Comparison of the GeneXpert® MTB/RIF Test and Conventional Methods in the Diagnosis of Mycobacterium tuberculosis.

BACKGROUND: The objective of this study is to evaluate the performance of the GeneXpert MTB/RIF system in Mycobacterium tuberculosis (MTB) diagnosis and the detection of rifampicin resistance in pulmonary and extrapulmonary clinical samples. METHODS: A total of 849 samples (611 pulmonary and 238 extrapulmonary), which were sent to the laboratory of our hospital on suspicion of MTB, were included in the study. The samples cultured on Lowenstein Jensen medium and Mycobacteria Growth Indicator Tubes. All samples were also tested with the GeneXpert MTB/RIF test. The drug susceptibility test was determined using the Bactec MGIT 960 system. RESULTS: MTB grew in the culture in 84 (9.8%) of all samples, and 78 (9.1%) were found to be positive by the GeneXpert MTB/RIF test, while acid-fast bacillus (AFB), MTB/RIF test, and culture positivity were 41 (6.7%), 74 (12.1%), and 75 (12.3%), respectively, in pulmonary samples, and these values were found to be 2 (0.8%), 4 (1.7%), and 9 (3.8%), respectively, in extrapulmonary samples. In the automated culture and susceptibility system, rifampicin resistance was detected in only one of 84 (2.6%) isolated strains. This resistant strain was also identified by the GeneXpert MTB/RIF test. According to the culture results of all samples examined, the sensitivity of the GeneXpert MTB/RIF test was calculated as 83.3%, specificity as 98.9%, PPV as 89.7%, and NPV as 98.1%. CONCLUSIONS: The GeneXpert MTB/RIF test used in the study was found to be highly successful, very quick, and requiring low workload in pulmonary samples and extrapulmonary samples in terms of sensitivity and specificity. It was observed that it can be used safely due to its high sensitivity, especially in AFB-positive samples.

As a Novel Procalcitonin Assay is Architect B∙R∙A∙H∙M∙S PCT; Comparison of Two Commercial Systems.

BACKGROUND: Procalcitonin (PCT) is the precursor structure of the calcitonin hormone with 116 amino acids. The measurement of serum procalcitonin is currently being safely used in community-acquired pneumonia, bacterial peritonitis and sepsis in the diagnosis, decision on the initiation of treatment, and follow-up of the response to treatment. In this study, it is aimed to compare PCT results obtained by the VIDAS PCT that makes measurements by the enzyme-dependent fluorescence (ELFA) method and Architect PCT method, a chemiluminescent microparticle immunoassay (CMIA) that has just been put into use, both of which are B∙R∙A∙H∙M∙S licensed and have method differences. METHODS: Serum samples of 109 patients from different clinics with a PCT request were included in the study. The sera were divided into two groups and the samples were immediately studied with two methods. Cohen's Kappa (κ) coefficient was used to determine concordance between the two methods. Other parameters were analyzed by the paired t-test, and their concordance was evaluated. RESULTS: In the concordance analysis study carried out by considering the significant cutoff value of 0.5 ng/mL in the clinical diagnosis of bacterial infections, the κ value was found to be 0.930, p < 0.001. Concordance was at an excellent level. Upon pairing and analyzing all the results regardless of the cutoff value, the Concordance Coefficient was found to be 0.958 (p < 0.001). It was observed that concordance was at an excellent level. CONCLUSIONS: Upon comparing the patient results obtained as a result of the study, it was observed that the concordance of the methods with each other was excellent. Larger and more comprehensive studies on this issue will be helpful.

Comparative evaluation of TK SLC-L, a rapid liquid mycobacterial culture medium, with the MGIT system.

BACKGROUND: The present study was conducted to assess the efficiency of using TK SLC-L (Salubris, Inc.) for the primary isolation of mycobacteria from clinical samples by comparing it to the MGIT detection system (Becton Dickinson Diagnostic Instrument Systems). Although TK SLC, a biphasic medium, has been evaluated previously, this is the first study to evaluate TK SLC-L, a liquid medium. METHODS: Clinical specimens from a total of 146 clinically suspected cases of tuberculosis were studied. Each processed sample was evaluated by ZN staining and inoculated into TK SLC-L and MGIT tubes. The TK SLC tubes were incubated in a MYCOLOR TK while the MGIT tubes were incubated in a MGIT system. Growth, indicated by automated systems, was confirmed through production of a smear and microscopic evaluation after ZN staining. RESULTS: Mycobacterial growth was positive in 35 TK SLC-L and in 34 MGIT samples. Although the growth detection time was approximately 3 to 5 days shorter, on average, with the MGIT system, the contamination rate was significantly lower using TK SLC-L. The total time spent for the repetition of cultures for contaminated samples in MGIT make the total return time for culture results equal to or longer than the time required by TK SLC-L. CONCLUSIONS: The TK Culture System using TK SLC-L is an efficient system and possible alternative to other rapid mycobacterial culture systems.

Could a step in the isolation of mycobacteria from sputum samples be eliminated by new decontamination kits?

The efficacy of two mycobacterial homogenization, decontamination and concentration kits, Mycoprosafe and Decomics, were compared. A total of 146 sputum samples were examined in this study; 46 (31.5%) mycobacterial isolates were recovered with Mycoprosafe, while 39 (26.7%) mycobacterial isolates were recovered with Decomics. These results, although very preliminary, indicate that Mycoprosafe and Decomics are similar in terms of ease of use and price. However, Decomics offers several advantages, including the need for less equipment, a more rapid detection time, and an easy shipping process; thus, pre-processing can be done anywhere.

Rapid detection of resistance in Staphylococcus aureus by using Quicolor ES.

Traditional microbiological methods are dependent on the growth of microorganisms, and hence require prolonged periods. The methods used to detect resistance in Staphylococcus aureus should have high sensitivity and specificity, yet provide results in a timely manner. The aim of this study was to evaluate the use of Quicolor (QC) ES(®) agar for the rapid detection of resistance in S. aureus. We evaluated 100 clinical S. aureus isolates. Resistance detection was performed using traditional microbiological methods. Methicillin resistance detection was evaluated using traditional and molecular microbiological methods. Traditional antibiotic susceptibility testing methods, such as disc diffusion, were conducted using QC ES and Mueller-Hinton (MH) media. The plates were incubated at 36 °C for 5, 6 and 24 h. Rapid results obtained using QC ES agar after 5 h of incubation were consistent with those using the overnight procedure with MH agar for 83 of the 100 S. aureus (including methicillin-susceptible S. aureus) strains. However, the correlation for oxacillin between MH (24 h) and QC ES (5 h) was not satisfactory (r = 0.770). The total agreement between QC ES and MH agar was 83% after 5 h, 89% after 6 h, and 94% after 24 h. The accurate and rapid detection of resistance in S. aureus is critical due to the associated therapeutic problems and infection control measures. We believe that the use of QC ES for S. aureus will reduce the delay in resistance detection, thus providing physicians and infection control practitioners with early information for better management.

Comparison of novel and familiar commercial kits for detection of C-reactive protein levels.

In this study, randomized patient sera were used to simultaneously evaluate an automated C-reactive protein (CRP) assay and a commercial semi-automated microCRP assay with respect to correlation, linearity, and accuracy. Patient specimens were analyzed; two independent assay runs were performed on i-CHROMA (Boditech Med Inc., Korea) and IMMAGE 800 (Beckman Coulter Inc., USA) analyzers to estimate the between- and within-run precision. All systems were calibrated, and quality-control materials were analyzed according to the manufacturer's instructions. The results using the control materials were within the respective manufacturers' specified limits. The comparison studies were designed using the CLSI EP9-2A guidelines. The mean serum CRP concentrations were 123.2 ± 123.5 mg/L (95 % confidence of interval (CI) 97.9-148.3) using the CRP assay and 130.1 ± 109.3 mg/L (95 % CI 107.9-152.4) using the microCRP assay. The variance values were σ = 15,252.6 and 11,935.8 for the CRP and microCRP assays, respectively. The concordance correlation coefficient value was calculated as 0.8314 (95 % CI 0.7594-0.8833). There was a significant correlation between the CRP and microCRP assays: r = 0.8392 and 95 % CI 0.7675-0.8902 (p < 0.0001). The CRP and microCRP detection methods were well correlated. The i-CHROMA has many advantages over the IMMAGE 800 with respect to space required, analysis time, and system setup/application costs in a laboratory. It may be an attractive instrument for small and intermediate medical centers.

Idiopathic granulomatous mastitis: an autoimmune disease?

PURPOSE: This study aimed to investigate the autoimmune basis of idiopathic granulomatous mastitis (IGM) by determining the anti-nuclear antibody (ANA) and extractable nuclear antigen (ENA) levels of patients diagnosed with IGM. MATERIAL AND METHODS: Twenty-six IGM patients were evaluated. Serum samples were analyzed for autoantibodies by indirect immunofluorescence (IIF) using a substrate kit that induced fluorescein-conjugated goat antibodies to human immunoglobulin G (IgG). IIF patterns were read at serum dilutions of 1 : 40 and 1 : 100 for ANA positivity. Using the immunoblot technique, the sera of patients were assayed at dilutions of 1 : 40 and 1 : 100 for human autoantibodies of the IgG class to 15 lines of highly purified ENAs. RESULTS: In the IIF studies for ANA, positivity was identified for four different patterns in the 1 : 40 diluted preparations, for three different patients in the 1 : 100 diluted preparations and only one pattern was identified at the 1 : 320 dilution. In the ENA studies, positivity was identified for four different pattern in the 1 : 40 dilution, and only one pattern was identified at the 1 : 100 dilution. CONCLUSION: This study was not able to support the eventual existence of an autoimmune basis for IGM.

[Distribution of blaOXA genes in Acinetobacter baumannii strains: a multicenter study]. / Acinetobacter baumannii Izolatlarinda blaOXA Genlerinin Dagilimi: Çok Merkezli Bir Çalisma.

Acinetobacter baumannii is the most important agent of nosocomial infections within the Acinetobacter genus. This gram-negative coccobacillus is intrinsically resistant to many antibiotics used in antimicrobial therapy, and capable of developing resistance including carbapenems. The objective of this study was to develop a multiplex real time polymerase chain reaction (qPCR) kit for OXA subgroups in A.baumannii, and to investigate the distribution of OXA subgroups in A.baumannii strains isolated from geographically different regions of Turkey. A total of 834 A.baumannii clinical isolates collected from different state and university medical centers in 13 provinces (Afyonkarahisar, Ankara, Bolu, Elazig, Erzurum, Isparta, Istanbul, Kahramanmaras, Konya, Sakarya, Van) between 2008-2011, were included in the study. The isolates were identified by conventional methods and automated systems [Vitek2 (bioMerieux, ABD) and Phoenix (BD Diagnostic, MD)]. The susceptibility profiles of the isolates were studied with automated systems and standard disc diffusion method. All samples were subjected to qPCR to detect blaOXA-51-like, blaOXA-23-like and blaOXA-58-like genes. A conventional PCR method was also used to detect blaOXA-24-like gene. The resistance rates observed during the study period were as follows: 96.8% for amoxicillin-clavulanate, 86.8% for ciprofloxacin, 74.7% for gentamicin, 71.7% for amikacin, 73.5% for cefaperozone-sulbactam, 72.1% for imipenem and 73% for meropenem. Six hundred and two (72.2 %) isolates were resistant to both imipenem and meropenem. Colistin was found to be the most effective antibiotic against A.baumannii isolates with 100% susceptibility rate. All isolates were positive for blaOXA-51-like, however blaOXA-24-like gene could not be demonstrated in any isolate. Total positivity rates of blaOXA-23-like and blaOXA-58-like genes were found as 53.7% and 12.5%, respectively, while these rates were 74.4% and 17.3% in carbapenem-resistant isolates, respectively. Twenty-five isolates were positive for both blaOXA-23-like and blaOXA-58-like genes. All of the carbapenem-resistant isolates have OXA type genes with the exception of blaOXA-24-like gene. The positivity rates for blaOXA-23-like and blaOXA-58-like genes varied for each center. In addition, there was a decrease in the frequency of blaOXA-58-like gene, however both blaOXA-23-like gene and carbapenem resistance rates increased during the study period. In conclusion, high rates of resistance to carbapenems were also remarkable but A.baumannii strains keep on sensitivity to colistin. Both blaOXA-23-like and blaOXA-58-like genes were shown to be widespread in carbapenem-resistant A.baumannii clinical isolates. However, blaOXA-23-like gene positive strains were increased throughout the study. Currently, multiplex qPCR is the best way for rapid diagnosis of resistant bacteria for prevention of hospital-acquired infections. The multiplex qPCR kit developed in this study could be useful for rapid diagnosis and identify the frequencies of blaOXA-23-like, blaOXA-51-like and blaOXA-58-like genes in carbapenem-resistant A.baumannii clinical isolates.

Comparison of fetuin-A and transforming growth factor beta 1 levels in patients with spondyloarthropathies and rheumatoid arthritis.

AIM: We investigated the serum transforming growth factor beta 1 (TGFß1) and fetuin-A levels, and determined the relationships between these biomarkers and disease activity, mobility and radiologic progression in patients with spondyloarthropathy (SpA) and rheumatoid arthritis (RA). METHOD: The study included 55 patients with SpA and 38 patients with RA, together with 28 healthy subjects. In AS patients, we assessed disease activity using the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), functional ability using the Bath Ankylosing Spondylitis Functional Index (BASFI), and mobility using the Bath Ankylosing Spondylitis Metrology Index (BASMI), radiologic progression using the Bath Ankylosing Spondylitis Radiology Index (BASRI). Serum fetuin-A and TGFß1 were determined using enzyme-linked immunosorbent assay (ELISA) equipment. RESULTS: Fetuin-A was significantly higher in the axial SpA and RA groups than in healthy subjects (P < 0.01). Serum TGFß1 and fetuin-A levels were similar in the peripheral SpA group and in healthy subjects. A significant positive correlation was found between the fetuin-A and TGFß1 levels in the axial SpA, peripheral SpA, and RA groups (r = 0.293, P = 0.009; r = 0.215, P = 0.04; r = 0.223, P = 0.05, respectively). Significant correlations were found between fetuin-A and the BASMI and BASRI values in the axial SpA patients (r = 0.444, P = 0.031; r = 0.486, P < 0.001, respectively). CONCLUSION: We conclude that Fetuin-A may be one of the steps that can be active in disease progression in axial SpA patients.

Overlooked hematological markers of disease activity in rheumatoid arthritis.

AIM: The aim of this study was to investigate the relationship between hematological markers and disease activity in patients with rheumatoid arthritis (RA). METHOD: The study was designed and performed in the Department of Rheumatology of the Sakarya University Faculty of Medicine. In total, 102 patients with RA were retrospectively enrolled. We used the Disease Activity Score of 28 joints (DAS28) instrument to evaluate disease activity. Laboratory assessments included complete blood cell counts, measurement of erythrocyte sedimentation rate (ESR) and assessment of C-reactive protein (CRP) level. Exclusion criteria included active infection and/or the presence of any hematological, cardiovascular or metabolic disorder. RESULTS: We found that the neutrophil lymphocyte ratio (NLR) and mean platelet volume (MPV) varied by disease activity status. NLR values correlated positively with the DAS28 scores of RA patients. Especially, higher NLR values (3.92 ± 0.31) were evident in the group exhibiting high-level disease activity, whereas the MPV values were lowest (7.11 ± 0.91 fL) in this group. Additionally, no significant difference was evident between DAS28 scores and platelet distribution width (PDW) values in patients with RA (r = -0.055, P = 0.124). CONCLUSIONS: We found that the MPV value may serve as a marker of the absence of acute-phase disease, and the NLR level as a marker of the presence of such disease, in patients with RA. More detailed analysis of disease activity is required to further explain the associations of the markers described above with disease activity.

Tuberculous arthritis of the elbow joint: A case report.

Tuberculous arthritis of the elbow joint is rare. A 57-year-old male patient presented with swelling, pain, and redness of the elbow. The symptoms first appeared one month ago; he was given antibiotic treatment after the diagnosis of septic arthritis at another center. The patient who did not improve with treatment was diagnosed with tuberculous arthritis according to the culture and was started on antituberculosis treatment. Tuberculous arthritis usually presents with chronic arthritis. However, it can also present in patients with septic arthritis.

Association of doripenem resistance with OXA-type carbapenemases in Acinetobacter baumannii isolates.

OBJECTIVES: To evaluate the in vitro activity of doripenem in Acinetobacter baumannii (A. baumannii) clinical isolates that possess different OXA-type carbapenemases, and to evaluate the roles of these enzymes in the development of carbapenem resistance. METHODS: This retrospective study was conducted with 25 A. baumannii isolates at Sakarya University Training and Research Hospital, Sakarya, Turkey from June to October 2014. Antibiotic susceptibility testing was carried out using the Vitek-2 automated system (bioMérieux, Marcy l'Etoile, France). Minimum inhibitory concentrations (MICs) were determined using Etest strips (bioMérieux, Marcy l'Etoile, France). Quantitative polymerase chain reaction was performed in a Fluorion Instrument (Iontek, Istanbul, Turkey).  RESULTS: Isolates were divided into 5 groups based on their susceptibility profiles and OXA-type carbapenemase positivity. Group 2 isolates whose MIC of both meropenem and doripenem are in the range of 4-32 µg/mL were negative for both blaOXA-23 and blaOXA-58. Group 3 isolates whose MIC of meropenem and doripenem is in the range of 4-32 µg/mL, blaOXA-23 is positive, and blaOXA-58 is negative. Group 5 isolates whose MIC of meropenem is more than 32 µg/mL, and that of doripenem is in the range of 16-32 µg/mL were positive for both blaOXA-23 and blaOXA-58.  CONCLUSION: The blaOXA-23 and blaOXA-58 gene combinations may confer resistance with a much greater MIC of both meropenem and doripenem. But the blaOXA-58 presence alone was not correlated with doripenem resistance.

Endocan, TGF-beta, and ADMA as Risk Factors for Endothelial Dysfunction and Possible Vascular Disease in Patients with Subclinical Hypothyroidism.

PURPOSE: Although the relationship between atherosclerosis and overt hypothyroidism has been confirmed, it remains controversial in cases of subclinical hypothyroidism. Higher TSH and similar T4 suggest differences in set-points or differences due to diagnostic limitations regarding subclinical hypothyroidism. Endothelial dysfunction (ED) is a marker rather than a precursor of cardiovascular disease. Asymmetric dimethylarginine (ADMA) and endocan are known as novel markers of ED in various diseases. Transforming growth factor-beta (TGF-ß) has a protective role against autoimmune diseases such as thyroiditis. This study aimed to determine the relationships between serum ADMA, endocan, TGF-ß, and the high-sensitivity C-reactive protein (hs-CRP) levels, a proven indicator of ED, in patients with SH. METHODS: Thirty-five patients with SH and 21 age- and sex-matched euthyroid subjects were included in the study. The levels of TSH, FT4, lipid parameters, endocan, ADMA, TGF-ß, and hs-CRP were measured. RESULTS: No significant differences in age or sex were found between the patient and control groups (p=0.294 and 0.881, respectively). Mean TSH level was higher in the patient group (p=0.005), whereas mean fT4 level was similar in two groups (p=0.455). The average hs-CRP, endocan, TGF-ß l level in the patient group was higher than control group (p=0.001; P=0.012; P=0.025; P<0.01 respectively). A positive correlation was found between the endocan and ADMA levels (r=0.760, p=0.000). ADMA levels also were positively correlated with hs-CRP. Both the TSH and low-density lipoprotein cholesterol (LDL-C) levels were positively correlated with the hs-CRP level. CONCLUSIONS: Subclinical hypothyroidism is associated with increased levels of serum endocan, ADMA, and TGF-ß, which are new markers for ED. In particular, ADMA was correlated with both endocan and hs-CRP levels. These findings are suggestive for increased risk of ED and subsequent development of atherosclerosis in patients with SH.

Roles of claudin-5 and von Willebrand factor in patients with rheumatoid arthritis.

Rheumatoid arthritis (RA) is a chronic inflammatory disorder that affects approximately 1% of the world's population. The pathogenesis of RA is not understood fully. It is assumed that endothelial function is associated with the proinflammatory state of RA. Endothelial dysfunction/activation reflects the increased level of von Willebrand factor (vWF) and a shift toward prothrombotic activity of the endothelium. The present study was performed to investigate the possible relationships between vWF and claudin-5 and the level of disease activity in patients with RA. The study population was divided into four groups according to the disease activity score in 28 joints (DAS28): remission group (RG), 18 patients (DAS28 < 2.6); low disease activity group (LDAG), 23 patients (DAS28 > 2.6-3.2); moderate disease activity (MDAG), 23 patients (DAS28 > 3.2-5.1); high disease activity group (HDAG), 14 patients (DAS28 > 5.1); and control group (CG), 10 healthy subjects. Claudin-5 and vWF assessment were derived from serum samples gathered from the patients known to have RF and anti-CCP titers in the normal ranges. A high positive association of claudin-5 and vWF with the MDAG was observed (P < 0.001). The results of our study indicated that the relationship between vWF and claudin-5, which are indicators of endothelial cell dysfunction and tight junction activity, may be a predictor of disease activity. Further studies are required to investigate these pathways to shed light on the roles of claudin-5 and vWF in the progression of inflammation and other vascular conditions.

[Rare Case of Strongyloides stercoralis with Vitamin B12 Deficiency]. / B12 Vitamin Eksikligi Olan Nadir Strongyloides stercoralis Vakasi.

Strongyloidiyasis is endemic in tropical and subtropical regions, and mostly soil transmitted nematode disease that is seen as sporadic cases in Turkey. As may be asymptomatic in healthy individuals, it may even cause death in immunosuppressive people. We report a case of Strongyloides stercoralis infection in a patient, 29 years old young male was admitted to our institution with diarrhea who has got vitamin B12 deficiency and eosinophilia. The case represents an extremely rare and in our knowledge, it is the first case in Sakarya.

Demodex spp. Infestation in a breast-cancer patient: A case report.

Demodex folliculorum and Demodex brevis are obligatory parasites that live in sebaceous glands and follicles. When immune system becomes suppressed by any reason, patients become vulnerable to obligatory parasites like D. folliculorum and D. brevis. Immune system becomes suppressed in cancer patients who undergo chemotherapy, and as a result these patients become vulnerable to infestations. In our case, a 45 year-old female has been admitted to oncology clinic for a medical treatment of breast cancer. Her systematic physical examination was normal, except redness on her cheeks and forehead. There was no abnormality in biochemical and haematological laboratory values. We have decided to apply chemotherapy of Adriamycin, cyclophosphamide and 5-fluorouracil. Due to the itchy redness on her cheeks and forehead, we had performed an examination for demodex before chemotherapy; and we have identified 20 mites/cm(2) on her right and left cheeks, and 15 mites/cm(2) on her forehead. When our patient had came our clinic with increasing complaint of itchy rash, after the first course of chemotherapy we have reexamined demodex. The result of microscopic examination revealed large amount of demodex of 50 mites/cm(2) on her right and left cheeks and 30 mites/cm(2) on her forehead, which were nearly 2.5-times higher than the previous examination. This increase probably was associated with immune suppression of chemotherapy.

Associations between Demodex species infestation and various types of cancer.

Tumor-associated immune system cells secrete protease and cytokines that can inhibit the immune response. In particular, T-cell effector functions could be inhibited, potentially causing an increase in parasitic infestations. Demodex species are common inhabitants of normal hair follicles. Humans are the specific host for two species Demodex folliculorum and D. brevis. The aim of this study was to investigate the incidence and infestation of D. folliculorum and D. brevis in patients with cancer. In the present study, 101 patients with cancer were selected from among patients who were diagnosed and treated for cancer. The cancer patients were divided into four groups according to cancer type. Slides were examined for parasites using light microscopy at magnifications of ×40 and ×100. Infestation was defined as having at least five living parasites/cm(2) of skin. The ages of the patients with cancer ranged between 38 and 82 years, with a mean of 65.5±10.1 years. It was determined that 77 of the 101 (76.2%) cancer patients were positive for Demodex species. Infestation was positive in 18 (47.4%) of the 38 cases in the breast cancer group, 7 (29.2%) of the 24 cases in the lung cancer group, 5 (18.5%) of the 27 cases in the gastrointestinal system cancer group, and 2 (16.7%) of the 12 cases in the urogenital system cancer group. Results showed that the rate of Demodex species infestation was higher in patients with breast cancer. Thus, cancer - and particularly breast cancer - is a risk factor for Demodex species infestation.