIMUD), participated in the study. Identification of bacteria was performed with automated bacterial identification systems (VITEK2, bioMérieux, France or Phoenix, BD, USA). Antibiotic susceptibility tests were performed in one center with the Kirby-Bauer disc diffusion method and in other centers with automated antibiotic susceptibility test systems (VITEK2, bioMérieux, France or Phoenix, BD, USA), and the results were evaluated according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Antibiotic susceptibility ratios were statistically analyzed using either the chi-square or Fisher's exact test. A p-value of &lt; 0.05 was considered statistically significant. Antibiotic susceptibility test results of a total of 4030 strains; 1152, 1139, and 1739 belonging to November 2019, November 2020, and July 2021, respectively; were examined. While cefotaxime and ceftazidime susceptibility rates in E.coli strains increased during the pandemic period compared to previous period (p= 0.04, p= 0.001, respectively); nitrofurantoin sensitivity (p= 0.02) and extended-spectrum beta-lactamase (ESBL) ratios (p&lt; 0.001) were found to be decreased. It was determined that the susceptibility rates of all other examined antimicrobials did not change statistically. It was observed that the susceptibility rates of all antibiotics in K.pneumoniae isolates decreased during the pandemic period, but the ESBL rates increased between 2019-2020 (p= 0.01) and decreased between 2020-2021 (p= 0.02). It was found that ESBL rates increased before and after the pandemic. It was observed that the susceptibility to ciprofloxacin (p= 0.0001), levofloxacin (p= 0.003), and gentamicin (p= 0.005) in S.aureus strains increased during the pandemic period. No significant changes were observed in other antibiotic susceptibility rates. Methicillin resistance of S.aureus (M","PeriodicalId":18509,"journal":{"name":"Mikrobiyoloji bulteni","volume":"57 4","pages":"507-534"},"PeriodicalIF":1.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54230015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[An Important Problem in AdV-36 Seropositive Obesity Patients: Leptin Resistance].","authors":"Özge Altınok, Turan Onur Bayazıt, Süleyman Büyükaşık, Ali Ağaçfidan, Halil Alış","doi":"10.5578/mb.20239946","DOIUrl":"10.5578/mb.20239946","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Adenoviruses are naked viruses with an icosahedral nucleocapsid containing a 36 kb linear double-stranded DNA genome that encodes 30-40 proteins. The word \"obesity\" in Latin means \"because of feeding\". Obesity is an energy metabolism pathology that paves the way for physical and psychological problems with excessive fat accumulation that can impair health. Body mass index (BMI), unaffected by gender and age, is the most useful indicator of overweight and obesity at the population level. The concept of infectobesity was first introduced in 1978 after the data showed that viruses might also play a role in obesity cases. In the same year, adenovirus 36 (AdV-36) was isolated from the stool of a six-year-old girl with diabetes who was admitted to the hospital with the complaint of enteritis. One of the adipokines important for obesity is leptin. Leptin regulates food intake and energy metabolism by having a \"negative feedback\" effect on the hypothalamus. Leptin acts as a sensor that acutely regulates energy metabolism by creating hunger and satiety signals and it also regulates the amount of body fat and the required weight of the person by adjusting its concentration in the plasma according to the nutritional status. Changes in body weight and metabolic status are often associated with acute or chronic inflammatory processes. Human cells infected by AdV-36 showed greater differentiation and higher lipid accumulation than uninfected control cells, which increases the prevalence of obesity. There are two fractions of serum leptin, protein-bound and free form. The balance between these two fractions depends on serum leptin and soluble leptin receptor (sLR) plasma concentration, which is adversely affected by BMI. AdV-36 infection reduces norepinephrine and leptin levels. These two effects contribute to obesity by increasing appetite and food intake. In this study, it was aimed to determine the presence of immunoglobulin G against AdV-36 in the blood serum of obesity patients (BMI≥ 30) and healthy weight individuals (18.5≤ BMI≤ 25), and also aimed to determine and compare the leptin and soluble leptin receptor levels of these individuals. In this study, 10 ml of blood was collected on an empty stomach from obese individuals (n= 101; BMI≥ 30) and healthy individuals (n= 96; 18.5≤ BMI≤ 25) between the ages of 18-55. All participants consisted of who were not taking any medication and were not immunosuppressed. Blood samples separated into their serum were analyzed for AdV-36 IgG, leptin, and soluble leptin receptor levels. Mean, standard deviation, and percentage values were calculated by descriptive statistical analysis. The data with normal distribution were evaluated with the paired and independent sample t-test and data with abnormal distribution were evaluated with the paired and independent sample Mann-Whitney U test. Findings with a p-value less than 0.05 were considered statistically significant. In conclusion, leptin levels in obese individu","PeriodicalId":18509,"journal":{"name":"Mikrobiyoloji bulteni","volume":"57 4","pages":"568-579"},"PeriodicalIF":1.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54229991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[A Case of Mycobacterium abscessus Identified by Suspicious Gram Staining in the Blood Culture of a Patient with Chronic Renal Failure].","authors":"Rıza Adaleti,&nbsp;Nilgün Kansak,&nbsp;Neslihan Arıcı,&nbsp;Ahmet Balıkçı,&nbsp;Yasemin Uzunöner,&nbsp;Sebahat Aksaray","doi":"10.5578/mb.20239956","DOIUrl":"10.5578/mb.20239956","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Mycobacterium abscessus (M.abscessus), which is from the group of non-tuberculosis mycobacteria and is widely found in the natural environment, has been reported with increasing frequency as the causative agent of various infections; especially in the lower respiratory tract and in immuncompromised people. In this report, a case of M.abscessus, which developed tubular adenoma, pancytopenia and sepsis on the basis of chronic renal failure (CRF) was diagnosed by suspecting the causative agent in the Gram stain examination prepared from blood culture, was presented. A 49-year-old patient with CRF, who had complaints of weight loss, weakness, and loss of appetite for the last six months, admitted to the emergency department with a 7-8-day history of severe diarrhea and fever. Besides other tests, as the white blood cell count was 1.6 x 103/µl, neutrophil count was 80.6%, hemoglobin was 9.3 g/ dl and the platelet value was 36 x 103/µl in the blood samples, the patient was first taken into internal medicine service and then to the intensive care unit with a preliminary diagnosis of hypotension and sepsis. Meropenem and teicoplanin were started with the preliminary diagnosis of peritonitis in the internal medicine service. In addition to other tests, on the fifth day of antibiotic treatment, two consecutive sets of blood cultures were taken and sent to the microbiology laboratory. A positive signal was obtained from two aerobic blood culture samples at 42 and 45 hours of incubation in the BacT/Alert device. No bacteria were observed in the Gram staining of these samples and Erhlich Ziehl Neelsen (EZN) staining was performed because the structures considered as dye residues were noted as a result of the examination. Acid-fast bacteria were observed in the EZN-stained slide examination, and a panic report was given to the clinician. The patient died shortly after the notification was made in the evening hours. On culture plates inoculated after a positive signal, at the end of two days of aerobic incubation at 37 °C, small smooth S colonies grew on chocolate and sheep blood agar. Growing bacteria were detected as positive by EZN staining and identified as M.abscessus with 99.9% confidence by MALDI-TOF MS. After the bacterium was named as M.abscessus, the isolates were sent to the tuberculosis central laboratory of Süreyyapaşa Chest Diseases and Thoracic Surgery Hospital for molecular typing. After DNA extraction from the growing colonies and polymerase chain reaction (PCR), they were typed using the GenoType NTM-DR (Hain Lifescience GmbH, Germany) kit and identified as M.abscessus, consistent with the MALDITOF MS result. After the species level identification, the erm, rrl (clarithromycin, azithromycin), and rrs (kanamycin, amikacin, and gentamicin) genes were investigated in the isolate, and it was determined that the bacteria were resistant to macrolides and sensitive to aminoglycosides. In the clinic, it should be noted that, non-tuberculous myco","PeriodicalId":18509,"journal":{"name":"Mikrobiyoloji bulteni","volume":"57 4","pages":"682-689"},"PeriodicalIF":1.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54229989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Pasteurella multocida Pneumonia with Hemoptysis in an Immunocompetent Case].","authors":"Işılay Gökçe Benk Uğur,&nbsp;Elif Seren Tanrıverdi,&nbsp;Mehmet Özgel","doi":"10.5578/mb.20239954","DOIUrl":"10.5578/mb.20239954","url":null,"abstract":"<p><p>Pasteurella species are gram-negative bacilli found in healthy pets' oropharynx and gastrointestinal tract flora. In humans, skin and soft tissue infections develop most frequently with the bite or scratching of animals such as cats or dogs. At the same time, they cause infections in the respiratory tract, mainly in patients with chronic lung disease or immunosuppressive patients. In this case report, a rare case of pneumonia caused by P.multocida bacteria in a patient with bronchiectasis was presented. A young male patient was admitted to the emergency department of our hospital with complaints of hemoptysis, cough with phlegm, and weight loss. The patient's blood pressure was 140/82 mmHg and SO2= 94%. Rales and rhonchi were detected in the lower left lung during the examination. Standard thorax tomography revealed prominent cystic structures and pneumonic infiltrates in the left lower lobe. Laboratory findings were normal. The Coronavirus disease-2019 (COVID-19) quantitative real-time polymerase chain reaction (qRt-PCR) test was found to be negative in the nasopharyngeal swab sample taken from the patient. Fiberoptic bronchoscopy was performed on the patient to investigate the presence of endobronchial lesion or foreign body aspiration. Culture and cytological evaluation was requested from the bronchial lavage taken. Gram-negative coccobacilli were seen among dense polymorphonuclear leukocytes in the Gram stain of the sample. Acid-fast bacilli were not detected with Ehrlich Ziehl Neelsen stain. In the lavage culture evaluated after 24 hours, colonies growing in blood and chocolate media were stained and gramnegative coccobacilli were observed. The isolate was identified as 96.0% P.canis with the automated Vitek 2 (Biomerieux, France) system. It was determined that the isolate was susceptible to levofloxacin, trimethoprim-sulfamethoxazole, amoxicillin-clavulanic acid, penicillin, ciprofloxacin and cefotaxime in the antibiogram performed by disc diffusion test according to EUCAST v13.0 guideline criteria. Sequence analysis of the isolate obtained from the culture was performed on the ABI Prism 310 Genetic Analyzer (Applied Biosystems, USA). Sequence analysis of the isolate revealed 99.85% homology with P.multocida (GenBank accession no: NG_115137.1). Although Pasteurella multocida pneumonia is not commonly observed, the presence of underlying bronchiectasis in this patient facilitated the establishment of the bacteria. In order not to miss the diagnosis of pneumonia due to P.multocida, microbiological evaluation and molecular typing should be performed in the samples taken from the respiratory tract in patients with chronic respiratory diseases such as bronchiectasis.</p>","PeriodicalId":18509,"journal":{"name":"Mikrobiyoloji bulteni","volume":"57 4","pages":"667-674"},"PeriodicalIF":1.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54230013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[In vitro Activity of Rifabutin and Clofazimine to Macrolide-Resistant Mycobacterium abscessus Complex Clinical Isolates].","authors":"Süheyla Sürücüoğlu,&nbsp;Nuri Özkütük,&nbsp;Hörü Gazi,&nbsp;Cengiz Çavuşoğlu","doi":"10.5578/mb.20239951","DOIUrl":"10.5578/mb.20239951","url":null,"abstract":"<p><p>Mycobacterium abscessus complex (MABSC) is one of the most resistant bacteria against antimicrobial agents. The number of agents that can be used by oral route, such as macrolides, is limited in antimicrobial therapy. In recent years, rifabutin and clofazimine have gained importance as they can be administered by oral route and have shown synergistic effects with macrolides and aminoglycosides. The aim of this study was to determine the in vitro activity of rifabutin and clofazimine against clinical isolates of MABSC resistant to macrolides. A total of 48 MABSC isolates obtained from respiratory tract and other clinical samples in the Tuberculosis Laboratories of the Faculty of Medicine of Manisa Celal Bayar and Ege Universities were included in the study. Subspecies differentiation and aminoglycoside and macrolide resistance of the isolates were determined by GenoType NTM-DR test. Rifabutin and clofazimine susceptibilities were determined by standard broth microdilution method. Of the MABSC isolates 42 were identified as M.abscessus subsp. abscessus, three as M.abscessus subsp. bolletii and three as M.abscessus subsp. massiliense. None of the isolates exhibited rrs and rrl mutations indicating acquired macrolide resistance and aminoglycoside resistance. However, the erm(41) T28 genotype which is associated with inducible macrolide resistance was detected in 41 (85%) of the strains. All M.abscessus subsp. massiliense isolates were found to be genotypically susceptible to macrolides. The minimum inhibitory concentration (MIC) range values for rifabutin were 0.0625 to 32 µg/mL, while for clofazimine, the range was 0.0625 to 1 µg/mL. Rifabutin MIC values were significantly higher (mean 5.98 µg/mL vs 0.5 µg/mL, p= 0.026) in the isolates with macrolide resistance. There was no correlation between macrolide resistance and clofazimine MIC values (mean 0.25 µg/mL vs. 0.214 µg/mL, p= 0.758). The MIC50 and MIC90 values for rifabutin were 1 and 8 µg/mL, respectively, while for clofazimine they were 0.25 and 0.5 µg/mL. Macrolide resistance was found to be higher in isolates with rifabutin MIC values above the MIC50 value (p= 0.045). In conclusion, the determination of higher rifabutin MIC values in isolates resistant to macrolides suggested that susceptibility testing should be performed before adding rifabutin to the treatment regimen. The low MIC values of clofazimine in all strains indicated that it may be used as a first choice in the combination therapy. However, further studies using a larger number of clinical isolates and applying genotypic and phenotypic susceptibility tests are needed to determine threshold MIC values to assist clinicians in making treatment decisions.</p>","PeriodicalId":18509,"journal":{"name":"Mikrobiyoloji bulteni","volume":"57 4","pages":"639-649"},"PeriodicalIF":1.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54229996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Comparative Analysis of the Effect of Different Nucleic Acid Extraction Methods on SARS-CoV-2 Quantitative Real-Time Reverse Transcription Polymerase Chain Reaction Results].","authors":"Taylan Bozok,&nbsp;Ali Öztürk","doi":"10.5578/mb.20239948","DOIUrl":"10.5578/mb.20239948","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of Coronavirus diseases-2019 (COVID-19) disease. Rapid and accurate detection of the virus is vital to prevent transmission and effectively manage the pandemic. The gold standard diagnostic method for this agent is the real-time reverse transcription polymerase chain reaction (qrRT-PCR) test conducted on respiratory tract samples and one of the most critical steps affecting the sensitivity of this test is the nucleic acid extraction stage. However, restrictive factors such as reagent supply and storage conditions limit the testing capacity. Therefore, innovative and cost-effective alternatives are needed to speed up testing and minimize pre-processing steps. The aim of this study was to evaluate the impact and applicability of different methods to enhance the efficiency of the nucleic acid extraction stage in the SARS-CoV-2 qrRT-PCR test. As an alternative to the routinely used viral nucleic acid extraction buffer (vNAT), the modified vNAT method (MvNAT), which includes centrifugation, the R1-R2 kit and the heat treatment (HT) method, was applied to 118 respiratory tract samples. Samples determined with threshold cycle values of (Cq) of ≤ 35 (n= 10), &gt; 35 (n= 42), indeterminate (n= 56) in routine results and negative controls (n= 10) were included in the study. The RNA quantities obtained after extraction for each method were measured and recorded using a spectrophotometric measurement device. All samples were processed using the SARS-CoV-2 qrRT-PCR kit targeting the RdRp region. The results were statistically analyzed using unpaired and paired t-tests and results with a p-value of &lt; 0.05 were considered statistically significant. Excluding negative control samples, while the standard method yielded a Cq value of 48.1% (mean Cq value (Cqmean)= 39.5 ± 6.9) for a total of 108 samples, the MvNAT method produced a Cq value of 11.1% (Cqmean= 38.4 ± 5.2), the R1-R2 kit yielded 14.8% (Cqmean= 35.9 ± 7.1) and HT method resulted in 25% (Cqmean= 31.4 ± 6.3). When the variability in target gene Cq values was analyzed in all samples compared to the standard method, the HT method significantly provided lower Cq values (n= 16; p= 0.007; paired t-test) while the MvNAT method and R1-R2 kit yielded higher Cq values (n= 6; p= 0.025, n= 11; p= 0.004; paired t-test). Sensitivity rates were MvNAT= 31.6%, R1-R2= 57.9%, HT= 84.2%, with 100% specificity for all three methods. The HT method demonstrated a positive extraction efficiency because it is fast, easy and not dependent on reagents. Although this method provided lower Cq values than the standard method, especially in samples with a high viral load, it should be considered that it also has the potential to yield false-negative results in samples with Cq&gt; 35. With this study, it was concluded that the extraction phase of the SARS-CoV-2 qrRT-PCR test can be carried out using various methods that do not require kits or reagents,","PeriodicalId":18509,"journal":{"name":"Mikrobiyoloji bulteni","volume":"57 4","pages":"597-607"},"PeriodicalIF":1.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54229993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Fungal Keratitis Associated with Curvularia lunata: First Case Report from Türkiye].","authors":"Sedef Zeliha Öner,&nbsp;Saniye Küçükakın Yaka,&nbsp;Tahsin Akçaoğlu,&nbsp;Caner Vural,&nbsp;Uğur Yılmaz,&nbsp;Çağrı Ergin","doi":"10.5578/mb.20239957","DOIUrl":"10.5578/mb.20239957","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Fungal keratitis is a medical emergency that is among the most common causes of blindness in developing countries. The type of the agent may vary depending on the geographical conditions under which the patient lives, trauma exposure, the use of contact lenses and profession. Curvularia spp. is a saprophytic genus that rarely causes systemic disease in humans and has 250 species identified to date. They proliferate in soil and plants and spread to the environment with their spores and the formation of blackish and fluffy colonies is its most well-known morphological feature. There may be difficulties in cultivating brown (dematiaceous) fungi. Due to the similarity between the genera, conventional methods remain inadequate for diagnosis. In this report, a case of fungal keratitis associated with C.lunata was presented. Seventy-five years-old female patient admitted to the hospital with the symptoms of stinging pain, blurred vision, and swelling in the right eye. Her symptoms had begun four days ago after her eye was hit by a plant. The patient who had a history of peripheral neuropathy due to diabetes mellitus (DM) was hospitalized with a preliminary diagnosis of keratitis, and in the cultures of the patient's corneal scraping samples, the filamentous, black pigment-forming colonies of the pathogen growing on 5% sheep blood agar and potato dextrose agar showing an aerial hyphal structure, were stained with lactophenol cotton blue and examined under the microscope. The microscopic examination revealed geniculate conidiophores with brown pigmentation. On top of these structures were tetralocular macroconidia, one of which appeared to be larger than the main axis. The fungus was subjected to molecular identification with the prediagnosis of Curvularia/Bipolaris. DNA extraction of the ITS region polymerase chain reaction amplification and Sanger sequencing were performed for molecular identification. Sanger sequencing identified the agent to be Curvularia lunata with a similarity rate of 99.79% (NCBI-GenBank Nucleotide ID: OR365075). In vitro antifungal susceptibility of C.lunata was evaluated by microdilution method. Itraconazole and amphotericin B showed higher activity against C.lunata compared to other antifungals while fluconazole was the least active antifungal. Intrastromal and subconjunctival voriconazole injection was applied to the patient who was unresponsive to empirically initiated oral moxifloxacin and different topical treatments (vancomycin, ceftazidime, flucanozole, ganciclovir, cyclopentolate hydrochloride, hyaluronic acid and trehalose). After injection, right penetrating keratoplasty was applied due to increased thinning of the ulcerated area. No pathogen was detected in cultures taken after keratoplasty. Rare fungi should be considered in cases of keratitis that are difficult to treat. Fungal keratitis caused by brown fungi are clinically similar to each other and effective treatment protocols cannot be implemented without a","PeriodicalId":18509,"journal":{"name":"Mikrobiyoloji bulteni","volume":"57 4","pages":"690-697"},"PeriodicalIF":1.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54229995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Investigation of Virulence Factors, Phylogenetic Group Features, and the Presence of ST131 Clone in Escherichia coli Isolates, a Urinary Tract Infection Agent in Children].","authors":"Selin Gamze Kılıç,&nbsp;Duygu Öcal,&nbsp;Alper Tekeli,&nbsp;İştar Dolapçı","doi":"10.5578/mb.20239944","DOIUrl":"10.5578/mb.20239944","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Urinary tract infection (UTI) caused by Escherichia coli is a significant health issue in children. Today especially E.coli O25b/ST131, defined as a pandemic clone, is a serious public health problem due to its high virulence and antimicrobial resistance rates. In this study, a total of 200 (100 first and 100 recurrent UTI-causing) E.coli isolates from urine samples sent to the Ankara University School of Medicine Cebeci Training and Research Hospital Central Laboratory between January and September 2021 with the preliminary diagnosis of UTI in pediatric patients aged three to 18 years were analyzed for antimicrobial resistance rates, phylogenetic group distributions, virulence factor frequencies and whether they belong to the O25b/ST131 clone. It is aimed in this study that, the obtained data will shed light on new studies for diagnosis, treatment and prophylaxis options that can be developed for more effective UTI management by contributing to the surveillance studies in our country. Antimicrobial susceptibility of E.coli isolates identified by conventional methods was evaluated by Kirby-Bauer disc diffusion method and extended spectrum beta-lactamase (ESBL) production was evaluated by double disc synergy test. Polymerase chain reaction (PCR) was used for the investigation of phylogenetic grouping, the O25b/ST131 clone, virulence genes and the molecular level classification of the isolates detected as uropathogenic E.coli (UPEC). Pulsed-field gel electrophoresis (PFGE) was performed with the isolates collected at different times from the same patient. The highest antimicrobial resistance rates observed were against ampicillin (n= 100, 50%), cefazolin (n= 99, 49.5%), trimethoprim-sulfamethoxazole (n= 55, 27.5%), amoxicillin-clavulanic acid (n= 43, 21.5%) and cefotaxime (n= 43, 21.5%). In recurrent UTI agents, resistance rates were higher for cefotaxime (n= 29, 29%), trimethoprim-sulfamethoxazole (n= 35, 35%) and cefepime (n= 25, 25%) and in O25b/ST131 isolates (n= 67) the rates were higher for amikacin (n= 3, 4.5%), gentamicin (n= 10, 14.9%) and ciprofloxacin (n= 17, 25.4%) when compared to the first UTI agents and non-O25b/ ST131 isolates (p&lt; 0.05). It was found that 29% (n = 58) of the isolates were multidrug resistant (MDR) and 19% (n = 38) produced ESBL.The rate of recurrent UTI agents was found to be higher among ESBL producing isolates and/or MDR isolates (n= 36, 62% and n= 27, 71%, respectively, p&lt; 0.05). It was found that 45.5% (n= 91) of the isolates were in D, 37.5% (n= 75) in B2, 12.5% (n= 25) in A, and 4.5% (n= 9) in B1 phylogenetic groups and isolates belonging to B2 and D phylogenetic groups had higher antibiotic resistance rates and carried more virulence genes (p&lt; 0.05). Of the isolates, 33.5% (n= 67) were found to belong to the O25b/ST131 clone, no significant difference was found between the O25b/ST131 rates among the first and recurrent UTI agents (p&gt; 0.05). It was determined that the isolates most frequently carry virul","PeriodicalId":18509,"journal":{"name":"Mikrobiyoloji bulteni","volume":"57 4","pages":"535-552"},"PeriodicalIF":1.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54230011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}