[Investigation of Efflux Pump Genes in Resistant Mycobacterium tuberculosis Complex Clinical Isolates Exposed to First Line Antituberculosis Drugs and Verapamil Combination]. / Birinci Seçenek Antitüberküloz Ilaçlara ve Verapamil Kombinasyonuna Maruz Birakilan Dirençli Mycobacterium tuberculosis Kompleks Klinik Izolatlarindaki Efluks Pompa Genlerinin Arastirilmasi.

Tuberculosis (TB) is caused by Mycobacterium tuberculosis, still one of the most common life-threatening infectious diseases worldwide. Although drug resistance in M.tuberculosis is mainly due to spontaneous chromosomal mutations in genes encoding drug target or drug activating enzymes, the resistance cannot be explained only by these mutations. Low permeability of the cell wall, drug inactivating enzymes and especially efflux pumps (EPs) are other mechanisms of drug resistance in mycobacteria. Efflux pump inhibitors (EPIs) binding to M.tuberculosis EPs were shown to inhibit efflux of anti-TB drugs, to enhance M.tuberculosis killing, to reduce drug resistance and to produce synergistic effects with first line anti-TB drugs. In this study, we aimed to determine the minimum inhibitory concentration (MIC) of first-line anti-TB drugs in the presence of verapamil (VER) and the expression of 21 putative EP genes belonged to the ATP-binding cassette (ABC), major facilitator superfamily (MFS) and resistance-nodulation-division (RND) families which might have caused the resistance in nine M.tuberculosis complex clinical isolates resistant to all of the first line anti-TB drugs. MIC values of the isolates were determined in 96-well U-bottom plates by the resazurin microtiter test (REMA) method based on the color change principle. According to the determined MIC values of each isolate, freshly grown cultures in Middlebrook 7H9 broth were exposed to first-line anti-TB drugs and MIC of first-line anti-TB drugs in the presence of VER (½ MIC) at 37°C for 48 hours for RNA extraction. The non-drug exposed cultures were used as control. Total RNA was extracted using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) and then treated with DNase I (Thermo Fischer Scientific Inc., Waltham, MA). Complementary DNA (cDNA) from the extracted RNAs was synthesized with the "First strand cDNA synthesis kit" (Thermo Fischer Scientific Inc., Waltham, MA) using oligo primers. The expression levels of efflux pump genes by quantitative realtime polymerase chain reaction (qRt-PCR) were performed using the QuantiTect SYBR Green Rt-PCR Kit (Qiagen, Germany). The housekeeping sigma factor gene sigA (Rv2703) was used as internal control in qRt­PCR assays. Relative quantification of the clinical isolates was determined by the 2-∆∆Ct method by comparing the expression levels of efflux genes in cultures exposed to primary anti-TB drugs and VER with those of non-drug exposed cultures. MIC values of nine isolates by REMA method was determined between 32-512 µg/mL, 1-128 µg/mL, 2-32 µg/mL, 4-16 µg/mL and 15.62-250 µg/mL for streptomycin (SM), isoniazid (INH), rifampicin (RIF), ethambutol (EMB) and VER, respectively. In the presence of ½ MIC VER, it was determined that the MIC of SM decreased 2-32 fold in eight isolates, the MIC of INH decreased by 2-8 fold in nine isolates, the MIC of RIF decreased by 2-16 fold in eight isolates, and the MIC of EMB decreased 2-4 fold in only five isolates. There was an increase in the expression of Rv1273c, Rv1456c, Rv1457 and Rv1819 efflux pump genes from the ABC family, Rv1634 and Rv0842 from the MFS family and Rv3823 efflux from the RND family in isolates exposed to ½ MIC of first-line anti-TB drugs stress. Rv1456c and Rv1819 were found to be associated with SM resistance, Rv1273c with EMB resistance, Rv1457, Rv0842 and Rv3823 with both RIF and EMB resistance, and Rv1634 with INH, RIF and EMB resistance. It was determined that there was a decrease in the expression levels of eight efflux pump genes from the ABC family (Rv1456c, Rv1457c, Rv1458c, Rv0194, Rv1272c, Rv1686c, Rv1687c, Rv1819c), six from MFS family (Rv0842, Rv0849, Rv1634, Rv2265, Rv2456c, Rv0876c) and two from RND family (Rv0507, Rv0676c) in isolates exposed to MIC of first-line anti-TB drugs in the presence of VER (½ MIC). Further studies with clinical isolates are needed to investigate the EPIs that can be used in alternative therapy and to determine the contribution of EPs to the development of resistance due to the increasing TB resistance.

[The Mutations on embA, embB and embC Gene Region in Ethambutol-Resistant and Susceptible Clinical Mycobacterium tuberculosis Complex Isolates]. / Etambutole Dirençli ve Duyarli Mycobacterium tuberculosis Kompleksi Klinik Izolatlarinda embA, embB ve embC Gen Bölgesi Mutasyonlari.

Ethambutol (EMB) is one of the first-line drugs used in the standard combination therapy for tuberculosis (TB) caused by Mycobacterium tuberculosis complex (MTC), and resistance to drugs that play a key role in treatment is increasing worldwide. Mutations in the embCAB operon that have been confirmed to be associated with resistance are responsible for EMB resistance. In this study, it was aimed to determine the frequency and patterns of mutations in embA, embB and embC gene regions in clinical MTC isolates found to be phenotypically resistant and susceptible to EMB. A total of 64 MTC isolates, 44 of resistant to EMB and 20 of susceptible to EMB, isoniazid, rifampicin, and streptomycin by conventional phenotypic drug susceptibility test, were included in the study. Following the DNA isolation, embA, embB and embC gene regions associated with EMB resistance were amplified with specific primer sequences. The PCR products were cycle sequenced using the Bigdye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems, USA) and electrophoretically separated on the ABI PRISM 3130XL Genetic Analyzer (Applied Biosystems, USA). Mutated gene regions were identified by aligning sequence analysis data in multiple sequence analysis programs. In the study, genomic mutations in the embCAB operon were detected in 68.2% (30/44) of the EMB resistant isolates. Mutations in the embB gene region were detected in 66% (29/44) of the resistant isolates, 76% (22/29) of these mutations were at codon 306 and the most common mutation patterns in this codon were determined as ATG→GTG (M306V; 58.6%; 17/29), ATG→ATA, ATC or ATT (M306I; 17.2%; 5/29). Other mutations in the embB gene region were determined as Y334H (3.4%; 1/29), D354A (6.9%; 2/29), E378A (3.4%; 1/29), G406C (3.4%; 1/29), M423I (3.4%; 1/29) and E521A (3.4%; 1/29). Of the 44 EMB-resistant isolates, mutations were detected in one (2.3%) of the isolate in the embA gene region (L330L) and in two (4.5%) of the isolates in the embC gene region (T270I in one isolate and T270I and E305E in the other isolate). Of the phenotypically EMB susceptible isolates, mutation was detected in only one (5%) of the isolates in the embA gene region (E180G). In our study, it was determined that mutations frequently occur in codon 306 of the embB gene in EMB-resistant MTC isolates and this mutation has a potential role in the development of EMB resistance. However, it was concluded that the absence of mutations does not exclude phenotypic EMB resistance. Our results will shed light on the molecular epidemiology of embCAB operon mutations that cause EMB resistance in our country.

Possible relation between expression of circulating microRNA and plasma cytokine levels in cases of pulmonary tuberculosis.

INTRODUCTION: Tuberculosis (TB) is a life-threatening infection and early diagnosis is critical for treatment and prevention of transmission. There is evidence of correlation between miRNA expression and cytokine regulation during TB infection. The aim of this study was to determine the relationship between expression levels of miRNAs in plasma and cytokine levels as a potential biomarker for genetic predisposition and/or early diagnosis of TB infection. METHODOLOGY: The expression levels of 86 miRNAs were examined in plasma samples of 44 TB patients and 44 healthy controls by qRT-PCR using BioMarkTM 96.96 Dynamic Array (Fluidigm Corporation, South San Francisco, CA, USA) system. The levels of plasma TNF-α, IFN-γ, IL-1ß, IL-4, IL-6, IL-8, IL-10, and IL-12/P40 were examined with ELISA. RESULTS: We identified dysregulation of 18 miRNAs which included upregulation of miR-1, miR-7-5p, miR-9-5p, miR-10a-5p, miR-10b-5p, miR-100-5p, miR-106b-5p, miR-128-3p, miR-133a-3p, miR-143-3p, miR-193a-5p, miR-200b-3p, miR-205-5p, miR-210-3p, and miR-296-5p, and downregulation of miR-15b-5p, miR-16-5p, and miR-25-3p in plasma samples of patients with pulmonary TB (p < 0.05). A significant correlation between the expression levels of miR-1, miR-7-5p, miR-9-5p, miR-10a-5p, miR-10b-5p, miR-15b-5p, miR-100-5p, miR-143-3p, miR-193a-5p, miR-200b-3p, miR-210-3p and cytokine levels of TNF-α, IFN-γ, IL-1ß, IL-8 and IL-10 was identified (p < 0.05). CONCLUSIONS: We demonstrated that altered expression levels of plasma miRNAs consistent with immunological response have the potential to serve as non-invasive biomarkers for early diagnosis of pulmonary TB. Additional investigations with larger sample sizes will be required to confirm our findings and to determine if miRNAs can be possible targets for TB management strategies.

[Investigation of pncA, rpsA and panD Gene Mutations Associated with Resistance in Pyrazinamide-Resistant Mycobacterium tuberculosis Isolates and Spoligotyping]. / Pirazinamid Dirençli Mycobacterium tuberculosis Izolatlarinda Direnç ile Iliskili pncA, rpsA ve panD Gen Mutasyonlari ve Spoligotiplerin Arastirilmasi.

Pyrazinamide (PZA) is one of the first-line anti-tuberculous drugs used in the treatment of tuberculosis (TB). Considering the ability of PZA to shorten the treatment period from 9-12 months to six months by eliminating persistent bacilli, it appears to be an important cornerstone of TB therapy. While the main mechanism causing the PZA resistance is pncA mutations at a rate of 70-97%, it has been determined that rpsA and panD mutations can also cause resistance. In this study, we aimed to investigate the pncA, rpsA and panD gene mutations, the efficiency of the pyrazinamidase (PZAse) enzyme test in determining PZA resistance, the drug susceptibility and their families in PZA-resistant Mycobacterium tuberculosis isolates. Totally 46 PZA resistant M.tuberculosis isolates were included in the study. The pncA, rpsA and panD mutations caused by PZA resistance were investigated by in-house PCR followed by DNA sequencing method. Drug susceptibility was determined with Bactec MGIT 960 (Becton Dickinson, USA) system, the presence of PZAse was evaluated by colorimetric PZAse enzyme assay and the families were determined by the spoligotyping method. Of the 46 PZA-resistant isolates, 24 (52.2%) were identified as PZA monoresistant, 11 (23.9%) multidrug resistant (MDR)-TB and 11 (23.9%) poly drug resistant (PDR)-TB. Gene mutations associated with resistance were detected in 73.9% (34) of PZA-resistant M.tuberculosis isolates. The pncA, rpsA and panD mutations were found in 71.7% (33), 28.2% (12) and 4.3% (2) of the isolates, respectively. The coexistence of pncA/rpsA and pncA/panD gene mutations were determined in 12 and two isolates, respectively. The pncA gene mutations were observed in 3 (33.3%) of 9 (19.6%) isolates whose enzyme presence was detected by the colorimetric PZAse test. In the pncA gene, eight different point mutations in the form of missense mutation;A226C (27.3%), A152C (24.2%), C169G (21.2%) A422C (9.1%), G145A (6.1%), A29G (6.1%), A424G (3%) and T464G (3%) were detected. In the rpsA gene, A636C (42.9%) silent and G1318A (42.9%) missense mutations and in the panD gene, C66G (50%) nonsense and A145G (50%) missense mutations were the most common mutations detected. As a result of genotyping of PZA resistant isolates, the most common genotypes were found in T1 cluster with 17 (36.9%) isolates; followed by the families of Beijing with 7 (15.2%) isolates, H3 with 6 (13%) isolates, TUR with 5 (10.9%) isolates, and LAM 9 with 4 (8.7%) isolates, respectively. In addition, 2 (4.3%) isolates belonging to the ORPHAN family and one isolate belonging to each of LAM TUR, LAM 2, LAM 7, T2, T5-RUS1 families were identified. Our study is the first to investigate all pncA, rpsA and panD gene mutations that have been found to cause PZA resistance in Turkey. Epidemiological studies on PZA resistance will make important contributions to the determination of resistance mechanism and the development of methods that will provide rapid diagnosis for the detection of resistance.

[Legionella Species Isolated in the Water Systems of Ships and Their Molecular Characterization]. / Gemilerin Su Sistemlerinden Izole Edilen Legionella Türleri ve Moleküler Karakterizasyonu.

Legionella species are generally found in nature and in water resources, and they are gram negative bacilli that can cause pneumonia by being transmitted from water systems to humans via aerosol or aspiration. Legionnaires' disease caused by this agent continues to be a public health problem in cruise ships. In this study, it was aimed to determine the prevalence of the colonization of Legionella species by culture method and to determine the molecular characterization of the isolated Legionella in water samples taken from the water systems of the ships docking in Mersin International Port. A total of 158 cold water samples were taken from 18 ferry and/or cargo ships docking in Mersin International Port between December 2014 and June 2015. Fifty-four of the samples were obtained from tanks, 68 from taps and 36 from shower heads. All samples were centrifuged and inoculated from the pellet onto "Buffered Coal Yeast Extract" (BCYE) (Oxoid, CM0655, UK) agar medium supplemented with iron pyrophosphate, L-cysteine and α-ketoglutarate (Oxoid, SR0110, UK). The culture plates were incubated for 10-15 days in microaerophilic environment in a desiccator at 37°C. The suspicious colonies grown in cultures were serogrouped by latex agglutination test (Oxoid, DR0800M, UK) and fluorescent antibody method (m-Tech Monoclonal Technologies, Inc., USA). For the molecular analysis of Legionella species grown in culture, DNA isolation was made from Legionella colonies and then polymerase chain reaction amplification was performed using specific primer sequences targeting the rpoB gene region of the Legionella genome. Direct DNA sequencing of rpoB gene products was performed in the "ABI PRISM 3130XL Genetic Analyzer" (Applied Biosystems, USA). The DNA sequences were typed by BLAST analysis and the determined types, and NCBI (National Center for Biotechnology Information) reference Legionella sequences were phylogenetically compared with the Neighbor-Joining comparison method by using the Mega 7 program. Legionella spp. was isolated in 18 (11.4%) of 158 samples. Of these, four (7.4%, 4/54) were detected from the tank, 11 (16.2%, 11/68) from the tap and three (8.33%, 3/36) from the shower head. After the latex agglutination test performed from the growing bacterial colonies, five (27.8%) were serogrouped as Legionella spp., four (22.2%) as Legionella pneumophila sg 5, two (11.1%, each) as L.pneumophila sg 1,L.pneumophila sg 8 and Legionella bozemanii and one (5.6%) as L.pneumophila sg 3. Two (11.1%) of the isolates grown in culture could not be serogrouped. Molecular characterization of 12 Legionella isolates could be performed. One of them was serologically serogrouped as L.bozemanii, and it was found to be 99% similar to Legionella rubrilucens when compared with NCBI Legionella sequence data in the BLAST program. One isolate that could not be differentiated by serogrouping was identified as Legionella erytra in the BLAST program after DNA sequence analysis. The remaining 10 isolates (55.6%, n= 18) were confirmed as L.pneumophilia after the comparison with reference NCBI sequences. In this study, it was determined that 11.4% of the water samples collected from the water systems of the ships docking in Mersin International Port were contaminated with Legionella species. The detected Legionella species have an important potential source of infection for the captain, ship workers and passengers travelling on the ships. In this respect, this study reveals the necessity of establishing studies to improve the risk management of Legionella in the water systems of ships.

[Longitudinal Monitoring of Seroconversion Status in SARS-CoV-2 RT-PCR Positive Healthcare Workers]. / SARS-CoV-2 RT-PCR Pozitif Saglik Çalisanlarinda Serokonversiyon Durumunun Boylamsal Izlenmesi.

The impact of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome 2 (SARS-CoV-2) still continues. The duration of the immune response in individuals recovering from COVID-19 and its protection against future SARS-CoV-2 infection are not fully understood. This study aimed to longitudinally evaluate anti-SARS-CoV-2 seroconversion status in healthcare workers with positive SARS-CoV-2 Real-time reverse transcription polymerase chain reaction (rRT-PCR), test in Mersin University Hospital. A total of 68 healthcare workers with positive SARS-CoV-2 rRT-PCR test between 19 April and 27 November 2020 were included in the study. Blood samples were collected from healthcare workers for SARS-CoV-2 antibody testing in the 1st, 3rd and 5th months following PCR positivity. Healthcare workers were classified as symptomatic, asymptomatic and reinfected according to their clinical findings, and rRT-PCR cycle thresholds (Ct) were recorded. Elecsys Anti-SARS-CoV-2 (Roche Diagnostics, Germany) kit was used for antibody testing. Of the 68 healthcare workers; 46 were classified as symptomatic, 15 as asymptomatic, and seven as reinfected. Twenty-seven (39.7%) of the healthcare workers were male and 41 (60.3%) were female, and the mean age was 36.4 ± 9.04. Seroconversion was detected in 45 (66.2%) of 68 healthcare workers in the study, and only one person had sero-negative result at the end of the 5th month. While seroconversion was detected in 78.3% (n= 36/46) of symptomatic healthcare workers, it was observed in 26.7% (n= 4/15) of the asymptomatic healthcare workers. Seroconversion was detected in only one of the seven reinfected healthcare workers after primary infection. After reinfection, seroconversion was observed in five of seven reinfected healthcare workers. Antibody response was not detected in two of them after both infections. According to the rRT-PCR Ct values; the median of Ct value was found significantly lower in healthcare workers with seroconversion (23.26, IQR= 18.45-27.30), than the ones without seroconversion (36.20, IQR= 33.09-37.56) (p< 0.001). In those who had reinfection, the mean Ct value (31.77 ± 6.62) detected during the primary infection period was statistically higher than the Ct value (22.44 ± 5.54) detected during reinfection (p= 0.008). The most frequently recorded symptoms in healthcare workers were myalgia (57.3%), fatigue (51.5%), headache (51.5%) followed by sore throat (36.7%), fever (33.8%), cough (27.9%), diarrhea (23.5%) and dyspnea (16.2%). In addition, fever (52%) and fatigue (80.6%) were found to be significantly higher in seroconversion-positive healthcare workers than in those without seroconversion (p= 0.028; p= 0.005, respectively). As a result, a higher rate of antibody response was detected in healthcare workers who had symptomatic infection than those who were asymptomatic. It has been observed that patients with asymptomatic primary infection and without antibody response were more susceptible to reinfection. In addition, it was observed that the probability of immune response increased when the viral load increased (Ct value decreased) in symptomatic infections. Although these findings provide important information about the short-term seroconversion status of healthcare personnel; longer-term and larger-scale studies are needed to evaluate the long-term effectiveness of seroconversion and to better understand the effectiveness of the immune response developed after SARS-CoV-2 vaccine administrations.

The Prevalence of Hepatitis E Virus Infection in the Adult Turkish Population: A Systematic Review of the Literature and Prevalence Study in Blood Donors in Mersin Province.

BACKGROUND: The hepatitis E virus (HEV) is an RNA virus that causes acute hepatitis, and can become chronic in immunocompromised patients, though this is rare. The frequency of HEV infection varies, depending on factors such as geographical region, socioeconomic level, and age. Despite limited studies on the adult population in Turkey, there is no current information about HEV frequency in our country. Therefore, we aimed to scrutinize the data found from such studies, in comparison to our own results. METHODS: A total of 900 volunteers who applied to donate blood to the University Hospital Blood Center and accepted the use of their data were enrolled in the study. Serum anti-HEV IgG antibody (Ab) was examined by the enzyme-linked immunosorbent assays method. The donors' location, occupation, and animal contact status were determined. In addition, we evaluated the full text and conference papers (in Turkish or English) of Turkey-based HEV seroprevalence studies from 1990-2020, investigating the adult population. RESULTS: The average age of the 900 volunteers in the study was 35.22 ± 9.60 years, of whom 889 (98.7%) were men. Anti-HEV IgG was positive in 12.8% of the serum samples. The average age of the volunteers who were seropositive was 40.40 ± 9.72 years, and 98.2% were men. No association was found between anti-HEV IgG positivity and occupation, place of residence, and contact with animals. An evaluation of the studies conducted in Turkey reveals that the average HEV infection seroprevalence is 9.52% in the healthy population, and the prevalence is increased in the region of Southeastern Anatolia. Patients with acute hepatitis and hemodialysis also had increased rates. CONCLUSION: The anti-HEV IgG seropositivity rate in healthy blood donors in Mersin province was 12.8%, and was similar to the rates reported earlier in our country. However, this rate, found in a sample of individuals from a healthy society, causes concern about what the frequency may be in sick people. Wide-ranging community screening is needed.

[Comparison of Real Time PCR Cycle Threshold Values in Symptomatic and Asymptomatic COVID-19 Patients]. / Semptomatik ve Asemptomatik COVID-19 Hastalarinda Gerçek Zamanli PCR Döngü Esik Degerlerinin Karsilastirilmasi.

Patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) show different clinical courses ranging from asymptomatic to severe infection requiring intensive care treatment and death. Real-time reverse transcription polymerase chain reaction (rRT-PCR), used in the diagnosis, screening and surveillance of coronavirus-2019 (COVID-19), provides the viral load as a cycle threshold (Ct) value. It has been reported that the Ct value may be related to the course of the infection and the clinical condition of the patient. In this study, it was aimed to compare the Ct and C reactive-protein (CRP) results of symptomatic and asymptomatic patients who were found to be positive with rRT-PCR. Between 14 April and 29 August 2020, a total of 355 patients aged 18 years and older with positive SARS-CoV-2 rRT-PCR test were included in the study. The COVID-19 rRT-PCR test was performed with Bio-speedy SARS-CoV-2 rRT-PCR kit (Bioeksen, Turkey) versions, the kit targeting the RdRp gene region, and the dual gene kit versions targeting the N and ORF1ab gene regions were used. Patients were classified as symptomatic and asymptomatic according to their clinical findings. Ct and CRP results of the patients were analyzed statistically. Of the 355 patients included in the study, 237 (66.7%) were symptomatic and 118 (33.2%) were asymptomatic patients. The mean age of symptomatic patients (46.68 ± 18.03) was observed significantly higher than asymptomatic patients (38.27 ± 13.82) (p<0.001). When the patients are evaluated according to the age groups, the rate of asymptomatic patients was significantly higher in the 21-39 age group, while the rate of symptomatic patients was significantly higher in 65 years and older group (p<0.05). The rate of comorbidity was significantly higher in symptomatic patients (n= 69, 29.1%) than in asymptomatic patients (n= 11, 9.3%) (p<0.001). Hypertension (12.2%), diabetes mellitus (9.7%), chronic respiratory disease (9.3%) and cardiovascular diseases (5.5%) were the most common diseases in symptomatic patients. However, among these, hypertension and chronic respiratory disease were found significantly higher in symptomatic patients (p<0.05). Increased CRP rate in symptomatic patients (64.6%) was found significantly higher than asymptomatic patients (27.3%) (p<0.001). The median of Ct value was found significantly higher in asymptomatic patients (26.34, IQR= 19.78-35.48), than in symptomatic patients (21.77, IQR= 17.81-26.51) (p<0.001). Regarding the medians of Ct values obtained from target genes; RdRp gene Ct value was found significantly higher in asymptomatic patients than in symptomatic patients (p<0.001). However, no statistical difference was found between symptomatic and asymptomatic patients in the ORF1ab and N genes Ct value medians (p> 0.05). As a result, it was observed that SARS-CoV-2 PCR positive patients were symptomatic in the presence of advanced age and comorbidity. Increased CRP value at the time of admission to the hospital was found significantly higher in symptomatic patients. Ct value has been shown to be lower in symptomatic patients, as expected. Although Ct and CRP values are thought to be useful in monitoring the clinical course and prognosis of patients with COVID-19, more detailed studies are needed to prove their clinical value.

[Dihydropteroate Synthase (DHPS) Gene Mutations and Mitochondrial Large Subunit (mtLSU) rRNA Genotype Variations in Pneumocystis jirovecii Strains]. / Pneumocystis jirovecii Izolatlarinin Dihidropteroat Sentaz (DHPS) Gen Mutasyonlari ve Mitokondriyal Büyük Alt Birim (mtLSU) rRNA Genotip Varyasyonlarinin Belirlenmesi.

Pneumocystis jirovecii is an atypical fungus that causes Pneumocystis pneumonia (PCP) in HIV/AIDS and immunocompromised patients. Antibiotics containing sulfa and sulfone groups are widely used in PCP prophylaxis and treatment. Especially, long-term use of trimethoprim sulfamethoxazole (TMP-SMX) is known to cause certain point mutations associated with drug resistance in the P.jirovecii dihydropteroate synthase (DHPS) gene. In addition, DHPS and mitochondrial large subunit (mtLSU) rRNA genotype characterization provides important data on the epidemiology of P.jirovecii. In this study, it was aimed to investigate the DHPS and mtLSU rRNA gene polymorphisms of P.jirovecii strains isolated from immunocompromised patients in Mersin University Hospital. In this study, 16 P.jirovecii positive samples, which isolated from 96 patients samples, between August 2016 and February 2018, were included. P.jirovecii mtLSU rRNA genotypes were determined by sequence analysis according to polymorphisms at the 85th and 248th nucleotide positions. Nested PCR and RFLP method was applied for mutation analysis of DHPS locus, 165th and 171st nucleotide positions. In the DHPS mutation analysis, 12/16 (75%) wild type (W165/W171) and 4/16 (25%) mutant type (M165/W171) were detected. Two mutant types belonged to HIV/AIDS positive patients with PCP and had a history of prophylaxis; the other 2 mutant types belonged to patients with colonization. In the study, a history of prophylaxis in 3 (19%) of the 16 patients were recorded, and mutant type was detected in these 2 of 3 patients. According to mtLSU-rRNA analysis, 3 different genotypes were obtained from 16 P.jirovecii isolates. In our region, genotype 2 (43.75%; n= 7) was the most common genotype, genotype 1 (37.5%; n= 6) was the second common and genotype 3 (18.75%; n= 3) was the least one. Genotype 4 was not detected in our region. When DHPS and mtLSU-rRNA were evaluated as multilocus, five different genotypes were observed. As a result, these findings provided important data on P.jirovecii epidemiology in our region and potential drug-resistant strains showed a risk of transmission in immunosuppressive patients. Multicenter studies involving more P.jirovecii isolates are needed to better define the epidemiology of P.jirovecii in our region and in our country.

[Investigation of Pneumocystis jirovecii Infection and Colonization in Immunocompromised Patients with Pneumonia]. / mmün Sistemi Baskilanmis Pnömonili Hastalarda Pneumocystis jirovecii Enfeksiyon ve Kolonizasyonlarinin Arastirilmasi.

Pneumocystis jirovecii is an atypical fungus that causes P.jirovecii pneumonia (PCP) in immunocompromised patients. Currently, while the incidence of AIDS-related PCP is decreasing, PCP has become more common in HIV-negative immunosuppressive patients as a result of increased diseases requiring immunosuppressive therapy. In this study, it was aimed to investigate PCP and colonizations by microscopy, polymerase chain reaction (PCR) and Krebs von den Lungen-6 (KL-6) tests in symptomatic immunosuppressive inpatients with the sign of radiologically atypical pneumonia in Mersin University Hospital. A total of 96 patients, between August 2016 and February 2018 were included in the study. Seventy two (75%) of the 96 patients were under immunosuppressive therapy. P.jirovecii was investigated in the respiratory tract samples [sputum (n= 88), tracheal aspirate (n= 6) and bronchoalveolar lavage (n= 2)] by mtLSUrRNA nested PCR and microscopic staining methods [immunofluorescence assay (IFA), Toluidine Blue O (TBO)], and KL-6 levels were tested in serum samples. P.jirovecii was detected in 16 (16.7%) samples by PCR, in five (5.2%) samples by IFA, in three (3.1%) samples by TBO stain method. When IFA was taken as a reference test, sensitivity and specificity of TBO and PCR were calculated as 60% and 100%; 100% and 87.9%, respectively. In P.jirovecii PCR positive patients, the distribution of underlying diseases; cancer (n= 6), hematological malignancy (n= 3), HIV/AIDS (n= 3), COPD (n= 2), and interstitial lung disease (n= 2) were found as 11 (68.75%) of the 16 positive patients, received immunosuppressive therapy (HIV positive non-Hodgkin lymphoma); of the 3 (18.75%) patients of were immunocompetent, and only 2 (12.5%) were HIV/AIDS. Five of the 16 PCR positive the patients that have positive microscopic examination were definited PCP [HIV/AIDS (n= 3), lung cancer (n= 1), interstitial lung disease (n= 1)]; three patients were PCR positive and microscopy negative probable PCP [multiple myeloma (n= 1), interstitial lung disease (n= 1), cholangiocellular carcinoma (n= 1)] and eight other patients were identified as colonized. In the study, when the frequency of the detection of P.jirovecii was evaluated according to the underlying diseases, it was found statistically significantly higher only in HIV/AIDS patients (p= 0.012). When KL-6 was evaluated among the patients defined as PCP/possible PCP and colonization, sensitivity and specificity were determined as 62.5% and 75%, respectively. As a result, nested PCR method was found as sensitive and successful for the detection of P.jirovecii from sputum samples. KL-6 test was not found sufficient for the differentiation of colonization and the infection in PCR positive patients. The results obtained in the study showed that PCP should be on the differential diagnosis list according to the immune status and the clinical features of the inpatients. More researchs are required with more patients to achieve for detailed reliable results in these groups. In addition, molecular epidemiological studies related to genotyping and resistance against anti-PCP drugs are needed to understand P.jirovecii infections in our region and country.

Association of cytokine gene polymorphisms with susceptibility to cutaneous leishmaniasis in a Turkish population.

AIMS: The objective of this study was to determine the association of TNF-α -308 G/A, IFN-γ +874 T/A, IL-12B + 1188 A/C, IL-10 -1082 G/A and IL-4 -590 C/T polymorphisms with susceptibility to CL. METHODS AND RESULTS: A total of 55 CL patients and 110 controls from Sanliurfa province of Turkey were included to this study. Polymorphisms were genotyped by 'polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)' and 'amplification refractory mutation system-PCR (ARMS-PCR)' methods. A statistically significant difference was noted in the allele (P < .001, P = .002) and genotype (P < .001, P = .001,) frequencies of TNF-α -308 G/A and IL-4 -590 C/T, respectively. TNF-α 308 GG versus GA genotype (OR = 19.556 [95% CI 8.310-46.019] P < .001), GG versus GA + AA genotype (OR = 20.444 [95% CI 8.707-48.004] P < .001) and G versus A allele (OR = 6.968 [95% CI 3.903-12.440] P < .001) revealed significant association with CL. IL-4 -590 CC versus TT + CT genotype (OR = 2.049 [95% CI 1.025-4.096], P = .041) and C versus T allele (OR = 2.441 [95% CI 1.355-4.396], P = .002) revealed significant association with CL. CONCLUSION: Our study indicates that TNF-α 308 G/A and IL-4-590 C/T polymorphisms are significantly associated with susceptibility to CL. Individuals carrying A allele at TNF-α promoter -308 position and T allele at IL-4 promoter -590 position are at a higher risk for CL.

[Detection and Molecular Characterization of Human Adenoviruses from Acute Conjunctivitis Cases]. / Akut Konjunktivitli Olgularda Insan Adenovirüslerinin Belirlenmesi ve Moleküler Karakterizasyonu.

Human adenoviruses (hAdV) can cause a wide range of clinical diseases in children and adults that mainly affect respiratory, eye and gastrointestinal systems. Ocular hAdV infections have various clinical manifestations such as epidemic keratoconjunctivitis, pharyngoconjunctival fever and non-specific follicular conjunctivitis. The hAdV genotypes which can cause conjunctivitis vary according to geographic distribution. In the study, we aimed to determine the frequency of the presence of hAdV by molecular methods and to determine the types with phylogenetic analysis in conjunctival swab samples taken from patients diagnosed clinically as acute conjunctivitis. Conjunctival swab samples (n= 100) were taken from the patients with acute conjunctivitis who have admitted to Mersin University Faculty of Medicine Hospital Ophthalmology Clinic and 50 conjunctival swab samples taken from healthy individuals as a control, between September 2014-July 2017 were included in the study. Following the DNA isolation from swab samples, polimerase chain reaction (PCR) amplification was performed using specific primer sequences targeting the hexon gene region of the hAdV genome. In order to determine hAdV types, direct DNA sequence analysis of hexon gene products was performed in "ABI PRISM 3130XL Genetic Analyzer" (Applied Biosystems, Foster City, CA, USA). The obtained hAdV DNA sequences were typed by BLAST analysis and the identified genotypes were compared phylogenetically with the reference hAdV sequences of the NCBI In the study, 30 (30%, 30/100) of the swab samples of the patients with acute conjunctivitis were found positive for hAdV hexon gene PCR. The hAdV DNA was not found in the conjunctival swab samples belonging to the healthy individuals included as controls. A total 27 samples found as positive of the hexon gene PCR were genotyped by direct DNA sequence analysis. A total of 5 genotypes were identified and the most common genotypes were hAdV-8 (n= 17, 63%) and followed by hAdV-53 (n= 4, 14.8%), hAdV-4 (n= 4, 14.8%), hAdV-7 (n= 1, 3.7%) and hAdV-37 (n= 1, 3.7%). In this study, the prevalence of adenoviral conjunctivitis determined by hexon gene PCR in patients with clinical diagnosis of acute conjunctivitis was similar to the prevalence rate reported in other regions of the world. In our region, more than one type of hAdV type was associated with acute conjunctivitis. The predominant type was determined as hAdV-8 with a 63% ratio. These results will significantly contribute to the molecular epidemiology of hAdV types in conjunctivitis cases.

Serological evidence of Rift Valley fever virus among humans in Mersin province of Turkey.

BACKGROUND & OBJECTIVES: Rift Valley fever virus (RVFV) is a vector-borne pathogen that causes serious outbreaks among livestock, and severe symptoms and mortality in humans. The virus is known to be widespread throughout African countries and Arabian peninsula. The aim of the present study was to investigate the seroprevalence of RVFV infection among human populations of Mersin province, Turkey. METHODS: A region-wide serological survey was conducted on humans residing in rural and urban areas of Mersin province located in the subtropical mediterranean region of Turkey from July 2011- January 2014. Plasma samples were tested for the presence of anti-RVFV antibodies using commercially available indirect immunofluorescence assay. RESULTS: The overall past infections were detected in 48 (4.9%) of the 977 human blood samples. The RVF virus- specific IgG positivity was detected in 33 (4.9%) of the 677 blood samples obtained from the urban area and in 15 (5%) of the 300 samples obtained from the rural area. There was no statistically significant difference in the distribution of RVFV IgG positivity rates between urban and rural areas (p = 0.933); though difference was significant between the rural areas (p = 0.029). INTERPRETATION & CONCLUSION: The study confirmed for the first time, the presence of the RVFV antibody in the urban and rural areas of mediterranean province of Mersin in Turkey, suggesting wide circulation of RVFV in the human population.