The impact of the COVID-19 pandemic on the circulation, seasonal distribution, and research of other respiratory pathogens in Turkey.

INTRODUCTION: Respiratory infections are one of the world's most common infectious diseases. Following the species, numbers, and seasonal distribution of acute respiratory agents is important for the protection of public health. Our study aimed to determine the effect of the COVID-19 pandemic on the circulation and seasonal distribution of non-SARS-CoV-2 respiratory tract agents and research on non-SARS-CoV-2 agents. METHODS: The results of the Multiplex PCR respiratory panel of 3702 nasopharyngeal swab samples sent between January 2018 and December 2021 were evaluated retrospectively. Scientific articles on acute respiratory infections between 2010 and 2021 from Turkey were analyzed in Scopus for bibliometric analysis. RESULTS: 1.382 pathogens were detected. During the pandemic, the number of non-SARS-CoV-2 pathogens was found to be statistically significantly lower than before the pandemic. It was determined that while the most frequent agent before the pandemic was the Adenovirus, the most frequent agent was the RSV-A during the pandemic. Our network analysis of keywords indicated that academic interest in 2020-21 was directed toward COVID-19, which coincides with the pandemic period. CONCLUSIONS: Our study determined the fact that the incidence, species, and seasonal distribution of non-SARS-COV-2 respiratory agents changed after the onset of the pandemic. Increasing the identification and following-up of these pathogens in health organizations and also presenting these data to literature and sharing with academics is important. We are of the opinion that the results of our study shall shed light on the epidemiology of changing respiratory infections and the prevention and following-up of future health problems.

Male Human Papillomavirus Infection and Genotyping in Turkey.

BACKGROUND: High-risk (HR) Human Papillomavirus (HPV) has been shown to play an important role in men in various locations in Turkey. This study aims to screen the male persistent infection with the high-risk human papillomavirus (HPV) genotype status in Turkey to provide a reference basis for formulating prevention strategies for the development of genitourinary tract neoplasia. METHODS: The HPV QUANT-21 Quantitative RT-PCR Kit® was used to identify and quantify low-risk HPV (HPV 6, 11, 44) and high-risk (HPV 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 73, 82) from male individuals in Turkey. RESULTS: Of the total 1304 samples, 473 were positive for at least one HPV genotype, with an overall frequency of 36.2%. Two-hundred fifty-four patients were positive only for one or more LR   HPV genotypes (54%), and 219 patients were positive for one or more HR HPV genotypes (46%). The LR HPV genotype frequency was 53.7%, while the HR HPV genotype frequency was 46.3%. Our technology had the positive advantage of being able to calculate concentrations for each genotype. Genotype 51 was second in frequency but had the highest average concentration of 5.38 log (copies/sample). CONCLUSION: The presence and genotype of the virus before HPV vaccination are also of increasing importance. The data obtained will serve as a guide for prevention strategies, especially vaccination. Based on our findings there is a need of new estimates of the efficacy of currently available HPV vaccines and to develop a screening program to prevent and reduce the incidence of genitourinary tract neoplasias in Turkey. Further studies are planned to measure and define the high levels of infection that may lead to the development of cervical tumors. Using this technique, it may be possible to make clinical decisions about the extent of cytological alterations.

Analysis of the Prevalence and Quantification of viral load of different human papillomavirus types in Turkish women population.

BACKGROUND: Persistent infection with high-risk (HR) Human Papilloma Virus (HPV) genotypes has been shown to play a significant role in the development of cervical intraepithelial neoplasia (CIN) and CC (cervical cancer). The present study aimed to determine the distribution and quantification of viral load of HPV genotypes in numerous genital samples obtained from women undergoing routine gynaecological care in different regions of Turkey. METHODS: HPV typing was done by HPV QUANT-21 Quantitative RT-PCR Kit®, which is intended for the specific identification and quantification of low-risk (HPV 6, 11, 44) and high-risk (HPV 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 73, 82) from female subjects in Turkey. RESULTS: From the total of 5975 samples, 2777 were positive for at least one HPV genotype, with an overall frequency of 46.4%. 1695 patients were positive for only one or more LR-HPV genotypes (61%) and 812 patients were positive for one or more HR-HPV genotypes (29%). The frequency of LR-HPV genotypes was 31.4%, while the frequency of HR-HPV genotypes was 118.8%. Our tecnology had a positive advantage to calculate the concentration of each genotypes. Although genotype 52 ranked fifth in frequency, it showed the highest mean concentration, with a value of 5.38 log (copies/sample). CONCLUSION: The presence and genotype of viruses before HPV vaccination have also gained importance. The data obtained would provide guidance for prevention strategies, mainly of vaccination. We decided to add a new estimate to the effectiveness of currently available HPV vaccines and the development of screening programs to prevent and decrease the incidence of CC in Turkey. Further studies would be planned to measure and define the high infection level that can lead to the development of cervical neoplasia. Using this tecnology could give us a clinical desicion to degree the cytological changes.

Screening for Latent Tuberculosis in Children With Immune-mediated Inflammatory Diseases Treated With Anti-tumor Necrosis Factor Therapy: Comparison of Tuberculin Skin and T-SPOT Tuberculosis Tests.

OBJECTIVES: This study aims to analyze the coherence between T-SPOT tuberculosis test (T-SPOT.TB) and tuberculin skin test (TST) with different cut-off values in screening latent tuberculosis infection (LTBI) both prior to and at the sixth month of anti-tumor necrosis factor (anti-TNF) treatment. PATIENTS AND METHODS: This prospective multicentric study included 57 children (34 girls, 23 boys, mean age 12.4±3.9 years; range, 6 to 18 years) diagnosed with immune-mediated inflammatory diseases (IMIDs) evaluated with TST and T-SPOT.TB for screening LTBI both prior to and at the sixth month of treatment with anti-TNF agents. Coherence between two tests was analyzed for TST cut-off values suggested by the local guidelines and also for different possible cut-off values of TST. RESULTS: Tuberculin skin test was positive (≥5 mm) in 28.1% (n=16) of patients in the screening prior to treatment and in 33.3% (n=19) at the sixth month of treatment. T-SPOT.TB test was positive in 8.8% (n=5) of patients both prior to and at the sixth month of treatment. Coherence between two tests was poor or fair when compared with all possible TST cut-off values both prior to and at the sixth month of anti-TNF therapy. CONCLUSION: Our results show poor coherence between T-SPOT.TB and TST for all possible cut-off values of TST. Thus, using both tests would be beneficial in screening LTBI until further studies bring new evidence on the subject.

Microscopy of Gram-stained urethral smear in the diagnosis of urethritis: Which threshold value should be selected?

The aim of this study was to investigate the sensitivity of GSS in the diagnosis of urethritis in patients who present to the outpatient clinic with symptoms of urethritis. Sixty-three male patients who presented to our outpatient clinic with symptoms of urethritis between January and March 2018 were evaluated. Urethral smear samples obtained from patients were evaluated both by GSS examination and by Real-time Multiplex Polymerase Chain Reaction (rt-MPCR) assay. The sensitivity and specificity of GSS in detecting gonococcal urethritis (GU) and nongonococcal urethritis (NGU) were calculated for threshold values of ≥5 and ≥2 PMNL/HPF. The mean age was 33.2 ± 7.1 years. According to the rt-MPCR results, 14 patients had GU and 27 patients had NGU. A threshold value of ≥5 PMNL/HPF in the GSS demonstrated 92.9% sensitivity in the diagnosis of GU and 55.6% sensitivity in the diagnosis of NGU. A threshold value of ≥2 PMNL/HPF reached 100% sensitivity for GU and 92.6% sensitivity for NGU. A cut-off value of ≥5 PMNL/HPF in the GSS has low sensitivity in the diagnosis of NGU. On the other hand, a threshold value of ≥2 PMNL/HPF seems to have higher sensitivity in the diagnosis of both GU and NGU.

HIV prevalence among men who have sex with men in Istanbul.

OBJECTIVES: The re-emergence of the HIV epidemic among men who have sex with men (MSM) represents a serious health issue. This study aimed to assess the HIV prevalence among MSM in a very low prevalence population of a large city. METHODS: A public campaign to raise awareness of HIV infection and to provide access to anonymous testing was conducted in places frequented by MSM and through a mobile phone application. No identity information was requested from individuals contacting the call centre, and anonymous and free HIV testing was offered proactively. Those who agreed to have a test were provided a code number, which was used in blood sampling procedures. RESULTS: Of 1200 subjects who contacted the call centre, 197 consented to undergo HIV testing and visited the laboratory to give a blood sample. Twenty-five subjects were found to have a reactive ELISA result on two different occasions plus a positive Western blot test result. Thus, the HIV prevalence in this group of MSM was 12.7%. CONCLUSIONS: MSM remain a high risk group for HIV infection in a low prevalence setting, and thus represent a key target population for diagnostic and therapeutic interventions.

Prevalence and Seasonal Distribution of Respiratory Viruses During the 2014 - 2015 Season in Istanbul.

BACKGROUND: Acute respiratory tract infection (ARTI) is one of the most common infections worldwide, causing significant morbidity and mortality. OBJECTIVES: This study was conducted to determine the prevalence and seasonal distribution of respiratory viruses in our region, in children and adults with a pre-diagnosis of ARTI. METHODS: A total of 845 nasopharyngeal swab specimens were analyzed with the RespiFinder Smart 22 kit (PathoFinder BV, Netherlands) and the Rotor-Gene 6000 real-time PCR system. RESULTS: At least one pathogen was detected in 612 (72.4%) of the specimens. Overall, 902 pathogens were detected; 821 (91%) were viruses and 81 (9%) were bacteria. The most commonly detected pathogens were influenza A virus (IFV-A) (n = 219), influenza B virus (IFV-B) (n=157), rhinovirus/enterovirus (n = 107), human bocavirus (HBoV) (n = 91), respiratory syncytial virus (RSV) A/B (n = 64), adenovirus (n = 56), human coronaviruses (n = 51), Mycoplasma pneumoniae (n = 49), parainfluenza viruses (n = 40), human metapneumovirus (n = 36), Bordetella pertussis (n = 15), Legionella pneumophila (n = 11), and Chlamydophila pneumoniae (n = 6), respectively. Among the 215 (25.4%) co-infected cases, IFV-A/HBoV and IFV-A/IFV-B were the most common co-infections. IFV-A was the most prevalent agent in all age groups except for children under 5 years of age, in whom RSV A/B was the most common pathogen. Approximately two thirds of the respiratory viruses were detected in early spring and winter, with peaks in January, March, and April. CONCLUSIONS: With regard to the prevalence and seasonal distribution of respiratory viruses, our epidemiological data for the 2014 - 2015 season in Istanbul showed a predominance of IFV-A infections with a peak activity in early spring. Enhanced surveillance and early detection of respiratory viral pathogens can be useful in the diagnosis, treatment, and prevention of ARTIs, and for guiding the development of appropriate public health strategies.

The prevalence of giardia intestinalis in dyspeptic and diabetic patients.

Background and Aims. We aimed to investigate the prevalence of Giardiasis in patients with dyspepsia and patients with diabetes mellitus. Methods. 400 patients and 100 healthy persons were included in this clinical prospective study. The number of patients in each group was equal, 200 dyspeptic and 200 diabetic, respectively. The antigen of G. lntestinalis was determined in the stool specimens by ELISA method. Results. The frequency of Giardiasis was 7% in dyspeptic and 15% in diabetic patients. There was no positive results in any of the healthy persons. There was a significant difference in prevalence rate of Giardiasis between patients with dyspepsia and diabetes mellitus (P < 0.05). Conclusions. These results revealed that the prevalence of Giardiasis in dyspepsia and with diabetes mellitus was high in our country. This is the first study investigating the prevalence of Giardiasis in diabetic patients. To investigate Giardiasis in diabetic patients, who have dyspepsia or not, may be a good approach for public health.