Genotype Distribution and Prevalence of Human Papillomavirus in Head and Neck Cancer Samples from Istanbul, Turkey.

Human papillomavirus (HPV)-associated tumors account for a significant proportion of head and neck squamous cell carcinomas (HNSCC) in developed countries. In recent years, there has been a rise of HPV infections associated with HNSCC, especially HPV16, which is the most commonly detected type in oral and oropharyngeal cancers. To investigate the frequency of HPV-driven HNSCC among patients living in Turkey, HPV DNA positivity and p16INK4A expression were assessed in primary tumor biopsies (n = 106). Eighteen out of one hundred and six (19%) HNSCC tumors showed p16INK4A overexpression, and 26/106 cases (24.5%) were positive for HPV DNA. Sixteen out of twenty-six samples were positive for both HPV DNA and p16INK4A staining. HPV16 could be isolated from 22/26 samples (84.6%) and was found to be the most frequently detected HPV type. This study represents the largest cohort of Turkish patients with HNSCC characterized according to HPV status and p16INK4A expression. Our data suggest that HPV16 infection, along with smoking, contribute to the development of HNSCC.

Frequency of CCR5-Δ32, CCR2-64I and SDF1-3'A alleles in HIV-infected and uninfected patients in Istanbul, Turkey.

INTRODUCTION: Co-receptors involved in cell entry of the human immunodeficiency virus (HIV) and mutations in genes encoding their ligands may play a role in the susceptibility to infection and resistance to the progression of the infection. The best studied mutations that can exist in these genes are the CCR5-Δ32, CCR2-64I and SDF1-3'A mutations. The frequency of these mutations vary from continent to continent and even from region to region. However, there is limited information on their distribution throughout the Turkish population. Istanbul is the city with the highest number of documented HIV-infected patients in Turkey, which can be attributed to the population size. The aim of this study was to determine the distribution of three AIDS-related gene variants among HIV-infected and uninfected population in Istanbul, Turkey and to estimate the contribution of these variants to susceptibility or resistance to HIV. METHODOLOGY: A total of 242 healthy individuals and 200 HIV-positive patients were included in the study. CCR5 polymorphisms were genotyped by polymerase chain reaction. CCR2 and SDF1 polymorphisms were genotyped using PCR restriction fragment length polymorphism (PCR-RFLP). RESULTS: The allelic frequencies for CCR5-Δ32, CCR2-64I and SDF1-3'A were 4.07%, 19.8% and 28.7%, respectively. No individual was found to carry the homozygous CCR5-Δ32 mutation in either cohort. No polymorphism was found to be significantly elevated in the HIV-infected cohort compared to the healthy group. CONCLUSIONS: The distribution of CCR5-Δ32, CCR2-64I, and SDF1-3'A variants does not differ between HIV-infected and uninfected patients. CCR2-64I and SDF1-3'A frequencies are relatively high where as the frequency of CCR5-Δ32 is low.

Syphilis seroprevalence among HlV-infected males in Istanbul, Turkey / Seroprevalencia de la sífilis entre hombres infectados con el HIV en Estambul, Turquía

Abstract Syphilis has become a serious issue for human immunodeficiency virus (HIV)-infected patients worldwide in recent years; however, the studies related to HIV coinfection and syphilis reinfections in Istanbul, Turkey, are limited. Ourobjective was to determine the seroprevalence of syphilis among HIV-infected men in the city which has one of the highest HIV prevalence rates in Turkey. Two hundred and forty four (244) HIV-positive men were evaluated at Istanbul Medical Faculty, Department of Medical Microbiology from March to June 2018. Serum samples were screened for the presence of antibodies against Treponema pallidum using the chemilumines-cent microparticle immunoassay (CMIA). Samples found to be positive were investigated with the rapid plasma reagin (RPR) test and the T. pallidum hemagglutination assay (TPHA). The patients completed a questionnaire for sociodemographic data. The mean age was found to be 41.8 years; 35.6% were men who havesexwith men (MSM). The overall seroprevalence of syphilis among the patients was 19.3%. MSM had a significantly higher seroprevalence than heterosexual patients (28.7%). In Turkey, there is a high seroprevalence of syphilis in HIV-infected patients, MSM being the most affected group. Therefore, HIV-infected patients should be screened for syphilis at least annually and should be informed about sexually transmitted diseases (STDs).

Resumen En los últimos años, la sífilis se ha convertido en un problema grave para los pacientes infectados por el virus de la inmunodeficiencia humana (HIV) en todo el mundo; sin embargo, los estudios relacionados con la coinfección por HIV y las reinfecciones por sífilis en Estambul, Turquía, son limitados. Nuestro objetivo fue determinar la seroprevalencia de la sífilis entre los hombres infectados por el HIV en Estambul, ciudad con las tasas de prevalencia del HIV más altas de Turquía. Se evaluaron 244 hombres con HIV entre marzo y junio de 2018 en la Facultad de Medicina de Estambul, Departamento de Microbiología Médica. Las muestras de suero se analizaron para detectar la presencia de anticuerpos contra Treponema pallidum con un inmunoensayo de micropartículas quimioluminiscentes (CMIA). Las muestras que resultaron positivas en dicha prueba se investigaron con la prueba de reagina plasmática rápida (RPR) y el ensayo de hemoaglutinación T. pallidum (TPHA). Los pacientes completaron un cuestionario de datos sociodemográficos. La media de la edad fue de 41,8 anos; 35,6% eran hombres que tienen sexo con hombres (HSH). La seroprevalencia global de sífilis entre los pacientes fue del 19,3%. Los HSH tuvieron una seroprevalencia significativamente mayor que los pacientes heterosexuales (28,7%). En Turquía, existe una alta seroprevalencia de la sífilis en pacientes infectados por el HIV y los HSH son el grupo más afectado. Por lo tanto, los pacientes infectados por el HIV deben someterse a la detección de sífilis al menos una vez al año y deben ser informados sobre las enfermedades de transmisión sexual (ETS).

Syphilis seroprevalence among HIV-infected males in Istanbul, Turkey.

Syphilis has become a serious issue for human immunodeficiency virus (HIV)-infected patients worldwide in recent years; however, the studies related to HIV coinfection and syphilis reinfections in Istanbul, Turkey, are limited. Our objective was to determine the seroprevalence of syphilis among HIV-infected men in the city which has one of the highest HIV prevalence rates in Turkey. Two hundred and forty four (244) HIV-positive men were evaluated at Istanbul Medical Faculty, Department of Medical Microbiology from March to June 2018. Serum samples were screened for the presence of antibodies against Treponema pallidum using the chemiluminescent microparticle immunoassay (CMIA). Samples found to be positive were investigated with the rapid plasma reagin (RPR) test and the T. pallidum hemagglutination assay (TPHA). The patients completed a questionnaire for sociodemographic data. The mean age was found to be 41.8 years; 35.6% were men who have sex with men (MSM). The overall seroprevalence of syphilis among the patients was 19.3%. MSM had a significantly higher seroprevalence than heterosexual patients (28.7%). In Turkey, there is a high seroprevalence of syphilis in HIV-infected patients, MSM being the most affected group. Therefore, HIV-infected patients should be screened for syphilis at least annually and should be informed about sexually transmitted diseases (STDs).

Mutations in Core Gene Region of Hepatitis B Virus in Patients with Chronic Hepatitis B.

BACKGROUND: The HBV core protein plays a major role in host immune response. Mutations occurring in the HBV core gene may cause alterations in the major epitopes being effective in the host immune response. Until now, the persistent effects of core gene mutations on HBV infections have not been fully understood. The aim of this study is to analyze the core gene mutations for epitopes in the T lymphocytes [T helper (Th) and cytotoxic (CTL)] and B cell and C terminal region in patients with chronic hepatitis using ultra-deep pyrosequencing (UDPS) method. METHODS: Eleven patients with chronic hepatitis B infection were included in the study. Amplification of the core gene was performed by a conventional PCR method. Mutations in the epitopes for T lymphocytes (Th and CTL) and B cell and in the C terminal region of HBV core gene were screened by UDPS. These mutations were analyzed in HBeAg positive and negative patients. RESULTS: The minimum percentages of amino acid substitutions were found with 0.9% in HBeAg positive patients and 1.2% in negative patients. The number of missense mutation was higher in patients with HBeAg positive than negative patients (p < 0.005). The number of amino acid substitutions in the region of aa49 - 69 in the Th epitopes was found to be the highest in both HBeAg positive and negative patients. The mutation frequency was higher in the C-terminal region of the core protein compared to the Th, CTL, and B cell regions and these were more common in subjects with high-grade fibrosis. Some types of mutations (V27I, R47H, Y132I, R174STOP, S181P, Q182K) were only detected in subjects with liver cirrhosis. CONCLUSIONS: Unlike literature, our results show that there is no significant increase in number of mutations in the core gene of the virus during the anti-HBe positive period. The role of low abundance variants and mutations in the immune system can be understood using methods such as UDPS in the near future.

Analysis of Hepatitis C Virus NS5A Region in Patients with Cirrhosis Using an Ultra-Deep Pyrosequencing Method.

BACKGROUND: HCV (Hepatitis C Virus) is genetically more diverse than HBV and HIV (Human Immunodeficiency Virus) and exists as quasispecies within infected individuals. This is due to the lack of efficient proofreading of the viral RNA-dependent RNA polymerase. Consequently, quasispecies emerge depending on the mutation rate of the viral polymerase, which may display a high level of genetic variability in a population. In infected individuals, HCV replicates and circulates as quasispecies composed of a complex mixture of different but closely related genomes that undergoes continuous change due to competitive selection and cooperation between arising mutants. The aim of this study is to investigate mutations in the NS5A region as a whole, including ISDR, PKRBD, IRRDR, and V3 of HCV genotype 1b cirrhosis patients being naive and nonresponders, treated with IFN (interferon) + ribavirin (RBN) by using an ultra-deep pyrosequencing method (UDPS). METHODS: During the study, five patients (four females, and one male, mean age 59.8 ± 11 years) with HCV related cirrhosis were analyzed. Three patients received IFN + RBN for six months, but two patients did not receive any therapy. HCV-RNA concentrations in patients' sera were determined using a COBAS AMPLICOR HCV MONITOR Test, Version 2.0. Genotyping was performed by using a commercial reverse hybridization method, Line Probe Assay. The quasispecies for the NS5A region were investigated using UDPS. RESULTS: All five patients were HCV genotype 1b (Mean Child-Pugh score 7.2 ± 1.9, 2 pts Child A, 2 pts Child B, and one pt Child C) but only one patient had hepatocellular carcinoma (HCC). A total of 19 different mutations were detected in each of the five patients (ranging from 3 to 6 mutations per patient). In all five patients, several mutations in the ISDR and PKR-BD regions were detected. On the other hand, mutations in the V3 and IRRDR regions were only detected in one patient. CONCLUSIONS: UDPS is a new sequencing technology and a very sensitive method in detection of quasispecies with low frequency NS5A region mutations. These mutations may affect the antiviral response and development of HCC. However, further studies in larger number of patients should be conducted to clarify this hypothesis.

Analysis of potential antiviral resistance mutation profiles within the HBV reverse transcriptase in untreated chronic hepatitis B patients using an ultra-deep pyrosequencing method.

The potential antiviral resistance mutations within hepatitis B virus (HBV) reverse transcriptase (RT) region for nucleos(t)ide analogues (NA) are not well known. Especially, the effect of pre-existing antiviral drug resistance mutations in untreated patients in comparison to the resistance developed after treatment is not still clear. Sixteen naive chronic hepatitis B patients were studied. None of the patients had received NA treatment prior to the serum samples being collected. Forty-two potential NA resistance (NAr) mutation sites were screened by ultra-deep pyrosequencing (UDPS). After therapy, mutations conferring treatment resistance were detected by LiPA. Serum samples taken before treatment showed no classic primary or compensatory/secondary drug resistance mutations. However, NAr mutations found in 6 isolates (37.5%) involved 7 positions including rtL91I, rtT128I, rtQ215P, rtF221Y, rtN238D, rtC256S, and rtI266G. Substitutions at 3 NAr mutation sites (rtT128I, rtN238D, and rtC256S) were detected in 3 unresponsive patients developing drug resistance after NA treatment. One patient with rtI266G mutation also developed drug resistance after lamivudine (LAM) therapy. However, the relationship between rtI266G mutation and NA drug resistance was not previously reported. These results suggest that association of potential mutations besides the primary and secondary/compensatory resistance mutations should be investigated. Investigation of NAr mutations before treatment may be important for the success of the treatment.

Relationship between oral anaerobic bacteria and otitis media with effusion.

OBJECTIVE: In this study hypothesing the translocation of oral bacteria from oropharynx into the middle ear cavity may be involved in the pathogenesis of otitis media with effusion (OME), we aimed to investigate the presence and similarity of Fusobacterium nucleatum and Treponema denticola in saliva, nasopharyngeal secretion and the middle ear effusion samples from the children with OME. METHODS: Totally 20 children with OME undergoing myringotomy and ventilation tube placement were attended. Stimulated saliva samples were collected after otorhinolaryngological and oral examinations were done. The middle ear effusion and nasopharyngeal secretions were collected during the operations. The presence of F. nucleatum and T. denticola were detected using 16SrRNA-based PCR. The clonal similarities of the bacteria were detected in the samples which the same bacteria had been detected in each samples of the same child. After DNA sequencing, clonal similarity was determined by 16SrRNA gene clone library analysis. The sequences from each clone were compared with similar sequences of reference organisms by FASTA search. RESULTS: T. denticola was detected only in four (20%) saliva and in one (5%) nasopharyngeal sample. F. nucleatum was detected in 11 (55%) saliva, eight (40%) nasopharyngeal and six (30%) middle ear effusion samples. Sequences from F.nucleatum clones derived from three different anatomic sites within patients were similar in 33% of OME patients, indicating their genetic relatedness. CONCLUSIONS: Bacteria involved in this process most likely originate from the oropharynx since they show a close genetic relatedness with their oropharyngeal counterparts.

Clinical features of hepatitis B virus genotypes in Turkish patients.

OBJECTIVE: To investigate the relationship between hepatitis B virus (HBV) genotypes and hepatitis B early antigen (HBeAg) as well as the hepatitis C antibody, alanine aminotransferase (ALT) levels and liver inflammation and damage in chronic patients of hepatitis B. METHODS: The study was conducted at the Department of Microbiology, Istanbul University, Istanbul, Turkey, between June 2002 and February 2003. Randomly selected 63 patients of chronic hepatitis B represented the study population. Biochemical and virological activities, and histopathological stages were determined in all the patients. All serum samples were investigated for the presence of hepatitis B virus DNA by nested polymerase chain reaction (PCR). The product of the reaction was sequenced by using Long Read Tower automated DNA sequencer. Clinical characteristics and laboratory features of the patients were compared using Mann-Whitney Rank Sum test, Kruskal Wallis test and Chi Square test for statistical analysis. RESULTS: Genotype D was the only type found in all patients. Of the 63 patients studied, 16 (25.4%) tested positive for HBeAg. Hepatitis B antigen-negative patients were more elderly than those who were positive (p < 0.05). The degree of hepatic inflammation, fibrosis stage and alanine aminotransferase levels were similar in both the groups (p > 0.05). Liver cirrhosis was present in 2 (4%) of the patients in the negative group. In terms of gender, the serum alanine aminotransferase levels were significantly higher in male patients than in females (p < 0.05). CONCLUSION: There was no relationship between the genotype of the patients and their response to the therapy since there was only one genotype detected in the study. The results showed that the hepatitis e antibody-negativity was not associated with good prognosis, while less necrotic activity, and alanine aminotransferase levels were not correlated with the severity of the disease.

In Vitro Antifungal Activity of Ankaferd Blood Stopper Against Candida albicans.

BACKGROUND: Candida albicans is a memeber of the oral flora that can lead to various complications in immunosupresive patients after oral surgery processes. Ankaferd Blood Stopper® (ABS) is a medical plant extract that is safe to use in patients with dental surgery bleedings in Turkey. OBJECTIVE: The study evaluated the antifungal activity of ABS medicinal plant extract against C albicans using the agar diffusion and broth microdilution methods. METHODS: The plant extract antifungal activity was assessed in vitro either by applying the ABS extract directly and by applying different concentrations of ABS onto Candida culture. For these experiments, an agar diffusion method was used. To determine the minimum inhibitory concentration (MIC), a broth microdilution method was used. RESULTS: Different volumes of the active substance (10, 20, 30, and 40 µL) were applied onto Candida (0.5 McFarland solution) cultivated plate; Candida growth was inhibited in accordance with the volumes of ABS. However, when various dilutions of ABS (1:2, 1:20, 1:40, and 1:80) were added as drops containing 20 µL, no antifungal effects were found. No MIC values were identified using broth microdilution. When different dilutions of ABS containing 100 µL of 0.5 McFarland solution of C albicans were cultured depending on the time (10, 20, 30, and 40 minutes), the effect of the duration was not significant. CONCLUSION: The various tests were carried out to investigate antifungal effects of ABS on Candida, but none were found.

Decreased prohepcidin levels in patients with HBV-related liver disease: relation with ferritin levels.

BACKGROUND: Levels of prohepcidin, a homeostatic regulator of iron absorption, are altered in chronic hepatitis C and liver cirrhosis. However, data on the potential alterations of prohepcidin in patients with HBV-related liver disease are scarce. We investigated whether serum prohepcidin is related to iron overload and perenchymal dysfuction in HBV-related liver disease. METHODS: Three groups of subjects were studied: 66 patients with chronic hepatitis B, 32 patients with HBV-related cirrhosis, and 42 healthy controls without evidence of liver disease. Serum levels of prohepcidin were determined by enzyme-linked immunosorbent assay. RESULTS: Serum prohepcidin levels were significantly lower in patients with HBV-related cirrhosis (175.85 ± 71.5 ng/ml) than in patients with chronic hepatitis B (209.02 ± 62.7 ng/ml P < 0.05) and controls (222.4 ± 128.4 ng/ml, P < 0.05). After adjustment for potential confounders, prohepcidin was found to be an independent predictor of ferritin levels in multiple linear regression analysis (ß = -1.10, t = -3.11, P < 0.01). CONCLUSION: These results demonstrate that prohepcidin levels are reduced in patients with HBV-related cirrhosis and are an independent correlate of serum ferritin.

Transmission routes of chronic hepatitis C and their relation to HCV genotypes.

BACKGROUND/AIMS: Hepatitis C virus transmission routes in chronic hepatitis C patients, the relationship between the viral genotype and the transmission routes were studied. MATERIAL AND METHODS: Genotyping was performed by using a commercial reverse hybridization method, Line Probe Assay. RESULTS: Genotyping of 108 HCV RNA positive patients revealed four different types (1, 2, 3, and 4) and some mixed types. Subtype 1b was the most common (n=82). Subtype 1a and 3a were detected in six patients, 2a/2c was detected in seven patients, and 4c/4d was detected in one patient respectively. Six subjects revealed mixed infections. Three of them were 1a+1b, two of them were 1b+4a, and one of them was 1b+2a/2c. Genotype 1b was most common in all groups. In 38.8% of the 108 patients with a history of blood or blood product transfusions, 16.6% of patients with a history of surgery, 15.7% of patients had an anamnesis of dental treatment and, 12.9% of patients receiving dialysis. CONCLUSION: Before the routine screening of blood donor practices became mandatory, the most common route of HCV infection was blood transfusions. The other risk factors of transmission such as tattoos, piercings, iatrogenic infections and intravenous drug usage have not been recorded for any of these patients in our study. The patient with a history of surgery had the genotype 1b as the most common genotype. The genotype 1b was determined in 75.9% of the whole patient population of the study.

An atypical form of necrotizing periodontitis.

BACKGROUND: Necrotizing ulcerative gingivitis/periodontitis are considered necrotizing periodontal diseases. This case report presents an atypical form of necrotizing periodontitis, which does not fit into this classification. METHODS: A 12-year-old child was referred to our clinic for gingival inflammation, extensive alveolar bone loss, and tooth mobility. Clinical and microbiologic examinations were carried out, and radiographs were taken. Clinical examination revealed soft and hard tissue destruction up to the mucogingival junction at the right maxillary premolar and mandibular incisors. Unusual infections or abnormalities in systemic functions were not detected through clinical and laboratory evaluations made at the Pediatrics Department, Istanbul University. Although an intensive established treatment protocol for necrotizing periodontitis was completed, management of long-standing health conditions could not be achieved because of recurrence of the disease, which caused us to repeat this treatment protocol at short intervals. RESULTS: Investigation led to a diagnosis of an atypical form of necrotizing periodontitis because the disease had a recurrent acute phase even under a standard treatment protocol. CONCLUSIONS: Our patient exhibits an unusual, necrotizing form of periodontal disease. The reason for the rapid rate of periodontal disease progression remains unclear.

Salivary detection of periodontopathic bacteria and periodontal health status in dental students.

OBJECTIVE: Saliva may become a potential source of contamination through vertical and horizontal transmissions as well as cross-infections. This study aims to use saliva as a screening tool to detect putative periodontal pathogens in a young population with fairly good oral hygiene. MATERIALS AND METHODS: Stimulated saliva samples were obtained from 134 dental students (20.5+/-1 years, range 18-22 years). Among those, 77 subjects also completed a periodontal examination including attachment loss, modified dental, gingival and plaque indices (AL, mDI, GI and PI). The test bacteria were identified using a 16S rRNA-based PCR detection method. RESULTS: One or more of the test bacteria was found in 67% of the subjects. Prevotella nigrescens was detected as single bacterium in 16% of the subjects followed by Treponema denticola (4%), Porphyromonas gingivalis (2%), Aggregatibacter (formerly Actinobacillus) actinomycetemcomitans (1%) and Tannerella forsythia (1%). Two or more pathogens were detected in 42% of the subjects. Clinical examination revealed health with no attachment loss (AL) in 84% of the students. In no AL group, 38% of the students were pathogen free while this was 25% for students in localized AL group (p>0.05). There was a statistically significant association between the detection of salivary periodontal pathogen in general and higher PI (p=0.018) and GI (p=0.043). CONCLUSION: Within the limits of this study, it is possible to detect all six periodontal pathogens in the saliva of dental students. Although a correlation can be observed between the presence of salivary periodontal pathogen and clinical signs of inflammation such as plaque accumulation and gingival bleeding, detection of specific bacteria in saliva is not related to the presence of localized AL based on the presented study population.