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Özen S, Kanik Yüksek S, Dinç B, Üçkardeş F, Konca HK, Erat T, Güney AY, Güneş Ö, Coşkun ZN, Gülhan B, Bayhan Gİ, Çöplü N, Parlakay ANÖ, Özbek NY. Catheter-related Infections in Pediatric Patients Due to a Rare Pathogen: Herbaspirillum huttiense. Pediatr Infect Dis J 2024:00006454-990000000-00826. [PMID: 38621150 DOI: 10.1097/inf.0000000000004350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
BACKGROUND Herbaspirillum species are nonfermenting, aerobic, helical or curved, Gram-negative bacteria belonging to the class Betaproteobacteria, order Burkholderiales. To date, only a few studies have reported on the epidemiology, clinical symptoms, antibiotic susceptibility profiles, treatment and outcomes of Herbaspirillum huttiense -related infections in pediatric patients. METHODS The aim of this study was to present 3 years of H.Huntiense data, antibiotic susceptibility profiles, systemic antibiotics and antibiotic lock therapy (ALT) options and clinical outcomes. RESULTS Fourteen episodes of infection in 12 patients were included in this retrospective study. The patients had a male/female ratio of 1:1 and a median age of 160.5 months (range, 3-198 months). Catheter-related bloodstream infection (CRBSI) was detected in 11 patients. Only 1 patient developed catheter-related infective endocarditis. The patient's catheter was removed, and she was successfully treated with systemic antibiotics for 4 weeks. Systemic antibiotics were used in all infections related to H. huttiense . In septic, critically ill patients, the catheter was removed, and systemic antibiotics were started. Port catheters were removed in 5 patients. ALT was performed in clinically stable patients. ALT using amikacin was administered to 6 patients through the port catheter. Two patients had a 2nd attack. After the 2nd ALT treatment, 1 patient cured, and the catheter of the other patient was removed due to persistent microbial growth in cultures. Antimicrobial susceptibility testing of the reported isolates showed susceptibility to meropenem (90%), ceftazidime (87%) and piperacillin/tazobactam (65%), with 92% resistance to colistin. CONCLUSION H. huttiense is an emerging pathogen in CRBSI. Piperacillin/tazobactam, ceftazidime and meropenem appear to be good therapeutic options for the treatment of H. huttiense infections. ALT and systemic antibiotics can be used in H. huttiense -CRBSI to sterilize and preserve the central venous catheter.
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Affiliation(s)
- Seval Özen
- From the Department of Pediatric Infectious Diseases
| | | | - Bedia Dinç
- Department of Medical Microbiology, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Fatih Üçkardeş
- Department of Biostatistics and Medical Informatics, Adiyaman University, Adiyaman, Turkey
| | | | - Tuğba Erat
- From the Department of Pediatric Infectious Diseases
| | | | - Ömer Güneş
- From the Department of Pediatric Infectious Diseases
| | | | - Belgin Gülhan
- From the Department of Pediatric Infectious Diseases
| | | | - Nilay Çöplü
- Department of Medical Microbiology, Ankara Bilkent City Hospital, Ankara, Turkey
| | | | - Namik Yaşar Özbek
- Department of Pediatric Hematology/Oncology and Pediatric Bone Marrow Transplantation Unit, Ankara Bilkent City Hospital, Ankara, Turkey
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Salman E, Dinç B. Elevated levels of anti-Golgi antibodies: An early sign of seronegative rheumatoid arthritis. Scand J Immunol 2024:e13369. [PMID: 38566362 DOI: 10.1111/sji.13369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
Anti-Golgi antibodies are uncommon antibodies that exhibit specific, polarized cytoplasmic staining on the Hep-2 substrate. The objective of our study was to identify the clinical and laboratory features associated with anti-Golgi antibodies. We examined 4.5 years of data from a Turkish tertiary hospital in this retrospective cohort analysis. The indirect immunofluorescence staining patterns, antinuclear antibody (ANA) titres and clinical data of all patients were obtained from the hospital record system. A total of 146,055 ANAs were detected, of which 224 patients (0.15%) exhibited anti-Golgi antibody staining. In total, 39.4% of diagnosed patients had autoimmune diseases (AIDs). Of the AIDs, 26 (46.4%) were rheumatoid arthritis (RA). This is a very high rate and another remarkable point is that 17 (65.3%) of these patients had seronegative RA. High-titre results (1 ≥ 1/320) were more common in patients with AID. Anti-Ro52 was prevalent in 50% of extractable nuclear antigen (ENA)-positive patients, making it a remarkable finding. The majority of individuals with high-titre anti-Golgi antibodies had AID, particularly RA. The majority of these patients also tested negative for anti-cyclic citrullinated peptide (anti-CCP) and rheumatoid factor (RF). Finally, high-titre anti-Golgi antibodies may be an important serologic marker for seronegative RA in the Turkish population.
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Affiliation(s)
- Emrah Salman
- Department of Immunology, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Bedia Dinç
- Department of Microbiology, Ankara Bilkent City Hospital, Ankara, Turkey
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Bayhan Gİ, Gülleroğlu NB, Çetin S, Erat T, Yıldız S, Özen S, Konca HK, Yahşi A, Dinç B. Radiographic findings of adenoviral pneumonia in children. Clin Imaging 2024; 108:110111. [PMID: 38368746 DOI: 10.1016/j.clinimag.2024.110111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/20/2024]
Abstract
OBJECTIVE Adenovirus pneumonia is a common cause of community-acquired pneumonia in children and can mimic bacterial pneumonia, but there are few publications on its radiographic features. This study has evaluated the chest radiography findings of community-acquired adenovirus pneumonia in children. The frequency of radiological findings mimicking bacterial pneumonia was investigated. The clinical features of patients with adenovirus pneumonia possessing radiological findings mimicking bacterial pneumonia were also evaluated. MATERIALS AND METHODS The chest radiographs of patients diagnosed with adenovirus pneumonia were retrospectively reviewed. The chest radiographs were interpreted independently by a pediatric infectious disease specialist and a pediatric radiologist. Chest radiography findings mimicking bacterial pneumonia (bacterial-like) were specified as consolidation +/- pleural effusion. Other findings on chest radiography or a completely normal chest X-ray were specified as findings that were compatible with "typical viral pneumonia". RESULTS A total of 1407 patients were positive for adenovirus with respiratory multiplex PCR. The 219 patients who met the study criteria were included in the study. Chest radiographs were normal in 58 (26.5 %) patients. The chest radiograph findings mimicked bacterial pneumonia in 41 (18.7 %) patients. CONCLUSION Adenovirus pneumonia occurs predominantly in children aged five years and younger, as with other viral pneumonias. The radiographic findings in adenovirus pneumonia are predominantly those seen in viral pneumonia. Increasing age and positivity for only adenovirus without other viruses on respiratory multiplex PCR were associated with the chest radiograph being more likely to be "bacterial-like". Adenovirus may lead to lobar/segmental consolidation at a rate that is not very rare.
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Affiliation(s)
- Gülsüm İclal Bayhan
- Ankara Yıldırım Beyazıt University, Faculty of Medicine, Ankara City Hospital, Department of Pediatric Infectious Disease, Turkey.
| | | | - Selin Çetin
- Ankara City Hospital, Department of General Pediatrics, Turkey
| | - Tuğba Erat
- Ankara City Hospital, Department of Pediatric Infectious Disease, Turkey
| | - Selin Yıldız
- Ankara City Hospital, Department of Pediatric Infectious Disease, Turkey
| | - Seval Özen
- Ankara City Hospital, Department of Pediatric Infectious Disease, Turkey
| | - Hatice Kübra Konca
- Ankara City Hospital, Department of Pediatric Infectious Disease, Turkey
| | - Aysun Yahşi
- Ankara City Hospital, Department of Pediatric Infectious Disease, Turkey
| | - Bedia Dinç
- Ankara City Hospital, Department of Microbiology, Turkey
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Bayhan Gİ, Altan I, Mercan H, Özkaya Parlakay A, Coşkun ZN, Dinç B, Gülhan B, Kanik-Yüksek S. Is SARS-CoV-2 Now More Like the Seasonal Coronaviruses Following Its Evolution? Pediatr Infect Dis J 2024:00006454-990000000-00800. [PMID: 38534261 DOI: 10.1097/inf.0000000000004327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
BACKGROUND SARS-CoV-2 has evolved significantly since the beginning of the COVID-19 pandemic. COVID-19 mortality has decreased due to increased population immunity and possibly the reduced intrinsic severity of the new variants. SARS-CoV-2 is now considered an endemic virus, but the extent to which its clinical findings resemble those of seasonal coronaviruses (sCoV) is not fully understood. METHODS Pediatric patients under 18 years of age who were sent for SARS-CoV-2 polymerase chain reaction real-time reverse transcription polymerase chain reaction between January 1, 2022 and January 14, 2023 and whose results were positive were included in this study. To include only symptomatic COVID-19 patients in the study, asymptomatic patients who were positive in their screening tests were excluded. For the sCoV patients' group, patients who had a respiratory viral polymerase chain reaction assay between January 10, 2022 and January 11, 2023 and were positive for any type of sCoV were included in the study. The 2 groups were compared for clinical and laboratory characteristics. RESULTS The study included 213 patients with COVID-19 and 194 patients with sCoV infection. Fever was a more common symptom in patients with COVID-19. sCoV was associated with lower respiratory involvement while increasing age was protective. The likelihood of hospitalization was decreased by increasing age but increased by the presence of comorbid conditions and lower respiratory tract involvement. The type of virus had no effect on the likelihood of hospitalization. CONCLUSIONS In conclusion, sCoV infections carry a higher risk for lower respiratory involvement than COVID-19, and COVID-19 has a milder course than sCoV infections in children.
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Affiliation(s)
- Gülsüm İclal Bayhan
- From the Department of Pediatric Infectious Disease, Faculty of Medicine, Ankara Yildirim Beyazit University
| | | | | | - Aslinur Özkaya Parlakay
- From the Department of Pediatric Infectious Disease, Faculty of Medicine, Ankara Yildirim Beyazit University
| | | | - Bedia Dinç
- Department of Microbiology, Ankara City Hospital, Ankara, Turkey
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Mızrak M, Sarzhanov F, Demirel F, Dinç B, Filik L, Dogruman-Al F. Detection of Blastocystis sp. and Dientamoeba fragilis using conventional and molecular methods in patients with celiac disease. Parasitol Int 2024; 101:102888. [PMID: 38499283 DOI: 10.1016/j.parint.2024.102888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/20/2024]
Abstract
Blastocystis sp. and Dientamoeba fragilis are intestinal protists, which are common worldwide, but the pathogenic role of these organisms in gastrointestinal diseases is still controversial. This study aimed to investigate the frequency of Blastocystis sp. and D. fragilis in stool samples from adult patients with celiac disease (CD) by using conventional and molecular methods. A total of 75 patients with CD and 75 healthy individuals were included in this study. Fresh stool specimens collected from each individual were analyzed by conventional and molecular methods. The overall prevalence of Blastocystis sp. and D. fragilis was 41.3% (31/75) and 24% (18/75) in patients with CD, and 46.7% (35/75) and 13.3% (10/75) in healthy controls, respectively. There was no statistically significant difference in the prevalence of Blastocystis sp. and D. fragilis between CD patients and healthy individuals. Blastocystis sp. subtypes were identified in 20 CD and 16 control patients and the overall subtype distribution was observed as ST1 13.9%, ST2 30.6%, and ST3 55.6%. The prevalence of Blastocystis sp. and D. fragilis in adults with CD is similar to the prevalence of protozoa in healthy adults. In this study, the most prevalent Blastocystis subtype was ST3 and the most frequent allele was a34 in both CD patients and healthy individuals. No significant difference was found between the two groups in terms of the detection rates of Blastocystis sp. and D. fragilis, and it is thought that both protists may be colonisers of the intestinal microbiome.
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Affiliation(s)
- Muzaffer Mızrak
- Yozgat City Hospital, Department of Microbiology, Yozgat, Turkey
| | - Fakhriddin Sarzhanov
- Khoja Akhmet Yassawi International Kazakh-Turkish University, Faculty of Medicine, Turkistan, Kazakhstan
| | - Filiz Demirel
- Health Science University, Ankara City Hospital, Department of Medical Microbiology, Ankara, Turkey.
| | - Bedia Dinç
- Health Science University, Ankara City Hospital, Department of Medical Microbiology, Ankara, Turkey
| | - Levent Filik
- Ankara Training and Research Hospital, Department of Gastroenterology, Ankara, Turkey
| | - Funda Dogruman-Al
- Gazi University, Faculty of Medicine, Department of Medical Microbiology, Division of Medical Parasitology, Ankara, Turkey
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Özen S, Karabiçak N, Uzuntaş ST, Kanik-Yüksek S, Yildiz S, Güder L, Üçkardeş F, Şahin S, Dinç B, Özyörük D, Parlakay ANÖ, Bayhan Gİ. Three Cases of Catheter-related Bloodstream Infection Caused by Phialemonium curvata : A Case Report and Literature Review. Pediatr Infect Dis J 2023:00006454-990000000-00622. [PMID: 37922485 DOI: 10.1097/inf.0000000000004142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
BACKGROUND With recent developments in the field of microbiology, an increasing number of yeasts and molds with the potential to cause infections in humans are identified every year. In addition to the challenges in identifying clinical isolates, there is limited antifungal susceptibility data available for Phialemonium species, leading to uncertainty in optimal treatment recommendations. METHODS In this article, catheter-related bloodstream infections caused by Phialemonium curvata (previously Phialemonium curvatum ) in 3 immunosuppressed patients are presented. Furthermore, the literature was reviewed to identify the clinical spectrum and treatment approaches for the reported infections. RESULTS The cases presented here were analyzed along with 24 cases reported in the literature. Among all cases, 21 (77.7%) patients had an underlying condition. Nine (33.3%) patients had hematological/oncological malignancies and solid organ transplants. Twenty-two (81.4%) patients had a history of device or invasive interventions. Surgical procedures, removal of contaminated devices or tissue were found to reduce the risk of death by 86.7%. Correspondence analysis revealed a significant association between antifungal treatment and outcome ( P < 0.001). The correspondence analysis could explain 53.9% of this relationship. Monotherapy and combination therapy were associated with survival. While salvage treatment or no antifungal therapy was associated with mortality, intravitreal injection or topical application of voriconazole was associated with sequelae. CONCLUSIONS Surgical intervention and removal of contaminated devices or tissue should be considered at an early stage.
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Affiliation(s)
- Seval Özen
- From the Department of Pediatric Infectious Diseases, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Nilgün Karabiçak
- National Mycology Reference Laboratory, Public Health Institution of Turkey, Ankara, Turkey
| | - Sema Turan Uzuntaş
- Department of Medical Microbiology, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Saliha Kanik-Yüksek
- From the Department of Pediatric Infectious Diseases, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Selin Yildiz
- From the Department of Pediatric Infectious Diseases, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Latife Güder
- From the Department of Pediatric Infectious Diseases, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Fatih Üçkardeş
- Department of Biostatistics and Medical Informatics, Adiyaman University, Adiyaman, Turkey; and
| | - Seda Şahin
- Department of Pediatric Hematology and Oncology, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Bedia Dinç
- Department of Medical Microbiology, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Derya Özyörük
- Department of Pediatric Hematology and Oncology, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Asli Nur Özkaya Parlakay
- From the Department of Pediatric Infectious Diseases, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Gülsüm İclal Bayhan
- From the Department of Pediatric Infectious Diseases, Ankara Bilkent City Hospital, Ankara, Turkey
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Aydoğan S, Kırca F, Gözalan A, Toyran A, Başyiğit T, Omay İ, Dinç B. [Viral Respiratory Tract Infection Agents Detected Between Years 2019-2021, COVID-19, and Co-Infections]. MIKROBIYOL BUL 2023; 57:650-659. [PMID: 37885392 DOI: 10.5578/mb.20239952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
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.
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Affiliation(s)
- Sibel Aydoğan
- University of Health Sciences, Ankara Bilkent City Health Training and Research Center, Department of Medical Microbiology, Ankara, Türkiye
| | - Füsun Kırca
- Ankara Bilkent City Hospital, Laboratory of Medical Microbiology, Ankara, Türkiye
| | - Ayşegül Gözalan
- Alanya Alaaddin Keykubat University Faculty of Medicine, Department of Medical Microbiology, Antalya, Türkiye
| | - Alparslan Toyran
- Ankara Bilkent City Hospital, Laboratory of Medical Microbiology, Ankara, Türkiye
| | - Tuğcan Başyiğit
- Ankara Bilkent City Hospital, Laboratory of Medical Microbiology, Ankara, Türkiye
| | - İpek Omay
- Ankara Bilkent City Hospital, Laboratory of Medical Microbiology, Ankara, Türkiye
| | - Bedia Dinç
- University of Health Sciences, Ankara Bilkent City Health Training and Research Center, Department of Medical Microbiology, Ankara, Türkiye
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Özkan-Ahmetoğlu M, Demirel F, Taşar MA, Dinç B, Sarzhanov F, Dogruman-Al F. Investigation of intestinal parasites by conventional and molecular methods in children with gastrointestinal system complaints. Parasitol Res 2023; 122:1361-1370. [PMID: 37036521 DOI: 10.1007/s00436-023-07836-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/30/2023] [Indexed: 04/11/2023]
Abstract
Intestinal parasitic infections are a global health problem that causes morbidity and mortality, especially in children living in rural areas. In this study, stool samples of pediatric patients with gastrointestinal complaints were examined by conventional and molecular methods to determine the prevalence of intestinal parasites. A total of 100 pediatric patients with gastrointestinal complaints and 50 healthy children were included in the study. Stool samples were collected from each child and examined by direct microscopic examination (native-Lugol method), formol-ethyl acetate concentration technique, Kinyoun's acid-fast staining, and Wheatley trichrome staining methods. Real-time PCR was used for the detection of Blastocystis spp. and D. fragilis in the stool samples. Sanger sequencing was used to identify Blastocystis spp. subtypes. One or more intestinal parasites were found in 12% (n = 100) of the patient group and 1% (n = 50) of the control group using conventional techniques. By using real-time PCR, Blastocystis spp. was discovered in 14% (14/100) of the patient group and 8% (4/50) of the control group. There was no significant difference in the frequency of Blastocystis spp. between the two groups. The most prevalent Blastocystis subtype was ST1 and the most frequent allele was a2 among the samples successfully amplified and sequenced. D. fragilis was detected in 17% (17/100) of the patient group and 8% (4/50) of the control group by real-time PCR. The prevalence of D. fragilis was not significantly different between the patient and control groups, as well. Blastocystis spp. and D. fragilis were found in high prevalence in pediatric patients with gastrointestinal complaints in this study. Although the role of these protists as a pathogen in humans is still controversial, it is supposed to the presence of the parasites are associated with gastrointestinal disorders such as diarrhea, abdominal pain, nausea, and vomiting. More case-control studies are needed to understand the pathogenic or commensal role of these parasites on the intestinal microbiota, especially in both patients with gastrointestinal disorders and healthy individuals.
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Affiliation(s)
- Merve Özkan-Ahmetoğlu
- Department of Medical Microbiology, Ankara Training and Research Hospital, Health Science University, Ankara, Türkiye
| | - Filiz Demirel
- Department of Medical Microbiology, Ankara Bilkent City Hospital, Ankara, Turkey.
| | - Medine Ayşin Taşar
- Department of Pediatrics, Ankara Training and Research Hospital, Health Science University, Ankara, Türkiye
| | - Bedia Dinç
- Department of Medical Microbiology, Ankara Bilkent City Hospital, Health Science University, Ankara, Türkiye
| | - Fakhriddin Sarzhanov
- Faculty of Medicine, Khoja Akhmet Yassawi International Kazakh-Turkish University, Turkistan, Kazakhstan
| | - Funda Dogruman-Al
- Division of Medical Parasitology, Department of Medical Microbiology, Faculty of Medicine, Gazi University, Ankara, Türkiye
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Erat T, Parlakay AÖ, Gülhan B, Konca HK, Yahşi A, Özen S, Koçkuzu E, Dinç B, Yüksek SK, Bayhan Gİ. Emergency in Group A Streptococcal Infections: Single center data from Turkey. Pediatr Infect Dis J 2023:00006454-990000000-00407. [PMID: 37053596 DOI: 10.1097/inf.0000000000003926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Affiliation(s)
- Tuğba Erat
- Department of Pediatric Infectious Diseases Ankara City Hospital Ankara, Turkey
| | - Aslinur Özkaya Parlakay
- Department of Pediatric Infectious Diseases Ankara Yildirim Beyazit University Ankara City Hospital Ankara, Turkey
| | - Belgin Gülhan
- Department of Pediatric Infectious Diseases Ankara City Hospital Ankara, Turkey
| | - Hatice Kübra Konca
- Department of Pediatric Infectious Diseases Ankara City Hospital Ankara, Turkey
| | - Aysun Yahşi
- Department of Pediatric Infectious Diseases Ankara City Hospital Ankara, Turkey
| | - Seval Özen
- Department of Pediatric Infectious Diseases Ankara City Hospital Ankara, Turkey
| | - Esra Koçkuzu
- Department of Pediatric Intensive Care Unit Ankara City Hospital Ankara, Turkey
| | - Bedia Dinç
- Department of Medical Microbiology Ankara City Hospital Ankara, Turkey
| | - Saliha Kanik Yüksek
- Department of Pediatric Infectious Diseases Ankara City Hospital Ankara, Turkey
| | - Gülsüm İclal Bayhan
- Department of Pediatric Infectious Diseases Ankara Yildirim Beyazit University Ankara City Hospital Ankara, Turkey
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Sarigüzel FM, Koç AN, Sağiroğlu P, Atalay MA, Borlu A, Canöz Ö, Dinç B. Molecular epidemiology and antifungal susceptibilities of Aspergillus species isolated from patients with invasive aspergillosis. Rev Assoc Med Bras (1992) 2023; 69:44-50. [PMID: 36820712 PMCID: PMC9937602 DOI: 10.1590/1806-9282.20220441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/15/2022] [Indexed: 02/19/2023]
Abstract
OBJECTIVE The aim of this study was to evaluate the demographic data, molecular epidemiology, and in vitro antifungal susceptibility results of patients with Aspergillus isolated from various clinical specimens. METHODS A total of 44 Aspergillus strains were studied. The definition of invasive aspergillosis in patients was made according to European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) criteria. Strains were phenotypically and molecularly identified. Demographic characteristics of patients and genotypes of strains were evaluated. Phylogenetic analysis was done by the The Unweighted Pair-Group Method with Arithmetic Mean (UPGMA). Antifungal susceptibility of strains was determined according to The Clinical and Laboratory Standards Institute (CLSI)-M61-Ed2 and The European Committee on Antimicrobial Susceptibility Testing (EUCAST). RESULTS A total of 11 patients were classified as proven and 33 as probable invasive aspergillosis. There was a statistically significant difference in age groups, subdisease, neutropenic, and receiving chemotherapy between groups. A total of 23 strains were identified as Aspergillus fumigatus, 12 as Aspergillus niger, 6 as Aspergillus flavus, and 3 as Aspergillus terreus. Phylogenetic analysis revealed five different genotypes. No statistical difference was found in the comparisons between patients groups and genotype groups. There was a statistically significant difference between genotype groups and voriconazole, posaconazole, and itraconazole Minimum Inhibition Concentration (MIC). CONCLUSION Accurate identification of strains and antifungal susceptibility studies should be performed due to azole and amphotericin B resistance. Genotyping studies are important in infection control due to identifying sources of infection and transmission routes.
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Affiliation(s)
- Fatma Mutlu Sarigüzel
- Erciyes Üniversitesi, Faculty of Medicine, Department of Medical Microbiology – Kayseri, Turkey.,Corresponding author:
| | - Ayse Nedret Koç
- Erciyes Üniversitesi, Faculty of Medicine, Department of Medical Microbiology – Kayseri, Turkey
| | - Pınar Sağiroğlu
- Erciyes Üniversitesi, Faculty of Medicine, Department of Medical Microbiology – Kayseri, Turkey
| | - Mustafa Altay Atalay
- Erciyes Üniversitesi, Faculty of Medicine, Department of Medical Microbiology – Kayseri, Turkey
| | - Arda Borlu
- Erciyes Üniversitesi, Faculty of Medicine, Department of Public Health – Kayseri, Turkey
| | - Özlem Canöz
- Erciyes Üniversitesi, Faculty of Medicine, Department of Medical Pathology – Kayseri, Turkey
| | - Bedia Dinç
- Ankara Bilkent City Hospital, Department of Medical Microbiology – Ankara, Turkey
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Bayhan Gİ, Özkubat Korkmaz I, Şahiner ES, Tekeli N, Akdağ AG, Uyan Erten AZ, Taşbaşı AB, Göre B, Doğru M, Kırca F, Dinç B. Are SARS-CoV-2 viral loads in children lower than in adults? J Infect 2023; 86:e13-e14. [PMID: 36029921 PMCID: PMC9398939 DOI: 10.1016/j.jinf.2022.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 02/04/2023]
Affiliation(s)
- Gülsüm İclal Bayhan
- Department of Pediatric Infectious Disease, Ankara City Hospital, Yildirim Beyazit University, Turkey,Corresponding author
| | | | | | - Nazlı Tekeli
- Department of General Pediatrics, Ankara City Hospital, Turkey
| | - Ahmet Gökhan Akdağ
- Division of Intensive Care, Department of Internal Medicine, Ankara City Hospital, Turkey
| | | | | | - Burak Göre
- Department of Internal Medicine, Ankara City Hospital, Turkey
| | - Mustafa Doğru
- Department of Internal Medicine, Ankara City Hospital, Turkey
| | - Fisun Kırca
- Department of Microbiology, Ankara City Hospital, Turkey
| | - Bedia Dinç
- Department of Microbiology, Ankara City Hospital, Turkey
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12
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Öcalan F, Mumcuoğlu İ, Ünaldı Ö, Bakkaloğlu Z, Dinç B. [Evaluation of Antibiotic Susceptibility, Biofilm Production and Clonal Analysis of Corynebacterium striatum Isolates]. MIKROBIYOL BUL 2023; 57:1-13. [PMID: 36636842 DOI: 10.5578/mb.20239901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this study, it was aimed to determine the possible factors affecting the clinical importance of Corynebacterium striatum isolates, which were accepted as infectious or contamination/colonization agents, by comparing their clinical and microbiological characteristics, antimicrobial susceptibility results, biofilm forming abilities and genotypic characteristics. The patients with C.striatum growth in the clinical samples sent to the laboratory were evaluated as infection or contamination/colonization with the evaluation of the examination findings and other laboratory parameters by the relevant physician. This study included 58 isolates, 29 of which were considered as infection and 29 as contamination/colonization. Length of hospital stay, presence of underlying disease [diabetes mellitus (DM), neurological disease, ischemic heart disease, chronic kidney disease, solid tumor], surgical operation status in the last month, and antibiotic use in the last three months of the patients were examined. Identification of the bacterial type was made with MALDI-TOF MS (Bruker/Germany) system. Antimicrobial susceptibility tests were performed by disc diffusion and gradient diffusion method and evaluated according to EUCAST standards. Biofilm production was determined in 96-well microtiter plates on negatively charged polystyrene surfaces. Clonal analyzes were performed by PFGE method using Xba1 enzyme. It was observed that there was no difference in terms of demographic characteristics in the two patient groups included in the study. It was observed that C.striatum strains isolated from outpatients were mostly found in the contamination/ colonization group. The presence of diabetes mellitus, ischemic heart disease, chronic kidney disease and solid tumor was not statistically different in the two patient groups. It was observed that C.striatum strains grown in the samples of patients with neurological disease were mostly found in the infectious agent group (p= 0.025). It has been observed that C.striatum strains grown purely in culture were mostly found in the infectious agent group (p= 0.001). Biofilm production was found to be significantly higher in the infectious agent group (p= 0.015). In antimicrobial susceptibility tests, it was observed that there was widespread multidrug resistance (MDR) in both groups and there was no significant difference between the groups in terms of antimicrobial susceptibility. In our study, it was determined that the strains showed very different PFGE patterns and were not clonally related to each other. In this study, it was determined that the demographic characteristics and comorbidities of the patients were not helpful in evaluating the clinical significance of C.striatum. Biofilm production was observed to be a common virulence factor in C.striatum strains. It was thought that there may be difficulties in the treatment of C.striatum in the future due to the widespread MDR detection among this bacterium strains. Our study contributes to draw attention to the increase in C.striatum infections, resistance and virulence factors.
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Affiliation(s)
- Fatma Öcalan
- Ankara City Hospital, Laboratory of Medical Microbiology, Ankara, Türkiye
| | - İpek Mumcuoğlu
- Ankara City Hospital, Laboratory of Medical Microbiology, Ankara, Türkiye
| | - Özlem Ünaldı
- TR Ministry of Health, General Directorate of Public Health, Department of Microbiology Reference Laboratory and Biological Products, Ankara, Türkiye
| | - Zekiye Bakkaloğlu
- TR Ministry of Health, General Directorate of Public Health, Department of Microbiology Reference Laboratory and Biological Products, Ankara, Türkiye
| | - Bedia Dinç
- Ankara City Hospital, Laboratory of Medical Microbiology, Ankara, Türkiye
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13
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Kirca F, Aydoğan S, Gözalan A, Kayipmaz AE, Özdemir FAE, Tekçe YT, Beşer İO, Gün P, Ökten RS, Dinç B. Comparison of clinical characteristics of wild-type SARS-CoV-2 and Omicron. Rev Assoc Med Bras (1992) 2022; 68:1476-1480. [PMID: 36417656 PMCID: PMC9683927 DOI: 10.1590/1806-9282.20220880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/06/2022] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE This study aimed to investigate the effect of mutations by comparing wild-type SARS-CoV-2 and Omicron regarding clinical features in patients with COVID-19. It also aimed to assess whether SARS-CoV-2 cycle threshold value could predict COVID-19 severity. METHODS A total of 960 wild-type and 411 Omicron variant patients with positive results in SARS-CoV-2 real-time reverse transcriptase polymerase chain reaction test from oropharyngeal and/or nasopharyngeal samples during their hospital admissions were included in this retrospective study. The reference symptoms of the patients were obtained from the hospital database. The correlation between chest computed tomography findings and the "cycle threshold" of patients with wild-type SARS-CoV-2 was assessed. RESULTS Cough, fever, shortness of breath, loss of taste and smell, and diarrhea were found to be statistically significantly higher (p=0.001; 0.001; 0.001; 0.001; and 0.006; respectively) in the wild-type cohort, while in the Omicron cohort, sore throat and headache were found to be statistically significantly higher (p=0.001 and 0.003, respectively). An inverse relationship was found between chest computed tomography findings and viral load. CONCLUSION This study revealed that the Omicron variant tended to infect predominantly the upper respiratory tract and showed decreased lung infectivity, and the disease progressed with a milder clinical course. Therefore, the study showed that the tropism of the virus was changed and the viral phenotype was affected. It was also found that SARS-CoV-2 viral load did not predict COVID-19 severity in patients with wild-type SARS-CoV-2.
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Affiliation(s)
- Füsun Kirca
- Ankara Şehir Hastanesi, Department of Medical Microbiology – Ankara, Turquia.,Corresponding author:
| | - Sibel Aydoğan
- Ankara Şehir Hastanesi, Department of Medical Microbiology – Ankara, Turquia
| | - Ayşegül Gözalan
- Alanya Alaaddin Keykubat University, Department of Medical Microbiology – Antalya, Turquia
| | | | | | - Yasemin Tezer Tekçe
- Ankara Şehir Hastanesi, Department of Infectious Disease and Clinical Microbiology – Ankara, Turquia
| | - İpek Omay Beşer
- Ankara Şehir Hastanesi, Department of Medical Microbiology – Ankara, Turquia
| | - Pınar Gün
- Ankara Şehir Hastanesi, Department of Medical Microbiology – Ankara, Turquia
| | | | - Bedia Dinç
- Ankara Şehir Hastanesi, Department of Medical Microbiology – Ankara, Turquia
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14
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Öcal DF, Öztürk FH, Şenel SA, Sinaci S, Yetişkin FDY, Keven C, Dinç B, Turgut E, Oluklu D, Tekin ÖM, Şahin D. The influence of COVID-19 pandemic on intrauterine fetal demise and possible vertical transmission of SARS-CoV-2. Taiwan J Obstet Gynecol 2022; 61:1021-1026. [PMID: 36427967 PMCID: PMC9482846 DOI: 10.1016/j.tjog.2022.03.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2022] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE The impact of COVID-19 on intrauterine fetal demise (IUFD) and vertical transmission of the SARS-CoV-2 from the mother to the fetus are crucial issues of the COVID-19 pandemic. In the current study, we aimed to detect the pandemic's influence on the IUFD and evaluate the vertical transmission of the SARS-CoV-2 through analysis of placental tissues collected from PCR positive women with IUFD above 20 weeks of gestation. MATERIALS AND METHODS The pregnant women above 20 weeks of gestation and had a fetus intrauterine demised during pandemic were included in the study. The pregnant women screened for COVID-19. Vertical transmission searched from placental tissues of COVID-19 positive women by RT-PCR tests for the presence of SARS-CoV-2 RNA. The number of IUFD before the pandemic and during the pandemic compared to assess the influence of the COVID-19 pandemic on the IUFD ratio. RESULTS Among 138 pregnant women with IUFD, 100 of them could screen for COVID-19 status. RT-PCR test results of 6 of the screened pregnant women were positive for SARS-CoV-2. Placental tissues of these six women were analyzed, and one test result was positive for SARS-CoV-2 RNA. The IUFD ratio was significantly increased during the pandemic. CONCLUSION It is clear that COVID-19 increases the IUFD ratio. Previous data for vertical transmission of SARS-CoV-2 during the second trimester is limited. We present the third case of literature that has positive placental results for SARS-CoV-2 RNA in the second trimester of pregnancy.
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Affiliation(s)
- Doğa Fatma Öcal
- Department of Obstetrics and Gynecology, Turkish Ministry of Health, Ankara City Hospital, Ankara, Turkey,Corresponding author. Akşemsettin Mah., 2308 Sk., No: 1/C-77, Mamak, Ankara, Turkey
| | - Filiz Halıcı Öztürk
- Department of Obstetrics and Gynecology, Turkish Ministry of Health, Ankara City Hospital, Ankara, Turkey
| | - Selvi Aydın Şenel
- Department of Obstetrics and Gynecology, Turkish Ministry of Health, Ankara City Hospital, Ankara, Turkey
| | - Selcan Sinaci
- Department of Obstetrics and Gynecology, Turkish Ministry of Health, Ankara City Hospital, Ankara, Turkey
| | - Fatma Didem Yücel Yetişkin
- Department of Obstetrics and Gynecology, Turkish Ministry of Health, Ankara City Hospital, Ankara, Turkey
| | - Can Keven
- Department of Obstetrics and Gynecology, Turkish Ministry of Health, Ankara City Hospital, Ankara, Turkey
| | - Bedia Dinç
- Department of Medical Microbiology, Turkish Ministry of Health, Ankara City Hospital, Ankara, Turkey,University of Health Sciences, Istanbul, Turkey
| | - Ezgi Turgut
- Department of Obstetrics and Gynecology, Turkish Ministry of Health, Ankara City Hospital, Ankara, Turkey
| | - Deniz Oluklu
- Department of Obstetrics and Gynecology, Turkish Ministry of Health, Ankara City Hospital, Ankara, Turkey
| | - Özlem Moraloğlu Tekin
- Department of Obstetrics and Gynecology, Turkish Ministry of Health, Ankara City Hospital, Ankara, Turkey,University of Health Sciences, Istanbul, Turkey
| | - Dilek Şahin
- Department of Obstetrics and Gynecology, Turkish Ministry of Health, Ankara City Hospital, Ankara, Turkey,University of Health Sciences, Istanbul, Turkey
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15
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Özkul G, Kehribar EŞ, Ahan RE, Köksaldı İÇ, Özkul A, Dinç B, Aydoğan S, Şeker UÖŞ. A Genetically Engineered Biofilm Material for SARS-CoV-2 Capturing and Isolation. Adv Mater Interfaces 2022; 9:2201126. [PMID: 36248312 PMCID: PMC9538133 DOI: 10.1002/admi.202201126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/10/2022] [Indexed: 06/16/2023]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously infecting people all around the world since its outbreak in 2019. Studies for numerous infection detection strategies are continuing. The sensitivity of detection methods is crucial to separate people with mild infections from people who are asymptomatic. In this sense, a strategy that would help to capture and isolate the SARS-CoV-2 virus prior to tests can be effective and beneficial. To this extent, genetically engineered biomaterials grounding from the biofilm protein of Escherichia coli are beneficial due to their robustness and adaptability to various application areas. Through functionalizing the E. coli biofilm protein, diverse properties can be attained such as enzyme display, nanoparticle production, and medical implant structures. Here, E. coli species are employed to express major curli protein CsgA and Griffithsin (GRFT) as fusion proteins, through a complex formation using SpyTag and SpyCatcher domains. In this study, a complex system with a CsgA scaffold harboring the affinity of GRFT against Spike protein to capture and isolate SARS-CoV-2 virus is successfully developed. It is shown that the hybrid recombinant protein can dramatically increase the sensitivity of currently available lateral flow assays for Sars-CoV-2 diagnostics.
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Affiliation(s)
- Gökçe Özkul
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - Ebru Şahin Kehribar
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - Recep Erdem Ahan
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - İlkay Çisil Köksaldı
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - Aykut Özkul
- Department of VirologyFaculty of Veterinary MedicineAnkara UniversityDışkapıAnkara06110Turkey
| | - Bedia Dinç
- Medical Microbiology Laboratory and Department of Clinical Microbiology and Infectious DiseasesAnkara Bilkent City HospitalHealth Sciences UniversityAnkara06800Turkey
| | - Sibel Aydoğan
- Medical Microbiology Laboratory and Department of Clinical Microbiology and Infectious DiseasesAnkara Bilkent City HospitalHealth Sciences UniversityAnkara06800Turkey
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Abstract
OBJECTIVE This study aimed to evaluate the distribution of intestinal parasites in refugee and native patients who applied to a territory hospital in Turkey. METHODS A total of 17911 patients who were admitted to our hospital between January 2018 and January 2019 were evaluated retrospectively in terms of intestinal parasites. The patients' stool samples were investigated for the existence of intestinal parasites by direct wet mount preparation, formalin ether concentration technique and cellophane tape method. The data obtained were compared between patient groups according to the examination method. RESULTS The overall prevalence of E. vermicularis in refugee children was found twice higher than that in native patients and the most common symptom was abdominal pain in these patients. Intestinal parasite detection rates were significantly higher in the stool concentration method than in the direct wet mount examination. Cutaneous complaints and protein energy malnutrition/growth retardation were the most common clinical conditions besides gastrointestinal symptoms in patients with intestinal parasitosis. CONCLUSION In our study, the prevalence of Blastocystis sp. in refugees was found to be higher than in the normal population. Intestinal parasitic infections should be investigated with proper diagnostic methods especially in children with PEM/GR and cutaneous symptoms in addition to gastrointestinal problems.
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Affiliation(s)
- Filiz Demirel
- University of Health Sciences Turkey, Ankara Training and Research Hospital, Clinic of Medical Microbiology, Ankara, Turkey
| | - Bedia Dinç
- University of Health Sciences Turkey, Ankara Training and Research Hospital, Clinic of Medical Microbiology, Ankara, Turkey
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17
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Sarıkaya A, Mumcuoğlu İ, Baran I, Aksoy A, Dinç B. Comparision of Colistin Broth Disc Elution, Rapid Resapolymyxin NP and Broth Microdilution Methods in Determining Colistin Sensitivity in Acinetobacter, Pseudomonas and Enterobacterales species. MIKROBIYOL BUL 2022; 56:404-415. [DOI: 10.5578/mb.20229703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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18
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Mumcuoğlu İ, Çağlar H, Erdem D, Aypak A, Gün P, Kurşun Ş, Çakır EY, Aydoğan S, Kırca F, Dinç B. Secondary bacterial infections of the respiratory tract in COVID-19 patients. J Infect Dev Ctries 2022; 16:1131-1137. [PMID: 35905017 DOI: 10.3855/jidc.16724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 04/29/2022] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION Secondary Bacterial Infections (SBIs) of the respiratory system are one of the biggest medical concerns in patients undergoing hospitalization with a diagnosis of COVID-19. This study aims to provide relevant data for the initiation of appropriate empirical treatment after examining the etiology and antimicrobial resistance of SBIs in COVID-19 patients under care in the Intensive Care Units (ICUs) in the largest pandemic hospital of our country. METHODOLOGY Between March 16, 2020 and December 31, 2021, 56,993 COVID patients were hospitalized, of which 7684 were admitted to ICUs. A total of 1513 patients diagnosed with SBIs have been included in this study. During the course of the study, demographic data, clinical course, etiology and antimicrobial resistance data of all patients were collected. RESULTS The most common causative agents of SBIs were inferred as Acinetobacter baumanii (35.1%), Staphylococcus aureus (15.2%), Klebsiella pneumoniae (12.3%) and Pseudomonas aeruginosa (10.4%). The isolation rates of carbapenem-resistant and colistin-resistant A. baumannii, K. pneumoniae and P. aeruginosa were 83.7%; 42.7%, 79.2%, and 5.6%, 42.7%, 1.7%, respectively. Acinetobacter pittii clustering was seen in one of the ICUs in the hospital. Multidrug resistant 92 (5.4%) Corynebacterium striatum isolates were also found as a causative agent with increasing frequency during the study period. CONCLUSIONS SBI of the respiratory system is one of the major complications in patients hospitalized with COVID-19. The antimicrobial resistance rates of the isolated bacteria are generally high, which indicates that more accurate use of antibacterial agents is necessary for SBIs in patients hospitalized with COVID-19 diagnosis.
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Affiliation(s)
- İpek Mumcuoğlu
- Department of Medical Microbiology, Dr. Abdurrahman Yurtaslan Ankara Oncology Training and Research Hospital, Ankara, Turkey.
| | - Hatice Çağlar
- Department of Medical Microbiology, Ankara City Hospital, Ankara, Turkey
| | - Deniz Erdem
- Department of Medical Microbiology, Ankara City Hospital, Ankara, Turkey
| | - Adalet Aypak
- Department of Infectious Diseases and Clinical Microbiology, Ankara City Hospital, Ankara, Turkey
| | - Pınar Gün
- Department of Medical Microbiology, Ankara City Hospital, Ankara, Turkey
| | - Şenol Kurşun
- Department of Medical Microbiology, Ankara City Hospital, Ankara, Turkey
| | - Esra Yakışık Çakır
- Department of Anaesthesiology and Reanimation Ankara, Ankara City Hospital, Ankara, Turkey
| | - Sibel Aydoğan
- Department of Medical Microbiology, Ankara City Hospital, Ankara, Turkey
| | - Fisun Kırca
- Department of Medical Microbiology, Ankara City Hospital, Ankara, Turkey
| | - Bedia Dinç
- Department of Medical Microbiology, Ankara City Hospital, Ankara, Turkey
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Şener B, Kirbaş E, Sancak B, Gözalan A, Evren E, Karahan ZC, Zeytinoğlu A, Dinç B, Alp A, Dizman GT, Metan G, Birengel S, Gülten E, Taşbakan M, Ayhan M. PERFORMANCE EVALUATION OF SIX DIFFERENT SARS-CoV-2 ANTIBODY IMMUNOASSAYS: DISEASE SEVERITY AND SERUM SAMPLING TIME AFFECT THE SENSITIVITY. Jpn J Infect Dis 2022; 75:388-394. [PMID: 35354702 DOI: 10.7883/yoken.jjid.2021.636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Comparative validation data and clinical performance data are essential for the reliable interpretation of SARS-CoV-2 antibody test results. This study aimed to assess the performance of six SARS-CoV-2 IgG immunoassays in different disease severity settings. Four automated chemiluminescence immunoassays Access (Beckman Coulter), Architect (Abbott), Atellica-IM (Siemens) and Elecsys (Roche) and two ELISA assays (SARS-CoV-2 IgG-S1-based and NCP IgG, Euroimmun) were evaluated in 143 patients and 50 pre-pandemic control sera. Accuracy and precision tests were performed for validation. Overall sensitivity differed between 73.38-88.65%, being higher in spike protein-based assays. Specificity was ≥ 98% in all immunoassays. IgG response was lower for the samples taken <20 days post-symptom onset (87.30%) than for the samples taken ≥20 days post-symptom onset (94.80%). Higher rate of antibody was detected in the clinically moderate disease group. In the asymptomatic and mild group more antibody positivity was detected with spike protein-based assays. Clinical performance of the immunoassays differs according to disease severity and antigen targeted; moderate disease leading to highest rate of IgG response. All the assays tested were eligible for the detection of SARS-CoV-2 IgG however, spike-based assays revealed relatively higher sensitivity than the nucleoprotein-based assays particularly in the asymptomatic and mild disease severity.
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Affiliation(s)
- Burçin Şener
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Turkey
| | - Ekin Kirbaş
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Turkey
| | - Banu Sancak
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Turkey
| | - Ayşegül Gözalan
- Department of Medical Microbiology, Faculty of Medicine, Alaaddin Keykubat University, Turkey
| | - Ebru Evren
- Department of Medical Microbiology, Faculty of Medicine, Ankara University, Turkey
| | - Zeynep Ceren Karahan
- Department of Medical Microbiology, Faculty of Medicine, Ankara University, Turkey
| | - Ayşın Zeytinoğlu
- Department of Medical Microbiology, Faculty of Medicine, Ege University, Turkey
| | - Bedia Dinç
- Medical Microbiology Laboratory, Ankara Bilkent City Hospital, Turkey
| | - Alpaslan Alp
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Turkey
| | - Gülçin Telli Dizman
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Medicine, Hacettepe University, Turkey
| | - Gökhan Metan
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Medicine, Hacettepe University, Turkey
| | - Serhat Birengel
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Medicine, Ankara University, Turkey
| | - Ezgi Gülten
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Medicine, Ankara University, Turkey
| | - Meltem Taşbakan
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Medicine, Ege University, Turkey
| | - Müge Ayhan
- Department of Clinical Microbiology and Infectious Diseases, Ankara Bilkent City Hospital, Turkey
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Evren K, Akçay E, Yücel M, Bal AZ, Erdinç FŞ, Dinç B, Kalkancı A. [A case of Peritonitis Caused by Wickerhamomyces anomalus (Candida pelliculosa) Related to Peritoneal Dialysis]. MIKROBIYOL BUL 2021; 55:665-672. [PMID: 34666666 DOI: 10.5578/mb.20219718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fungal peritonitis is less commonly seen than bacterial peritonitis in patients undergoing peritoneal dialysis (PD), but it is a serious complication with high morbidity and mortality. It often results in catheter loss and modifying therapy from PD to hemodialysis. The causative organisms are often Candida species. In this report, a PD-associated peritonitis caused by Wickerhamomyces anomalus (Candida pelliculosa), a rare fungal infection agent with increasing clinical importance by causing different clinical pictures was presented. An outpatient peritoneal fluid culture was sent from a 48-yearold male patient, who had been undergoing continuous peritoneal dialysis (CAPD) for 9 years, due to abdominal pain and blur in peritoneal fluid during dialysis. The patient admitted to the emergency department four days later due to the persistence of his complaints. A sample of peritoneal fluid was taken in the emergency department and sent to the laboratory for microbiological analysis. In the direct microscopical examination of the peritoneal fluid; cell number was determined as 210/mm3, and no microorganisms were seen in the Gram and methylene blue staining. The patient was admitted to the nephrology service with a pre-diagnosis of PD-associated peritonitis. Enterobacter aerogenes was grown in the peritoneal fluid culture which was sent from the dialysis outpatient clinic four days ago. The peritoneal fluid sample sent from the emergency department was inoculated on 5% sheep blood , EMB and chocolate agars and no growth was detected. As the patient's complaints and peritoneal fluid leukocyte count continued to increase, peritoneal fluid cultures were repeated and recurrent growth of yeast was detected in cultures. The yeast was identified as Candida pelliculosa by matrix assisted laser desorption ionization time-of-flight mass spectrofotometry (MALDI-TOF) VITEK®MS (bioMerieux, France). The species identification was confirmed by sequencing the target ITS gene regions on the rRNA and the isolate was identified as 100% Wickerhamomyces anomalus (sexual reproduction form of Candida pelliculosa, teleomorph). The reference microdilution method was performed according to the recommendations of the Clinical and Laboratory Standards Institute (CLSI) in order to test the antifungal susceptibility. After 24 hour incubation, the minimal inhibitory concentrations (MIC) were determined as 0.03 μg/ml for amphotericin B, 0.125 μg/ml for caspofungin 0.125 μg/ml for voriconazole, 0.03 μg/ ml for itraconazole and 4 μg/ml for fluconazole. Fluconazole and anidulafungin were started for the treatment of fungal peritonitis. The patient's peritoneal dialysis catheter was removed and hemodialysis was applied to the patient. Clinical and laboratory symptoms regressed with antifungal therapy and the patient's anidulafungin treatment was discontinued for 14 days after the catheter removal. In conclusion, in patients undergoing CAPD, as in our case, fungal pathogens should also be considered although it is rare, when there is no laboratory and clinical improvement, and the response to treatment is not complete in PD-associated peritonitis to prevent delays in diagnosis and treatment.
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Affiliation(s)
- Kübra Evren
- University of Health Sciences, Ankara Training and Research Hospital, Clinic of Medical Microbiology, Ankara, Turkey
| | - Eda Akçay
- University of Health Sciences, Ankara Training and Research Hospital, Clinic of Medical Microbiology, Ankara, Turkey
| | - Mihriban Yücel
- University of Health Sciences, Ankara Training and Research Hospital, Clinic of Medical Microbiology, Ankara, Turkey
| | - Ayşe Zeynep Bal
- University of Health Sciences, Ankara Training and Research Hospital, Clinic of Nephrology, Ankara, Turkey
| | - Fatma Şebnem Erdinç
- University of Health Sciences, Ankara Training and Research Hospital, Clinic of Infectious Diseases and Clinical Microbiology, Ankara, Turkey
| | - Bedia Dinç
- University of Health Sciences, Ankara Training and Research Hospital, Clinic of Medical Microbiology, Ankara, Turkey
| | - Ayşe Kalkancı
- Gazi University Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkey
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21
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Salman E, Çelikbilek N, Aydoğan S, Özdem B, Gökay S, Kırca F, Toyran A, Bilici Salman R, Dinç B. [Investigation of the Relationship of Systemic Immune-Inflammation Index, C-Reactive Protein and Interleukin-6 with Viral Dynamics in Patients with COVID-19]. MIKROBIYOL BUL 2021; 55:539-552. [PMID: 34666654 DOI: 10.5578/mb.20219706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Coronaviruses are enveloped, positivepolarity, single-stranded RNA viruses that can cause respiratory and gastrointestinal tract infections, less likely to cause infections with hepatic, neurological and nephrotic involvement. A novel coronavirus termed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in the city of Wuhan, China, and caused an outbreak of unusual viral pneumonia at the end of 2019. This study aimed to reveal the relationship between systemic immune-inflammation index (SII), C-reactive protein (CRP) and interleukin-6 (IL-6) and viral dynamics in COVID-19 patients. This retrospective, single-center study was conducted in Ankara City Hospital from April 1 to May 31, 2020. A total of 338 hospitalized patients who had positive results in SARS-CoV-2 reverse transcrytase polymerase chain reaction (RT-PCR) test from nasopharyngeal and oropharyngeal samples during their hospital admission were included in this study. Patients were divided into three groups according to their ward/intensive care unit, intubation and mortality situation and their clinical data were evaluated. Correlation analysis was performed to determine the relationship between viral dynamics and laboratory parameters such as SII, the neutrophil-to-lymphocyte ratio (NLR), the lymphocyte-to-CRP ratio (LCR), the lymphocyte-to-monocyte ratio (LMR), the platelet-to-lymphocyte ratio (PLR), CRP, IL-6 ferritin, albumin levels and lymphocyte count. Advanced age, low Ct value, increase in IL-6, increase in SII, decrease in albumin, increase in ferritin, decrease in lymphocyte count, increase in NLR, decrease in LCR, decrease in LMR, increase in PLR and increase in CRP levels were found statistically significantly different in all three groups (p<0.001; p= 0.02; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001; p<0.001, respectively). Statistical analysis revealed a significant negative correlation between serum IL-6, NLR, LCR and CRP values with Ct values (p<0.01, r= -0.233; p= 0.021, r= -0.126; p=0.004, r= -0.156 and p= 0.011, r= -0.138, respectively) and a significant positive correlation between Ct values and lymphocyte count and albumin levels (p= 0.005; r= 0.151 and p= 0.050; r= 0.106, respectively). Severe progression was observed in patients with advanced age, low Ct value, high IL-6 levels, high SII, hypoalbuminemia, high ferritin levels, lymphopenia, high NLR, low LCR, low LMR, high PLR and high CRP. In these patients hospitalization in intensive care unit, intubation and mortality were found to be higher. High levels of IL-6, NLR, LCR and CRP, lymphopenia and hypoalbuminemia were associated with low PCR Ct values.
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Affiliation(s)
- Emrah Salman
- Ankara City Hospital, Clinic of Basic Immunology, Ankara, Turkey
| | | | - Sibel Aydoğan
- Ankara City Hospital, Clinic of Medical Virology, Ankara, Turkey
| | - Birsen Özdem
- Ankara City Hospital, Clinic of Medical Microbiology, Ankara, Turkey
| | - Sibel Gökay
- Ankara City Hospital, Clinic of Medical Microbiology, Ankara, Turkey
| | - Fisun Kırca
- Ankara City Hospital, Clinic of Medical Microbiology, Ankara, Turkey
| | - Alparslan Toyran
- Ankara City Hospital, Clinic of Medical Microbiology, Ankara, Turkey
| | - Reyhan Bilici Salman
- Reyhan Bilici Salman, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Clinic of Rheumatology, Ankara,Turkey
| | - Bedia Dinç
- Ankara City Hospital, Clinic of Medical Microbiology, Ankara, Turkey
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22
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Köksaldı İÇ, Köse S, Ahan RE, Hacıosmanoğlu N, Şahin Kehribar E, Güngen MA, Baştuğ A, Dinç B, Bodur H, Özkul A, Şeker UÖŞ. SARS-CoV-2 Detection with De Novo-Designed Synthetic Riboregulators. Anal Chem 2021; 93:9719-9727. [PMID: 34192453 PMCID: PMC8265535 DOI: 10.1021/acs.analchem.1c00886] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/17/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 is a human pathogen and the main cause of COVID-19 disease, announced as a global pandemic by the World Health Organization. COVID-19 is characterized by severe conditions, and early diagnosis can make dramatic changes for both personal and public health. Low-cost, easy-to-use diagnostic capabilities can have a very critical role in controlling the transmission of the disease. Here, we are reporting a state-of-the-art diagnostic tool developed with an in vitro synthetic biology approach by employing engineered de novo riboregulators. Our design coupled with a home-made point-of-care device can detect and report the presence of SARS-CoV-2-specific genes. The presence of SARS-CoV-2-related genes triggers the translation of sfGFP mRNAs, resulting in a green fluorescence output. The approach proposed here has the potential of being a game changer in SARS-CoV-2 diagnostics by providing an easy-to-run, low-cost diagnostic capability.
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Affiliation(s)
- İlkay Çisil Köksaldı
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Sıla Köse
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Recep Erdem Ahan
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Nedim Hacıosmanoğlu
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Ebru Şahin Kehribar
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Murat Alp Güngen
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Aliye Baştuğ
- Department of Infectious Diseases and Clinical
Microbiology, Health Science University Turkey, Ankara City
Hospital, 06800 Ankara, Turkey
| | - Bedia Dinç
- Department of Infectious Diseases and Clinical
Microbiology, Health Science University Turkey, Ankara City
Hospital, 06800 Ankara, Turkey
| | - Hürrem Bodur
- Department of Infectious Diseases and Clinical
Microbiology, Health Science University Turkey, Ankara City
Hospital, 06800 Ankara, Turkey
| | - Aykut Özkul
- Faculty of Veterinary Medicine, Department of
Virology, Ankara University, 06110 Ankara,
Turkey
- Biotechnology Institute, Ankara
University, 06135 Ankara, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
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23
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Güngör AA, Demirdağ TB, Dinç B, Azak E, Yazal Erdem A, Kurtipek B, Özkaya Parlakay A, Sarı N. A case of infective endocarditis due to Herbaspirillum Huttiense in a pediatric oncology patient. J Infect Dev Ctries 2020; 14:1349-1351. [PMID: 33296351 DOI: 10.3855/jidc.13001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 11/02/2020] [Indexed: 10/31/2022] Open
Abstract
Infective endocarditis (IE) is an infection of the endocardium and/or heart valves that involves thrombus formation (vegetation). This condition might damage the endocardial tissue and/or valves. An indwelling central venous catheter is a major risk factor for bacteremia at-risked pediatric populations such as premature infants; children with cancer and/or connective tissue disorders. Herbaspirillum huttiense is a Gram-negative opportunistic bacillus that may cause bacteremia and pneumonia rarely in this fragile population. Herein we report the very first case of bacteremia and IE in a pediatric oncology patient caused by H. huttiense.
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Affiliation(s)
| | - Tugba B Demirdağ
- Pediatric Infectious Diseases Department, Yildirim Beyazit University, Ankara City Hospital, Ankara, Turkey.
| | - Bedia Dinç
- Department of Medical Microbiology, Ankara City Hospital, Ankara, Turkey.
| | - Emine Azak
- Department of Pediatric Cardiology, Ankara City Hospital, Ankara, Turkey.
| | - Arzu Yazal Erdem
- Department of Pediatric Heamatology and Oncology, Ankara City Hospital, Ankara, Turkey.
| | - Burçin Kurtipek
- Department of Pediatric Heamatology and Oncology, Ankara City Hospital, Ankara, Turkey.
| | - Aslinur Özkaya Parlakay
- Pediatric Infectious Diseases Department, Yildirim Beyazit University, Ankara City Hospital, Ankara, Turkey.
| | - Neriman Sarı
- Department of Pediatric Heamatology and Oncology, Ankara City Hospital, Ankara, Turkey.
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Cesur S, Kınıklı S, Cesur S, Yücel M, Ataman Hatipoğlu Ç, Dinç B. Determination of polymyxin B, minocycline, colistin and phosphomycin susceptibilities in Acinetobacter baumannii strains showing carbapenem resistant multidrug resistance phenotype. Journal of Health Sciences and Medicine 2018. [DOI: 10.32322/jhsm.456990] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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25
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Kınıklı S, Kaya Kılıç E, Arslan K, Cesur S, Ataman Hatipoğlu Ç, Yağcı S, Dinç B. Assessment of the performance of CHROMagar Candida media in identification of candida strains. Journal of Health Sciences and Medicine 2018. [DOI: 10.32322/jhsm.440907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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26
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Cesur S, Kınıklı S, Doğan K, Büyükdemirci A, Yağcı S, Ataman Hatipoğlu Ç, Kılıç EK, Dinç B. Investigation of the presence of metallo-beta-lactamase enzyme in two different phenotypic methods in carbapenem resistant Acineobacter baumannii strains isolated from clinical specimens. Journal of Health Sciences and Medicine 2018. [DOI: 10.32322/jhsm.410890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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27
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Kabakçı Alagöz G, Karataylı SC, Karataylı E, Celik E, Keskin O, Dinç B, Cınar K, Idilman R, Yurdaydın C, Bozdayı AM. Hepatitis C virus genotype distribution in Turkey remains unchanged after a decade: performance of phylogenetic analysis of the NS5B, E1, and 5'UTR regions in genotyping efficiency. Turk J Gastroenterol 2015; 25:405-10. [PMID: 25254523 DOI: 10.5152/tjg.2014.7083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND/AIMS Hepatitis C virus (HCV) genotyping has a considerable effect on therapy. The aim was to determine the change in prevalence of HCV genotypes in Turkey during the last decade and to compare the performance of DNA sequencing of different targets in the HCV genome (NS5B, E1, and 5'UTR). MATERIALS AND METHODS Five hundred HCV RNA-positive patients (226 males, 274 females) were included in the study. The NS5B, E1, and 5'UTR regions of the HCV genome were amplified by polymerase chain reaction (PCR) in patients where possible. Amplified PCR products were sequenced directly, and phylogenetic analysis was performed. A commonly used database, namely www.hcv.lanl.gov, was also used to determine the genotypes. RESULTS Phylogenetic analysis of the NS5B, E1, and 5'UTR regions showed that 1b was the most frequent genotype, with percentages of 92.5%, 93.5%, and 87.7%, respectively. Genotype 1a was the second most prevalent genotype, with ratios of 6.7%, 5.6%, and 6.6%, whereas genotype 2a was detected in proportions of 0.4%, 0.2%, and 0.8%, respectively. Genotype 5 or 6 was not detected among patients. The phylogenetic analysis showed discordant results with 18 patients' genotypes for different targets. The phylogenetic analysis showed similar results with the hcv.lanl.gov database for the E1 and NS5B sequences. CONCLUSION There has been no change in genotyping profiles of Turkey during the last decade, representing 1b as the most prevalent subtype, followed by 1a. Phylogenetic analysis of HCV indicated high performance compared with the hcv.lanl.gov database when sequences of E1 and NS5B regions were analyzed.
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Celik I, Karatayli E, Cevik E, Kabakçi SG, Karatayli SC, Dinç B, Cinar K, Yalçin K, Idilman R, Yurdaydin C, Bozdayi AM. Complete genome sequences and phylogenetic analysis of hepatitis delta viruses isolated from nine Turkish patients. Arch Virol 2011; 156:2215-20. [PMID: 21984217 DOI: 10.1007/s00705-011-1120-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 09/14/2011] [Indexed: 12/18/2022]
Abstract
Hepatitis delta virus (HDV) is a subviral agent of hepatitis B virus (HBV), and its life cycle is dependent on HBV. It is commonly accepted that HDV has eight distinct genotypes. In this study, the complete nucleotide sequences of HDV genomes isolated from nine Turkish patients were obtained by RT-PCR using two pairs of primers that cover the entire HDV genome. PCR products were sequenced directly. The results showed that these 9 isolates were approximately 1680 base pairs in length and clustered in the genotype HDV-1 branch when phylogenetic analysis was done with the sequences together with the complete sequences of HDV genomes representing each genotype retrieved from GenBank. Analysis of a portion of the large hepatitis D antigen (L-HDAg) gene showed that sequence similarity among these Turkish isolates is between 87.4 and 97.1%, and the Turkish isolates have the most sequence similarity to HDV-1 (90.5%), while they have the least sequence similarity to HDV-3 (64.1%). Full-genome analysis indicates that the sequence similarity is between 80.7 and 95.4%, and the highest sequence similarity is 84.8% (between the Turkish isolates and HDV-1). The lowest sequence similarity is 56.4% (between the Turkish isolates and HDV-3). In conclusion, phylogenetic analysis shows that the Turkish HDV isolates belong to HDV-1.
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Affiliation(s)
- Inci Celik
- Department of Gastroenterology, Institute of Hepatology, School of Medicine, Ankara University, Cebeci, Turkey
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Biri A, Bozdayi G, Ciçfti B, Dinç B, Yücel A, Rota S. The detection of CMV in amniotic fluid and cervicovaginal smear samples by real-time PCR assay in prenatal diagnosis. Arch Gynecol Obstet 2005; 273:261-6. [PMID: 16001197 DOI: 10.1007/s00404-005-0020-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Accepted: 03/29/2005] [Indexed: 10/25/2022]
Abstract
OBJECTIVE There is no specific antiviral therapy or a vaccine, which could be safely administered to the pregnant women with primary human cytomegalovirus (CMV) infection. Therefore, prenatal diagnosis has a critical role in the management of pregnancy, complicated by this disease. In this study, we investigated the prevalence and clinical consequences of human CMV infection from cervicovaginal smear and amniotic fluid samples of pregnant women by using real-time polymerase chain reaction (RT-PCR) assay, in one of the Obstetrics and Gynecology outpatient clinics of Turkey. The identification of reliable prognostic markers of fetal disease remains the main purpose and a major challenge on this issue. METHODS Two hundred and six samples, of which 135 were cervicovaginal smear and 71 were amniotic fluid, were enrolled in the study. The DNAs of the samples were extracted by using Roche Diagnostic (Roche, Germany) kit and amplifications of these DNAs were studied by using Light-Cycler system (Roche Germany) as being quantitative. Anti-CMV IgM antibodies in the samples were studied by both MEIA (Imx system, Abbot Laboratories, USA) and a commercial ELISA kit (Radim SPA, Italy) while anti-CMV IgG antibodies were studied by MEIA (Axsym system, Abbot Laboratories, USA). RESULTS Human CMV DNA was found to be positive in 1.5% (2 in 135) of cervicovaginal smear and 1.4% (1 in 71) of amniotic fluid samples by RT-PCR. IgM and IgG were found to be negative in all of the cervicovaginal smear samples by both MEIA and ELISA, while IgG antibody was found to be positive in only one of the amniotic fluid samples by MEIA. CONCLUSION With RT-PCR assay, we have found the prevalence of human CMV in pregnant women similar to epidemiologic reports, which have been described earlier. Whereas the fetus with positive amniotic fluid in favor of human CMV had an intrauterine growth restriction resulted in intrauterine exitus, no symptoms were observed in the infants of the other two pregnant women with positive RT-PCR results. The fact that the clinical consequence of the newborn whose amniotic fluid evaluation revealed human CMV infection by RT-PCR made us think that this molecular diagnosis method may be a reliable assay in prenatal diagnosis of this pathogen.
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Affiliation(s)
- Aydan Biri
- School of Medicine, Department of Obstetrics and Gynecology, Gazi University, Besevler, Ankara, Turkey.
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30
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Rota S, Bozdayi G, Doğan B, Dinç B. [Investigation of herpes simplex virus DNA by real-time polymerase chain reaction in the clinical samples]. MIKROBIYOL BUL 2004; 38:233-8. [PMID: 15490842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The aim of this study was to investigate the presence of Herpes simplex virus (HSV) type 1 and type 2 DNA from the clinical samples sent to our routine laboratory, by real-time polymerase chain reaction (PCR). A total of 328 samples collected from 306 female and 7 male patients who were admitted to different outpatient clinics were included in the study. The samples included 235 cervical swab samples (of which 150 were from pregnant women), 77 amniotic fluid, 8 blood, 6 cerebrospinal fluid (CSF), one pericardial fluid and one cervical biopsy. DNA extraction were performed with High Pure Viral Nucleic Acid Kit (Roche, Germany) and amplified in Light Cycler (Roche, Germany) with a commercial amplification mix (Metis Biotechnology, Ankara). HSV-DNA positivity were found in 2.1% of the cervical samples (three of 150 pregnant and two of 85 non-pregnant women), two of the blood samples and one of the CSF sample, while there were no positive result for the other clinical specimens. It can be concluded that, real-time PCR would be preferred in conditions requiring rapid diagnosis such as HSV infections of central nervous system and HSV suspected infections of immunosupressed patients, as a rapid and practical method.
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Affiliation(s)
- Seyyal Rota
- Gazi Universitesi Tip Fakültesi, Tibbi Mikrobiyoloji Anabilim Dali, Ankara
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