Genotyping and Identification of Antigen B Gene Polymorphism of Echinococcus granulosus in Edirne, Thrace, and the First Report of Genotype G2 (Tasmanian Sheep Strain) in Turkey

Background: Echinococcus granulosus is the causative agent of cystic echinococcosis in humans and livestock. It is common worldwide. Cystic echinococcosis is still an important public health problem in Turkey, which is an endemic region. Aims: To genotype Echinococcus granulosus isolates and investigate antigen B gene polymorphism in Thrace, Turkey. Study Design: A cross-sectional study. Methods: Seventy-five hydatid cyst materials obtained between June 2020 and May 2021 were included in the study. Hydatid cyst materials were collected from 12 humans from various hospitals in Edirne and 63 from slaughterhouse animals during the same period. Cyst materials were localized in 8 livers and 4 lungs in humans, 23 livers and 17 lungs in cattle, and 13 livers and 10 lungs in sheep. In the first step, the 12S ribosomal RNA gene was amplified by polymerase chain reaction for all samples and run on an agarose gel. Band patterns were used for strain typing. Then, the selected samples that represented each of the band patterns obtained by single-strand conformation polymorphism analysis were sequenced for AgB1, AgB2, mt-CO1, and mt-ND1 genes. Results: Three different genotypes in Edirne, Thrace, Turkey, were observed for Echinococcus granulosus: G1 (domestic sheep strain), G2 (Tasmanian sheep strain), and G3 (buffalo strain). G1 was the dominant genotype in Edirne, and G3 was the second most common. Additionally, polymorphism in AgB1 and AgB2 gene regions was found. Conclusion: This study is the first to report on Echinococcus granulosus G2 (Tasmania sheep strain) in Turkey and G3 (buffalo strain) and antigen B polymorphism in Thrace. The study results will contribute to the prevention and control programs for cystic echinococcosis in Turkey and worldwide.

Case of Prolonged Viral Shedding: Chronic, Intermittan COVID-19?

COVID-19 is a pandemic that has been affecting the entire world and has caused the death of approximately 2.8 million people. Although the duration of viral shedding varies, an average of 7-10 days is accepted. It is still unclear whether prolonged viral shedding means prolonged contagious period and whether COVID-19 will become chronic or not. This article presents a case with hematological malignancy (lymphoma) with the longest polymerase chain reaction positivity that we could find in the literature (110 days in total).

[A case of Infective Endocarditis Caused by Pseudoclavibacter species]. / Pseudoclavibacter spp.'nin Etken Oldugu Enfektif Endokardit Olgusu.

Infective endocarditis is an infectious disease usually caused by bacteria, including streptococci, staphylococci, and enterococci. In this report, a case of infective endocarditis in which Pseudoclavibacter spp. detected as the causative agent was presented. A 66-year-old female patient was admitted to our hospital with weight loss, malaise, and lumbar pain. A 2/6 murmur was detected in the physical examination of the patient, who had a history of mitral valve surgery nine years earlier. Blood sample was collected for culture and vancomycin [1 g/24 hours, intravenously (IV)] and gentamicin (80 mg/8 hours, IV) therapy were started. Gram-positive bacilli were detected on the second day of incubation in the blood culture bottle incubated in the BacT/ALERT 3D microbial detection system (bioMerieux, France). High uptake in the focal area of the mitral valve on positron emission tomography-computerized tomography (PET-CT) was interpreted as infective endocarditis. The patient was considered to be at very high risk for surgery and she was discharged after the vancomycin treatment completed for 42 days. For bacterial identification, DNA was isolated using a commercial kit (Invitrogen PureLink Genomic DNA Mini Kit; ThermoFisher Scientific, Waltham, MA, USA), and the 16S rRNA gene was amplified by a polymerase chain reaction (PCR) assay using universal primers 27F and 1492R. Sequence analysis of the PCR product was carried out on an Applied Biosystems 3730XL DNA Analyzer with an Applied Biosystems BigDye Terminator v3.1 Cycle Sequencing Kit (ThermoFisher Scientific, Waltham, MA, USA). A 1366 bp long sequence of the isolate was analyzed using the Basic Local Alignment Search Tool (BLAST) in GenBank and the sequence was 99% compatible with Gulosibacter spp. (GenBank sequence ID: LR884222.1, identity 1365/1366 bp) and Pseudoclavibacter spp. (GenBank sequence ID: FJ375951.1, identity 1364/1366 bp). Upon the negative result of nitrate reduction test of bacterium that was oxidasepositive, the bacterium was considered as Pseudoclavibacter spp. Linezolid, clindamycin, and tetracycline susceptibilities were determined by using the disc diffusion method. The isolate was susceptible to linezolid and resistant to clindamycin and tetracycline. It was also susceptible to penicillin [minimum inhibitory concentration (MIC) = 0.002 µg/ml], vancomycin (MIC= 0.25 µg/ml), and rifampicin (MIC= 0.003 µg/ml) and was categorized as "susceptible, increased exposure" to ciprofloxacin (MIC= 0.25 µg/ml), as determined by using a gradient strip test. Pseudoclavibacter species are non-spore-forming, non-motile, catalase-positive, aerobic gram-positive bacilli belonging to the Microbacteriaceae family. A limited number of clinical cases due to Pseudoclavibacter species have been reported. In the present case, gram-positive bacilli were considered to be the causative agent of infective endocarditis because of the growth of the same bacteria in six bottles of blood cultures taken at different times and increased focal involvement on PET-CT. To our knowledge, this is the second reported case of infective endocarditis due to Pseudoclavibacter species. In conclusion, in cases of clinical compliance in patients with prosthetic heart valves, gram-positive bacilli should be considered causative agents of infective endocarditis and in such cases, a range of microbiological assays should be used for identification.

Serological Follow-up of Human Cystic Echinococcosis in the Thrace Region, Turkey.

Background: Parasites of the genus Echinococcus are common worldwide and are important cestodes that cause serious infections in humans and animals. This retrospective study evaluated the indirect hemagglutination (IHA) test results of serum samples obtained from patients with a pre-diagnosis of cystic echinococcosis (CE) within ten years. In addition, the role of the IHA test results of the patients in the follow-up of the treatment and determining possible recurrences was investigated. Methods: The IHA test results of 2426 serum samples of patients with a pre-diagnosed CE admitted to Trakya University Health Center for Medical Research and Practice in Edirne, Turkey, between January 2011 and December 2020 were evaluated retrospectively. The data of 53 patients with CE who had medical treatment and/or postoperative follow-up serological records were evaluated. Results: Of 2426 IHA tests, 376 (15.5%) were seropositive, and 2050 (84.5%) were seronegative. It was determined that 376 serum samples detected as positive belonged to 207 patients with CE. Of 207 CE patients, 109 (52.7%) were female and 98 (47.3%) were male. The most common organ involvement was the liver in 186 (89.9%) cases. Of 53 patients, 16 were considered relapse cases. The median follow-up period for 16 recurrent cases was 31.8 (1-77) months. Our results showed a statistically significant correlation between long-term serological follow-up and recurrence detection (P=0.034). Conclusion: Long-term serological follow-up after treatment is considered useful in determining possible recurrent cases. CE is an important public health problem for endemic regions, including our country, and we think our study results will contribute to the status and follow-up of the disease.

[A rarely isolated bacterium in microbiology laboratories: Streptococcus uberis]. / Mikrobiyoloji laboratuvarlarinda nadir izole edilen bir etken: Streptococcus uberis.

Streptococcus uberis is a gram-positive bacterium that is mostly responsible for mastitis in cattle. The bacterium rarely has been associated with human infections. Conventional phenotyphic methods can be inadequate for the identification of S.uberis; and in microbiology laboratories S.uberis is confused with the other streptococci and enterococci isolates. Recently, molecular methods are recommended for the accurate identification of S.uberis isolates. The aim of this report is to present a lower respiratory tract infection case caused by S.uberis and the microbiological methods for identification of this bacterium. A 66-year-old male patient with squamous cell lung cancer who received radiotherapy was admitted in our hospital for the control. According to the chest X-Ray, patient was hospitalized with the prediagnosis of ''cavitary tumor, pulmonary abscess''. In the first day of the hospitalization, blood and sputum cultures were drawn. Blood culture was negative, however, Candida albicans was isolated in the sputum culture and it was estimated to be due to oral lesions. After two weeks from the hospitalization, sputum sample was taken from the patient since he had abnormal respiratory sounds and cough complaint. In the Gram stained smear of the sputum there were abundant leucocytes and gram-positive cocci, and S.uberis was isolated in both 5% sheep blood and chocolate agar media. Bacterial identification and antibiotic susceptibility tests were performed by VITEK 2 (Biomerieux, France) and also, the bacterium was identified by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) based VITEK MS system as S.uberis. The isolate was determined susceptible to ampicillin, erythromycin, clindamycin, levofloxacin, linezolid, penicillin, cefotaxime, ceftriaxone, tetracycline and vancomycin. 16S, 23S ribosomal RNA and 16S-23S intergenic spacer gene regions were amplified with specific primers and partial DNA sequence analysis of 16S rRNA polymerase chain reaction (PCR) products were performed by 3500xL Genetic Analyzer (Applied Biosystems, USA). According to the partial 16S rRNA gene sequencing results, bacterium was confirmed as S.uberis. This report makes a significant contribution to the number of case reports of human infections caused by S.uberis as the identification was performed by current microbiological methods in our case. In conclusion, S.uberis should be evaluated as an opportunistic pathogen among the immunosuppressed patients and in addition to phenotypic bacteriological methods, the other recent microbiological methods should also be utilized for the identification.

Molecular Characterization of Human and Animal Isolates of Echinococcus granulosus in the Thrace Region, Turkey.

OBJECTIVE: Echinococcus granulosus is the causative agent of cystic echinococcosis in humans and many domestic animals, and remains an important global health problem. The aim of this study was to genotype E. granulosus isolates obtained from humans and animals in the Thrace Region of Turkey. MATERIAL AND METHODS: A total of 58 isolates were obtained from patients who underwent surgery at several hospitals and from animals at a slaughterhouse in the province of Edirne. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of ribosomal internal transcribed spacer 1 fragments, and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) of the partial mitochondrial NADH dehydrogenase subunit 1 (ND1) gene, was used to characterize human and animal E. granulosus isolates. To investigate the genetic characteristics of isolates, deoxyribonucleic acid (DNA) sequencing of the mitochondrial cytochrome c oxidase subunit 1 (CO1) and ND1 genes was performed. RESULTS: Fifty-eight E. granulosus isolates, including 42 from human, 13 from cattle and 3 from sheep were, analyzed. The results indicated two distinct genotypes: the G1 (sheep strain) and G7 (pig strain) genotypes. The sheep strain was shown to be the most common genotype of E. granulosus affecting humans, sheep and cattle. Among the concatenated partial CO1 and ND1 sequence data, eight haplotypes of Echinococcus species were identified in the present study. CONCLUSION: This is the first report indicating that the E. granulosus pig strain is present in humans in this region. We suggest that new strategies be designed for E. granulosus control programs in Turkey.

[Antifungal susceptibilities of Aspergillus spp. strains isolated from invasive aspergillosis cases]. / Invazif aspergillozlu olgulardan izole edilen Aspergillus spp. suslarinin antifungal duyarliliklari.

Aspergillus species found abundantly in the outer environment and hospital setting may lead to serious morbidity and mortality particularly in patients with suppressed immunity. This retrospective study was aimed to investigate the antifungal susceptibilities of Aspergillus spp. isolated from aspergillosis cases being hospitalized. Aspergillus spp. isolated from samples of the patients with suspected fungal infections between January of 2002 and October of 2007, were investigated. A total of 678 samples (420 lower respiratory tract, 202 sterile body fluids, and 56 biopsy/tissue specimens) from 569 patients were included in the study. The samples were incubated in 25 degrees C and 35 degrees C on brain-heart-infusion agar supplemented with blood and on Sabouraud dextrose agar. Gram and Giemsa stained samples were also examined by microscopy. Mold type of fungi were identified by conventional techniques. "Invasive aspergillosis" was described according to criteria of Invasive Fungal Infections Cooperative Group of the European Organization for Research and Treatment of Cancer. A. fumigatus (n = 8), A. flavus (n = 2) and A. niger (n = 2) were isolated from 12 patients' samples (2.1%), 9 of them were lower respiratory tract and one of each was ascid, brain biopsy and pleural fluid specimens. All of those patients have had an underlying diseases such as malignancy. The susceptibility of the isolates to caspofungin, voriconazole, itraconazole and amphotericin B was tested by broth microdilution susceptibility testing and to posaconazole by E-test (AB Biodisk, Sweden). The lowest minimum inhibitory concentration (MIC) (< or = 0.125 microg/ml) values were detected for caspofungin and posaconazole for Aspergillus spp., however, the highest MIC values were detected for amphotericin B (> 1 microg/ml). MIC values of the all strains except one, were detected as < or = 0.5 microg/ml for voriconazole and itraconazole. In one A. niger strain itraconazole MIC value was 2 microg/ml. Since the number of other species was low, MIC50 value was determined only for A. fumigatus strains and it was found that the highest MIC50 value was for amphotericin B (2 microg/ml) and the lowest MIC50 values were for posaconazole (0.064 microg/ml), caspofungin (0.064 microg/ml), itraconazol (0.25 microg/ml) and voriconazol (0.25 microg/ml). Since caspofungin and posaconazole revealed the lowest MIC values, they should be taken into consideration in choice of therapy of aspergillosis cases in our hospital.