Phylogenetic Characterization of Orthohantavirus dobravaense (Dobrava Virus).

We report complete coding sequences of Orthohantavirus dobravaense (Dobrava virus) Igneada strains and phylogenetic characterization of all available complete coding sequences. Our analyses suggested separation of host-dependent lineages, followed by geographic clustering. Surveillance of orthohantaviruses using complete genomes would be useful for assessing public health threats from Dobrava virus.

Is adenotonsillectomy safe in covid-19 era? Investigation of sars-cov2 in adenoid and tonsil tissues.

OBJECTIVES: COVID-19 has seriously altered physicians' approach to patients and diseases, with a tendency to postpone elective procedures. Tonsillectomy, alone or with adenoidectomy, is one of the most common surgeries performed by otolaryngologists. Although they are generally accepted as elective surgeries, they significantly improve the quality of life, and postponing these surgeries for a long time can have deteriorative effects on the patients. We aimed to investigate the presence of SARS CoV-2 in the adenotonsillectomy materials to find out if performing adenotonsillectomy is safe during the COVID-19 pandemic. METHODS: Forty-eight tissue samples from 32 patients that underwent tonsillectomy with or without adenoidectomy were investigated whose SARS-CoV-2 RT-PCR test in the samples obtained from nasopharyngeal (NP) and oropharyngeal (OP) swabs were negative within 24 h before the operation. While 16 patients underwent only tonsillectomy and one of their tonsils was investigated, 16 of the patients underwent adenotonsillectomy and their adenoid tissues were sent along with one of their tonsils. SARS-CoV-2 viral RNA was investigated with Real-Time PCR in tissue samples. RESULTS: Two (4.2%) tissue samples had positive PCR tests for SARS-CoV-2, while 46 of them were negative. One of the positive patients had undergone tonsillectomy with the indication of chronic recurrent tonsillitis, and the other patient had undergone adenotonsillectomy for obstructive adenotonsillar hypertrophy. PCR test was positive in the adenoidectomy specimen and negative in the tonsillectomy specimen in this patient. CONCLUSIONS: Adenotonsillectomy can be done safely in asymptomatic patients without a history of Covid-19, with a negative PCR test result obtained within the last 24 h.

[Spread of armA 16S rRNA Methylase Gene in a Tertiary Hospital and Errors in Aminoglycoside Susceptibility Results of Rapid Susceptibility Test Systems]. / Bir Üniversite Hastanesinde armA 16S rRNA Metilaz Geninin Yayilimi ve Hizli Duyarlilik Test Sistemlerinde Belirlenen Aminoglikozid Duyarlilik Hatalari.

Aminoglycosides (AGs) are actively used in combination therapies against carbapenem resistant gram negative species in recent years. Spread of 16S rRNA methylases which can cause high-level resistance to AG antibiotics, limits this treatment choice. Although there are some studies showing that errors in determining AG susceptibility in automated systems may be related to the armA gene, one of the 16S rRNA methylase genes, the exact reason for these errors is not yet known. In our study, we aimed to investigate the relevance of 16S rRNA methylases to the discrepancies between VITEK 2.0 and disc diffusion test results for amikacin (AK) and gentamicin (GEN) susceptibility of Acinetobacter baumannii and Klebsiella pneumoniae isolates. All K.pneumoniae and A.baumannii isolates from 1st January-10th February 2018 were collected prospectively and included in the study. Additionally, two initial isolates from July 2017 (one K.pneumoniae and one A.baumannii isolate) for which first discrepant susceptibility results were determined, were also included. Amikacin and gentamicin susceptibility results of 37 isolates [A. baumannii (n= 20) and K.pneumoniae (n= 17)] were evaluated together with VITEK 2.0 system, disc diffusion and gold standard broth microdilution methods and minor error (mE), major error (ME) and very major error (VME) rates were calculated. The rmtB, rmtC and armA genes in isolates were investigated by polymerase chain reaction (PCR) and the relationship between the presence of 16S rRNA methylases and false susceptibility results were examined. In addition, disc diffusion test results were evaluated at the end of four, six, eight hours and one night incubation periods to examine the effect of the double zone phenotype observed in 13 of the study isolates on rapid susceptibility tests. All disc diffusion test results were found to be compatible with broth microdilution test results. When the VITEK 2.0 system and the broth microdilution test were compared, 10.3% and 12.1% VME and 8.1% and 5.4% mE were detected for AK and GEN susceptibility results, respectively. While rmtB and rmtC genes were not detected in the study isolates, armA gene was positive in eight (47.1%) of 17 K.pneumoniae isolates and in 15 (75%) of 20 A.baumannii isolates. All three VMEs in A.baumannii isolates were detected in AK susceptibility results. Two of those were armA gene positive and one was armA gene negative isolates. All four VMEs in K. pneumoniae isolates were detected in GEN susceptibility results only, and all of these isolates were armA gene positive. No direct correlation was found between the errors detected in the VITEK 2.0 system susceptibility results and the double zone phenotype. When the isolates were evaluated in the 4-16 hours incubation time interval, it was observed that resistant colonies could be detected after a minimum of six hours of incubation period in the inhibition zone surrounding the aminoglycoside discs. To the best of our knowledge this is the first report of armA producing A.baumannii from Turkey. The high rate of armA gene positivity detected in our isolates suggested that the prevalence of armA gene increased in our country or at least in our region, in recent years. In the AG susceptibility results of the VITEK 2.0 system, the rate of VME above the acceptance criterion has shown that the errors occurred were not directly related to armA gene positivity or double zone phenotype. Finally, our study results indicated that AG susceptibility results should be evaluated minimum six hours later of incubation while implementing rapid susceptibility tests.

[Seroprevalence of pertussis toxin antibody in Manisa province of Turkey, after six years implementation of acellular pertussis vaccine]. / Hücre içermeyen bogmaca asi uygulamasinin altinci yilinda Türkiye'nin Manisa ilindeki pertussis toksin antikoru seroprevalansi.

Vaccination is the most effective way of preventing pertussis disease. Turkey commenced a routine infant immunization program using whole cell (wP) pertussis vaccine in 1968. Immunization accelerated in 1985 after participation of Turkey in the Expanded Programme on Immunization initiated by the World Health Organization. Acellular vaccine (aP) replaced wP in 2008 and a booster was added to age 6 in 2010. The immunization programme was successful in reducing the morbidity rate from 20.58 per 100.000 in 1970 to the lowest level of 0.01 per 100.000 in 2009. However, reduction of vaccine-induced protection and reduced natural boosting of circulating Bordetella pertussis are likely to increase the susceptibility of the population. As a result, morbidity rate increased from 0.09 per 100.000 to 0.41 per 100.000 in 2015 compared to the previous year. The aim of this epidemiological study was to determine the seroprevalence of pertussis toxin (PT) antibodies among healthy people and its association with various social determinants in Manisa province in Turkey, 6 years after aP replaced wP vaccine. The study was conducted as a cross-sectional study with a sample of 1250 people that was randomly selected from the over 2 years of age population in Manisa in 2014. Seroprevalence of PT antibody was determined as the dependent variable of the study. Independent variables of the study were; gender, age, migration in the last 5 years, occupational class, perceived income, house ownership, number of people per room, annually per capita equivalent income. The presence of anti-PT IgG was detected by quantitatively using a commercially available ELISA kit. The antibody levels were categorized into groups according to pertussis infection or vaccination immune response status. The groups consisted of undetectable (< 5 IU/ml), mid-range (5-< 62.5 IU/ml: more than one year previously), high (62.5-< 125: with in 12 months) and very high (≥ 125 IU/ml: with in 6 months) antibody levels. The test results with ≥ 5 IU/ml were defined as seropositive. Level > 100 IU/ml detected among adolescent and adult participants indicated acute or recently recovered pertussis infection. Chi-square test was used to evaluate association between social determinants and pertussis seropositivity. The seroprevalence of the whole study population was 58.1% (95% CI 55.32-60.79) and no association was found with any of the social determinants. The highest seroprevalence was found among 2-9 age group (68.3%) followed by 70-79 age group (63.5%). The lowest seroprevalence was found among 20-29 age group (50.9%) followed by 10-19 age group (51.6%). When seropositivity levels according to ages were compared, it was found that there was a decrease one year after the first vaccination at 2nd, 4th and 6th months and the booster at the 6th year, with a lowest rate (19%) in 11 year-old. The highest seropositivity (77.3%) with a level of >100 IU/ml (13.6%) were detected at age 15 among all adolescent and adult participants. Adding an adolescent booster to immunization schedule and recommendation of vaccine to elderly people should be considered to reduce the incidence of pertussis disease in Turkey.

West Nile Virus Seroprevalence in Manisa Province: A Population-based Study.

Objective: West Nile Virus (WNV), which causes widespread outbreaks in different parts of the world, is a risk to public health in Turkey, too. Community-based study data are needed to identify measures against possible outbreaks. This study aimed to determine the seroprevalence of community-based WNV in Manisa and to investigate the relationship between sociodemographic and socioeconomic variables. Methods: We included individuals older than two years of age (N=1,317,917) registered in the Manisa Province Family Medicine Information System. Selected participants (n=1233) were determined by a simple random sampling method. Specific IgG antibodies against WNV were investigated in serum samples using a commercial ELISA test (Euroimmun, Germany). The relationship between age, gender, location, education and income level, occupation, population density, altitude, the location of the toilet in the house, and the presence of hypertension, diabetes mellitus and cardiovascular disease variables were analyzed by chi-square, Fisher's exact test and t-test. Adjusted odds ratio (OR) with95% confidence interval (CI) for each variable were calculated by the logistic regression method to explain potential risks. Results: WNV IgG antibodies were detected in 47 (3.8%) sera samples by ELISA. Seroprevalence was significantly correlated with independent variables of advanced age, presence of hypertension, diabetes mellitus and cardiovascular disease, low level of education and income, living in low altitude areas and the location of the toilet. In multivariate analysis; age (every one-year increase) (OR:1.05; 95% CI:1.02-1.07; p <0.001), equivalent annual income per capita below 3265 TL (OR:3.21; 95% CI: 1.53-6.73; p=0.002), and living areas below 132 meters altitude (OR=3.21; 95% CI 1.26-8.15; p=0.014) were found to be the risk factors for WNV seropositivity. Conclusion: In Manisa province, WNV IgG seroprevalence was detected as 3.8% with ELISA method. Older age, low income and living in regions with a low altitude were found to be associated with increased seropositivity significantly.

[Inappropriately ordered tests from hepatitis B vaccinated subjects]. / Hepatit B asili kisilerden gereksiz test istekleri.

Laboratory testing for viral hepatitis B constitutes a vast burden regarding the cost and the workload for health care system for many countries including ours. There are several reports stating that the cost in question is not always necessary. As a consequence of larger scale vaccination programmes, an increase in unnecessary hepatitis B testing is expected in vaccinated individuals. The present retrospective study aims to determine the rate of inappropriately ordered tests from vaccinated individuals and to discuss the causes and possible solutions of this problem. Laboratory records of 56.349 subjects admitted to Dokuz Eylul University Hospital, Izmir, during 2007 and 2009, were evaluated retrospectively for hepatitis B serological test results. Unnecessary testing was defined as the requests for HBsAg, anti-HBc, anti-HBc IgM, HBeAg and anti-HBe tests from those who had positive anti-HBs and negative anti-HBc results. The cost burden was calculated by taking account the prices recommended by the Department of Social Security. The appropriateness of anti-HBs test orders were not taken into evaluation since specific clinical conditions (immune response disorders, HIV infection, chronic hemodialysis, newborns of HBsAg positive mothers, contact with HBsAg carriers) were not clarified. It was found that among the 17.869 samples tested for both anti-HBs and anti-HBc, 4402 (24.6%) were ordered from subjects who were vaccinated against hepatitis B virus (anti-HBs positive, anti-HBc negative status). Thus, 11.405 (12.9%) tests out of a total of 88.174 hepatitis B tests (HBsAg, anti-HBc, anti-HBc IgM, HBeAg, anti-HBe) were unnecessarily ordered. Social security services and/or individuals paid approximately 59.000 USD for these unnecessary tests in three years, leading to an economic loss of approximately 20.000 USD yearly. Providing appropriate feedback to clinicians and reflex test application (to order a test according to the results of previous tests in accordance to diagnostic test algorithms) were considered to be useful in prevention of the problem.

Characterization of Bartonella taylorii Strains in Small Mammals of the Turkish Thrace.

Rodents play role as a reservoir for some Bartonella species which cause different clinical manifestations in humans. Bartonella spp. existence in rodents of Turkish Thrace has been detected for the first time, and the risky habitat types were evaluated for the infection. Ninety individuals belonging to three small rodent species were screened by PCR, and the overall prevalence of Bartonella infection was 22.2%. The strains were characterized molecularly based on the phylogenetic analyses of two housekeeping genes, rpoB and gltA. They clustered with B. taylorii. The significant effects of habitat types and rodent species on Bartonella infections were observed. It was detected that B. taylorii prevalence was the highest in the swamp forest habitat and A. flavicollis species. The present study demonstrates that A. flavicollis is the reservoir of B. taylorii in the European part of Turkey.

Dynamics of Puumala hantavirus outbreak in Black Sea Region, Turkey.

BACKGROUND: Some of the hantavirus species in Euro-Asia cause haemorrhagic fever with renal syndrome (HFRS) in humans. The first documented human hantavirus infection in Turkey was diagnosed in 2009. This report describes the dynamics of the first hantavirus outbreak that emerged in humans in the Western Black Sea Region of Turkey. METHODS: All the suspected cases of hantavirus infection were admitted to the Infectious Diseases and Clinical Microbiology Department at the Zonguldak Bülent Ecevit University Hospital in Zonguldak, Turkey. The patients were carefully interviewed, examined and evaluated using routine laboratory tests and hantavirus diagnostic tools. Hantavirus-reactive antibodies (IgM and IgG) in serum samples were detected via enzyme immune assay (EIA) and immunofluorescence assay (IFA) in the acute and convalescence stages of the disease. The presence of hantavirus ribonucleic acid (RNA) was analysed via reverse transcription polymerase chain reaction (RT-PCR) in serum and urine samples. A focus reduction neutralization test (FRNT) was performed to confirm specific hantavirus serotypes. In addition, a case-control study was conducted to identify possible risk factors for hantavirus transmission in the outbreak area. A control group was composed of asymptomatic individuals who were seronegative for hantavirus IgM and IgG and living in the outbreak area. RESULTS: A total of 55 suspected cases of hantavirus infection were admitted to the inpatient clinic between February and June of 2009. Twenty-four patients were diagnosed with acute HFRS via EIA or IFA. In 22 of the 24 infected patients, Puumala virus (PUUV) was identified as the causative hantavirus type by detecting IgM in the acute stage and an increase in the IgG level in follow-up serum samples. PUUV was also verified as the infecting agent by FRNT in two of the 24 cases. Among the 24 laboratory-confirmed HFRS cases, 21 (87.5%) were males and 3 (12.5%) were females, and the mean age was 45.92 years (standard deviation ± 16.90 years). Almost all these individuals were living in villages or rural areas. The 24 HFRS cases were matched with 26 healthy controls for statistical analyses and according to binary logistic regression analysis, and dealing with rodent control activities in gardens or in annexes of their homes (p = 0.021 and Odds ratio [OR] = 17.11) and being male (p = 0.019 and OR = 22.37) were detected as statistically significant risk factors for hantavirus infection. The most commonly observed clinical complaints were fatigue (95.8%), shivering (91.7%), fever (87.1%), headache (70.8%) and nausea (70.8%). Haemodialysis was required for four patients (16.7%). Except for the first case diagnosed with acute hantavirus infection, no patient died. The mean delay time to hospital admission from initiation of symptoms was 5.3 days, the mean duration of febrile days was 2.6 days, and the mean duration of hospital stay was 8.5 days. CONCLUSION: Hantaviruses are circulating in Turkey and causing sporadic or epidemic infection in humans. Additional investigations are needed to better understand the dynamics of hantaviruses in this country.

A novel genetic lineage of Tula orthohantavirus in Altai voles (Microtus obscurus) from Turkey.

Orthohantaviruses (family Hantaviridae order Bunyavirales) are emerging pathogens with a significant impact on human health. They are transmitted via aerosolized excreta of rodents which also act as reservoir hosts, constituting a unique route for dispersion. Dobrava-Belgrade and Puumala orthohantaviruses have been previously reported from Anatolia, in rodents, case reports and occasional outbreaks. We have collected rodents at several locations during a surveillance study in eastern Anatolia. The specimens were morphologically-identified and various tissues were screened via a generic orthohantavirus reverse transcription polymerase chain reaction assay. DNA barcoding via mitochondrial cytochrome b sequencing was performed in rodents with detectable orthohantavirus sequences. High throughput sequencing was performed for viral genome characterization. Fifty rodents were collected and identified morphologically as Microtus spp. (96%) and Apodemus spp. (4%). Orthohantavirus sequences were detected in lung and spleen or liver tissues of 4 voles (8%), barcoded as Microtus obscurus. The virus sequences were identified as Tula orthohantavirus (TULV) and near-complete genomic segments of the prototype viral genome, tentatively named as the Tula orthohantavirus-Turkey (TULV-T), could be characterized. Putative open reading frames for viral nucleocapsid and a nonstructural protein on the S segment, glycoproteins G1 and G2 on the M segment and viral replicase on the L segment were identified on the TULV-T. Several minor sequence variants were further characterized. No evidence of recombination could be detected and pairwise comparisons displayed over 95% amino acid sequence identities to various Eurasian TULV strains. Phylogenetic analyses revealed distinct clustering of all genome segments from previously-characterized TULV strains via various approaches and models. Here, TULV-T constituted a novel lineage, forming an intermediate among Asian and European TULV lineages. This report describes the initial documentation of TULV circulation and its potential reservoir in Anatolia. The extent of virus dispersion, alternate hosts or outcomes of human exposure require elucidation.

A metagenomic survey identifies Tamdy orthonairovirus as well as divergent phlebo-, rhabdo-, chu- and flavi-like viruses in Anatolia, Turkey.

We employed a direct metagenomic approach via next-generation sequencing for a cross-sectional investigation of viruses in 10 tick pools, collected from Aegean, Mediterranean and central Anatolian locations in Turkey. Sequences from all genome segments of Tamdy orthonairovirus (family Nairoviridae) were characterized in ticks collected from a Meriones tristrami. We further obtained near-complete L and partial S segments of several tick-associated phleboviruses (family Phenuiviridae), including Tacheng tick virus 2 and a novel virus, tentatively named as the tick phlebovirus Anatolia. Partial NS5-coding region of recently-described flavi-like virus (Tacheng tick virus 8) was further detected. Moreover, near-complete and polymerase-coding regions of arthropod-associated rhabdoviruses as well as sequences closely-related to the members of the newly-proposed virus family, the Chuviridae, were characterized. Despite origins of the viral sequences could not be fully elucidated, the findings suggest the circulation of diverse arthropod and tick-associated viruses in Anatolia. Occurrence and outcome of vertebrate exposure and probable health impact of these viruses require further investigation. We also report the initial detection of Tamdy orthonairovirus, an established human pathogen, which should be included in the diagnostic workup of infections with unknown etiology.

PCR and serology were effective for identifying Chlamydophila pneumoniae in a lower respiratory infection outbreak among military recruits.

During endemic infections, the sensitivity of diagnostic tests and rapid diagnosis of the respiratory tract pathogens is particularly important. Utilization of just one diagnostic technique, such as serological tests or polymerase chain reaction (PCR)-based detection methods, during outbreaks of lower respiratory tract infections (LRI) can result in some of the patients being missed. In this study we aimed to investigate the etiology of LRI in military recruits in Izmir, Turkey, among whom several pneumonia cases have been reported and 47 patients have been hospitalized. Nasopharyngeal swabs were used for PCR analysis of Chlamydophila pneumoniae, Mycoplasma pneumoniae and Legionella spp. Serum samples were collected in the acute and convalescent phase of infection for C. pneumoniae and M. pneumoniae. Thirty-nine patients were diagnosed with C. pneumoniae infection by PCR and/or serology. Diagnoses were established by PCR in the acute phase of infection in 40.4% of the group. Based on the results of these studies, PCR is a useful method for early detection and identification of C. pneumoniae-related LRI outbreaks. However, this technique is not sufficient to detect all positive cases per se. After effective therapy and introduction of appropriate infection control measures, the outbreak ceased without mortality. This is the first closed-community C. pneumoniae outbreak report from Turkey.