1
|
Guldemir D, Usluca S, Nalbantoglu AS. Genome Sequencing of Leishmania infantum Causing Cutaneous Leishmaniosis from a Turkish Isolate with Next-Generation Sequencing Technology. Acta Parasitol 2021; 66:75-80. [PMID: 32691361 DOI: 10.1007/s11686-020-00252-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/06/2020] [Indexed: 11/26/2022]
Abstract
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 ).
Collapse
Affiliation(s)
- Dilek Guldemir
- Public Health General Directorate, Microbiology Reference Laboratories Department, National Parasitology Reference Laboratory, Saglik Mah. Adnan Saygun Cad. No:55, Sihhiye, 06100, Ankara, Turkey.
- Department of Parasitology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey.
| | - Selma Usluca
- Public Health General Directorate, Microbiology Reference Laboratories Department, National Parasitology Reference Laboratory, Saglik Mah. Adnan Saygun Cad. No:55, Sihhiye, 06100, Ankara, Turkey
| | - Ayse Serpil Nalbantoglu
- Department of Parasitology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
| |
Collapse
|
2
|
Usluca S, Çelebi B. [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]. MIKROBIYOL BUL 2020; 54:306-317. [PMID: 32723285 DOI: 10.5578/mb.69011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
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.
Collapse
Affiliation(s)
- Selma Usluca
- General Directorate of Public Health, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
| | - Bekir Çelebi
- General Directorate of Public Health, Department of Zoonotic and Vector-borne Diseases, Ankara, Turkey
| |
Collapse
|
3
|
Atalay HT, Uysal BS, Sarzhanov F, Usluca S, Yeşilırmak N, Özmen MC, Erganiş S, Tefon AB, Dogruman-Al F, Bilgihan K. Rose Bengal-Mediated Photodynamic Antimicrobial Treatment of Acanthamoeba Keratitis. Curr Eye Res 2020; 45:1205-1210. [DOI: 10.1080/02713683.2020.1731830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | | | - Fakhriddin Sarzhanov
- Departments of Medical Microbiology, School of Medicine, Gazi University , Ankara, Turkey
- School of Medicine, Akhmet Yassawi International Kazakh-Turkish University , Turkestan, Kazakhstan
| | - Selma Usluca
- Microbiology Reference Laboratories and Biological Products Department, National Parasitology Reference Laboratory , Ankara, Turkey
| | - Nilüfer Yeşilırmak
- Department of Ophthalmology, School of Medicine, Yıldırım Beyazıt University , Ankara, Turkey
| | | | - Sidre Erganiş
- Departments of Medical Microbiology, School of Medicine, Gazi University , Ankara, Turkey
| | | | - Funda Dogruman-Al
- Departments of Medical Microbiology, School of Medicine, Gazi University , Ankara, Turkey
| | - Kamil Bilgihan
- Departments of Ophthalmology, Gazi University , Ankara, Turkey
| |
Collapse
|
4
|
Usluca S, Babur C, Kurtcebe Ö, Topluoğlu S, Kılıç S. Evaluation of Malaria Blood Smears Sent to National Malaria Reference Laboratory. Turkiye Parazitol Derg 2019; 43:165-169. [PMID: 31865650 DOI: 10.4274/tpd.galenos.2019.6410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
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.
Collapse
Affiliation(s)
- Selma Usluca
- General Directorate of Public Health, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
| | - Cahit Babur
- General Directorate of Public Health, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
| | - Özlem Kurtcebe
- General Directorate of Public Health, Department of Zoonotic and Vector-borne Diseases, Ankara, Turkey
| | - Seher Topluoğlu
- General Directorate of Public Health, Department of Zoonotic and Vector-borne Diseases, Ankara, Turkey
| | - Selçuk Kılıç
- General Directorate of Public Health, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
| |
Collapse
|
5
|
Usluca S, Çelebi B, Babür C. [Method Verification of Inhouse Real-time Polymerase Chain Reaction for Detection of Toxoplasma gondii]. MIKROBIYOL BUL 2019; 53:442-450. [PMID: 31709941 DOI: 10.5578/mb.68415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
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.
Collapse
Affiliation(s)
- Selma Usluca
- General Directorate of Public Health, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
| | - Bekir Çelebi
- General Directorate of Public Health, Department of Zoonotic and Vectorial Diseases, Ankara, Turkey
| | - Cahit Babür
- General Directorate of Public Health, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
| |
Collapse
|
6
|
Usluca S, Celebi B, Karasartova D, Gureser AS, Matur F, Oktem MA, Sozen M, Karatas A, Babur C, Mumcuoglu KY, Taylan Ozkan A. Molecular Survey of Babesia microti (Aconoidasida: Piroplasmida) in Wild Rodents in Turkey. J Med Entomol 2019; 56:1605-1609. [PMID: 31143936 DOI: 10.1093/jme/tjz084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Indexed: 06/09/2023]
Abstract
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.
Collapse
Affiliation(s)
- Selma Usluca
- General Directorate of Public Health, Microbiology Reference Laboratories and Biological Products Department, Ankara, Turkey
| | - Bekir Celebi
- General Directorate of Public Health Department of Zoonotic and Vectorial Diseases, Ankara, Turkey
| | - Djursun Karasartova
- Department of Microbiology, Hitit University, Faculty of Medicine, Corum, Turkey
| | - A Semra Gureser
- Department of Microbiology, Hitit University, Faculty of Medicine, Corum, Turkey
| | - Ferhat Matur
- Biology Department, Dokuz Eylul University, Faculty of Science, Izmir, Turkey
| | - M Ali Oktem
- Department of Microbiology and Clinical Microbiology, Dokuz Eylul University, Faculty of Medicine, Izmir, Turkey
| | - Mustafa Sozen
- Biology Department, Zonguldak Bulent Ecevit University, Faculty of Science, Zonguldak, Turkey
| | - Ahmet Karatas
- Biology Department, Nigde Omer Halisdemir University, Faculty of Science, Nigde, Turkey
| | - Cahit Babur
- General Directorate of Public Health, Microbiology Reference Laboratories and Biological Products Department, Ankara, Turkey
| | - Kosta Y Mumcuoglu
- Department of Microbiology and Molecular Genetics, Parasitology Unit, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Aysegul Taylan Ozkan
- Department of Microbiology, Hitit University, Faculty of Medicine, Corum, Turkey
| |
Collapse
|
7
|
Karasartova D, Gureser AS, Gokce T, Celebi B, Yapar D, Keskin A, Celik S, Ece Y, Erenler AK, Usluca S, Mumcuoglu KY, Taylan-Ozkan A. Bacterial and protozoal pathogens found in ticks collected from humans in Corum province of Turkey. PLoS Negl Trop Dis 2018; 12:e0006395. [PMID: 29649265 PMCID: PMC5916866 DOI: 10.1371/journal.pntd.0006395] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 04/24/2018] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
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. Ticks are important vectors for different kind of pathogens, both of medical and veterinary importance, while tick-borne diseases (TBDs) are increasing all over the world. In Turkey, many important human and zoonotic TBDs such as, Lyme borreliosis, rickettsiosis, anaplasmosis, ehrlichiosis, tularemia, bartonellosis, babesiosis, theileriosis, and hepatozoonosis have been reported. Nonetheless, there is lack of research-based information concerning the epidemiology, ecology, and vector diversity of these tick-borne pathogens. In this study, we aimed to investigate broad-range bacterial and protozoan vector-borne pathogens by PCR/RT-PCR and sequencing, those ticks infesting humans in the Corum province. Spotted fever group rickettsiae and lymphangitis-associated rickettsiae, Borrelia afzelii, Anaplasma spp., Ehrlichia spp. were detected. Babesia microti was detected in Hyalomma marginatum infesting humans. Interestingly zoonotic pathogens like Babesia ovis, Babesia occultans, Theileria spp, Hepatozoon felis, Hepatozoon canis, and Hemolivia mauritanica were also detected, showing the role of ticks for diseases also of veterinary importance. This study provides important data for understanding the epidemiology of tick-borne pathogens and it is hoped that these results will challenge clinicians and veterinarians to unify their efforts in the management of TBDs.
Collapse
Affiliation(s)
| | | | - Tuncay Gokce
- Department of Biology, Faculty of Arts and Science, Hitit University, Corum, Turkey
| | - Bekir Celebi
- National High Risk Pathogens Reference Laboratory, Public Health Institution of Turkey, Ankara, Turkey
| | - Derya Yapar
- Department of Infectious Diseases and Clinical Microbiology, Hitit University, Corum, Turkey
| | - Adem Keskin
- Department of Biology, Faculty of Science and Arts, Gaziosmanpasa University, Tokat, Turkey
| | - Selim Celik
- Emergency Medicine, Hitit University Corum Training and Research Hospital, Corum, Turkey
| | - Yasemin Ece
- Emergency Medicine, Hitit University Corum Training and Research Hospital, Corum, Turkey
| | - Ali Kemal Erenler
- Department of Emergency Medicine, Faculty of Medicine; Hitit University, Corum, Turkey
| | - Selma Usluca
- National Parasitology Reference Laboratory, Public Health Institution of Turkey, Ankara, Turkey
| | - Kosta Y. Mumcuoglu
- Parasitology Unit, Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Aysegul Taylan-Ozkan
- Department of Medical Microbiology, Hitit University, Corum, Turkey
- Department of Medical and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia, Northern Cyprus
- * E-mail:
| |
Collapse
|
8
|
Sonmez C, Usluca S, Hakki Usluca I, Kalipci I, Sezen F, Resat Atalay C, Kilic S. Evaluation of Symptomatic Patients with Resistant Discharge. Acta Dermatovenerol Croat 2018; 26:1-7. [PMID: 29782292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
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.
Collapse
Affiliation(s)
- Cemile Sonmez
- Cemile Sonmez , PhD, Public Health General Directorate Ministry of Health, Adnan Saygun Street No: 55 , Sihhiye Ankara, Turkey;
| | | | | | | | | | | | | |
Collapse
|
9
|
Taylan-Ozkan A, Yasa-Duru S, Usluca S, Lysen C, Ye J, Roellig DM, Feng Y, Xiao L. Cryptosporidium species and Cryptosporidium parvum subtypes in dairy calves and goat kids reared under traditional farming systems in Turkey. Exp Parasitol 2016; 170:16-20. [PMID: 27373430 DOI: 10.1016/j.exppara.2016.06.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
Abstract
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.
Collapse
Affiliation(s)
- Aysegul Taylan-Ozkan
- Department of Medical Microbiology, Faculty of Medicine, Hitit University, Corum 19200, Turkey
| | - Sibel Yasa-Duru
- Department of Internal Medicine, Faculty of Veterinary Medicine, Kirikkale University, Kirikkale 71450, Turkey
| | - Selma Usluca
- National Parasitology Laboratory, Turkish National Public Health Agency, Ankara 16100, Turkey
| | - Colleen Lysen
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Jianbin Ye
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30329, USA; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Dawn M Roellig
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Yaoyu Feng
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Lihua Xiao
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30329, USA
| |
Collapse
|
10
|
Abstract
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.
Collapse
Affiliation(s)
- Selma Usluca
- Department of Parasitology, Dokuz Eylül University, İzmir, Turkey
| | | | | | | |
Collapse
|
11
|
Inceboz T, Usluca S, Over L, Yalcin G, Tuncay S, Ozkoc S. The Epidemiology Research of Blastocystis hominis in the Dokuz Eylül University Medical Faculty Hospital between 2005 and 2009. TurkiyeParazitolDerg 2011; 35:72-6. [DOI: 10.5152/tpd.2011.19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
12
|
Usluca S, Aksoy U. [Microsporidium spp. infection in an immunocompromised child diagnosed by polymerase chain reaction]. MIKROBIYOL BUL 2010; 44:679-683. [PMID: 21063982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
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.
Collapse
Affiliation(s)
- Selma Usluca
- Dokuz Eylül Üniversitesi Tıp Fakültesi, Parazitoloji Anabilim Dalı, İzmir, Türkiye.
| | | |
Collapse
|
13
|
Usluca S, Inceboz T, Over L, Tuncay S, Yalçin G, Arcak SS, Ozkoç S, Aksoy U, Akisü C. [The distribution of intestinal parasites detected in The Dokuz Eylul University Medical Faculty Hospital between 2005 and 2008.]. Turkiye Parazitol Derg 2010; 34:27-31. [PMID: 20340084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
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.
Collapse
Affiliation(s)
- Selma Usluca
- Dokuz Eylül Universitesi Tip Fakültesi Parazitoloji Anabilim Dali, Inciralti, Izmir, Türkiye
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Aksoy U, Ozdemir MH, Usluca S, Toprak Ergönen A. [Biosafety profile of laboratory workers at three education hospitals in Izmir, Turkey]. MIKROBIYOL BUL 2008; 42:469-476. [PMID: 18822891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
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.
Collapse
Affiliation(s)
- Umit Aksoy
- Dokuz Eylül Universitesi Tip Fakültesi, Parazitoloji Anabilim Dali, Izmir.
| | | | | | | |
Collapse
|
15
|
Aksoy U, Akisü C, Bayram-Delibaş S, Ozkoç S, Sahin S, Usluca S. Demographic status and prevalence of intestinal parasitic infections in schoolchildren in Izmir, Turkey. Turk J Pediatr 2007; 49:278-282. [PMID: 17990581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
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).
Collapse
Affiliation(s)
- Umit Aksoy
- Department of Parasitology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | | | | | | | | | | |
Collapse
|
16
|
Aksoy U, Akisu C, Sahin S, Usluca S, Yalcin G, Kuralay F, Oral AM. First reported waterborne outbreak of cryptosporidiosis with Cyclospora co-infection in Turkey. ACTA ACUST UNITED AC 2007; 12:E070215.4. [PMID: 17370959 DOI: 10.2807/esw.12.07.03142-en] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In September 2005, an outbreak of cryptosporidiosis with co-infection of Cyclospora occurred in western Turkey, in a village about 25 kilometres from Izmir, the country’s third largest city.
Collapse
Affiliation(s)
- U Aksoy
- Department of Parasitology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey.
| | | | | | | | | | | | | |
Collapse
|
17
|
Tuncay S, Inceboz T, Over L, Yalçin G, Usluca S, Sahin S, Delibaş SB, Aksoy U. [The evaluation of the techniques used for diagnosis of Entamoeba histolytica in stool specimens]. Turkiye Parazitol Derg 2007; 31:188-193. [PMID: 17918056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
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.
Collapse
Affiliation(s)
- Sema Tuncay
- Dokuz Eylül Universitesi Tip Fakültesi, Parazitoloji Anabilim Dali, Izmir, Turkey
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Abstract
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.
Collapse
Affiliation(s)
- Samil Hizli
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Faculty of Medicine, Dokuz Eylül University, Izmir 35350, Turkey.
| | | | | | | | | | | | | |
Collapse
|
19
|
Usluca S, Yalçin G, Over L, Tuncay S, Sahin S, Inceboz T, Aksoy U. [The distribution of intestinal parasites detected in the Dokuz Eylul University Medical Faculty Hospital between 2003 and 2004]. Turkiye Parazitol Derg 2006; 30:308-12. [PMID: 17309035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
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.
Collapse
Affiliation(s)
- Selma Usluca
- Dokuz Eylül Universitesi Tip Fakültesi Parazitoloji Anabilim Dali, Inciralti, Izmir, Turkey
| | | | | | | | | | | | | |
Collapse
|