Investigation of group A rotavirus G10, G12 genotypes emerging in patients with acute gastroenteritis in a tertiary care hospital

Rotaviruses are the most common cause of viral gastroenteritis with the highest mortality and morbidity rates in children aged 0-5 years. The aim of this study was to determine the frequency of rotavirus infection in patients whose stool samples were sent to microbiology laboratory to investigate the etiology of diarrhea, to investigate the rotavirus genotypes that are common in our region and G10, G12 genotypes that have recently become common in the world. Fecal samples of 476 patients aged between 0-92 years who applied between November 2016 and February 2018 were studied via immunochromatographic rapid test and enzyme-linked immunosorbent assay (ELISA) methods. ELISA positive samples were studied by nested reverse transcriptase chain reaction (RT-PCR) and genotyped by agarose gel electrophoresis. Rotavirus was found positive in 18.3% and 17% of stool samples by immunochromatographic test and ELISA, respectively. All ELISA positive samples were also detected as positive by RT-PCR. 18.5% of female patients and 15.7% of male patients were found to be positive and rotavirus positivity was not statistically significant between genders. The frequency of rotavirus in different age groups was 23.5% (6-12 years), 17.3% (13-24 months) and 16% (25-36 months). It was determined that rotavirus cases were most common in the spring. G1, G2, G3, G4, G9, G10, and G12 were detected in 37%, 7.4%, 16.1%, 6.2%, 9.9%, 2.5%, 26% of the samples, respectively. G12 was the most common genotype after G1. The most common G and P genotype combination was G1P[8] (17.2%). This was followed by G12P[8] (11.11%) and G3P[8] (11.11%). P[8] (53%) was found to be the dominant P genotype. In this study, it was observed that rotavirus, which is the cause of childhood diarrhea, can also be encountered in advanced ages and even new genotypes that infect humans worldwide may also be the causative agents. Therefore, we concluded that it is important to investigate new genotypes such as G10 and G12 in molecular epidemiological studies

Investigation of enteroviruses, herpesviruses (1, 2, 6, 7), flaviruses and phleboviruses in patients with atypical meningitides/encephalitis by polymerase chain reaction

Bu çalışmada, atipik menenjit/ensefalitli hastalarda, PZR yöntemi ile herpesvirüsler (tip 1,2,6,7), enterovirüsler (EV), flavivirüsler ve flebovirüslerin araştırılması ve epidemiyolojik veri elde edilmesi amaçlanmıştır. Ankara'da iki farklı hastanenin Çocuk Enfeksiyon Bölümü'ne Ekim 2011-Aralık 2015 tarihleri arasında nörolojik şikayetlerle başvuran, 0-18 yaş arasındaki 100 hastadan beyin omurilik sıvısı (BOS) örnekleri toplanmıştır. Nükleik asit ekstraksiyonu ve cDNA sentezi için ticari kitler kullanılmıştır. HSV1/2 gerçek zamanlı PZR (LightCycler® HSV1/2 QualKit, Roche, Almanya); enterovirüsler, flavi- ve flebovirüsler geleneksel PZR yöntemi ile araştırılmış ve ayrıca çeşitli menenjit etkenlerini saptayabilen gerçek zamanlı multipleks PZR yöntemi (MeningoFinder® 2SMART, Hollanda) kullanılmıştır. Çalışılan 100 örneğin 7'si (%7) viral etkenler (2 HSV1, 4 HHV6, 1 EV) açısından pozitif; diğer etkenler negatif bulunmuştur. HHV6 pozitif saptanan 4 hastanın 2'si 1-6 aylık, 1'i 13-36 aylık ve diğeri ise 4-6 yaş grubundadır. HHV6 pozitif hastaların 3'ü menenjit, 1'i viral ensefalit; HSV1 pozitif hastalar viral ensefalit; EV pozitif hasta ise menenjit ön tanısı almıştır. Merkezi sinir sistemi enfeksiyonlarında çok sayıda virüs etken olabilmektedir ve etkeni saptanabilen olgu sayısı düşüktür. HSV1 viral ensefalit etkenleri arasında başlarda yer alsa da, HHV6 ile nadir karşılaşılmaktadır. Ayrıca HHV6'nın etken olma durumu, latent bir virüs olması nedeniyle her olguda kesin değildir. Yine de bu etkenlerin, MSS enfeksiyonlarında rolü olabileceği için, tanı algoritmalarında değerlendirilmesi gerekmektedir.The aim of this study was to investigate the impact of enteroviruses (EV), herpesviruses (types 1,2,6,7), flaviviruses and phleboviruses in patients with atypical meningitis/encephalitis and to obtain epidemiological data. One hundred cerebrospinal fluid (CSF) specimens were collected from 100 patients (age:0-18) that presented with neurological complaints at Paediatric Infections Clinics of two hospitals in Ankara from October 2011 to December 2015. Commercial kits were used for nucleic acid extraction and cDNA synthesis. A commercial real time PCR assay (LightCycler® HSV1/2 QualKit, Roche, Germany) was employed for HSV1/2 detection; enteroviruses, flaviviruses, phleboviruses were investigated by in house PCR methods. Also a commercial real time multiplex PCR method (MeningoFinder® 2SMART, The Netherlands), which can detect various meningitis agents, was used. A total of 7 specimens (7%) were positive for viral agents (2 HSV1, 4 HHV6, 1 EV) and other agents tested were negative. Two of HHV6 positive patients were 1-6 months old, 1 was 13-36 months old and the other was 4-6 years old. HHV6 was detected in 3 patients with meningitis, in 1 patient with viral encephalitis, HSV1 was detected in 2 patients with viral encephalitis and EV positive patient had meningitis. Many viral agents can cause central nervous infections and detectable number of cases is low. Although HSV1 is the most common agent in viral encephalitis cases, HHV6 is a rare agent. Thus, these viral agents that might have a role in CNS infections, should be considered in diagnostic algorithms

Enterococcus Faecalis ve Diş Hekimliğindeki Yeri

Mikroorganizmalar, sahip oldukları çeşitli virülans faktörleri ve geliştirdikleri veya var olan direnç mekanizmaları nedeniyle dirençli enfeksiyonlara neden olabilmektedir. Diş hekimliğinde de dirençli enfeksiyonlara neden olan önemli fırsatçı patojenlerden birisi olan Enterococcus faecalis, periodontal dokularda, kök kanallarında ve implant çevresinde tedavisi zor hatta bazen mümkün olmayan, tekrarlayan enfeksiyonlara neden olmaktadır. Enterococcus faecalis’in sahip olduğu önemli virülans faktörlerinin yanı sıra biyofilm oluşturabilme yeteneği elimine edilmesini zorlaştırmaktadır. Enterococcus faecalis’in kolonize olduğu ve biyofilm oluşturduğu subgingival dokulardan, kök kanallarından ve implant çevresinden elimine edilebilmesi için çeşitli ajanlar uygulanmaktadır. Ancak, oluşturduğu biyofilm nedeniyle E. faecalis dental dokularda dirençli ve tekrarlayan enfeksiyonlara neden olmaya devam etmekte ve halen E. faecalis üzerinde bakterisidal etki gösterirken çevre dokulara zarar vermeyecek ideal biyo-uyumlu ajanların bulunması için araştırmalar devam etmektedir

Emergence of rotavirus G9 in 2012, as the dominant genotype in Turkish children with diarrhea, in a university hospital in Ankara

Introduction: Rotavirus infection is a major cause of morbidity and mortality in infants and young children with diarrhea throughout the world

HPV types and E6/E7 mRNA expression in cervical samples from Turkish women with abnormal cytology in Ankara, Turkey

Background/aim: Human papillomaviruses have been established as a risk factor for invasive carcinoma of the uterine cervix. HPV E6/ E7 oncogene expression has recently emerged as a promising biomarker to determine the risk for progression to high-grade cervical lesions. The aim of this study was to evaluate HPV mRNA and DNA detection in samples with abnormal cytology. Materials and methods: Cervical specimens were obtained at the Department of Obstetrics and Gynecology via cervical brushes during January–October 2011. Liquid-based cytology slides were evaluated according to the 2001 Bethesda System. Cytology specimens from a total of 81 women with abnormal cytology were included. Real-time PCR and NASBA assays were performed to detect HPV DNA and E6/E7 mRNA, respectively. Results: HPV DNA was identified in 73 samples (90.1%). HPV E6/E7 mRNA expression was observed in 45 samples (55.6%). A statistically significant difference was observed among cytological diagnosis groups. In 25 patients, a biopsy was performed during the follow-up. HPV DNA was detected in all of these patients. HPV E6/E7 expression was present only in CIN I–III diagnosed patients. Conclusion: The E6/E7 mRNA test is a robust indicator of cytological atypia and correlates better with progressive lesions than DNA assays

[Multicenter investigation of bufavirus in the etiology of viral central nervous system infections of adults and children].

Bufavirus (BuV) is a newly-identified parvovirus in the family of Parvoviridae. Metagenomic analysis of fecal samples from children in Burkina Faso with acute diarrhea showed a highly divergent parvovirus, which was named bufavirus (BuV). The global distribution, epidemiology and genetic characteristics of BuVs infections are obscure. It was first discovered as an agent causing gastroenteritis but the association of BuV infections with various clinical presentations mostly remain to be explored. The aims of this study were to investigate probable impact of BuV in central nervous system infections in a region where it was previously reported to cause human infections and to detect enteroviruses (EV) which are reported as a cause of central nervous system infections in our country. The study was undertaken in three institutions in Ankara province, Central Anatolia, Turkey. Patients, clinically diagnosed with febrile disease and/or central nervous system infections of presumed viral etiology, were enrolled in the study with informed consent. Cerebrospinal fluid specimens were collected from 93 children attended to Gazi University Hospital and Dışkapı Yıldırım Beyazıt Hospital from October 2011-April 2015 and 33 adult patients, attended to Hacettepe University Hospital from June 2012 to March 2013. Clinical history and follow-up, physical examination and standard laboratory findings of the patients were recorded. Nucleic acid extraction was performed via commercially available spin-column assays and complementery DNA (cDNA) synthesis was performed by using commercially available cDNA synthesis kit with randomised hexamer primers. BuV detection was carried out by in house nested-polymerase chain reaction (PCR) utilized with previously-described primers. EV detection was carried out by in house PCR with pan-enterovirus primers. Seventy-four percent (93/126) and 26% (33/126) of the patients were children (0-18) and adults (19-86), respectively. In all patients, bacterial, mycobacterial and fungal cultures were negative, as well as PCR for herpes simplex virus (HSV) types 1 and 2. PCR results of all samples were negative for BuV and EV. This is the first study that evaluates a probable association of BuV and central nervous system infections. Although Parvovirus B19, a well-characterized human pathogen can rarely cause encephalitis, our findings did not confirm such an association for BuV in this preliminary investigation. However, long-term evaluation of individual cases with unknown etiology is required to reveal the relationship of the virus with specific environments

Evaluation of the results of MOTAKK hepatitis C virus RNA genotyping and hepatitis delta virus external quality assessment programs during 2015-2016.

To evaluate the HCV RNA genotyping and HDV RNA tests that are performed in molecular microbiology laboratories in Turkey as part of a national external quality assessment programme, MOTAKK (Moleküler Tanıda Kalite Kontrol) (English translation: Quality control in molecular diagnostics)