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Article ; Online: Respiratory viruses in the healthy middle ear and middle ear with otitis media with effusion.

Durmaz, Bengul / Abdulmajed, Olkar / Durmaz, Rıza / Koroglu, Mehmet / Arı, Oguz / Celik, Serdal / Kalcioglu, Mahmut Tayyar

Journal of medical virology

2021 Volume 93, Issue 11, Page(s) 6140–6147

Abstract: To investigate the presence of respiratory viruses in the middle ear cavity of the individuals with a healthy middle ear and the children with otitis media with effusion (OME). A total of 72 middle ear samples were collected from 25 children with OME ( ... ...

Abstract	To investigate the presence of respiratory viruses in the middle ear cavity of the individuals with a healthy middle ear and the children with otitis media with effusion (OME). A total of 72 middle ear samples were collected from 25 children with OME (Group 1) and 47 individuals with no middle ear disease (Group 2). Multiplex real-time polymerase chain reaction was used to investigate the presence of 20 different respiratory viruses. Virus results were compared with bacteriomes of the same populations. At least one respiratory virus was detected in 56% of the patients in Group 1 and 12.8% of the individuals in Group 2. The viral co-infection rate for Group 1 and 2 was 8% and 2.1%, respectively. In Group 1, adenovirus was the most frequently detected virus with a rate of 24%, either alone (16%) or concurrent with other viruses (8%), followed by influenza B (12%), rhinovirus, and bocavirus (8%) each. Parainfluenza 4, coronavirus OC43, and RSV A/B were detected in 4% of the sample each. In Group 2, rhinovirus was detected in two samples (4.3%) followed by adenovirus, coronavirus OC43, coronavirus E299, and coronavirus NL63 with a rate of 2.1% each. The detection rate of respiratory viruses was significantly higher in children aged 6 to 11 years. There was no positive association between virus and bacteria found in the middle ear cavity. The current study has provided comprehensive data indicating the presence of diverse respiratory viruses in the healthy middle ear cavity. Our results also suggest that respiratory viruses might have a contribution to OME pathogenesis.
MeSH term(s)	Adenoviruses, Human/isolation & purification ; Bacteria/isolation & purification ; Child ; Child, Preschool ; Coinfection ; Coronavirus/isolation & purification ; Ear, Middle/virology ; Female ; Human bocavirus/isolation & purification ; Humans ; Infant ; Male ; Orthomyxoviridae/isolation & purification ; Otitis Media with Effusion/microbiology ; Otitis Media with Effusion/virology ; Paramyxoviridae/isolation & purification ; Rhinovirus/isolation & purification ; Virus Diseases/virology ; Viruses/isolation & purification
Language	English
Publishing date	2021-07-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.27151
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Article: Mutations Observed in the SARS-CoV-2 Spike Glycoprotein and Their Effects in the Interaction of Virus with ACE-2 Receptor.

Durmaz, Bengül / Abdulmajed, Olkar / Durmaz, Rıza

Medeniyet medical journal

2020 Volume 35, Issue 3, Page(s) 253–260

Abstract: Coronaviruses (CoVs) classified in the Coronaviridae family infect a very large spectrum of vertebrate group. Seven CoVs that cause human disease consist of Alpha-CoVs, which are HCoV-229E, and NL63 and beta-CoVs, which are MERS-CoV, SARS-CoV, HCoV-OC43, ...

Abstract	Coronaviruses (CoVs) classified in the Coronaviridae family infect a very large spectrum of vertebrate group. Seven CoVs that cause human disease consist of Alpha-CoVs, which are HCoV-229E, and NL63 and beta-CoVs, which are MERS-CoV, SARS-CoV, HCoV-OC43, HCoV-HKU1, and SARS-CoV-2. SARS-CoV-2 is an enveloped, positive-polarity, single-stranded RNA virus responsible for a new Coronavirus disease 2019 (COVID-19). The mutagenic ability of the SARS-CoV-2 directs its evolution and genome variability, thus allowing viruses to escape from host immunity and develop drug resistance. Tracing viral mutations is also important for the development of new vaccines, antiviral drugs, and diagnostic systems. During replication in the host cell, genomic mutations occur in the virus and these mutations are transferred to new generations. For this reason, systematic monitoring of mutations in the SARS-CoV-2 genome allows observation of the national and international molecular epidemiology of the virus. SARS-CoV-2 spike (S) glycoprotein is vital in the binding of the virus to the host cell receptor that is angiotensin converting-enzyme 2 (ACE2), membrane fusion, vaccine studies and immune response to the virus. Therefore, mutations in the gene encoding the S glycoprotein and especially the possible variations in the receptor binding domain (RBD) in S gene are important issues to be emphasized. In this article, information about the mutations observed in the SARS-CoV-2 S glycoprotein and their possible effects are presented.
Keywords	covid19
Language	English
Publishing date	2020-09-30
Publishing country	Turkey
Document type	Journal Article ; Review
ZDB-ID	3035195-9
ISSN	2149-4606 ; 2149-2042
ISSN (online)	2149-4606
ISSN	2149-2042
DOI	10.5222/MMJ.2020.98048
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Article ; Online: Mycobiome in the Middle Ear Cavity with and Without Otitis Media with Effusion.

Durmaz, Rıza / Durmaz, Bengül / Arı, Oğuz / Abdulmajed, Olkar / Çelik, Serdal / Kalcıoğlu, Mahmut Tayyar

Turkish archives of otorhinolaryngology

2022 Volume 59, Issue 4, Page(s) 261–270

Abstract: Objective: No data have yet been published revealing the composition and the diversity of fungal communities (mycobiome) in the human middle ear cavity. The presented study investigated the mycobiome in the middle ear cavities of individuals with ... ...

Abstract	Objective: No data have yet been published revealing the composition and the diversity of fungal communities (mycobiome) in the human middle ear cavity. The presented study investigated the mycobiome in the middle ear cavities of individuals with healthy middle ears and patients with otitis media with effusion. Methods: A total of 77 middle ear and four adenoid samples were collected from 47 individuals (35 children and 12 adults) in Group 1 and from 20 children in Group 2. The mycobiome profile was analyzed with nuclear ribosomal internal transcribed spacer 2 (ITS2) based metabarcoding using an Illumina MiSeq metagenomics kit. Results: ITS2-based metabarcoding detected 14 different genera and 17 different species with a mean relative abundance of ≥1% in the samples analyzed. Mycobiome profile was similar between the adenoid tissue and the middle ear cavity, between Groups 1 and Group 2, and between children and adults. Conclusion: The species
Language	English
Publishing date	2022-02-22
Publishing country	Turkey
Document type	Journal Article
ISSN	2667-7474
ISSN (online)	2667-7474
DOI	10.4274/tao.2021.2021-10-4
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Article: The effect of gestational weight gain on serum total oxidative stress, total antioxidant capacity and gut microbiota.

Cömert, Tuğba Küçükkasap / Akpinar, Funda / Erkaya, Salim / Durmaz, Bengül / Durmaz, Riza

Bioscience of microbiota, food and health

2022 Volume 41, Issue 4, Page(s) 160–167

Abstract: This study aimed to investigate the effect of gestational weight gain on total oxidative stress (TOS), total antioxidant capacity (TAC), oxidative stress index (OSI), dietary antioxidant intake, and the gut microbiome. The study was carried out on 40 ... ...

Abstract	This study aimed to investigate the effect of gestational weight gain on total oxidative stress (TOS), total antioxidant capacity (TAC), oxidative stress index (OSI), dietary antioxidant intake, and the gut microbiome. The study was carried out on 40 pregnant women divided as follows: a) normal prepregnancy weight and gestational weight gain of 11.5-16.0 kg (n=10) b) normal prepregnancy weight and gestational weight gain of >16.0 kg (n=10) c) obese before pregnancy and gestational weight gain of 5-9 kg (n=10) and d) obese before pregnancy and gestational weight gain of >9.0 kg (n=10). Serum TOS and TAC levels, dietary antioxidant intake, and microbiome diversity of the gut microbiome were evaluated during the third trimester of pregnancy. A positive correlation was found between body mass index (BMI) in the third trimester and serum TOS levels and OSI. In women with normal prepregnancy weight, an increase in the
Language	English
Publishing date	2022-05-24
Publishing country	Japan
Document type	Journal Article
ISSN	2186-6953
ISSN	2186-6953
DOI	10.12938/bmfh.2022-010
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Article ; Online: The effect of pre-pregnancy obesity on gut and meconium microbiome and relationship with fetal growth.

Cömert, Tuğba Küçükkasap / Akpinar, Funda / Erkaya, Salim / Durmaz, Bengül / Durmaz, Riza

The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians

2022 , Page(s) 1–9

Abstract: Objective: To investigate the effect of pre-pregnancy obesity on maternal and newborn microbiomes and fetal growth.: Methods: Individuals who gained body weight in accordance with the recommendations during pregnancy and normal gestastional age are ... ...

Abstract	Objective: To investigate the effect of pre-pregnancy obesity on maternal and newborn microbiomes and fetal growth. Methods: Individuals who gained body weight in accordance with the recommendations during pregnancy and normal gestastional age are included in the study and were separated into two groups, normal ( Results: The stool samples of mothers who were obese before pregnancy harbored a higher (59.9 versus 52.3%) relative abundance of Firmicutes and a lower (7.1 versus 4.1%) relative abundance of Proteobacteria than the stool samples of mothers with normal body weight pre-pregnancy. In contrast, in the meconium samples of mothers who were obese pre-pregnancy, compared to those of mothers who had a normal body weight pre-pregnancy, the phylum Firmicutes was less (56.0 versus 69.0%) abundant and Proteobacteria (9.0 versus 8.5%) was more abundant. There was a negative correlation between pre-pregnancy BMI, birth weight, weight/height ratio and alpha diversity indices (Shannon and Chao1). Conclusions: Pre-pregnancy obesity can affect pregnant and newborn gut microbiota, which might related to fetal growth of the newborn.
Language	English
Publishing date	2022-11-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2077261-0
ISSN	1476-4954 ; 1057-0802 ; 1476-7058
ISSN (online)	1476-4954
ISSN	1057-0802 ; 1476-7058
DOI	10.1080/14767058.2022.2148098
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Zs.A 3510: Show issues

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Article ; Online: Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology.

Karabudak, Sema / Ari, Oguz / Durmaz, Bengul / Dal, Tuba / Basyigit, Tugcan / Kalcioglu, Mahmut Tayyar / Durmaz, Riza

Journal of medical microbiology

2019 Volume 68, Issue 8, Page(s) 1148–1158

Abstract: Purpose: This study aimed to investigate the effect of smoking on the buccal microbiome and to analyse the descriptive ability of each of the seven hypervariable regions in their 16S rRNA genes.: Methodology: Microbiome compositions of 40 buccal swab ...

Abstract	Purpose: This study aimed to investigate the effect of smoking on the buccal microbiome and to analyse the descriptive ability of each of the seven hypervariable regions in their 16S rRNA genes. Methodology: Microbiome compositions of 40 buccal swab samples collected from smokers (n =20) and non-smokers (n =20) were determined using 16S rRNA sequencing. Seven different 16S rRNA hypervariable regions (V2, V3, V4, V6-7, V8 and V9) in each sample were amplified using the Ion Torrent 16S Metagenomics kit and were sequenced on the Ion S5 instrument. Results: Seven hypervariable regions in the 16S rRNA gene were successfully sequenced for all samples tested. The data obtained with the V2 region was found to be informative but the consensus data generated according to a number of operational taxonomic unit reads gathered from all seven hypervariable regions gave the most accurate result. At the phylum level, no statistically significant difference was found between smokers and non-smokers whereas relative abundances of Veillonella atypica, Streptococcus australis, Prevotella melaninogenica, Prevotella salivae and Rothia mucilaginosa showed significant increases in the smoker group (P-adj=0.05). Alpha diversity results did not show a significant difference between the two groups; however, beta diversity analysis indicated that samples of smoker and non-smoker groups had a tendency to be clustered within themselves. Conclusion: The results of the current study indicate that smoking is a factor influencing buccal microbiome composition. In addition, sequencing of all seven hypervariable regions yielded more accurate results than those with any of the single variable regions.
MeSH term(s)	Adult ; Bacteria/classification ; Bacteria/genetics ; Female ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Microbiota/genetics ; Middle Aged ; Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Smoking ; Young Adult
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2019-06-14
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	218356-0
ISSN	1473-5644 ; 0022-2615
ISSN (online)	1473-5644
ISSN	0022-2615
DOI	10.1099/jmm.0.001003
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Article: Ishal etkeni olarak enterotoksijenik Bacteroides fragilis.

Durmaz, Bengül

Mikrobiyoloji bulteni

2002 Volume 36, Issue 1, Page(s) 99–103

Abstract: The etiology of almost half of the diarrheal diseases has not been cleared yet, in spite of modern diagnostic methods. Bacteroides fragilis strains which secrete an enterotoxin are termed as enterotoxigenic B.fragilis (ETBF). These strains are associated ...

Title translation	Enterotoxigenic Bacteroides fragilis as a factor in diarrhea.
Abstract	The etiology of almost half of the diarrheal diseases has not been cleared yet, in spite of modern diagnostic methods. Bacteroides fragilis strains which secrete an enterotoxin are termed as enterotoxigenic B.fragilis (ETBF). These strains are associated with diarrheal diseases in children above 1 year of age and in adults. B. fragilis toxin (BFT) stimulates intestinal secretion and in-vitro cytotoxic response in HT29/C1 cells. Recent studies suggest that BFT is related to inflammatory bowel disease and colon cancer by triggering nuclear activation with potential oncogene expression. In this review, the molecular pathogenesis, epidemiology and laboratory diagnosis of ETBF have been reviewed to focus on ETBF as a diarrheal agent.
MeSH term(s)	Bacteroides Infections/diagnosis ; Bacteroides Infections/epidemiology ; Bacteroides Infections/microbiology ; Bacteroides fragilis/pathogenicity ; Colonic Neoplasms/microbiology ; Diarrhea/diagnosis ; Diarrhea/epidemiology ; Diarrhea/microbiology ; Enterotoxins/biosynthesis ; Humans ; Inflammatory Bowel Diseases/microbiology
Chemical Substances	Enterotoxins
Language	Turkish
Publishing date	2002-01
Publishing country	Turkey
Document type	English Abstract ; Journal Article ; Review
ZDB-ID	985146-x
ISSN	0374-9096
ISSN	0374-9096
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Article: Prevalence of enterotoxigenic Bacteroides fragilis in patients with diarrhea: a controlled study.

Durmaz, Bengul / Dalgalar, Mehmet / Durmaz, Riza

Anaerobe

2005 Volume 11, Issue 6, Page(s) 318–321

Abstract: In this age matched controlled study performed in Malatya, a city in east region of Turkey, enterotoxigenic Bacteroides fragilis (ETBF) was investigated in stool specimens obtained from children and adults with and without diarrhea. A nested polymerase ... ...

Abstract	In this age matched controlled study performed in Malatya, a city in east region of Turkey, enterotoxigenic Bacteroides fragilis (ETBF) was investigated in stool specimens obtained from children and adults with and without diarrhea. A nested polymerase chain reaction (PCR) method was used to detect the enterotoxin gene of B. fragilis in a total of 418 stool samples, including 221 samples from 117 children (aged 0-16 years) and 104 adults (aged >16 years) with diarrhea, and 197 samples from 102 children and 95 adults as control group that was the same age group with those having diarrhea. ETBF was detected in 13 of 117 diarrheal children (11.1%) and 8 of 102 control children (7.8%) (P>0.05). In children aged 1-5 years, the rate of ETBF was significantly higher in patients than in controls (25% versus 9.5%, respectively; P<0.05). On the other hand ETBF was detected similar rates (2.2% and 2.4%, respectively) in children younger than 1 year in both patients and controls. ETBF positivity was not significantly difference between patient and control groups who were older than 5 years of age and adults. The frequency of ETBF in the controls was slightly higher in older persons than in younger ones; however, it was not significant. The rate of ETBF as the only enteropathogen in the patients with ETBF was significantly higher than in controls with ETBF (88% versus 39%, respectively; P<0.02). We found that in east region of Turkey, the prevalence of ETBF was higher in the childhood diarrhea, particularly in aged 1-5. As the only enteropathogen, ETBF may play an important role in diarrheal diseases. Persons after 6 years old can be carrier for ETBF regardless diarrhea.
Language	English
Publishing date	2005-12
Publishing country	England
Document type	Journal Article
ZDB-ID	1237621-8
ISSN	1075-9964
ISSN	1075-9964
DOI	10.1016/j.anaerobe.2005.06.001
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Article: Spread of a single clone Acinetobacter baumannii strain in an intensive care unit of a teaching hospital in Turkey.

Güdücüoglu, Hüseyin / Durmaz, Riza / Yaman, Gorkem / Cizmeci, Zeynep / Berktas, Mustafa / Durmaz, Bengul

The new microbiologica

2005 Volume 28, Issue 4, Page(s) 337–343

Abstract: Acinetobacter baumannii is an important nosocomial pathogen, especially in immunocomprimised patients and those hospitalized in intensive care units. After the first isolation of A. baumannii strains from the bronchial aspirates of two patients in the ... ...

Abstract	Acinetobacter baumannii is an important nosocomial pathogen, especially in immunocomprimised patients and those hospitalized in intensive care units. After the first isolation of A. baumannii strains from the bronchial aspirates of two patients in the intensive care unit (ICU) of our hospital as a pure culture, screening studies were performed to define possible source(s). A. baumannii strains isolated from bronchial aspirates and blood cultures of the patients in ICU were collected as a possible part of the outbreak. A total of 23 screening samples collected from equipment (7), hands (4) and gloves (2) of the staff, and from ten different body regions of the patients in the ICU were cultured. Antimicrobial susceptibility test of the isolates was performed by the standardized disk-diffusion method. All isolates were subtyped by antibiogram, arbitrarily primed polymerase chain reaction (AP-PCR) and pulsed-field gel electrophoresis (PFGE) typing methods. A total of 26 A. baumannii strains including eight clinical and 18 screening isolates were identified. All isolates were susceptible only to meropenem, tobramycin, and imipenem. There was at least a 96% resistance rate to the other antibiotics tested. Antibiogram typing showed that 24 of the 26 isolates were epidemiologically related, two were unique. AP-PCR yielded two types, one of which had 21 isolates, the other had five. PFGE fingerprinting revealed that all isolates were clonally related, including four closely related and 22 indistinguishable strains. Based on the results of PFGE which has been accepted as a reference method it can be concluded that A. baumannii strains isolated from our intensive care unit originated from a single type of strain.
MeSH term(s)	Acinetobacter Infections/epidemiology ; Acinetobacter Infections/microbiology ; Acinetobacter baumannii/classification ; Acinetobacter baumannii/genetics ; Acinetobacter baumannii/isolation & purification ; Acinetobacter baumannii/physiology ; Anti-Bacterial Agents/pharmacology ; Blood/microbiology ; Cluster Analysis ; Cross Infection/epidemiology ; Cross Infection/microbiology ; Cross Infection/transmission ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Bacterial/isolation & purification ; Drug Resistance ; Electrophoresis, Gel, Pulsed-Field ; Environmental Microbiology ; Exudates and Transudates/microbiology ; Hospitals, Teaching ; Humans ; Inhalation ; Inpatients ; Intensive Care Units ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Turkey/epidemiology
Chemical Substances	Anti-Bacterial Agents ; DNA, Bacterial
Language	English
Publishing date	2005-10
Publishing country	Italy
Document type	Journal Article
ZDB-ID	756168-4
ISSN	1121-7138 ; 0391-5352
ISSN	1121-7138 ; 0391-5352
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Zs.B 2267: Show issues

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Article: The prevalence of fecal colonization of enterococci, the resistance of the isolates to ampicillin, vancomycin, and high-level aminoglycosides, and the clonal relationship among isolates.

Kuzucu, Cigdem / Cizmeci, Zeynep / Durmaz, Riza / Durmaz, Bengul / Ozerol, Ibrahim Halil

Microbial drug resistance (Larchmont, N.Y.)

2005 Volume 11, Issue 2, Page(s) 159–164

Abstract: The gastrointestinal tract carriage of enterococci was searched in 150 hospitalized patients and 100 outpatients, and clonal relatedness of the isolates and their resistance to ampicillin, vancomycin, and high-level streptomycin and gentamicin were ... ...

Abstract	The gastrointestinal tract carriage of enterococci was searched in 150 hospitalized patients and 100 outpatients, and clonal relatedness of the isolates and their resistance to ampicillin, vancomycin, and high-level streptomycin and gentamicin were investigated. A stool sample or rectal swab collected from each patient was inoculated into appropriate media within an hour. Enterococcus species were identified by using conventional biochemical tests, API-20 Strep assay, and BBL crystal kit. Antibiotic susceptibility tests were performed using Kirby-Bauer disk diffusion method. A polymerase chain reaction (PCR) was used to detect vanA and vanB genes. Pulsed-field gel electrophoresis (PFGE) and arbitrarily primed-polymerase chain reaction (AP-PCR) methods were used for molecular typing of the strains. Enterococci were isolated from 90 (60%) of the specimens collected from 150 inpatients. Of these 90 isolates, 37 (41%) had high-level gentamicin resistance, 36 (40%) had high-level streptomycin resistance, and 50 (55.6%) had ampicillin resistance. Fecal colonization was found in 30% of the outpatients. Resistances to ampicillin, high-level streptomycin, and gentamicin were 13%, 10%, and 3%, in these patients' isolates, respectively. No vancomycin-resistant enterococci were detected by both agar diffusion and PCR assays in our study. Both typing procedures were applied on 78 Enterococcus strains isolated from inpatients. AP-PCR typing showed that 30 (50.8%) of the 59 E. faecium and 5 (50%) of the 10 E. faecalis strains were clonally related. These values were found to be 12 (20.3%) and two (20%) by PFGE, respectively. The typing procedures did not find any clustered strains in the six E. durans and three E. avium isolates. Neither PFGE nor AP-PCR result was significantly different among the sensitive and resistant strains. Our results indicate that the high prevalence of colonization with ampicillin and highlevel aminoglycoside-resistant enterococci is an important problem in our medical center. The high clonal diversity among the isolates indicates limited spread of antibiotic-resistant strains between patients.
MeSH term(s)	Aminoglycosides/pharmacology ; Ampicillin Resistance ; Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus/drug effects ; Enterococcus/genetics ; Feces/microbiology ; Humans ; Polymerase Chain Reaction ; Vancomycin Resistance
Chemical Substances	Aminoglycosides
Language	English
Publishing date	2005
Publishing country	United States
Document type	Journal Article
ZDB-ID	1290490-9
ISSN	1931-8448 ; 1076-6294
ISSN (online)	1931-8448
ISSN	1076-6294
DOI	10.1089/mdr.2005.11.159
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