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Signal amplification methods are the most preferred non-PCR molecular tools in diagnostic virology. The aim of signal amplification tests is to amplify and measure the signals obtained from the target DNA or RNA in clinical samples, instead of directly copying these molecules. With these characteristics, signal amplification methods do not pose any risk of contamination of the test samples, laboratory devices or working environment with amplified products. Approved signal amplification tests have been commercially available for detection and quantitation of HIV-1, HCV and HPV nucleic acids, as well as genotyping analysis of HPV. Signal amplification tests were first used in the early 1990s and have different working principles and special designs. These tests are now combined with new diagnostic techniques such as real-time PCR, the rolling circle method, luminex xMAP, DNA biosensor technology and sequence analysis, in the detection and genotyping of viral agents, multiplex analysis and the discovery of new and unknown viruses. In addition, approved signal amplification tests are used as the standard control methods for newly developed test designs. In this review, the working principles of signal amplification-based tests and their use in diagnostic virology are discussed in detail and examples of their use in other platforms are presented.

Hepatitis C virus (HCV) is an infectious agent transmitted mainly by the contact of blood and body fluids of infected people, causing acute and chronic hepatitis in humans with a high potential for chronicity, unlike other hepatitis viruses. Although a protective vaccine has not yet been developed due to the extreme variability of its antigenic structures, it has become possible to permanently treat HCV infections with direct-acting antiviral drugs recently introduced. Laboratory tests such as determination of genotype-subtype before the start of treatment and viral load monitoring by using quantitative molecular analyzes during treatment are critical for the success of treatment. Laboratory diagnosis of HCV infections is also important for infection control measures such as screening of blood and blood products and epidemiological surveillance. The most important difficulties encountered in the diagnosis of HCV are low positive serological test results, serological window period, lack of antibody production in immunosuppressive patients, the presence of multiple genotype-subtypes and genomic variations that complicate primary-probe design. In the past, immunoblotting tests using recombinant proteins had been used to confirm low titer serological test results. Nowadays, these tests have been replaced by molecular tests that provide early detection of acute infections as well as having high sensitivity and specificity. In this article, advantages and limitations of the methods used in the diagnosis and follow-up of HCV infections are discussed, and the current diagnostic algorithm based on the use of available tests in the management of HCV infections is reviewed.

Infections caused by multi drug-resistant gram-negative bacilli are increasingly reported worldwide. Colistin, tigecycline and aminoglycosides are almost the only and last choice antibiotics in the treatment of infections caused by carbapenem-resistant Enterobacterales members. Ceftazidime-avibactam is a novel antibiotic combination consisting of a broad-spectrum cephalosporin and avibactam with good antimicrobial activity against carbapenem-resistant Enterobacterales members. The aim of this study was to assess the in vitro activity of ceftazidime-avibactam and colistin against carbapenem-resistant Klebsiella pneumoniae isolates and to obtain local antimicrobial surveillance data. A total of 150 carbapenem-resistant K.pneumoniae isolates obtained from various clinical samples of the patients hospitalized in our hospital between 2018-2021 were included in the study. Duplicate isolates were excluded from the study. The isolates were recovered from blood (n= 72), tracheal aspirate (n= 40), wound (n= 20), biopsy and abscess (n= 10), steril body fluid (n= 5), and peripheral venous catheter (n= 3) samples. Isolates were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS, Bruker Daltonics, Germany). The minimum inhibitory concentration (MIC) values of the isolates for meropenem, colistin, ceftazidime, and ceftazidime-avibactam were determined by broth microdilution method. Susceptibility of the isolates to the tested antibiotics was evaluated by the European Committee of Antimicrobial Susceptibility Testing (EUCAST) criteria. The presence of carbapenemases (VIM, IMP, NDM, KPC, and OXA-48) was investigated by polymerase chain reaction (PCR) using specific primers. The mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5 genes were evaluated by PCR for plasmid-mediated colistin resistance. All K.pneumoniae isolates were found to be positive for at least one of the carbapenemase genes evaluated in the study. The blaOXA-48 gene was detected in 107 (71.3%), blaKPC gene in 25 (16.7%); blaNDM gene in 7 (4.7%), co-production of blaOXA-48 and blaKPC genes in 10 (6.7%), co-production of blaOXA-48 and blaNDM genes in 1 (0.6%) isolate. None of the isolates harbored the blaVIM and blaIMP genes. None of the mcr genes screened in the study were detected among the isolates. The susceptibility of the isolates to ceftazidime-avibactam and colistin was 92.7% (139/150) and 48% (72/150), respectively. The MIC50 and MIC90 values for meropenem, ceftazidime, ceftazidime-avibactam, and colistin of the isolates were determined as 32/256,128/128, 1/8, and 4/16 µg/ml, respectively. Of the ceftazidimeavibactam resistant isolates, seven were positive for blaNDM, three for blaKPC, and one for both blaOXA-48 and blaNDM genes. High ceftazidime-avibactam MIC levels (128 µg/ml) were detected in metallo-betalactamase producing isolates. Consequently, our data suggested that ceftazidime-avibactam exhibited as a good alternative therapeutic choice for carbapenem-resistant K.pneumoniae isolates. It is noteworthy that high rate of colistin resistance was detected in K.pneumoniae isolates. Another notable finding of this study is the increase in K.pneumoniae isolates producing blaKPC for our country. To prevent the development of resistance which is observed even in last-choice therapeutic antibiotics, the principles of rational antibiotic use should be followed. The appropriate antimicrobial susceptibility testing should be routinely performed for surveillance of ceftazidime-avibactam and colistin.

Amaç: Çok ilaca dirençli Gram negatif basillerin neden olduğu enfeksiyonlar dünya genelinde giderek daha fazla rapor edilmektedir. Seftazidim-avibaktam, karbapenem dirençli Entero- bacterales üyelerine ve Pseudomonas aeruginosa izolatlarına karşı iyi etkinlik gösteren yeni bir antibiyotik kombinasyonudur. Bu çalışmanın amacı, seftazidim-avibaktam ve kolistinin karbapenem dirençli P. aeruginosa izolatlarına karşı in vitro aktivitesini değerlendirmektir.Gereç ve Yöntem: Hastanemizde 2016-2021 yılları arasında hasta örneklerinden elde edilen toplam 100 karbapenem dirençli ve tekrar içermeyen P. aeruginosa izolatı çalışmaya dahil edildi. İzo- latlar MALDI-TOF MS (Bruker Daltonics, Almanya) ile tanımlandı. Meropenem, kolistin, seftazidim ve seftazidim-avibaktamın mini- mum inhibitör konsantrasyon (MİK) değerleri sıvı mikrodilüsyon yöntemi ile belirlendi. Karbapenemaz genlerinden bla KPC, bla NDM, bla OXA-48, bla IMP, ve bla VIM varlığı PCR ile araştırıldı.Bulgular: Bir bla VIM üreten izolat dışında izolatlarda karbapenemaz genleri saptanmadı. Seftazidim-avibaktam ve kolistinin duyarlılık oranları sırasıyla %90 (n=90) ve %100 (n=100) bulundu. P. aeruginosa izolatlarına karşı meropenem, seftazidim, seftazidim-avibaktam ve kolistin için MİK50 ve MİK90 değerleri sırasıyla 32/64, 8/64, 4/8, 0,5/2 μg/mL olarak bulundu.Sonuç: Verilerimiz seftazidim-avibaktamın karbapenem dirençli P. aeruginosa izolatlarının tedavisi için iyi bir alternatif seçenek olduğunu göstermektedir. Çalışma izolatları arasında kolistin direnci tespit edilmemesi dikkat çekicidir. Antibiyotiklere direnç gelişiminin önlenmesi için akılcı antibiyotik kullanımına önem verilmelidir. Seftazidim-avibaktam ve kolistin sürveyansı rutin anti- mikrobiyal duyarlılık testleri ile takip edilmelidir., Objective: Infections caused by multi drug-resistant Gram-neg- ative bacilli are increasingly reported worldwide. Ceftazi- dime-avibactam is a novel antibiotic combination that presents good activity against carbapenem-resistant Enterobacterales members and Pseudomonas aeruginosa isolates. The objec- tive of this study was to evaluate the in vitro activity of ceftazi- dime-avibactam and colistin against carbapenem-resistant P. aeruginosa isolates.Materials and Methods: A total of 100 carbapenem-resistant and non-duplicate P. aeruginosa isolates obtained from patient samples in our hospital between 2016-2021 were included in the study. The isolates were identified by MALDI-TOF MS (Bruker Daltonics, Germany). The minimum inhibitory concentration (MIC) values of meropenem, colistin, ceftazidime, and ceftazi- dime-avibactam were determined by the broth microdilution method. The presence of carbapenemase genes bla KPC, bla NDM, bla OXA-48, bla IMP, and bla VIM were investigated using PCR.Results: Carbapenemase genes were not detected among the isolates except for one isolate producing bla VIM. The susceptibil- ity rates of ceftazidime-avibactam and colistin were 90% (n=90) and 100% (n=100), respectively. The MIC50 and MIC90 values for meropenem, ceftazidime, ceftazidime-avibactam, and colistin against P. aeruginosa isolates were found to be 32/64, 8/64, 4/8, 0.5/2 μg/mL, respectively.

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.

Critically ill patients with COVID-19 in the intensive care units (ICU) are at elevated risk for candidemia. Prolonged ICU and COVID-19 management are important contributing factors. Improved infection control and antibiotic stewardship practices to curb irrational antimicrobial utilization are needed. Background We evaluated the epidemiology of candidemia among coronavirus disease 2019 (COVID-19) patients admitted to intensive care units (ICUs). Methods We conducted a retrospective multicenter study in Turkey between April and December 2020. Results Twenty-eight of 148 enrolled patients developed candidemia, yielding an incidence of 19% and incidence rate of 14/1000 patient-days. The probability of acquiring candidemia at 10, 20, and 30 days of ICU admission was 6%, 26%, and 50%, respectively. More than 80% of patients received antibiotics, corticosteroid, and mechanical ventilation. Receipt of a carbapenem (odds ratio [OR] = 6.0, 95% confidence interval [CI] = 1.6-22.3, P = .008), central venous catheter (OR = 4.3, 95% CI = 1.3-14.2, P = .02), and bacteremia preceding candidemia (OR = 6.6, 95% CI = 2.1-20.1, P = .001) were independent risk factors for candidemia. The mortality rate did not differ between patients with and without candidemia. Age (OR = 1.05, 95% CI = 1.01-1.09, P = .02) and mechanical ventilation (OR = 61, 95% CI = 15.8-234.9, P < .0001) were independent risk factors for death. Candida albicans was the most prevalent species overall. In Izmir, Candida parapsilosis accounted for 50% (2 of 4) of candidemia. Both C parapsilosis isolates were fluconazole nonsusceptible, harbored Erg11-Y132F mutation, and were clonal based on whole-genome sequencing. The 2 infected patients resided in ICUs with ongoing outbreaks due to fluconazole-resistant C parapsilosis. Conclusions Physicians should be aware of the elevated risk for candidemia among patients with COVID-19 who require ICU care. Prolonged ICU exposure and ICU practices rendered to COVID-19 patients are important contributing factors to candidemia. Emphasis should be placed on (1) heightened infection control in the ICU and (2) developing antibiotic stewardship strategies to reduce irrational antimicrobial therapy., National Institute of Health [R21 AI160098, R21 AI152018], M. H. N. was funded by the National Institute of Health (Grants R21 AI160098 and R21 AI152018).

Amac: Son yillarda Candida turlerine bagli enfeksiyon oranlarinda artis gozlenmesi ve antifungal duyarlilik sonuclarinin turlere gore farkliliklar sergilemesi gibi nedenlerle, Candida izolatlarinin hizli ve dogru bir sekilde tur duzeyinde tanimlanmasi gerekli hale gelmistir. Bu calismada, MALDI-TOF MS yonteminin, geleneksel ve molekuler yontemler ile tur duzeyinde tanimlanmis ve uzun sure -20°C’de saklanmis Candida klinik izolatlarini tanimlamadaki etkinligini arastirmak amaclanmistir. Gerec ve Yontem: Calismaya, 10 yildan daha uzun suredir -20°C’de saklanan, canlandirma islemi yapilmamis ve API® ID 32C, CHROMagar Candida ile PCR-RFLP gibi cesitli yontemlerle tanimlanmis 28 Candida izolati dahil edildi. Izolatlar yeniden pasajlandi ve MALDI-TOF MS ile analiz edildi. Daha once tur duzeyinde tanimlanamayan bir izolat ile MALDI-TOF MS skoru dusuk olan diger bir izolat ITS dizileme ile analiz edildi. Ayrica calisma izolatlarimiz ile rutin kulturlerden izole edilmis 57 Candida susuna ait MALDI-TOF MS skorlari karsilastirildi. Bulgular: MALDI-TOF MS analizinde 11 (%39,3) izolat icin tur duzeyinde ve 15 (%53,6) izolat icin cins duzeyinde guvenilir tanimlama elde edilirken, iki izolat guvenilir tanimlama sinirlarinin disinda kalmistir. Cesitli yontemlerle ile tanimlanan 28 izolatin tamaminda, MALDI-TOF MS yontemi ile farkli skorlar elde edilse de tur duzeyinde dogru tanimlama yapilmistir. Sonuc: MALDI-TOF MS uzun sure saklanmis stok Candida izolatlarinin tanimlanmasinda geleneksel ve RFLP gibi molekuler yontemler ile kiyaslandiginda kolaylikla kullanilabilecek, dusuk maliyetli, hizli ve guvenilir bir yontemdir. Calismaya alinan izolatlar sinirli sayida olmakla birlikte, MALDI-TOF MS ile yapilan analizlerde Candida turleri icin alinan dusuk skor degerlerinin tanimlamada yararli olabilecegini dusunuyoruz.

Özet Messenger (haberci) ribonükleik asit (mRNA) moleküllerinin aşı veya genetik tedavi amaçlı kullanımında protein ekspresyonunun etkinliğini belirleyen önemli parametrelerden biri bu moleküllerin hücre içerisine iletilmesinde başvurulan yaklaşımlardır. Viral vektör aracılı olmayan genetik bilgi transferi olarak da tanımlanan mRNA temelli aşı sistemlerinin hücrelere verimli bir şekilde iletilebilmesi için birçok farklı yaklaşım denenmiştir. Bu yöntemlerden biri mRNA moleküllerinin herhangi bir taşıyıcı molekül olmaksızın çıplak olarak dokulara doğrudan verilmesidir. Çıplak mRNA hücre dışı RNazlar (extracellular RNases) tarafından hızla yıkılır ve hücre içerisine verimli bir şekilde alınamaz. Bu nedenle, mRNA'nın hücreye alınmasını kolaylaştıran çeşitli biyokimyasal (protamin ve penetre edici peptitler gibi) ve fiziksel-mekanik yöntemler (elektroporasyon ve gen tabancası gibi) geliştirilmiştir. Öncelikle terapötik kanser aşılarının iletiminde başvurulan farklı bir yaklaşım ise otolog dendritik hücrelere (DH) ex-vivo mRNA yüklenmesi ve transfekte edilen DH’lerin tekrar dokulara enjekte edilmesidir. Ölçeklenebilir üretim için ideal bir yaklaşım olmayan bu sistem salgınlara müdahalede veya toplumsal bağışıklamada yetersiz kalacağı için bu stratejiye alternatif olan üçüncü bir mRNA iletim sistemi olarak nanopartikül taşıyıcılar geliştirilmiştir. Lipit nanopartiküller, polimerler ve katyonik nano-emülsiyonlar gibi farklı taşıyıcı sistemleri içeren bu nanopartiküller protamin, kolesterol ve polietilenglikol gibi çeşitli moleküllerin eklenmesi ile modifiye edilebilmektedir. Aşılama ile ulaşılmak istenilen hedefe göre mRNA temelli sistemler intradermal, subkutan, intranazal, intrasplenik, intravenöz ve intramusküler enjeksiyon gibi çeşitli yollarla doku-hedefli veya sistemik olarak verilebilmektedir. Bu derleme makalede mRNA bazlı aşıların hücrelere ve dokulara verimli bir şekilde in-vivo iletilmesi için kullanılan tekniklerin bir özeti sunulmuştur. Abstract One of the important parameters determining the efficiency of protein expression in the use of messenger ribonucleic acid (mRNA) molecules for vaccine or genetic therapy is the approaches used in the delivery of these molecules into the cell.Many different approaches, also defined as non-viral vector-mediated gene transfer, have been triedin order toefficient delivery of mRNA-based vaccine systems to cells.One of these methods is delivery of naked mRNA molecules directly to tissues without any carrier molecules.Naked mRNA is rapidly degraded by extracellular RNases and cannot be efficiently taken into the cell.Therefore, various biochemical (such as protamine and penetrating peptides) and physical-mechanical methods (such as electroporation and gene gun) have been developed that facilitate the uptake of mRNA into the cell.A different approach, which is primarily used in the delivery of therapeutic cancer vaccines, is ex-vivo loading of mRNA into autologous dendritic cells (DCs) and re-injection of transfected DCs into tissues.Since this system, which is not an ideal approach for scalable production, will be inadequate in response to epidemics or in community immunization, nanoparticle carriers have been developed as a third mRNA delivery system as an alternative to this strategy.These carrier systems, include different designs such as lipid nanoparticles,polymersand cationic nano-emulsions, can be modified adding a variety of molecules such as protamine, cholesterol and polyethyleneglycol.mRNA based systems can be administered systemically or tissue-targeted by various means such as intradermal, subcutaneous, intranasal, intrasplenic, intramuscular and intravenous injections, depending on the target to be achieved by vaccinating.A summary of the techniques used for efficient in-vivo delivery of mRNA-based vaccines to cells and tissues was presented in this review article.

The arthroconidial yeasts Magnusiomyces capitatus and M. clavatus are emerging opportunistic pulmonary pathogens. They are closely related and difficult to distinguish based on morphological and physiological traits. We applied an SYBR® green-based quantitative PCR (qPCR) assay to identify the species. We analyzed 30 reference strains originating from clinical and environmental sources by targeting the Rpb2 gene encoding the second largest subunit of RNA polymerase II. The qPCR assays were tested by direct identification of M. capitatus and M. clavatus in spiked sputum and household dishwasher swabs, respectively, as models for clinical and environmental samples. The assays were proved to be reliable for species-level identification of both species, with 100% sensitivity and 100% specificity, lowest inter-assay deviations (RSDr ? 1.65%, R2 values >0.99), detection limit of 10 theoretical copy number of target DNA, and detection cell limit of ?5000 yeast cells from spiked sputum samples. The developed qPCR assay is a practical molecular approach for the detection of M. capitatus and M. clavatus that can be used as a stand-alone assay or in conjunction with culture-dependent approaches. © 2021, The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature.

Özet Hastalıktan iyileşmiş kişiler veya aşılanmış donörlerden toplanan konvalesan plazma ve bu plazmaların işlenmesi ile elde edilen immünglobulinler standart tedavilerin dışında, hayatı tehdit eden veya yeni ortaya çıkan ve spesifik tedavi seçenekleri kısıtlı olan enfeksiyonların tedavisinde başvurulan geleneksel uygulamalardır. İmmün tam kan transfüzyonu, konvalesan plazma veya plazma türevli hiperimmünglobulinler enfeksiyonu henüz geçirmekte olan hastalara aktarılarak hastaların enfeksiyona verdiği cevap ve iyileşme süreci desteklenir. Poliklonal antikorlarla pasif bağışıklamayı amaçlayan bu geleneksel yaklaşımlar dışında, rekombinan gen teknolojisi prensibine dayalı yeni tekniklerle üretilen patojene spesifik monoklonal ve poliklonal antikorlar da profilaksi ve tedavi amaçlı yaygın kullanımı olan ve benzer etkiyi hedefleyen yeni alternatiflerdir. Plazma türevli tedavilerin influenza virus, kanamalı ateş virüsleri, SARS-CoV ve MERS-CoV enfeksiyonlarının tedavisinde yararlı olabileceği yapılan araştırmalarla gösterilmiştir. Yakın zamanda yapılan birkaç çalışmada ise konvalesan plazmanın COVID-19 hastalarının tedavisinde yararlı olabileceğine dair kanıtlar sunulmuştur. Spesifik antiviral tedavilerin ve koruyucu bir aşının yokluğu da dikkate alındığında konvalesan plazma veya saflaştırılmış hiperimmünglobulin uygulamaları ülkelere göre değişmek üzere %3 ile %10’u bulan COVID-19 mortalite oranlarını azaltmada kısa sürede müdahaleimkanısunan umut vadeden seçenekler olarak görülmektedir. Standart önlemlere uyulması koşulu ile ulusal ve uluslararası resmi kurum ve kuruluşlar tarafından da desteklenen bu tedavi yaklaşımları pandemi yönetiminde ve stoklanabilir özellikleri ile gelecekteki yeni olası bölgesel epidemiler için erken dönem tedavi seçeneği olarak değerlendirilmektedir. Bu derleme makaledeSARS-CoV-2 hastalarında konvalesan plazma ve hiperimmünglobulin kullanımının olası yararlılıkları ve bu tedavi yaklaşımı ile ilişkili olabilecek riskleri ele almak amaçlanmış ve bu konuda yürütülen güncel klinik çalışmaların bir özeti sunulmuştur. Abstract Convalescent plasma and immunoglobulins derived by processing these plasmas obtained from disease-healed individuals or vaccinated donors are traditional practices for the treatment of life-threatening or emerging infections for which no specific treatment exists. Immune whole blood transfusion, convalescent plasma or plasma-derived hyperimmunoglobulin are transferred to patients who have just had the infection, and the response and recovery process of the patients are supported. Apart from these traditional approaches aimed at passive immunization with polyclonal antibodies, pathogen-specific monoclonal and polyclonal antibodies produced by new techniques based on the principle of recombinant gene technology are also new alternatives that have a common use for prophylaxis and therapeutic purposes. Studies have shown that plasma-derived treatments can be useful in the treatment of influenza virus, hemorrhagic fever viruses, SARS-CoV and MERS-CoV infections. Also, several recent studies have provided evidence that convalescent plasma may be useful in the treatment of patients with COVID-19. Considering the absence of a protective vaccine and specific antiviral treatments, convalescent plasma or purified hyperimmunoglobulin treatmentsare seen aspromising options that offer a short-term intervention in reducing COVID-19 mortality rates ranging from 3% to 10%to vary according to countries. These treatment approaches, which are supported by national and international official institutions and organizations, provided that standard precautions are followed, are considered as early treatment options for pandemic management and new possible regional epidemics in the future because these are storable products. It is aimed to discuss the possible benefits of using convalescent plasma and hyperimmunoglobulin in SARS-CoV-2 patients and the risks that may be associated with this treatment approach, and a summary of current clinical studies conducted on this subject is presented in this review article.

Objective:To investigate the effects of different suture materials in the nasal cavity on encrustation and micro-organism colonisation.Methods:Four different suture materials were used to suture the nasal septum. The effects of suture materials on intranasal encrustation were evaluated with anterior rhinoscopy. The sutures were removed and evaluated in terms of micro-organism colonisation on the 7th and 21st post-operative days.Results:Monofilament sutures were found to cause less encrustation and micro-organism colonisation. There was increased late-stage encrustation if an absorbable monofilament suture remained in place for a long time. The removal of a non-absorbable monofilament suture in the early or late post-operative period made no difference in terms of micro-organism growth on the suture.Conclusion:The material and physical characteristics of sutures placed inside the nose may indirectly affect the healing process. It may be more appropriate to use different materials depending on the length of time the suture is to remain in place.

Urban life has led to the creation of human-made environments that, from a microbiological perspective, provide extreme life conditions. Certain non-ubiquitous microorganisms such as thermophilic members of the black yeast genus Exophiala are enriched within these habitats for which no counterpart is known in nature. Dishwashers consistently accumulate a number of specific black, white and red yeasts on the rubber seals of doors and in stagnant water at the interior. Several of these yeasts are primarily known as agents of human opportunistic infections. In this review, the literature data are supported by a screening study involving 937 households in 15 cities in Turkey. Fungi were detected in 230 samples (24.5 %). Using rDNA sequencing, the prevalent species were identified as Exophiala dermatitidis (n = 116), Candida parapsilosis (n = 44), E. phaeomuriformis (n = 35), Magnusiomyces capitatus (n = 22), Rhodotorula mucilaginosa (n = 15), and C. lusitaniae (n = 14). The possible role of dishwashers in transmitting disease is discussed.

PubMedID: 26373644 The present study compared two chemical-based methods, namely, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, to understand the misidentification of Exophiala dermatitidis and Exophiala phaeomuriformis. The study utilized 44 E. dermatitidis and 26 E. phaeomuriformis strains, which were partially treated with strong acids and bases for further evaluation. MALDI-TOF MS and ATR-FTIR spectroscopy data of the two Exophiala species were compared. Data groupings were observed for the chromic acid- and nitric acid-treated species when the black yeast sources were categorized as creosoted-oak sleepers, concrete sleepers, or dishwasher isolates. The MALDI-TOF MS data for the metalloenzyme-containing regions were consistent with the ATR-FTIR spectroscopy data. These results indicated that environmental isolates might contain metals not found in human isolates and might interfere with chemical-based identification methods. Therefore, MALDI-TOF MS reference libraries should be created for clinical strains and should exclude petroleum-associated environmental isolates. © 2015, Springer Science+Business Media New York.

The aim of this study was to investigate the effects of commonly used antibiotics on bacterial flora of the tonsil core. Patients who underwent tonsillectomy for recurrent chronic tonsillitis were included in the study. Three groups were formed: group 1 was treated for 10 days preoperatively with amoxicillin/clavulanic acid; group 2 was treated for 10 days preoperatively with clarithromycin; and group 3 included patients who underwent tonsillectomy without preoperative antibiotic use. The removed palatine tonsils were sent to our microbiology department in sterile tubes for bacteriological analysis. Seventy-three patients (group 1 = 19, group 2 = 20, group 3 = 34 patients) aged 3-18 years (mean 7 years) were included in the study. At least one bacterium was isolated from all tonsils, except for two cases in group 1; the difference in single bacterial growth among groups was not significant (p = 0.06). On the other hand, the numbers of patients with pathogenic bacterial growth was significantly lower in group 2 (n = 2) compared with group 1 (n = 10) and group 3 (n = 27) (p < 0.001). The bacterium isolated most frequently from the tonsils was Streptococcus viridans. Pseudomonas aeruginosa was the only pathogenic bacterium that grew in all three groups. Clarithromycin was more effective than amoxicillin/clavulanic acid in eradicating pathogenic bacteria in the tonsil core. Pseudomonas aeruginosa might be responsible for resistant or recurrent tonsil infections. To prevent endocarditis, antibiotic prophylaxis toward S. viridians, which is the most prevalent bacterium in the tonsil core, should be kept in mind for patients with heart valve damage.

PubMedID: 25476038 Dermatophytes are some of the most common fungal pathogens in both humans and animals. These fungi release enzymes (e.g., keratinases) that play roles in their pathogenesis. Little is known about their haemolytic and co-haemolytic (CAMP-like) activities; however, in bacteria, these components play significant roles in pathogenesis. This study characterised these two factors in 45 dermatophyte strains (representing the genera Arthroderma, Epidermophyton, Microsporum and Trichophyton) using Columbia agar (CA) supplemented with 5% bovine, ovine and equine erythrocytes. Haemolysis was best observed on CA supplemented with ovine erythrocytes followed by equine and bovine erythrocytes, while CAMP-like reactions occurred using bovine and ovine but not equine erythrocytes. Haemolytic and CAMP-like activities were best observed using ovine and bovine erythrocytes in CA in 44 and 38 strains at 7 and 3 days respectively. Most dermatophytes recovered from both symptomatic and asymptomatic lesions had haemolytic and CAMP-like activities. We suggest that the haemolytic and CAMP-like activities are not correlated with ecological characteristics, isolation sites or clinical manifestations of dermatophytic fungi. We also believe that this study has the potential to contribute to the existing literature on dermatophytes and dermatophyte pathogenesis. © 2014 Blackwell Verlag GmbH.

PubMedID: 25027275 The environmental isolation of opportunistic pathogenic black yeasts, which are responsible for a wide spectrum of human infections, is essential to understanding the ecology of clinical fungi. Extreme outdoor environments polluted with aromatic hydrocarbons support the growth of black yeasts in unlikely places, such as railway sleepers. However, there are limited data concerning the diversity of these fungi growing on polluted railway sleepers. In this investigation, we examined 845 railway sleeper samples, obtained from 11 Turkish cities representing altitudes from 25 to 1,893 m, and inoculated the samples onto mycological media for the isolation of black yeasts. Ninety-four samples (11.1 %) yielded positive results for black yeast, with creosoted oak sleepers having a significantly higher number of isolates than concrete sleepers (p < 0.05). Identification based on the ribosomal DNA (rDNA) internal transcribed spacer region revealed the highest prevalence of Exophiala phaeomuriformis, followed by Exophiala dermatitidis, Exophiala heteromorpha, Exophiala xenobiotica, and Exophiala crusticola. This study revealed that railway sleepers harboring black yeasts were predominantly (>75 %) populated with thermophilic species. We observed that altitude might have a significant effect on species diversity. Briefly, E. phaeomuriformis exhibited growth over a wide altitude range, from 30 to 1,893 m. In contrast, E. dermatitidis had a remarkable aversion to low altitudes and exhibited maximum growth at 1,285 m. In conclusion, we speculate that one can predict what species will be found on railway sleepers and their probability and that species diversity primarily depends on sleeper type and altitude height. We believe that this study can contribute new insights into the ecology of black yeasts on railway sleepers and the railway factors that influence their diversity. © 2014, Springer Science+Business Media New York.

Aim: In our study, correlation between serum alanine aminotransferase (ALT), histological activity index (HAI), HBeAg/antiHBe seroconversion and HBV-DNA levels in chronic hepatitisB (CHB) patients with higher ALT levels was investigated. Material and Method: Liver biopsy was performed on 31 untreated patients with CHB. Tissue HBV-DNA was measured from 19 samples from slides following histopathological examination and from the rest 12 from direct biopsy materials. Serum HBV-DNA was also measured for all patients. Hepatitis B serological pattern, Knodell HAI and ALT levels of the patients were analyzed and recorded. Results: Serum HBV-DNA levels of HBeAg(+) patients were found significantly higher than those in patients with HBeAg(-) (p

PubMedID: 26857806 The black yeast genus Exophiala is known to cause a wide variety of diseases in severely ill individuals but can also affect immunocompetent individuals. Virulence markers and other physiological parameters were tested in eight clinical and 218 environmental strains, with a specific focus on human-dominated habitats for the latter. Urease and catalase were consistently present in all samples; four strains expressed proteinase and three strains expressed DNase, whereas none of the strains showed phospholipase, haemolysis, or co-haemolysis activities. Biofilm formation was identified in 30 (13.8%) of the environmental isolates, particularly in strains from dishwashers, and was noted in only two (25%) of the clinical strains. These results indicate that virulence factors are inconsistently present in the investigated Exophiala species, suggesting opportunism rather than pathogenicity. © 2016 Blackwell Verlag GmbH.

Summary We investigated the epidemiological characteristics of both symptomatic and asymptomatic dermatophytic groin infections in 1970 women (age: 36.2 ± 12.5) during routine gynaecologic examinations. Bilateral groin samples were collected with sterile cotton swabs premoistened with sterile physiological saline. The samples were then separately inoculated onto Sabouraud glucose agar. Fungi were identified by sequencing the rDNA internal transcribed spacer region. Dermatophytes were recovered from five patients (four Trichophyton rubrum and one Arthroderma vanbreuseghemii, 0.25%) with a diagnosis of asymptomatic carriers (four) and tinea inguinalis (one). In one case, groin carriage converted into tinea inguinalis after 3 weeks. Analysis of risk factors indicated that patients of at least 49 years were more likely to be positive for dermatophyte isolation (P = 0.002). In conclusion, groin dermatophyte carriage is more common than tinea inguinalis and can potentially convert into a symptomatic infection.

Human papillomavirus types are the main tumor viruses in humans. High-risk human papillomavirus types, also called oncogenic human papillomaviruses, have been shown to be associated with cervical cancer, which is the leading cause of cancer mortality among women worldwide. High-risk human papillomavirus types are also associated with other anogenital cancers, and a subgroup of head and neck cancers. In addition, several studies have reported human papillomavirus types to be associated with some of the breast, lung, skin, and colon cancers. The proof that human papillomaviruses have a role in human oncogenesis has allowed the development of preventative and therapeutic strategies purposed at reducing the incidence and mortality rate of associated cancers. This article summarizes the main steps of the human papillomavirus life cycle and the functions of the viral proteins, and draws attention to carcinogenic mechanisms. In addition, this study presents a brief analysis of researches on cancer that were definitely or possibly associated with human papillomavirus and current information on prophylactic and therapeutic vaccine strategies against human papillomavirus infections and related cancers.

Summary Participation in competitive sports is popular and widely encouraged worldwide. Herein, we investigated 252 male and 67 female sports players, aged 16.4 ± 1.3 years, active in 15 different types of combat (n = 143) and non-combat (n = 176) sports. Of the 319 participants in this study, 11 (3.5%) players, including six wrestlers, four football players and one handball player, all of whom were men, harboured dermatophytic fungi. Briefly, Trichophyton tonsurans was present in three athletes, who were scalp carriers of the fungus. Furthermore, T. rubrum (4), T. interdigitale (3) and Arthroderma simii (1) were recovered from eight participants with tinea inguinalis (4), tinea pedis (2) or both (1). One patient was a trunk carrier of concomitant tinea pedis. All dermatophytic fungi were identified using both direction sequence of the rDNA regions spanning the internal transcribed spacers (ITS1 and ITS2) and 5.8 rRNA gene. Although sports-active individuals are active and sweat more, we observed a low prevalence of dermatophytosis, both in combat (5.2%) and non-combat sports participants (3.4%) (P > 0.05). However, dermatophyte infections require more attention and appropriate management to eradicate the infection and to prevent possible outbreaks. This study also documents the first case of zoophilic A. simii in Turkey.

Objective: This study aims to determine the rate of hepatitis A virus (HAV) seropositivity in adult HBsAg (+) patients from various regions of Turkey. Method: 137 adult (≥20 age) male patients admitted to Erzurum Maresal Cakmak Military Hospital in 2009 who were previously diagnosed as HBsAg(+) were included. The subjects were not vaccinated for HAV. Serum samples were analyzed by EIA (enzyme immunassay) using Abbott/AxSYM. Chi-square test was used for statistical analysis of serological data. Results: The Anti-HAV IgG (+) rates was 83.2% in the study populations (114/137), 61.5% (8/13) for those from Marmara region, 83.3% (13/16) for Mediterranean region, 84.6% (22/26) for Mid-Anatolian region, 66.7% (8/12) for Blacksea region, 87.5% (21/24) for East Anatolian region, 94.1% (32/34) for Southeast-Anatolian region. According to our study, no significant difference was found between seven geographical regions due to HAV seropozitivity rates (χ2= 9.511, p=0.147). The seven geographical regions were classified two main grups as East-Southeast Anatolia and other regions. The percentage of antiHAV positivity rate was significantly higher in EastOZET Amac: Bu calismanin amaci, Turkiye’nin degisik bolgelerinden gelen HBsAg pozitif eriskin hastalarda hepatit A virus (HAV) seropozitiflik oraninin saptanmasidir. Yontem: Erzurum Maresal Cakmak Asker Hastanesine 2009 yilinda gelen ve HBsAg pozitif olan, daha once HAV asisi yapilmamis 137 eriskin (≥20 yas) erkek hasta calismaya alinmistir. Serum ornekleri EIA (Abbott/AxSYM) yontemi ile calisilmis ve serolojik verilerin degerlendirilmesinde χ2 testi kullanilmistir. Bulgular: Calisma grubumuzdaki serum orneklerinde anti-HAV IgG pozitifligi %83,2 (114/137), Marmara Bolgesinde %61,5 (8/13), Ege Bolgesinde %83,3 (10/12), Akdeniz Bolgesinde %81,3 (13/16), Ic Anadolu Bolgesinde %84,6 (22/26), Karadeniz Bolgesinde %66,7 (8/12), Dogu Anadolu Bolgesinde %87,5 (21/24), Guneydogu Anadolu Bolgesinde %94,1 (32/34) olarak saptanmistir. Calisma bulgularimiza gore yedi cografik bolgenin HAV seropozotifligi arasinda istatistiksel olarak anlamli bir fark gorulmemistir (χ2= 9,511, p=0,147). Yedi cografik bolge Dogu-Guneydogu Anadolu ve diger bolgeler seklinde iki ana grup olarak siniflandirilmistir. Dogu-Guneydogu Anadolu grubunun 1 GATA, KBRN Bilim Dali, ANKARA 2 GATA, Tibbi Mikrobiyoloji Anabilim Dali, ANKARA 3 Maresal Cakmak Asker Hastanesi, ERZURUM Gelis Tarihi / Received : Kabul Tarihi / Accepted : Iletisim / Corresponding Author : Mesut ORTATATLI GATA, KBRN Bilim Dali, ANKARA Tel : +90 312 304 33 05 E-posta / E-mail : mortatatli@gata.edu.tr 29.05.2011 04.01.2012 DOI ID : 10.5505/TurkHijyen.2012.05924 Turk Hijyen ve Deneysel Biyoloji Dergisi Ortatatli M, Gumral R, Uckardes H, Kenar L. Degisik bolgelerden gelen eriskin HBsAg pozitif hastalarda Anti-HAV seropozitifligi. Turk Hij Den Biyol Derg, 2012; 69(2): 61-6. Cilt 69  Sayi 2  2012 Turk Hij Den Biyol Derg 62 Hepatit A virusu (HAV) Picornaviridae ailesi icinde yer alan, yaklasik 27-28 nm capinda, lineer pozitif polariteli ve tek sarmalli RNA iceren, zarfsiz bir virustur (1, 2). Hepatit A virusu dezenfektanlara ve isiya diger pikornavirusler’den daha direnclidir. Insana bulasma cogunlukla fekal-oral yolla olmaktadir. Hepatit A virus enfeksiyonu tum dunyada yaygin olarak gorulmekle beraber gelismekte olan ulkelerde ozellikle erken cocukluk doneminde daha sik rastlanmaktadir (3-5). HAV enfeksiyonu kucuk yaslarda hafif bir klinik tablo sergilerken, artan yasla beraber klinik bulgular daha agir ve uzun sureli olarak ortaya cikmaktadir (2-4). Sosyoekonomik duzey dusuklugu, kalabalik ortamlarda yasama, anne-babanin egitim duzeyinin dusuk olmasi, kirsal kesimde bulunma ile paralel olarak HAV prevalansi artmaktadir (3, 6). Eski ve yeni yapilan seropozitiflik arastirma sonuclari karsilastirildiginda HAV enfeksiyonu gecirme yasinin erken cocukluktan gec cocukluk, hatta genc eriskinlik donemine kaydigi gorulmektedir. Bu kayma, ulkelerin sosyoekonomik duzeylerindeki ilerleme ile aciklanmaktadir (1, 7). Ulkemizde 80 90’li yillarda yapilan calismalarda 20 yas uzerinde %90 ve daha fazla HAV seropozitifliginin saptandigi rapor edilirken, 2000’li yillarda yapilan calismalarda bu oranin dustugu gozlenmistir (3, 8-10). Kronik viral hepatitli hastalarda HAV ile superenfeksiyon, hepatitin seyrinin agirlasmasina neden olmakta, fulminan hepatit ve olum riskini arttirmaktadir (11-13). Bu calisma tanimlayici bir arastirma olarak planlanmis olup, Hepatit B virusu enfeksiyonu nedeniyle takip edilen eriskin erkek hastalarda asi ile korunulabilen bir etken olan HAV seroprevalansinin belirlenmesi amaclanmistir. GIRIS HBV TASIYICI HASTALARDA HAV POZITIFLIĞI (%91,4; 53/58) diger bolgeler grubuna (%77,2; 61/79) gore HAV seropozitiflik oraninda istatistiksel olarak anlamli bir yukseklik saptanmistir (χ2= 4,803; p=0,028). Sonuc: Hepatit A prevalansi farkli ulkelerde, hatta ayni ulkenin farkli bolgelerinde degismektedir. Saglikli bireylerde yapilan calismalarda en onemli risk faktorlerinin yas, sosyoekonomik duzey, kalabalik ortamda bulunmak oldugu belirtilmektedir. Calismamizda; farkli olarak HBsAg pozitif hastalarda anti-HAV seropozitifligi arastirilmis, Dogu-Guneydogu Anadolu Bolgesinde yasamanin diger bolgelere gore OR=3,13 kat (%95 guven araligi 1,09 – 9,01) risk artisi getirdigi saptanmistir. Ozellikle HBsAg pozitif hastalarda saglikli bireylere gore daha agir komplikasyonlarin gorulebilecegi ve mortalitenin daha yuksek olacagi beklenmesi nedeniyle HBV yonunden takip edilen tum hastalarda anti-HAV IgG bakilip, negatif olanlarin asilanmasinin gerekli oldugu kanisina varilmistir. Anahtar Sozcukler: Hepatit A, seropozitiflik, HBV tasiyici. Southeast Anatolia grup (91.4%; 53/58) compared to other regions grup (77.2%; 61/79) (χ2= 4.803; p=0.028). Conclusion: The prevalance of Hepatitis A varies in different countries and even in different regions of a specific country. Age, low socioeconomic level and worse living conditions have been reported as the most important risk factors in studies with healthy individuals. In this study where subjects with HBsAg(+) were evaluated for anti-HAV positivity, an increase in the risk was found as OR =3.13 times larger (95% confidence interval, 1.09-9.01) when especially living conditions in East-Southeast Anatolia was compared with other regions. It has been postulated that all patients monitored for chronic HBV infection should be assessed for anti-HAV IgG and negative individuals need to be vaccinated due to higher mortality and more severe complications in HBsAg(+) patients.

Mucormycosis (Zygomycosis) is a rare, invasive, opportunistic fungal infection of the paranasal sinuses, caused by a fungus of the order Mucorales. We report a case of rhinoorbital mucormycosis caused by Rhizopus oryzae in an acute lymphoblastic leukemia patient and review the 79 Mucormycosis cases reported in the last decade from Turkey. In our case, the diagnosis was made with endoscopic appearance, computerized tomography of the paranasal sinuses, and culture of the surgical materials. Following aggressive surgical debridement and parenteral amphotericin B therapy, the patient recovered completely. In Turkish literature, rhinocerebral manifestations were the most common form of the mucormycosis (64 cases), followed by pulmonary form (6 cases). The most common risk factor was hematologic malignancies (32 cases) and diabetes mellitus (32 cases), similar to those reported from the rest of the world. The etiologic agents responsible for the review cases were Rhizopus sp., Mucor spp., Rhizomucor spp., Rhizopus oryzae, Mucor circinelloides, and Lichtheimia corymbifera. Although various treatment modalities were used, amphotericin B was the mainstay of therapy. Mortality rate was found to be 49.4% in review cases. It seems that strong clinical suspicion and early diagnosis, along with aggressive antifungal therapy and endoscopic sinus surgery, have great importance for better prognosis in mucormycosis.

PubMedID: 21380767 Candida africana differs from the common strains of C. albicans and C. dubliniensis morphologically, physiologically, genetically, and, in particular, clinically. This fungal pathogen is primarily recovered from genital specimens, especially in vaginal specimens. In this investigation, we reexamined 195 vaginal C. albicans isolates for the presence of C. africana and C. dubliniensis by using hyphal wall protein 1 (HWP1) gene polymorphisms. All study isolates were confirmed to be C. albicans, and none were verified as either C. africana or C. dubliniensis. In conclusion, the HWP1 gene polymorphisms offer a useful tool in the discrimination of C. africana, C. albicans, and C. dubliniensis. Further studies may highlight the pathogenesis and importance of this yeast in vulvovaginal candidiasis. © 2011 Springer Science+Business Media B.V.

Emericella nidulans is a species that has only rarely been implicated in human disease after cataract surgery. Here, we report the first postoperative case in the literature, as far as we know. The patient was a 50-year-old patient presented with mild anterior uveitis one week after cataract surgery, and hypopion developed over the next two days. First microbiological evaluation and the results of direct microscopy and cultures of the anterior chamber and vitreous samples were found to be negative. Despite vigorous topical and intravitreal (vancomycin and amikacin) therapy, the endophthalmitis did not improve. Anterior chamber paracentesis, vitreous tap and finally complete vitrectomy with removal of the capsular bag including the intraocular lens (IOL) were performed. The anterior chamber, vitreous fluid samples and IOL were submitted to the microbiology laboratory: the culture yielded E. nidulans growth. Ocular inflammation resolved and vision improved on intravenous, subconjunctival and long-term oral voriconazole treatment. E. nidulans can be an important cause of ocular fungal infections including endophthalmitis, and voriconazole seems to be effective for the treatment of E. nidulans endophthalmitis.

PubMedID: 26281324 Background/aim: Mycological media that promote spore production are essential for the diagnosis of dermatophytosis. However, these culture media frequently become contaminated by multiple fungal or bacterial species during culture. The aim of this study was to compare the contamination rates of 6 culture media used for the isolation and identification of dermatophytes, including Borelli’s lactritmel agar (BLA), brain-heart infusion agar (BHIA), Lowenstein–Jensen agar (LJA), malt extract agar (MEA), potato dextrose agar (PDA), and Sabouraud glucose agar (SGA). Materials and methods: Agar plates were inoculated with 43 well-characterized dermatophyte strains, belonging to the genera Arthroderma, Epidermophyton, Microsporum, or Trichophyton. The agar plates were incubated at 26 °C and examined every 5 days for 1 month. Results: By the end of the incubation period, 97 of the 258 plates (37.6%) were contaminated by fungi. No bacteria were detected. Overall, BLA demonstrated the lowest rate of contamination, followed by SGA, MEA, BHIA, PDA, and LJA. Sequencing of the internal transcribed spacer region rDNA of the contaminant fungi revealed that Aspergillus and Penicillium species were the most common contaminants. Conclusion: Tese results suggest that nonenriched culture media types, such as BLA or SGA, reduced contamination during dermatophyte subculture. © TÜBİTAK.

Mucormycosis is increasingly common in patients with risk factors such as diabetes mellitus, neutropenia, and corticosteroid therapy. However, mucormycosis seems to be less common in patients with human immunodeficiency virus (HIV) infection compared to patients with other risk factors. Despite their lower virulence, Lichtheimia species should be regarded as emerging pathogens among Mucoralean fungi. We report a fatal case of pulmonary mucormycosis due to Lichtheimia ramosa in a 52-year-old man with an end-stage HIV infection. He had a cachectic appearance and his CD4 count was 8 cells/mm3. The fungal infection was diagnosed based on a positive sputum culture with histopathologic confirmation. The fungus was resistant to caspofungin, anidulafungin, and voriconazole [minimum inhibitory concentration (MCI) >32 µg/ml], whereas the E test MIC values of itraconazole, posaconazole, and amphotericin B were 0.38, 0.38, and 0.5 µg/ml, respectively. Although intravenous drug use is the main risk factor for the development of mucormycosis in HIV-infected patients, it may also develop in patients with low CD4 count, opportunistic infections and/or additional diseases, such as Kaposi's sarcoma or severe immunodeficiency, as in our case. © 2014 Springer Science+Business Media Dordrecht.

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.

PubMedID: 24219728 No consensus exists about whether contraceptives cause an increased risk of vaginitis, including vulvovaginal candidosis (VVC). We investigated 495 women (252 who used contraceptives; 243 who did not) for the presence of VVC. Antifungal susceptibility testing was performed for five antifungal agents and for boric acid, and three virulence factors were also examined. We recovered 129 (26.1%) monofungal populations from vaginal samples of women with acute VVC (AVVC, n = 18), symptomatic recurrent VVC (RVVC, n = 22) and asymptomatic RVVC (n = 28), as well as of other contraceptive users who carried Candida in their vaginas (n = 61). It is important to note that the women who had VVC used the same contraceptive methods (p > 0.05). Candida albicans was the most common species isolated (45%), followed by C. glabrata (40.3%). Most of the vaginal yeast isolates exhibited low minimum inhibitory concentration levels for the five antifungals tested. However, this was not the case for boric acid. In addition, the yeast fungi that was derived from the AVVC and RVVC patients showed higher amounts of haemolytic activity than the yeast fungi found among the controls (p < 0.05). The use of contraception does not predispose women to VVC (p > 0.05). Also, both host- and organism-related factors were required to achieve optimal clinical treatment for VVC. © 2013 Informa UK, Ltd.

Pityriasis versicolor is a common superficial mycotic disease of the skin which is caused by different species of Malassezia genus. The aim of this study was to contribute to the knowledge of the aetiology of pityriasis versicolor (PV) with a mycological study made according to the new species and additionally, the success of the different sampling techniques, duration and recurrence history of the disease, distribution of infecting strains according to the affected body sites were also investigated. In total, 146 patients with pityriasis versicolor were included in this study. Fungal elements could only be visualized by potassium hydroxide examination in 36.4% of the samples. Specimens obtained by scraping skin surface by a sterile scalpel and/or sterile sticky plaster (OpSite) were inoculated in plates containing modified Dixon's medium. Out of 146 samples, 109 (74.7%) yielded a growth which was considered to be Malassezia spp. in culture. Species level identification of suspicious Malassezia yeasts was made according to their macroscopic and microscopic features, and their physiological characteristics. Among the identified species, Malassezia globosa (65.1%) was the most commonly isolated species, followed by Malassezia obtusa (17.4%). However, four Malassezia isolates could not be identified at species level with conventional methods. While most of the patients suffered their first episode of pityriasis versicolor (76%), back of the trunk was the mostly affected body site (39%). In conclusion, Malassezia globosa was found to be the predominant species in pityriasis versicolor patients in our region, and culture of the specimen is necessary for the epidemiologic purposes.

PubMedID: 23591622 An in vitro hair perforation test is used to differentiate isolates of Trichophyton mentagrophytes and Trichophyton rubrum complexes because morphological criteria are insufficient. Here, we performed in vitro hair perforation tests using blond prepubertal hair and albino adult hair to determine whether they differentiate between fungal species. We tested 43 well-characterized dermatophyte strains, Arthroderma spp. [n = 4], Epidermophyton floccosum [n = 1], Microsporum spp. [n = 8], and Trichophyton spp. [n = 30], and examined hair perforation at 3-30 days postinoculation (p.i.). The perforation times were not significantly different between the two hair types (P > 0.05). The T. mentagrophytes complex strains perforated hair 4-5 days p.i., whereas T. rubrum complex strains perforated hair 13-30 days p.i., except for Trichophyton violaceum, which perforated hair after 6-7 days. Thus, the hair perforation test is highly sensitive (100 %) and specific (100 %) for differentiating T. mentagrophytes from T. rubrum complexes 5 days p.i. At 14 and 30 days, the sensitivity and negative predictive value of the test remained unchanged (100 %), but the specificity was reduced (64.3 and 14.3 %, respectively). Consistent with previous reports, we observed "perforating organs" of zoophilic Microsporum canis and geophilic Microsporum gypseum at 4 and 3 days, respectively. This paper offers a "low-cost" and "low-tech" alternative to differentiating dermatophyte species where standard morphological techniques fail and/or where molecular techniques are not a viable option. © 2013 Springer Science+Business Media Dordrecht.

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.

We investigated the epidemiological characteristics of both symptomatic and asymptomatic dermatophytic groin infections in 1970 women (age: 36.2 ± 12.5) during routine gynaecologic examinations. Bilateral groin samples were collected with sterile cotton swabs premoistened with sterile physiological saline. The samples were then separately inoculated onto Sabouraud glucose agar. Fungi were identified by sequencing the rDNA internal transcribed spacer region. Dermatophytes were recovered from five patients (four Trichophyton rubrum and one Arthroderma vanbreuseghemii, 0.25%) with a diagnosis of asymptomatic carriers (four) and tinea inguinalis (one). In one case, groin carriage converted into tinea inguinalis after 3 weeks. Analysis of risk factors indicated that patients of at least 49 years were more likely to be positive for dermatophyte isolation (P = 0.002). In conclusion, groin dermatophyte carriage is more common than tinea inguinalis and can potentially convert into a symptomatic infection.

Participation in competitive sports is popular and widely encouraged worldwide. Herein, we investigated 252 male and 67 female sports players, aged 16.4 ± 1.3 years, active in 15 different types of combat (n = 143) and non-combat (n = 176) sports. Of the 319 participants in this study, 11 (3.5%) players, including six wrestlers, four football players and one handball player, all of whom were men, harboured dermatophytic fungi. Briefly, Trichophyton tonsurans was present in three athletes, who were scalp carriers of the fungus. Furthermore, T. rubrum (4), T. interdigitale (3) and Arthroderma simii (1) were recovered from eight participants with tinea inguinalis (4), tinea pedis (2) or both (1). One patient was a trunk carrier of concomitant tinea pedis. All dermatophytic fungi were identified using both direction sequence of the rDNA regions spanning the internal transcribed spacers (ITS1 and ITS2) and 5.8 rRNA gene. Although sports-active individuals are active and sweat more, we observed a low prevalence of dermatophytosis, both in combat (5.2%) and non-combat sports participants (3.4%) (P0.05). However, dermatophyte infections require more attention and appropriate management to eradicate the infection and to prevent possible outbreaks. This study also documents the first case of zoophilic A. simii in Turkey.

PubMedID: 22563856 Macroconidia are among the most important indicators used to identify dermatophytic fungi, but several do not usually sporulate and/or produce macroconidia on Sabouraud glucose agar. Specifically, Microsporum audouinii, M. ferrugineum, Trichophyton concentricum, T. schoenleinii, T. verrucosum, and T. violaceum (including T. soudanense and T. yaoundei) rarely form macroconidia and, therefore, cannot be easily identified. In this study, we investigated the production of macroconidia on nine common laboratory media, including Borelli's lactritmel agar (BLA), modified Borelli's lactritmel agar (MBLA), brain heart infusion agar (BHIA), Christensen's urease agar in Petri dishes (UPA), cornmeal dextrose agar (CMDA), Lowenstein-Jensen agar (LJA), malt extract agar (MEA), oatmeal agar (OA), and potato dextrose agar (PDA). The performance of these media was evaluated using 18 rare-macroconidia producing isolates, including representative of the six species mentioned above. All cultures in this study were incubated at 26°C on the bench, and conidia formation on each was investigated at 5, 10, 15, 20, 25, and 30 days of incubation. BLA apparently improved macroconidia production after 15 days and was the most useful nutrient agar medium to induce these phenotypic characters in daily practice, closely followed by OA, PDA, and MBLA. © 2012 ISHAM.

PubMedID: 22528742 Fungal keratitis is a rare but sight-threatening infection of the cornea that may be caused by several fungal pathogens. A delay in diagnosis and inadequate treatment may even lead to loss of the affected eye. Fungal keratitis is often misdiagnosed as bacterial keratitis because isolation and identification of the fungal pathogen is difficult and requires experience, and fungal growth in culture requires time. In this report, a 14-year-old boy with recalcitrant Fusarium solani keratitis, unresponsive to initial therapy, is presented. CLSI M38-A2 in vitro antifungal susceptibility tests demonstrated that only amphotericin B (0. 5 µg/ml) had potent activity against F. solani; however, fluconazole (>64 µg/ml), itraconazole (>16 µg/ml), voriconazole (8 µg/ml), and posaconazole (>16 µg/ml) had high minimum inhibitory concentrations. In addition, caspofungin (>16 µg/ml) and anidulafungin (>16 µg/ml) exhibited high minimum effective concentrations. Repeated intrastromal voriconazole injections, topical voriconazole, and caspofungin combined with systemic antifungal agents improved of the corneal lesion with a significant increase in visual acuity. Intrastromal voriconazole injection may be used as an adjunctive treatment method for recalcitrant fungal keratitis with no prominent complications. The intrastromal route could be an effective route of administration of antifungal agents, especially for F. solani keratitis, as in this case. A combination of various antifungal agents administered by different routes prevented loss of the eye. © 2012 Springer Science+Business Media B.V.

Trichophyton tonsurans tinea gladiatorum is an emerging epidemic among combat-sport athletes across the globe. In the present study, we investigated the prevalence of symptomatic and asymptomatic dermatophytic infections among wrestlers in the National Greco-Roman Championship in Turkey. In total, 194 wrestlers from 32 provinces and 72 clubs were examined for scalp, trunk, groin, and toe web dermatophytic infections. We also administered a questionnaire to obtain information on the participants' lifestyles, wrestling characteristics, and risk factors for dermatophytic infections. The hairbrush method was used for scalp and trunk sampling, whereas a cotton swab was used for groin, toe web, and mat sampling. Three wrestling mats in the gymnasium were surveyed for dermatophytes using the touch preparation method. A total of 17 (8.8%) wrestlers harbored dermatophytes, and 22 strains were isolated: 13 (59.1%) T. tonsurans and 9 (40.9%) T. rubrum. These isolates were found on the scalp (8), trunk (2), forearm (1), hand (1), groin (3), and feet (7). In addition, we recovered 8 dermatophyte strains from the 150 mat samples (5.3%): T. rubrum in 6 samples (75%) and T. tonsurans in two samples (25%). T. tonsurans was only recovered from 11 out of 194 (5.7%) wrestlers. Scalp carriage represents the predominant (72.7%) clinical picture of a T. tonsurans infection in these Greco-Roman wrestlers in Turkey. © 2011 Springer Science+Business Media B.V. Acknowledgments The present study was partly supported by the Turkish Wrestling Federation. We gratefully acknowledge Mr. Önder Yaks¸i, the General Coordinator of the Turkish Wrestling Federation, who kindly helped in the organization of this study, making the present study possible. In addition, we appreciate and give our sincere thanks to two anonymous reviewers for their critical comments on earlier drafts of this paper.

HPV-DNA testing is widely used worldwide today and it has become an important part of cervical cancer screening programs. The aim of this study is re-evaluating the effectiveness of MY09/11 consensus primer system, which is one of the most widely used HPV-DNA tests, by using a different approach. In this study, MY09/11 consensus PCR and two different TaqMan-based type-specific PCR assays were used for investigation of the presence of 17 different HPV types in cervical smear samples. Of the 470 samples, 33.2% (156/470) were HPV-DNA positive by at least one of the three methods and remains were negative by all methods. A total of 220 different HPV isolates were identified in 149 samples by the type specific PCR, while the nine samples were positive by consensus PCR only. A single HPV type was detected in 64.4% (96/149) of the genotyped samples, and multiple HPV types were detected in the remaining 35.6% (53/149). MY09/11 PCR failed to detect 21.2% (33/156) of all HPV-DNA positive samples and the rates of false negative results were 18.75% (18/96) and 28.3% (15/53) in single and multiple infections, respectively. We conclude that highly sensitive type-specific PCR tests may be a useful tool for screening of cervical cancer.

Bloodstream infections (BSIs) are a major cause of healthcare-associated morbidity and mortality. Analyses of the frequency of microorganisms isolated from blood cultures and antibiotic susceptibility can provide clinicians with relevant information for the empirical treatment of patients. The purpose of the study was to investigate to frequency of microorganisms isolated from blood cultures and their sensitivity to antimicrobial agents between January 2009 and December 2010 at the Training Hospital of Gulhane Military Medical Faculty. Blood cultures were processed by automatized BACTEC/9050 (Becton Dickinson, Maryland, USA). The observed growth of microorganisms in culture media was identified by conventional methods and PhoenixTM 100 automatized systems (BD Phoenix System, Beckton Dickinson, USA).Antimicrobial susceptibility tests were performed by Kirby-Bauer disc diffusion method and automatized systems (BD Phoenix System, Beckton Dickinson, USA) in accordance with the recommendations of Clinical and Laboratory Standarts Institute (CLSI). In the study period among the 6823 blood culture samples, 957 (14%) yielded positive results. Results of 600 (8.7%) blood culture samples evaluated as contamination. Of the 957 isolated microorganisms, 61.0% were Gram negative, 31.1% were Gram positive and 7.8% were yeast. E.coli was the most frequently isolated species (15.9%), followed by Klebsiella spp (15.4%) and Coagulase Negative Staphylococcus (CNS) (13.2%). Twenty eight percent% of S. aureus and 89% of CNS isolates were resistant to methicillin. Only one isolate (1.73%) was resistant to glycopeptides among Enterococcus spp. ESBL (Extended-spectrum beta lactamase) was detected in 36.8% of E.coli and 51.3% of Klebsiella spp. isolates.

Crimean-Congo Hemorrhagic Fever (CCHF) is a fatal zoonotic viral infection. The agent belongs to the Nairovirus of the Bunyaviridae species. The virus naturally recycles in vector-vertebrate-vector. This study aimed to evaluate cases of tick bites admitted to Infectious Diseases and Emergency Departments in 2008, and to develop management recommendations of such cases. Fifty-seven patients who admitted to a hospital due to tick bites in 2008 were included in the study. A 10-day clinical follow-up was performed to assess for symptoms including fever, fatigue, abdominal pain, headache, nausea/vomiting, diarrhea, disseminated somatic pain, and other hemorrhagic signs. During this period, laboratory analyzes, including white blood cells, thrombocytes, aspartate aminotransferase, alanine aminotransferase, gamma-glutamyl transferase, lactate dehydrogenase, creatinine phosphokinase (CK), and pentylenetetrazol were performed. Personal data of the patients, location of the bite, and the removal of the tick were recorded.ResultsOf the 57 patients, 37% were from the city, and 63% were from rural areas. The tick was removed by health staff in 25 (44%) of the cases. The bites occurred on body areas including the head/neck, trunk, upper extremities, and lower extremities in 14%, 24%, 27%, and 13% of the cases, respectively. During the follow-up period, none of the patients exhibited any of the signs or symptoms listed above. Laboratory tests did not reveal any abnormalities, except for high levels of CK in 15 patients. Thus, 57 cases did not develop CCHF.Discussion and ConclusionSince 2002, CCHF has caused an increased mortality in Turkey, and has resulted in high anxiety and concern among the Turkish public regarding tick bites. This has resulted in a rise in the number of patients admitting to emergency departments with tick bites. Due to CCHF's incubation period, patients with tick bites should be evaluated for 10 days using a multidisciplinary approach involving both clinical and laboratory evaluations in order to prevent the unnecessary administration of ribavirine.

IntroductionIn this study, the mean daily and annual radiation exposure of the radiology department staff, other hospital health staff, and public volunteers was compared at Maresal Cakmak Military Hospital in Erzurum, Turkey.MethodsThe NEB.211 Dose–Rate Meter with a Gaiger–Müller counter was used to measure the amount of radiation. Six radiology department health staff carried the NEB.211 device during seven working hours. At the end of the day, total absorbed dosages were noted. The same measurements were also done for the six health staff of the other departments and six non-hospital volunteers. Seventeen additional hours were noted for the non-hospital volunteers. The mean value of 17 hours of daily measurements (3.31 mSv) was added to the both group's working hours measurements and the total daily radiation amounts were calculated.ResultsThere was no statistical difference between each three groups in working hours (p = 0.087), daily and annual equivalent dosages (for both p = 0.099).DiscussionThe radiology department health staff was exposed to radiation under the border of equivalent dosage which is determined by Turkish Automic Energy Authority. Public volunteers were seen as they were exposed the radiation over the determined border of equivalent dosage. Nonetheless, with changes depending on living standards, the physical properties of living spaces and geographical circumstances per capita exposed annual dosage is about 2.4–2.8 mSv throughout the world. There was no significant statistical difference between the amounts of equivalent dosage which were exposed to the radiology department health staff, the other hospital staff and public members.