Myroides odoratimimus: a New Threat with Persistent Infections, Multidrug Resistance, and the Potential for Hospital Outbreaks.

Myroides species have recently been reported more frequently in outbreaks in clinics and intensive care units (ICUs). In this study, we aimed to investigate the epidemic potential, antibiotic resistance profile, and risk factors of M. odoratimimus isolates that are increasingly being isolated from the ICUs of our hospital. Data from patients whose Myroides spp. were isolated from their clinical specimens over a 5-year period (September 2016 to January 2022) were retrospectively analyzed. Bacterial identification was performed using a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). The presence of antibiotic resistance genes was analyzed using polymerase chain reaction (PCR). Possible clonal associations between isolates were investigated using enterobacterial repetitive intergenic consensus (ERIC)-PCR. As a result, 66 isolates were identified as M. odoratimimus and one isolate was identified as M. odoratus. The blaMUS resistance gene was detected in all M. odoratimimus isolates, whereas sul2 was detected in ten isolates and tetX was detected in 11 isolates. No other resistance genes, such as blaTUS, were detected. Additionally, two different clonal association patterns were discovered in the 24 selected isolates through the ERIC-PCR method. The increase in the immunosuppressive patient population indicate the possibility of encountering this agent and other opportunistic pathogens more frequently in the future.

Tuberculous and non-tuberculous cervical lymphadenopathy incidence and distribution in Somalia from 2016 to 2020: A review of 241 cases.

Objective: To determine the incidence of tuberculous lymphadenitis (TBL) and other pathologies in cervical lymphadenopathies in Somalia and accompanying radiological findings. Methods: In this hospital-based retrospective study, the demographic characteristics, pathology results and radiological findings of 263 patients who underwent ultrasound (US)-guided cervical lymph node biopsy between January 2016 and February 2020 were analyzed. Results: Of 241 patients 118 men and 123 women (mean age 27.9 ± 18.1 years) included in the study, 46.1% (n = 111) were diagnosed as necrotizing granulomatous lymphadenitis (caseified, consistent with TBL) and 21.6% (n = 12, atypical lymphoid cells and n = 40, metastases) as malignancy. The most common type of metastasis was squamous cell cancer (n = 31), and the primary source of most of them was esophageal cancer (16/31, 51.6%). The age of patients with TBL was significantly lower than that of non-TBL (21.9 ± 14.6 vs. 41.9 ± 24.6, P = 0.003) and the incidence of TBL in pediatric patients was statistically higher (58.0% vs. 21.5%, P = 0.019). The rate of patients with TBL being localized at level 4 and level 5 was significantly more than non-TBL patients (18.0% vs. 10.0% and 23.4% vs. 10.8%, respectively, P = 0.01). Half of patients with TBL who have chest radiography had pathological findings; consolidation and bronchopneumonia were present in 52.6% of them. There were 2 patients with paravertebral abscess and one patient with gastrointestinal tuberculosis. Conclusion: In Somalia, in the presence of cervical lymphadenopathy, after diagnosis by using US-guided biopsy; primarily considering of TBL and malignancy, thoracic involvement should be investigated, and esophageal carcinoma must be excluded in terms of metastatic lymph node.

HIV Seroprevalence in Mogadishu, Somalia: a Retrospective Study between 2015 and 2019.

BACKGROUND: Acquired immunodeficiency syndrome (AIDS) remains a major global public health problem. This study aimed to obtain current epidemiological data on the Human immunodeficiency virus (HIV) infections in Mogadishu, Somalia. METHODS: This study included 92,270 anti-HIV test results reported for 82,954 different individuals between 2015 and 2019. HIV tests were performed using the Architect HIV Ag/Ab Combo assay and retested with the Elecsys HIV combi PT assay. RESULTS: HIV seropositivity was found to be 0.32% (269/82,954) in all individuals over a period of four years. Anti-HIV seropositivity in the 0 - 14, 15 - 19, 15 - 24, 15 - 49, and > 15 age groups were as follows: 0.17% (11/6,441), 0.17% (12/7,131), 0.15% (35/24,132), 0.37% (212/56,895), and 0.34% (258/76,513), respectively. In HIV-infected patients, anti-HBs, HBsAg, anti-HCV, and anti-TP (syphilis) seropositivity was found to be 30.3% (56/185), 9.54% (23/241), 1.24% (3/242), and 3.45% (2/58), respectively. CONCLUSIONS: The findings from this study provide comprehensive data on the HIV epidemiology in Somalia. We believe that the results presented in this study will contribute to the risk analysis and planning of preventive policies of national and global health organizations.

[Investigation of Azithromycin Minimum Inhibitory Concentration Values and Carbapenem Resistance in Salmonella and Shigella Clinical Isolates]. / Salmonella ve Shigella Klinik Izolatlarinda Azitromisin Minimum Inhibitör Konsantrasyon Degerlerinin ve Karbapenem Direncinin Arastirilmasi.

Increasing resistance to first-line antibiotics used in the treatment of infections caused by Salmonella and Shigella species is emerging. Azithromycin presents a good alternative treatment option for Salmonella and Shigella infections. However, there are limited data regarding the susceptibility of azithromycin in Turkey. In this study, we aimed to evaluate the susceptibility of Salmonella and Shigella species to azithromycin, to determine and compare the minimum inhibitory concentration (MIC) values and disk diffusion zone diameters. In addition, susceptibility to meropenem and first-line antibiotic options in isolates was also investigated. A total of 170 Salmonella, 76 Shigella clinical isolates collected between 2014 and 2018 in our hospital were tested for their susceptibility to azithromycin, meropenem, ampicillin, pefloxacin, trimetoprim-sulfamethoxazole, ceftazidime, and cefotaxime. Isolates were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry. The isolates were confirmed and serotyped by the reference laboratory using the conventional slide agglutination method. Susceptibility of the isolates to azithromycin and other antibiotics was evaluated by Kirby-Bauer disk diffusion method. MIC values of azithromycin were determined by the reference broth microdilution method. Combined disk diffusion test was used for the detection of extended spectrum beta-lactamase (ESBL) production. Polymerase chain reaction was performed for macrolide and carbapenem resistance genes and the detected resistance genes were confirmed by sequencing. Of the 76 Shigella isolates tested, 64 (84.2%) were identified as Shigella sonnei, 10 (13.2%) as Shigella flexneri, one (1.3%) as Shigella boydii, and one (1.3%) as Shigella dysenteriae. Among the 170 Salmonella isolates, 131 (77%) were identified as Salmonella enteritidis, 11(6.5%) as Salmonella Typhimurium, 8 (4.7%) as Salmonella Kentucky, 5 (2.9%) as Salmonella Paratyphi B, 4 (2.4%) as Salmonella Infantis, 3 (1.8%) as Salmonella Cholerasuis, and 8 (4.7%) as other serovars (Salmonella Agona, Salmonella Dabou, Salmonella Gallinarum, Salmonella Hadar, Salmonella Muenchen, Salmonella Newport, Salmonella Paratyphi C, Salmonella Senftenberg), respectively. ESBL production was determined as 7.9% (6/76) in Shigella isolates and 2.9% (5/170) in Salmonella isolates. A carbapenem resistant S.Senftenberg isolate positive for the blaOXA-48 resistance gene was detected in our study. Meropenem MIC value of the isolate was detected as > 32 µg/ml with gradient diffusion test. Among all isolates, only one S.boydii isolate was detected as resistant to azithromycin with a MIC value of 128 µg/ml. The isolate was positive for the existence of mphA gene by PCR. In the disk diffusion test, azithromycin inhibition zone diameters were ≥ 12 mm in all of the tested isolates, except for the azithromycin-resistant isolate, and the azithromycin MICs were determined as ≤ 16 µg/ ml by broth microdilution. Increasing resistance to commonly used antibiotics in Salmonella and Shigella species is emerging. The detection of a carbapenem-resistant Salmonella isolate in our study indicates that the spread of carbapenem resistance to other Enterobacterales species may cause global problems. Antimicrobial susceptibility testing of azithromycin for Salmonella and Shigella species has been difficult to establish due to the lack of approval in vitro breakpoints for all species. Consequently, our data shows that azithromycin exhibits as a good alternative therapeutic choice for the treatment of gastrointestinal diseases caused by Salmonella and Shigella species. Further studies are needed to provide appropriate in vitro breakpoints supported by clinical data.

The Prognostic Value of Vertebral Bone Density on Chest CT in Hospitalized COVID-19 Patients.

The aim of this study is to evaluate the prognostic value of the vertebral bone mineral density (BMD) on chest computed tomography (CT) in COVID-19 patients. The chest CT of hospitalized patients with COVID-19 pneumonia were evaluated for Pneumonia Severity Score (PSS) as the ratio of the volume of involved lung parenchyma to the total lung volume. In addition, BMD was manually measured from the vertebral corpus using axial CT images. The relationships of clinical variables, PSS and vertebral BMD with patient outcomes, namely mortality, intensive care unit (ICU) admission and mechanical ventilation were investigated. Lower BMD was defined as ≤100 HU. The study included 209 patients (118 males, 56.4%). As a result of the univariate analysis, the rates of mortality, ICU admission and mechanical ventilation were 17.2% (n = 36), 24.8% (n = 52), and 20.6% (n = 43), respectively, and they were significantly higher among the patients with lower BMD (38.1 vs 13.0%, p < 0.001; 33.4 vs 21.2%, p = 0.002; and 38.1 vs 8.2%, p < 0.001, respectively). In the mortality group, PSS was significantly higher (median, 9 vs 5; p < 0.001) and vertebral BMD was significantly lower (median, 83 vs 139; p < 0.001). Severe clinical incidence was significantly higher in patients with lower BMD compared to those with higher BMD (39.7 vs 24.7% and p = 0.028). There was a significant correlation between clinical classification and lower BMD (r = 0.152 and p = 0.028). The multivariate analysis revealed vertebral BMD [odds ratio (OR), 1.028; 95% CI, 1.011-1.045, p = 0.001) and lower BMD (OR, 4.682; 95% CI, 1.784-12.287, p = 0.002) as significant independent predictors of mortality. Vertebral BMD is a strong independent predictor of mortality that is reproducible and can be easily evaluated on the chest CT images of COVID-19 patients.

Does COVID-19 cause an increase in spleen dimensions? Possible effects of immune activation, hematopoietic suppression and microthrombosis.

PURPOSE: To radiologically examine how the spleen size, which has important functions in hematological and immunological balance, is affected in COVID-19. METHODS: Between July 1 and August 31, 2020, consecutive patients diagnosed with COVID-19 were analyzed. Among these patients, those who underwent chest computed tomography (CT) examination at the time of presentation, patients with follow-up CT due to clinical deterioration were included in the study. The CTs of the patients were evaluated in terms of spleen size and volume. RESULTS: A total of 160 patients (88 females, 55%) were included in the study. The mean time between the initial and follow-up CT was 7.2 ± 2.8 days. The splenic volume (244.3 ± 136.7 vs. 303.5 ± 156.3 cm3) and splenic index (421.2 ± 235.5 vs. 523.2 ± 269.4 cm3) values were significantly higher in the follow-up CT compared to the initial CT (p < 0.001). The increase in the splenic volume and splenic index values was 59.2 ± 52.4 cm3 and 101.9 ± 90.3 cm3 (p < 0.001), respectively. The COVID-19 severity score was significantly higher in the follow-up CT compared to the initial CT (3.7 ± 4.2 vs. 12.5 ± 5.7, respectively; p < 0.001). The spleen width measured separately on the initial and follow-up CTs showed a highest positive correlation (r = 0.982, p < 0.001). CONCLUSION: Our study indicates that spleen size increases slightly-moderately in the first stages of the infection, and this increase is correlated with the COVID-19 severity score calculated on the chest CT data, and in this respect, it is similar to infections presenting with cytokine storm.

Frequency of hepatic steatosis and its association with the pneumonia severity score on chest computed tomography in adult COVID-19 patients.

BACKGROUND: Recent studies of the coronavirus disease 2019 (COVID-19) demonstrated that obesity is significantly associated with increased disease severity, clinical outcome, and mortality. The association between hepatic steatosis, which frequently accompanies obesity, and the pneumonia severity score (PSS) evaluated on computed tomography (CT), and the prevalence of steatosis in patients with COVID-19 remains to be elucidated. AIM: To assess the frequency of hepatic steatosis in the chest CT of COVID-19 patients and its association with the PSS. METHODS: The chest CT images of 485 patients who were admitted to the emergency department with suspected COVID-19 were retrospectively evaluated. The patients were divided into two groups as COVID-19-positive [CT- and reverse transcriptase-polymerase chain reaction (RT-PCR)-positive] and controls (CT- and RT-PCR-negative). The CT images of both groups were evaluated for PSS as the ratio of the volume of involved lung parenchyma to the total lung volume. Hepatic steatosis was defined as a liver attenuation value of ≤ 40 Hounsfield units (HU). RESULTS: Of the 485 patients, 56.5% (n = 274) were defined as the COVID-19-positive group and 43.5% (n = 211) as the control group. The average age of the COVID-19-positive group was significantly higher than that of the control group (50.9 ± 10.9 years vs 40.4 ± 12.3 years, P < 0.001). The frequency of hepatic steatosis in the positive group was significantly higher compared with the control group (40.9% vs 19.4%, P < 0.001). The average hepatic attenuation values were significantly lower in the positive group compared with the control group (45.7 ± 11.4 HU vs 53.9 ± 15.9 HU, P < 0.001). Logistic regression analysis showed that after adjusting for age, hypertension, diabetes mellitus, overweight, and obesity there was almost a 2.2 times greater odds of hepatic steatosis in the COVID-19-positive group than in the controls (odds ratio 2.187; 95% confidence interval: 1.336-3.580, P < 0.001). CONCLUSION: The prevalence of hepatic steatosis was significantly higher in COVID-19 patients compared with controls after adjustment for age and comorbidities. This finding can be easily assessed on chest CT images.

[Current Approaches in the Diagnosis and Management of Congenital Cytomegalovirus Infections and the Situation in Turkey]. / Konjenital Sitomegalovirüs Enfeksiyonlarinin Tani ve Yönetiminde Güncel Yaklasimlar ve Türkiye'deki Durum.

Human cytomegalovirus (CMV) infections are common in all populations and CMV seroprevalence in women of childbearing age is in the range of 45-100% worldwide. CMV is the most common cause of congenital infections and is associated with fetal development defects and hearing loss. The risk of congenital infection is directly related to maternal immunity and is between 30-40% and 1-2% range in primary and non-primary infections, respectively. Only 5-10% of newborns with congenital infection are symptomatic at birth. Nearly 4% of these babies can die early in life, while 40-60% have to live with permanent sequelae such as sensorineural hearing loss, cognitive deficit and visual impairment. Asymptomatic newborns including those born from mothers with non-primary infections are also at risk for long-term sequelae. These sequelae often develop in the first 1-2 years of life and may extend up to 5-7 years, but the severity of damage reduces in time. CMV seroprevalence in women of childbearing age and pregnant women in Turkey is between 96% and 99.8%. Until recently, our knowledge about the frequency of congenital CMV infections in Turkey was derived from the studies based on the maternal screening tests. These studies, which were far from reflecting the true prevalence of congenital CMV infections, have begun to be replaced by newborn-based systematic screening studies. CMV DNA positivity was found to be 1.6-1.9% in saliva samples, while both saliva and urine and/or blood samples positivity was found to be 0.2-1.4% in the newborn screening studies carried out in Turkey. Glycoprotein B-1 (gB1) was the most frequently detected genotype (38.4-83.3%) in newborns in Turkey. Standard measures and preventive public health practices such as education of the mother, reducing the contact of pregnant women with virus-spreading children and the hand hygiene come into prominence in the prevention of maternal and congenital infections as a result of the absence of an approved vaccine or low protection of existing vaccines. Advanced measures, such as screening blood products especially for the people with immunodeficiency and serological screening of the in-vitro fertilization applications are also being considered. Monitoring of infected newborns and their mothers during pregnancy, postnatal diagnosis and providing counseling for the parents are also critical. Hearing loss can be detected at an early stage using screening tests that become a routine practice for all newborns. Thus, cognitive and psychosocial development of children affected by infection is supported by speech therapy, the use of hearing aids and other practices. However, it should be noted that hearing functions in infected newborns may be normal at birth, but these newborns are at risk for progressive sensorineural hearing loss. For early diagnosis of asymptomatic newborns, it is important to adopt CMV tests as a part of newborn screening programs. Another preventive approach is to treat the mother and the baby with antiviral drugs and preparations that directly target the virus. Passive immunization of the pregnant and the treatment of the symptomatic newborns with valganciclovir have yielded positive results. In this review article, maternal, fetal and newborn based current approaches used in the diagnosis and follow-up of congenital CMV infections have been discussed.

Zika Virus-associated Ocular and Neurologic Disorders: The Emergence of New Evidence.

BACKGROUND: It has been approximately 70 years since the discovery of the Zika virus (ZIKV). It had been established that the virus causes mild infections and is confined to Africa and Asia; however, major changes in the clinical and epidemiologic patterns of ZIKV infection have occurred in recent years. The virus has attracted intense interest because of the possible association of several autoimmune and neurodevelopmental disorders. METHODS: We present a summary of the articles that attempt to explain the ZIKV unknowns and strengthen the association with some disorders that are thought to be related to ZIKV, by describing the discovery milestones from the initial identification of the virus to the present day. RESULTS: New evidence strengthens the association between ZIKV infections and Guillain-Barré syndrome (GBS), microcephaly and various neurodevelopmental and ophthalmologic disorders as a result of numerous new clinical and experimental studies. CONCLUSIONS: The World Health Organization declared the end of the "Public Health Emergency of International Concern" in December 2016, but ZIKV and associated consequences remain a significant enduring public health challenge.

[Global spread of Zika virus epidemic: current knowledges and uncertainties]. / Zika virus salgininin küresel yayilimi: Güncel bilgiler ve belirsizlikler.

Zika virus (ZIKV) is an enveloped RNA virus that belongs to the Flaviviridae family. Although more than 60 years have passed since the discovery and first reported human cases of the virus, only a small number (< 10) of cases had been encountered in the literature until the last 10 years. Zika virus was known as a virus which caused sporadic infections and was confined to Africa and Asia along a narrow equatorial line. In 2007, however, the first major outbreak of ZIKV occurred in Yap Island (Micronesia), and so it was reported for the first time outside of Africa and Asia. Between the years of 2007 and 2014, ZIKV spreaded to island groups located in Southeast Asia and the Pacific Ocean, and in 2015-2016, it has spread to South and Central America and the Caribbean. Today, travel-related imported cases is still been reported in Europe, North America, and other countries in the Far East. According to the data from the World Health Organization and the Centers for Disease Control and Prevention, as of March 2016, ZIKV infections have already spread locally in more than 30 countries, and travel alerts have been issued for the countries where the virus is present. Zika virus infections are generally asymptomatic or may present with a moderate clinical picture (e.g. acute onset of fever, maculopapular rash, arthralgia, and nonpurulent conjunctivitis). Although no deaths were attributed to ZIKV infection over the past 60 years, as of November 2015, it has been suggested that three deaths in Brazil, including the death of a newborn with microcephaly, may be attributed to ZIKV infection. In addition, concurrent with outbreaks in 2013 in French Polynesia and in 2015 in Brazil, there have been significant rises reported in the incidence of some autoimmune and neurodevelopmental disorders, including Guillain-Barre syndrome and microcephaly; these reports have caused considerable international concern. There are many points that are still unclear about ZIKV, including: (1) intrauterine transmission risk, frequency, and effects of the infection on fetal development; (2) the probability of perinatal transmission and if so the possible risks; (3) association with autoimmune and neurological diseases, and presence of long-term sequelae risks after infection; (4) possible routes of transmission other than mosquito bites, such as sexual contact, blood transfusion, and other body fluids (saliva, semen, or urine); (5) presence of reservoir(s) and different mosquito vectors; (6) diagnostic difficulties including cross reactivity in serological tests and standardization of testing procedures; (7) severity of the infection in immunocompromised patients; and (8) the potential effectiveness of antiviral therapy or preventive vaccines. In this review, updated information and recommendations regarding ZIKV outbreaks and risks, and the epidemiology, diagnosis and characteristics of ZIKV infections, are summarized in light of the most recent literature.

Preservative solution for skeletal muscle biopsy samples.

CONTEXT: Muscle biopsy samples must be frozen with liquid nitrogen immediately after excision and maintained at -80°C until analysis. Because of this requirement for tissue processing, patients with neuromuscular diseases often have to travel to centers with on-site muscle pathology laboratories for muscle biopsy sample excision to ensure that samples are properly preserved. AIM: Here, we developed a preservative solution and examined its protectiveness on striated muscle tissues for a minimum of the length of time that would be required to reach a specific muscle pathology laboratory. MATERIALS AND METHODS: A preservative solution called Kurt-Ozcan (KO) solution was prepared. Eight healthy Sprague-Dawley rats were sacrificed; striated muscle tissue samples were collected and divided into six different groups. Muscle tissue samples were separated into groups for morphological, enzyme histochemical, molecular, and biochemical analysis. STATISTICAL METHOD USED: Chi-square and Kruskal Wallis tests. RESULTS: Samples kept in the KO and University of Wisconsin (UW) solutions exhibited very good morphological scores at 3, 6, and 18 hours, but artificial changes were observed at 24 hours. Similar findings were observed for the evaluated enzyme activities. There were no differences between the control group and the samples kept in the KO or UW solution at 3, 6, and 18 hours for morphological, enzyme histochemical, and biochemical features. The messenger ribonucleic acid (mRNA) of ß-actin gene was protected up to 6 hours in the KO and UW solutions. CONCLUSION: The KO solution protects the morphological, enzyme histochemical, and biochemical features of striated muscle tissue of healthy rats for 18 hours and preserves the mRNA for 6 hours.

The degree of mucosal damage to the small intestine and serum immunoglobulin G4 levels correlate with celiac disease.

BACKGROUND: Celiac disease (CD) is an immune-mediated and chronic inflammatory enteropathy, triggered by the ingestion of gluten in genetically susceptible individuals. Immunoglobulin G4 (IgG4)-related diseases are a recently defined emerging clinical condition, characterized by increased serum IgG4 concentrations. The aim of this study was to investigate whether IgG4 levels correlate with the titers of intestinal antibodies and the degree of mucosal damage in CD patients. MATERIALS AND METHODS: A total of 41 CD patients and 28 healthy controls were included in the study. All patients underwent a duodenal biopsy and were then diagnosed with the modified Marsh classification. Blood samples were obtained for IgG4 measurements. Serums were kept at -80 °C until the analysis was carried out and plasma IgG4 levels were determined using an enzyme-linked immune sorbent assay method with a diagnostic cutoff value of 135 mg/dl. RESULTS: The mean age of the CD and the control group was 26.8 ± 8.3 and 26.9 ± 6.2 years, respectively. The mean IgG4 levels were significantly higher in CD patients (283.21 ± 39.02 mg/dl) compared with the healthy control group (68.97 ± 15.89 mg/dl, P<0.0001). In the CD group, 27/41 patients and in the control group, 4/28 patients had high IgG4 levels (>135 mg/dl, P < 0.0001). A close correlation was found between the grade of mucosal damage, IgG4 levels, and antigliadin-IgA; the higher the grade Marsh score, the higher the measured IgG4 (P < 0.05). CONCLUSION: In our study, IgG4 levels of CD patients were higher than normal ranges whereas the results of the control group were within physiologic limits. We also showed for the first time that there was a correlation between IgG4 levels, autoantibody, and severity of mucosal damage. To the best of our knowledge, this is the first study to evaluate IgG4 levels and mucosal damage in CD patients.

Congenital cytomegalovirus infections and glycoprotein B genotypes in live-born infants: a prevalence study in Turkey.

BACKGROUND: Cytomegalovirus (CMV) infections are the leading cause of infectious hearing loss and central nervous system disease among children worldwide. In this study, we aimed to determine the birth prevalence of congenital CMV infection in live-born infants in Turkey. METHODS: In total, 944 consecutive live-born infants born from 926 pregnant women were included in this study. CMV-DNA was investigated in saliva samples of all newborns within the first 3 days after birth using TaqMan-based real-time PCR. RESULTS: The birth prevalence of congenital CMV infection in live-born infants was 1.91% (18/944), and all congenitally infected infants were asymptomatic at birth. The prevalence of congenital CMV infection was 16.7% (3/18) in twin pregnancies and 1.32% (12/908) in single pregnancies (p = 0.002). Genotyping analysis showed glycoprotein B-1 (gB1) to be the most frequently detected genotype at 83.3%. CONCLUSION: The study results suggest that the majority of congenital CMV infection in Turkey occurs following nonprimary maternal infection. We believe that congenital CMV infection and its long-term effects have been underestimated in our country, as infected infants are usually asymptomatic at birth.

[Current problems and recent advances in the molecular diagnosis of genital human papillomavirus infections]. / Genital insan papillomavirus enfeksiyonlarinin moleküler tanisinda karsilasilan sorunlar ve yeni gelismeler.

It was proven in the early 1980s that cervical cancer (CC) biopsy specimens and CC cell lines contain human papillomavirus (HPV) DNA sequences. In subsequent years, researchers discovered that the E6 and E7 genes of HPV are expressed in CC tissues and these oncoproteins interact with cellular proteins, including pRb and p53. Establishment of the relationship between HPV infections and CC led to increasing interest on this topic. Comprehensive epidemiological studies determined that specific types of HPV are major risk factors for CC. These HPV types, called high-risk or oncogenic types, are associated with other anogenital cancers and a subset of head and neck cancers. A number of commercial and in-house diagnostic techniques, each of which has a different approach and methodology, have been developed to diagnose HPV infections. HPV testing based on the detection of viral DNA has become an important part of CC screening programs. These screening-typing methods and combined approaches, which are used to diagnose and follow-up (management) HPV infections, have advantages and disadvantages. The choice of method is complicated by several factors and challenges that arise owing to the nature of the virus and the assay methodology. For example, a number of different HPV types can cause genital infections, multiple sequence variations are often observed even in the same HPV genotype, the detection sensitivity of the available methods is variable depending on the HPV genotypes and the viral DNA copy number in the samples examined. The capability for the detection of multiple infections and the ability to perform genotyping differ between the methods. The aim of this review is to summarize the methods used for the diagnosis and follow-up of HPV infections, and to share the current informations that may be helpfull for the choice of appropriate method. For this purpose, molecular-based HPV tests that were used in the past and their development processes were described briefly, then currently accepted and widely used methods for diagnosis, screening, and typing were discussed in detail, along with their advantages and disadvantages.

Coexistence of Epstein-Barr virus and Parvovirus B19 in tonsillar tissue samples: quantitative measurement by real-time PCR.

OBJECTIVE: In this study, we aimed to investigate the presence and copy number of six different viruses in tonsillar tissue samples removed surgically because of chronic recurrent tonsillitis or chronic obstructive tonsillar hypertrophy. METHODS: In total, 56 tissue samples (tonsillar core) collected from 44 children and 12 adults were included in this study. The presence of viruses was investigated using a new TaqMan-based quantitative real-time PCR assay. RESULTS: Of the 56 tissue samples, 67.9% (38/56) were positive for at least one of the six viruses. Epstein-Barr virus was the most frequently detected virus, being found in 53.6% (30/56), followed by human Parvovirus B19 21.4% (12/56), human adenovirus 12.5% (7/56), human Cytomegalovirus 5.4% (3/56), BK polyomavirus 1.8% (1/56), and Herpes simplex virus 1.8% (1/56). Precancerous or cancerous changes were not detected in the tonsillar tissue samples by pathologic examination, whereas lymphoid hyperplasia was observed in 24 patients. In contrast to other viruses, B19 virus was present in high copy number in tonsillar tissues. The rates of EBV and B19 virus with high copy number (>500.000 copies/ml) were higher in children than in adults, and a positive relationship was also found between the presence of EBV and the presence of B19 virus with high copy number (P=0.037). CONCLUSIONS: It is previously reported that some viral agents are associated with different chronic tonsillar pathologies. In the present study, the presence of B19 virus in tonsillar core samples was investigated quantitatively for the first time, and our data suggests that EBV infections could be associated with B19 virus infections or could facilitate B19 virus replication. However, further detailed studies are needed to clarify this observation.

Efficiency of MY09/11 consensus PCR in the detection of multiple HPV infections.

Human papillomavirus (HPV) DNA testing has become an important component of cervical cancer screening programs. In this study, we aimed to evaluate the efficiency of MY09/11 consensus polymerase chain reaction (PCR) for the detection of multiple HPV infections. For this purpose, MY09/11 PCR was compared to an original TaqMan-based type-specific real-time PCR assay, which can detect 20 different HPV types. Of the 654 samples, 34.1% (223/654) were HPV DNA positive according to at least one method. The relative sensitivities of MY09/11 PCR and type-specific PCR were 80.7% (180/223) and 97.8% (218/223), respectively. In all, 352 different HPV isolates (66 low-risk and 286 high-risk or probable high-risk types) were identified in 218 samples, but 5 samples, which were positive by consensus PCR only, could not be genotyped. The distribution of the 286 high-risk or probable high-risk HPVs were as follows: 24.5% HPV-16, 8.4% HPV-52, 7.7% HPV-51, 6.3% HPV-39, 6.3% HPV-82, 5.6% HPV-35, 5.6% HPV-58, 5.6% HPV-66, 5.2% HPV-18, 5.2% HPV-68, and 19.6% the other 8 types. A single HPV type was detected in 57.3% (125/218) of the genotyped samples, and multiple HPV types were found in the remaining 42.7% (93/218). The false-negative rates of MY09/11 PCR were found to be 17.4% in single infections, 23.3% in multiple infections, and 34.6% in multiple infections that contained 3 or more HPV types, with the condition that the low-risk types HPV-6 and HPV-11 be considered as a monotype. These data suggest that broad-range PCR assays may lead to significant data loss and that type-specific PCR assays can provide accurate and reliable results during cervical cancer screening.

Detection of major HPVs by a new multiplex real-time PCR assay using type-specific primers.

In this study, we aimed to develop a cost-effective, practical, and sensitive method to be used for the diagnosis of HPV infections. The presence of HPV-DNA was investigated in cervical smear samples using three different methods: MY09/11 consensus PCR, TaqMan-based type-specific real-time PCR, and SYBR Green-based multiplex PCR. Of the 315 samples, 21.6% (68/315) were HPV-DNA positive by using at least one of the three methods. The relative sensitivities of MY09/11 PCR, type-specific PCR, and multiplex PCR were found to be 86.8% (59/68), 91.2% (62/68), and 91.2% (62/68), respectively. Genotyping analyses were successfully carried out in 62 of 68 HPV-DNA positive samples, and 77 isolates (8 low-risk and 69 high-risk HPV) were identified, while six samples were determined to be positive by consensus PCR only and could not be genotyped. The type distribution of the 69 high-risk HPV strains was as follows: 37.7% HPV 16, 13.0% HPV 52, 11.6% HPV 58, 7.2% HPV 18, 7.2% HPV 31, 7.2% HPV 68, 4.3% HPV 35, 4.3% HPV 39, 4.3% HPV 82, 1.4% HPV 33, and 1.4% HPV 45. Our data suggests that the diagnosis of HPV infections using only consensus PCR may lead to epidemiologically significant data loss, and that our multiplex PCR is more sensitive than consensus PCR and lower in cost than the type-specific PCR. We believe that the SYBR Green-based multiplex PCR may be useful and cost-effective for other microbiological fields. In addition, type-specific screening of HPV-DNA gives more reliable results, but it may also be used in combination with consensus PCR if the type spectrum of the test is not large enough.

[Investigation of HPV-DNA in cervical smear samples by two different methods: MY09/11 consensus PCR and type-specific real-time PCR]. / Servikal Sürüntü Örneklerinde Iki Farkli Yöntemle HPV-DNA Varliginin Arastirilmasi: MY09/11 Konsensus PCR ve Tipe Özgül Gerçek Zamanli PCR.

Cervical cancer that has been proven to be associated with human papillomavirus (HPV) is the second most common cancer in women worldwide and is a leading cause of cancer deaths in women in developing countries. Cervical cancers can be detected in the early stages by screening programs since a long latency period exists between the beginning of HPV infection and the development of cervical cancer. HPV-DNA testing is widely used throughout the world and today is an important part of cervical cancer screening programs. In this study, we analyzed the presence of HPV-DNA in 356 cervical smear samples by two different methods which are MY09/11 consensus real-time polymerase chain reaction (Rt-PCR) and type-specific Rt-PCR. All samples were also tested by type-specific PCR, regardless of consensus PCR results. PCR analysis were performed using the type- specific primers and TaqMan probes that were designed for a total of 13 different HPV types; two low risk HPV and 11 high risk HPV types. A total of 142 different isolates, 95 being high risk HPV isolates, 39 low risk HPV isolates and eight unidentified isolates, were determined in 109 (30.6%) smear samples that were defined as HPV-DNA positive by at least one of the two methods. Frequencies of detection of high risk HPV types in HPV-positive samples were as follows respectively: HPV-16; 32 (33.7%), HPV-52; 12 (12.6%), HPV-58; 11 (11.6%), HPV-18; 7 (7.4%), HPV-31; 7 (7.4%), HPV-35; 7 (7.4%), HPV-68; 6 (6.3%), HPV-33; 4 (4.2%), HPV-82; 4 (4.2%), HPV-39; 3 (3.2%) and HPV-45; 2 (2.1%). Various cytologic atypia were reported in 84 (23.6%) smear samples according to the simultaneously performed cytopathologic examination. Single HPV type was detected in 72 (71.3%) and multiple HPV types were detected in 29 (28.7%) of 101 smear samples with the exception of the unidentified isolates by type-specific RtPCR. HPV-18, HPV-33 and HPV-35 had higher detection rates of 7.4, 3.7 and 3.0 fold in mixed infections than single ones, respectively. HPV-DNA could not be detected by MY09/11 consensus primers in 24 (23.8%) of 101 cervical smear samples that were accepted as HPV-DNA positive by type-specific PCR. Thus, investigation of the presence of HPV-DNA by only consensus primers would be insufficient for the diagnosis, treatment and follow-up of HPV infections. Initial assessment of smear samples by using consensus primers and genotyping only positive samples seem to be the most practical strategy for the diagnosis and screening of HPV infections throughout the world. When this situation is taken into consideration, we think that the current prevalence data in our country and around the world must be updated by using large-scale studies that apply new generation screening and diagnostic tests.

[Investigation of West Nile virus RNA in blood donors by real-time RT-PCR]. / Kan Donörlerinde Gerçek Zamanli RT-PCR ile Bati Nil Virusu RNA'sinin Arastirilmasi

West Nile virus (WNV), a member of Flaviviridae family, is an enveloped, icosahedral symmetric RNA virus. Primary reservoir hosts of WNV are birds, but the virus can cause various infections in humans and other mammals. The most common and natural transmission way of WNV infections is mosquito bites, however, humans can be infected by different routes. The most important non-mosquito transmission route is contaminated blood and blood products. In this study, we aimed to investigate the risk of WNV transmission through blood and blood products in Ankara, Turkey. The presence of WNV RNA was investigated by in house real-time reverse transcriptase-polymerase chain reaction (RT-PCR) in serum samples obtained from 729 healthy blood donors (mean age: 27.7 years; 711 were male), regardless of the donor's seropositivity status since the virus can be transmitted at the early stages of infection when seroconversion has not yet developed. Serum samples were collected in August-September 2009, the period when these infections are more frequent due to mosquito activity. The vast majority of donors (n= 702, 96.3%) have been inhabiting in Ankara and 569 (78%) of donors have had risk factors for arboviral infections (e.g. outdoor activity, mosquito and tick bites). WNV RNA was not detected by real-time RT-PCR analysis in any serum sample included in this study. According to the results of our study, it can be said that the risk of WNV transmission through blood and blood products is low in Ankara. However, WNV seropositivity was detected within the range of 0.56 to 2.4% among blood donors in previous studies and probable and confirmed WNV infections have been reported in our region. In addition, WNV outbreaks have emerged in some countries neighbouring Turkey recently. Thus, the risk of WNV transmission through blood and blood products should not be ignored and blood donor questionnaires should be evaluated in detail.

[Phenotypic and genotypic identification of Candida strains isolated as nosocomial pathogens]. / Hastane enfeksiyonu etkeni olarak izole edilen Candida suslarinin genotipik ve fenotipik olarak tanimlanmasi.

Over the last decade, there have been important changes in the epidemiology of Candida infections and antifungal agents used to treat these infections. In recent years, Candida species have emerged as important causes of invasive infections among patients in intensive care units. One of the main goals of this study was to evaluate the molecular epidemiology of infectious Candida species isolated in our hospital and accordingly supply data for hospital infection (HI) control. The other aim of this study was to evaluate effectiveness and practical applicability of traditional and molecular methods used to identify Candida isolates to the species level. A total of 77 Candida strains that were isolated from various clinical specimens of 60 hospitalized patients (29 male, 24 female; 7 were children) were included in the study. Fifty-seven (74%) of those isolates were defined as HI agents according to Centers for Disease Control and Prevention (CDC) criteria. The most common Candida species identified as agents of HI were C.albicans (22; 38.6%), followed by C.tropicalis (14; 24.6%), C.parapsilosis (13; 22.8%), C.glabrata (7; 12.3%) and Candida spp. (1; 1.75%). It was determined that bloodstream (26; 45.6%) and urinary tract infections (24; 42.1%) were the most frequently encountered nosocomial infections caused by Candida species. In addition it was detected that the most frequent causative agent of bloodstream infections was C.parapsilosis (10; 38.5%) and of urinary tract infections was C.albicans (12; 50%). The evaluation of advantages and disadvantages of traditional phenotypic methods [germ tube formation, chlamydospore formation in corn meal agar, growth at 45°C, colony characteristics on CHROMagar Candida medium, carbohydrate assimilation properties detected by API ID 32C (BioMerieux, France) system] and some molecular techniques [polymerase chain reaction (PCR) by using ITS-1, ITS-3 and ITS 4 primers, PCR-Restriction fragment length polymorphism (RFLP), PCRRFLP in which ITS1-ITS4 products cut by Msp I ve Bln I restriction enzymes] for the identification of Candida species revealed that CHROMagar Candida medium combined with API ID 32C kit yielded the same results (100% compatible) as molecular techniques for the species identification of Candida isolates. Since these phenotypic methods were simple and cost effective when compared to molecular techniques, they should be considered in the identification of Candida species.