Genome Sequencing of Leishmania infantum Causing Cutaneous Leishmaniosis from a Turkish Isolate with Next-Generation Sequencing Technology.

PURPOSE: Leishmania subgenus Leishmania causes leishmaniosis, which is a chronic systemic disease in humans and animals, in which the skin and visceral organs can be affected. The disease generally consists of three different clinical types in humans: visceral (kala-azar, VL), cutaneous (CL) and mucocutaneous leishmaniosis (MCL). According to the World Health Organization (WHO), leishmaniosis is still one of the world's most neglected diseases. It has been nearly 13-14 years since the completion of the first complete genome sequence of a Leishmania parasite. However, much information about these parasites remains to be elucidated, such as the causes of differences in tissue tropism. The aim of this study is to perform the whole-genome sequencing of Leishmania infantum causing cutaneous leishmaniosis from a Turkish isolate with next-generation sequencing technology. METHODS: Genomic sequencing was performed on the Illumina HiSeq 2500 platform. The TruSeq Nano DNA Low Throughput Library Prep Kit, compatible with the Illumina HiSeq 2500 platform, was used to generate the library. Synthesis sequencing (SBS) was performed with a HiSeq Rapid SBS Kit v2 to generate single-fragment reads (2 × 150 bp; PE) with two fragment end-to-end assemblies. Bioinformatics analyses were performed on the Geneious 11.0.5. ( www.genius.com ) platform. RESULTS: In our study, a high-quality whole-genome sequence (WGS) of L. infantum was successfully generated, and a total of 32,009,137 base pairs of genomic DNA from 36 chromosomes were obtained. The resulting genomic DNA sequence was submitted to the US National Center for Biotechnology Information (NCBI) GenBank ( www.ncbi.nlm.nih.gov ) database and registered under the name Leishmania infantum_TR01 (Lin_TR01). The following accession numbers were assigned by NCBI to the 36 chromosomes of the Lin_TR01 genome: CP027807, CP027810, CP027808, CP027811, CP027809, CP027812, CP027813, CP027814, CP027817, CP027818, CP027819, CP027815, CP027821, CP027816, CP027823, CP027820, CP027822, CP027824, CP027825, CP027826, CP027827, CP027828, CP027829, CP027830, CP027831, CP027832, CP027833, CP027834, CP027835, CP027836, CP027837, CP027838, CP027839, CP027840, CP027841, CP027842. As a result of the annotation of the Lin_TR01 genome, 3153 polymorphisms, 8324 genes, 8199 CDSs, 8109 mRNAs, 67 tRNAs, 11 rRNAs and 58 ncRNA were identified. Among the 8199 CDS obtained, 5278 encode hypothetical proteins. CONCLUSION: In this study, a high-quality WGS of Leishmania infantum was successfully obtained for the first time in Turkey. According to a review of WGS studies on this subject, the Lin_TR01 strain is the first strain to be isolated from cutaneous leishmaniosis. The reference genome of L. infantum JPCM5 (Peacock et al., 2007) was obtained from a visceral leishmaniosis case, in accordance with the classical tissue and organ tropism of the species. Lin_TR01 is the second whole-genome-sequenced strain in the world after the JPCM5 strain. The Lin_TR01 genome is the only L. infantum whole-genome sequence that is completed assembly level from 36 chromosomes among the genomes obtained thus far ( https://www.ncbi.nlm.nih.gov/genome/genomes/249 ).

[Comparison of Multiplex Nested PCR, In-house Real-Time PCR and Commercial Real-Time PCR Methods for the Detection of Plasmodium spp. from Blood Samples]. / Plasmodium spp.'nin Saptanmasinda Multipleks Nested PCR, In-house Gerçek Zamanli PCR ve Ticari Gerçek Zamanli PCR Yöntemlerinin Karsilastirilmasi.

Malaria is a life-threatening parasitic disease caused by the parasites belonging to Plasmodium genus. Microscopic examination of Giemsa stained blood smears is accepted as the gold standard diagnostic method. It is recommended to use more than one method in order to strengthen the laboratory diagnosis of malaria which is an important health problem in our country as in the whole world. In this study, it was aimed to compare the results of three different molecular methods and determine which molecular method could be used in the diagnostic algorithm to be applied. DNA was extracted from 280 whole blood sample stored in EDTA tubes using a commercial kit. Three different polymerase chain reaction (PCR) methods were used for the detection of Plasmodium spp. in DNA samples obtained and the results were compared. First, multiplex nested PCR was applied and then in-house real-time PCR (Rt-PCR) which was validated in our laboratory and a commercial Rt-PCR kit were applied. Multiplex nested PCR was accepted as the gold standard and 182 samples that were evaluated as Plasmodium spp. positive and 98 samples that were evaluated as negative were also studied by in-house and commercial Rt-PCR methods. In multiplex nested PCR's first step reaction 1670 base pairs (bp) band was observed in Plasmodium spp. positive samples and 117 bp band was observed in Plasmodium vivax positive samples in the second step reaction. Tm values of P.vivax positive samples were determined as 78-79 in the melting analysis of the in-house Rt-PCR. CT values of the positive samples in in-house Rt-PCR were between 20.03-31.71 and were between 17.26-34.94 in the commercial Rt-PCR. With the in-house Rt-PCR method 180 cases were determined as positive, while with the commercial Rt-PCR method 178 cases were determined as positive. Two samples with the in-house Rt-PCR and 4 samples with the commercial Rt-PCR were considered as false negative. When the sensitivity and specificity of the both methods were calculated, the sensitivity of the in-house Rt-PCR method was 0.98, the specificity was 0.97, the positive predictive value (PPV) was 98%, the negative predictive value (NPV) was 97%, the sensitivity of the commercial Rt-PCR was 0.97, the specificity was 0.95, the PPV was 97%, the NPV was 95%. A high level of agreement (κ: 0.953) was determined between the in-house and the commercial Rt-PCR methods. In order for a test to be accepted as a confirmatory test, its specificity must be high. It was decided that sensitivity and specificity of the in-house Rt-PCR were suitable for using this method in the laboratory diagnosis of Plasmodium species.

Rose Bengal-Mediated Photodynamic Antimicrobial Treatment of Acanthamoeba Keratitis.

Purpose: To evaluate the in vivo efficacy of rose bengal (RB)-mediated photodynamic antimicrobial therapy (PDAT) for treatment of Acanthamoeba castellanii keratitis (AK). Materials and Methods: An animal (rabbit) AK model was successfully achieved via intrastromal inoculation of a suspension of A. castellanii cells and trophozoites. Prior to RB-PDAT (pre-treatment, day-5), the severity of the induced corneal infection was graded numerically for epithelial defects, stromal edema, neovascularity, and stromal opacity/infiltration. The right eyes of rabbits (n = 18) were divided equally into three groups (n = 6/group): control (no treatment); 0.1% RB+518 nm irradiation (5.4 J/cm2); and 0.2% RB+518 nm irradiation (5.4 J/cm2). On post-treatment day-5, animals were euthanized, after which corneal buttons were excised and submitted for real-time polymerase chain reaction (RT-PCR) analysis. Results: Post-treatment clinical scores of the 0.1 and 0.2% RB groups indicated significant improvement compared to control group scores (pre-treatment clinical scores; 5.17 ± 0.98, 7.50 ± 0.62, and 6.17 ± 0.70 and post-treatment clinical scores; 4.50 ± 0.56, (p = .043), 3.50 ± 0.99 (p = .039), 6.83 ± 1.66 (p = .34), respectively). RT-PCR analysis revealed that the mean cycle threshold (Ct) values were significantly higher in treated-group corneas compared to control-group corneas, with no significant differences between treated-groups (Mean Ct values; 34.33, 34.5, and 29.67 for 0.1 and 0.2% RB, and control groups). There was a statistically significant negative correlation between post-treatment clinical scores and Ct values (r = -0.474, p-value 0.047). Conclusions: Our results demonstrate that RB-PDAT is effective in decreasing the parasitic load and clinical severity of AK.

Acanthamoeba Keratitis Associated with Scleral Contact Lens Use in a Keratoconus Patient.

To the best of our knowledge, this is the second reported case of Acanthamoeba keratitis (AK) as a result of scleral lens use and the first case of AK associated with Maxim scleral lens use (Accu-Lens, Inc., Lakewood, CO, USA). A 22-year-old male scleral lens user presented at the department of ophthalmology at Gazi University Hospital complaining of painful corneal opacities and erosion in the cornea of right eye. A real-time polymerase chain reaction assay (Primerdesign, Southampton, UK) was performed, and Acanthamoeba spp. DNA was amplified on the corneal specimen. A topical antimicrobial treatment was prescribed, and the symptoms had improved significantly at the 2-week follow-up. Contact lens wearers always run the risk of developing AK, even with gas-permeable scleral contact lenses. Therefore, AK must be considered as an important differential diagnosis in patients who use scleral contact lenses.

Evaluation of Malaria Blood Smears Sent to National Malaria Reference Laboratory

Objective: Although the disease has been eliminated in Turkey malaria continues to be a threat due to increase in the number of people coming from or going to countries where the disease is endemic. In this study, we aimed to evaluate blood smears sent to the National Malaria Reference Laboratory within the malaria surveillance system. Methods: From March 2016 to July 2018 a retrospective study was conducted to compare the results of Malaria Reference Laboratory and Public Health Laboratories. A total of 16.827 blood stains were sent to our laboratory for approval. Results: In Public Health Laboratories, 315 (1.88%) of the smears were positive, 16.510 (98.12%) were negative, and in the National Malaria Reference Laboratory 252 (1.50%) were positive, 16.466 were negative. In the Public Health Laboratories, one of the two samples considered to be malaria suspected was positive in the National Malaria Reference Laboratory and one was negative. In Public Health Laboratories 35.88% of smears were P. falciparum, 27.30% were Plasmodium spp., 20.96% were P. vivax, 14.92% were mixed infection, 0.63% were P. malariae, 0.31% were P. ovale, and in the Reference Laboratory 49.60% were Plasmodium spp., 29.37% were P. falciparum, 16.27% were P. vivax, 4.36% were mixed infection, 0.40% were P. malariae. Conclusion: In order to malaria surveillance system to be maintained in a healthy manner, preparation, staining, coding, packaging, transportation of blood slides is very important. Also if necessary, continuing training of laboratory staff working in malaria diagnosis is crucial.

[Method Verification of Inhouse Real-time Polymerase Chain Reaction for Detection of Toxoplasma gondii]. / Toxoplasma gondii'nin Inhouse Gerçek Zamanli Polimeraz Zincir Reaksiyonu ile Saptanmasinda Yöntemin Dogrulanmasi.

Toxoplasmosis is one of the most common parasitic infection in humans. Serological and molecular methods are used for diagnosis. Molecular methods are becoming increasingly preferred, since they lead to shortening of diagnostic time. In our study, it was aimed to determine Toxoplasma gondii by a cost-effective, quantitative, fast and reliable method without using a commercial kit, and apply method verification. T.gondii strain which was continued by mouse inoculation in our laboratory was used for method verification study. For this purpose DNA extraction was performed using a commercial kit. The limit of detection and, high and low positivity rates were determined by serial dilutions of DNA sample. Accuracy and certainty studies were performed using with TG-F, TG-R primers and TaqMan TG probe for method verification of the test. In the study with serial dilutions of DNA sample, detection limit was determined as 10-3 dilutions (0.028 copies/reaction). Furthermore 10-1 dilution (2.8 copies/reaction) was considered as high positive, 10-2 dilution (0.28 copies/reaction) was considered as low positive and method verification studies were performed. The accuracy of test was determined as 0.62 for high positive samples and 0.14 for low positive samples. CV value of intra-assay certainty was 0.62 for high positive samples and 0.14 for low positive samples, whereas, CV value of inter-assay certainty was calculated as 1.03 for high positive samples and 2.34 for low positive samples. Correlation coefficient was determined as 0.99. The coefficient of variation of inhouse realtime PCR method used in our study was found to be below 15%, and it was decided to be suitable for routine laboratory studies.

Molecular Survey of Babesia microti (Aconoidasida: Piroplasmida) in Wild Rodents in Turkey.

Babesia microti (Aconoidasida: Piroplasmida) (Franca, 1910) is an important tick-borne zoonotic parasite with rodents serving as reservoir hosts. In the present study, 536 rodents were captured from Burdur, Bartin, Giresun, and Yozgat provinces of Turkey between the years 2010 and 2012, and blood samples were examined for the presence of Babesia spp. using conventional PCR which targeted the 18S rRNA gene. The sequence analysis of PCR amplicons was tested for B. microti as well as for Hepatozoon spp., and Sarcocystis spp. Overall, 5.8% of the rodents were positive for B. microti: 41% in Myodes glareolus, 7.7% in Chionomys roberti, and 2% in Apodemus spp., whereas no Babesia DNA was detected in Mus macedonicus and Microtus spp. Six rodents were positive for Hepatozoon spp. and one rodent was positive for Sarcocystis spp. Overall, 14.9 and 4.5% of rodents captured from Bartin and Giresun provinces, respectively, were PCR positive for B. microti, whereas none of rodents captured in Burdur and Yozgat were positive for Babesia spp. The sequence data of B. microti from rodents revealed that all sequences belonged to the zoonotic genotype. Sequences of B. microti obtained from rodents of the Bartin province were genotypically closer to European isolates, whereas those obtained from rodents of the Giresun province were closer to Russian and Mongolian isolates.

Evaluation of Symptomatic Patients with Resistant Discharge.

The aim of this study was to detect the presence of Chlamydia trachomatis, Neisseria (N.) gonorrhoeae, Mycoplasma (M.) hominis, M. genitalium, Ureaplasma (U.) urealyticum, and Trichomonas (T.) vaginalis in patients with resistant discharge. The study also evaluated the concordance of the diagnostic tests. Samples from 156 patients were tested by direct microscopy and culture for T. vaginalis and Mycoplasma IES for M. hominis and U. urealyticum. Multiplex Polymerase Chain Reaction (PCR) was used to determine the presence of six agents. Statistical analyses were performed using the SPSS program. Out of 156 patients, 38 had positive result for the agents tested. Of these 38 patients, 28 (73.7%) had single agent positivity and 10 (26.3%) had multiple agent positivity. The detection rate of U. urealyticum, M. hominis, N. gonorrhoeae, C. trachomatis, T. vaginalis, M. genitalium specifically was 10.3%, 9.6%, 6.4%, 3.2%, 2.6%, 0.6% respectively. N. gonorrhoeae and U. urealyticum were the most common in male patients, while M. hominis and U. urealyticum were mostly found in female patients. Different methods used for detecting T. vaginalis were compared to find that interrater reliability was perfect for culture-direct microscopy (κ:0.85; P<0.001) and also for culture-PCR (κ:0.89; P<0.001). The interrater reliability was moderate (κ:0.53; P<0.001) for PCR-Mycoplasma IES test for M. hominis and fair (κ:0.21; P<0.007) for U. urealyticum. U. urealyticum and M. hominis were among the most commonly found sexually transmitted infections (STI) agents in patients with resistant discharge. Multiple agent positivity was high and should be kept in mind in every STI case.

Bacterial and protozoal pathogens found in ticks collected from humans in Corum province of Turkey.

BACKGROUND: Tick-borne diseases are increasing all over the word, including Turkey. The aim of this study was to determine the bacterial and protozoan vector-borne pathogens in ticks infesting humans in the Corum province of Turkey. METHODOLOGY/PRINCIPAL FINDINGS: From March to November 2014 a total of 322 ticks were collected from patients who attended the local hospitals with tick bites. Ticks were screened by real time-PCR and PCR, and obtained amplicons were sequenced. The dedected tick was belonging to the genus Hyalomma, Haemaphysalis, Rhipicephalus, Dermacentor and Ixodes. A total of 17 microorganism species were identified in ticks. The most prevalent Rickettsia spp. were: R. aeschlimannii (19.5%), R. slovaca (4.5%), R. raoultii (2.2%), R. hoogstraalii (1.9%), R. sibirica subsp. mongolitimonae (1.2%), R. monacensis (0.31%), and Rickettsia spp. (1.2%). In addition, the following pathogens were identified: Borrelia afzelii (0.31%), Anaplasma spp. (0.31%), Ehrlichia spp. (0.93%), Babesia microti (0.93%), Babesia ovis (0.31%), Babesia occultans (3.4%), Theileria spp. (1.6%), Hepatozoon felis (0.31%), Hepatozoon canis (0.31%), and Hemolivia mauritanica (2.1%). All samples were negative for Francisella tularensis, Coxiella burnetii, Bartonella spp., Toxoplasma gondii and Leishmania spp. CONCLUSIONS/SIGNIFICANCE: Ticks in Corum carry a large variety of human and zoonotic pathogens that were detected not only in known vectors, but showed a wider vector diversity. There is an increase in the prevalence of ticks infected with the spotted fever group and lymphangitis-associated rickettsiosis, while Ehrlichia spp. and Anaplasma spp. were reported for the first time from this region. B. microti was detected for the first time in Hyalomma marginatum infesting humans. The detection of B. occultans, B. ovis, Hepatozoon spp., Theileria spp. and Hemolivia mauritanica indicate the importance of these ticks as vectors of pathogens of veterinary importance, therefore patients with a tick infestation should be followed for a variety of pathogens with medical importance.

Cryptosporidium species and Cryptosporidium parvum subtypes in dairy calves and goat kids reared under traditional farming systems in Turkey.

Molecular characterizations of Cryptosporidium spp. in ruminants reared under traditional animal management systems are scarce and studies conducted thus far have revealed largely an absence of the pathogenic and zoonotic species Cryptosporidium parvum in pre-weaned animals. In this study, we examined Cryptosporidium species and subtype distribution in free-range pre-weaned dairy calves and goat kids with diarrhea. Cryptosporidium-positive specimens from pre-weaned calves on 10 farms and goat kids on 4 farms in Ankara, Balikesir, Corum, Kirikkale, and Kirsehir Provinces, Turkey were genotyped by PCR-restriction length polymorphism analysis of the small subunit rRNA gene, which identified C. parvum in 27 calves and 9 goat kids and Cryptosporidium ryanae in 1 calf. Among the C. parvum isolates successfully subtyped by DNA sequence analysis of the 60 kDa glycoprotein gene, three subtypes were detected in calves, including IIaA13G2R1 (20/23), IIdA18G1 (2/23), and IIdA20G1b (1/23), and four subtypes were detected in goat kids, including IIaA13G2R1 (3/8), IIaA15G1R1 (2/8), IIdA22G1 (2/8), and IIdA18G1 (1/8). Data of the study suggest that dairy calves reared in a traditional cow-calf system in Turkey are mainly infected with a C. parvum subtype rarely seen elsewhere, whereas goat kids are infected with diverse subtypes. As all five C. parvum subtypes found in this study are known human pathogens, pre-weaned farm animals could play a potential role in the transmission of human cryptosporidiosis.

Isospora belli in a patient with liver transplantation.

Isospora belli is an opportunistic protozoon which should be monitored in patients with gastrointestinal complaints such as abdominal pain, nausea and diarrhoea, in both immune-compromised and immune-competent patients. Our case was a 35 year-old male patient who had received a liver transplant because of cirrhosis and hepatic fibrosis. A diarrhoeic stool sample of the patient was sent to the laboratory for microbiological and parasitological analyses. Faecal occult blood was positive and bacteriological analysis was negative. Isospora belli infection was diagnosed by detection of the oocysts in stool samples. Per oral trimethoprim-sulphamethoxazole treatment was given in 500 mg bid dose for 10 days. At the end of the treatment, no oocyst of Isospora belli was seen but non-pathogenic cysts of Entamoeba coli and vacuolar forms of Blastocystis hominis were observed. Two months later the patient had abdominal pain, fatigue and diarrhoea again and parasitological re-evaluation showed oocysts of Isospora belli.

[The epidemiology research of Blastocystis hominis in the Dokuz Eylül University Medical Faculty Hospital between 2005 and 2009]. / Dokuz Eylül Üniversitesi Hastanesi'ne 2005-2009 Yillari Arasinda Basvuran Olgularda Blastocystis hominis Epidemiyolojisinin Arastirilmasi

OBJECTIVE: An investigation of Blastocystis hominis (B. hominis) prevalance in 17756 patients with gastrointestinal system complaints who presented at the parasitology laboratory of the Dokuz Eylul University Medical Faculty Hospital between January 2005 and December 2009 was carried out. METHODS: Fecal samples of all patients were examined using the native-Lugol and trichrome and Kinyoun acid-fast staining method after sedimentation in fecal concentration tubes. RESULTS: One or more parasites were detected in 1510 (8.50%) of the patients. The distribution of the intestinal parasites was as follows: B. hominis 778 (4.38%), nonpathogenic amoebas 343 (1.93%), Giardia intestinalis (G. intestinalis) 205 (1,15%), Enterobius vermicularis (E. vermicularis) 46 (0.25%), Entamoeba histolytica/Entamoeba dispar (E. histolytica/E. dispar) 34 (0.19%), and other rare parasites 104 (0.58%). The most frequently seen parasite was B. hominis in fecal samples of patients with gastrointestinal complaints in our study. Distribution of 778 patients with B. hominis due to parasite forms was determined as: vacuolar in 525 (67.49%), granular in 115 (14.78%), both vacuolar and granular in 138 (17.73%) cases. CONCLUSION: As B. hominis was the most frequently seen parasite in patients with gastrointestinal complaints, we suggest that the parasite should be considered as pathogenic and sufficient attention must be paid in routine stool examinations.

[Microsporidium spp. infection in an immunocompromised child diagnosed by polymerase chain reaction]. / Immün sistemi baskilanmis bir çocukta Microsporidium spp. Enfeksiyonunun polimeraz zincir reaksiyonu ile tanimlanmasi

Microsporidium spp. may lead to a variety of clinical pictures like sinusitis, keratoconjunctivitis, hepatitis, myositis, peritonitis, nephritis, encephalitis and pneumonia in case of immune deficiencies. In this report, a case of diarrhea due to Microsporidium spp. has been presented. A four years old male patient who was followed with the diagnosis of myotonic dystrophia, was admitted to the hospital with the complaints of respiratory distress and fever. Due to the history of recurrent infections, further investigations was carried out to clarify the immunological status of the patient, and the total IgA and IgM levels were found as 14 mg/dl and 30 mg/dl, respectively (normal values were; 18-160 and 45-200 mg/dl, respectively). Following bronchoscopy done to enlighten respiratory distress, the patient developed high fever and watery diarrhea. Since bacteriological cultures of the stool yielded Shigella spp., antimicrobial therapy with ciprofloxacin was initiated. Parasitological examination of the stool done by Weber's modified trichrome dye, yielded Microsporidium spp. microscopically and albendazole was added to the treatment. Presence of Microsporidium spp. was confirmed by polymerase chain reaction with the use of C1 and C2 primers (Metabion, Germany) targeted to Microsporidium spp. and besides a 270 bp band specific for Encephalitozoon intestinalis was also obtained. This case emphasized that in case of diarrhea the stool samples of the immunocompromised patients should be evaluated in terms of Microsporidium spp. in addition to the routine parasitologic examinations.

[The distribution of intestinal parasites detected in The Dokuz Eylul University Medical Faculty Hospital between 2005 and 2008.]. / Dokuz Eylül Universitesi Tip Fakültesi Arastirma ve Uygulama Hastanesi'nde 2005-2008 Yillari Arasinda Saptanan Bagirsak Parazitlerinin Dagilimi.

A retrospective evaluation of the data from 14,246 patients with gastrointestinal complaints who presented at the parasitology laboratory of the Dokuz Eylul University Medical Faculty Hospital between January 2005 and December 2008 was carried out. Fecal samples of all patients were examined using native-Lugol and the trichrome and Kinyoun acid-fast staining method after sedimentation in fecal concentration tubes. One or more parasites were detected in 1320 (9.3%) of the patients. The distribution of the intestinal parasites was as follows: Blastocystis hominis, 689 (4.83%); nonpathogenic amoebas, 108 (21.82%); Giardia intestinalis, 320 (2.24%); Enterobius vermicularis, 23 (0.16%); Entamoeba histolytica/Entamoeba dispar, 34 (0.24%); and other rare parasites, 78 (0.54%). The results of this study emphasize the fact that intestinal parasitic infections are still an important public health problem.

[Biosafety profile of laboratory workers at three education hospitals in Izmir, Turkey]. / Izmir'deki üç egitim hastanesinde laboratuvar çalisanlarinin biyogüvenlik profili.

The laboratory personnel in hospitals are at risk in terms of transmission of various infectious diseases. The aim of this study is to evaluate the knowledge, behavior and attitude of the health personnel who work in one university and two state hospitals in Izmir, Turkey, about biosafety. The study is an observational-sectional study. Participants were selected via random sampling method. The hospitals were visited on workdays determined by the random selection method and all of the personnel (doctor, technician, cleaning-staff) were included to the study. The data were analyzed statistically using Chi square test. Of the 183 participants included in the study, 106 were from Dokuz Eylül University School of Medicine Central Laboratory and 77 were from state hospitals. 62.8% of the participants were female, 37.2% were male and mean age of all was 32.8 +/- 6.9 years. 23.5% of the participants stated that they had previously taken education about biosafety (p= 0.002). It was determined that 91.3% of the participants were wearing gloves and 87.4% of them were wearing lab-coat during laboratory studies. A significant difference was observed between the hospitals in terms of use of gloves (p= 0.004). All the participants stated that they wash their hands and 43% of them indicated that their daily hand wash rate was > or = 10 times. It was determined that 38.3% of the participants consumed food or drinks in the laboratory, however, this rate was statistically significantly less in the university hospital laboratory (p= 0.000). The rate of participants who had been subjected to a microorganism in the last six months was 6.6%. Obedience to the biosafety rules in laboratory will not only provide a safer environment but also improve the quality of work. We believe that the results of this study will serve as a guide for future studies on laboratory biosafety.

Demographic status and prevalence of intestinal parasitic infections in schoolchildren in Izmir, Turkey.

Thirteen primary schools from nine areas were randomly selected in the shantytown and apartment districts in Izmir. Fecal specimens were evaluated with native-lugol, formalin-ethyl-acetate sedimentation and with trichrome staining for protozoa and helminths and with cellophane tape for Enterobius vermicularis. Of the study group, 33.4% had one or more parasites. The most common parasite was Blastocystis hominis (14.6%) followed by Enterobius vermicularis (10.1%) and Giardia intestinalis (7.8%). When parasitic distribution was evaluated in association with demographic features, a significant relation was found between the income level and parasitic infection prevalence. Multiple parasitic infections were more prevalent in crowded families (either extended or with many children). When parasitic infection prevalences in the 9-10 and 11-12 years of age groups were compared, the probability in the shantytown primary school group was significantly higher than in the apartment group (p<0.05).

[The evaluation of the techniques used for diagnosis of Entamoeba histolytica in stool specimens]. / Diskida Entamoeba histolytica'nin saptanmasinda kullanilan yöntemlerin birlikte degerlendirilmesi.

In this study, stool samples of 9378 patients from different clinics, who presented at the laboratory of the department of parasitology of the Dokuz Eylul University, Faculty of Medicine with several gastrointestinal complaints from January 2004 to May 2006, were examined. All stool samples were examined with the saline-Lugol method and, in suspicious cases, by trichrome staining, cultivation in Robinson's medium and/or antigen detection in stool with the Entamoeba CELISA Path kit. Forty-one cases (0.44%), in which Entamoeba histolytica/Entamoeba dispar cysts and/or trophozoites were detected by at least one method, were found to be positive. Out of these 41 cases, four methods were used in 24 cases, three methods in 14 cases, whereas only saline-Lugol and trichrome staining methods were used in 3 cases. Even though all 41 positive cases had been examined with the saline-Lugol method, only 25 cases were found to be positive with this method for E. histolytica/E. dispar cysts and/or trophozoites. The remaining 16 cases were diagnosed by the other three methods. Today it is necessary to distinguish E. histolytica from E. dispar because the patient does not need to be treated if E. dispar is identified whereas if E. histolytica is identified the patient needs urgent treatment. That's why it is necessary to get reliable results using diagnostic methods together and, when needed, by ELISA specific for E. histolytica.

Cryptosporidium parvum diarrhea in an infant with short bowel syndrome.

Cryptosporidium parvum is an underdiagnosed cause of diarrhea in children. The case of a 1-year-old girl with short bowel syndrome presenting with severe dehydrating diarrhea with a protozoon named C parvum is reported. Although the resection of the small bowel in this patient seemed to cause this severe infection with C parvum, more cases are needed to include the resection of the small bowel as a risk factor for Cryptosporidium infection and/or for a more severe form of diarrhea. Awareness of this infection among clinicians will help to diagnose this infection since special acid fast staining is made on special request.

[The distribution of intestinal parasites detected in the Dokuz Eylul University Medical Faculty Hospital between 2003 and 2004]. / Dokuz Eylül Universitesi Tip Fakültesi Arastirma ve Uygulama Hastanesi'nde 2003-2004 yillari arasinda saptanan bagirsak parazitlerinin dagilimi.

A retrospective evaluation of the data from 7,712 patients with gastrointestinal complaints who presented at the parasitology laboratory of the Dokuz Eylul University Medical Faculty Hospital between January 2003 and December 2004 was carried out. Fecal samples of all patients were examined using native-Lugol and the trichrome staining method after sedimentation by the fecal concentration tube. One or more parasites were detected in 495 (6.41%) of the patients. The distribution of the intestinal parasites was as follows: Blastocystis hominis 218 (44.04%), nonpathogenic amoebas 108 (21.82%), Giardia intestinalis 82 (16.57%), Enterobius vermicularis 50 (10.10%), Entamoeba histolytica 17 (3.43%) and other rare parasites 20 (4.04%). The results of this study were similar to those of other cities in the western part of Turkey and emphasize the fact that intestinal parasitic infections are still an important public health problem.