Evaluation of the Diagnostic Algorithms for Serodiagnosis of Syphilis.

We analyzed the performance parameters of the traditional and reverse algorithms to determine which is more convenient for serodiagnosis of syphilis. In total, 4,789 serum samples were obtained from a cross-sectional study. Venereal Disease Research Laboratory (VDRL), Treponema pallidum hemagglutination assay (TPHA), and chemiluminescent microparticle immunoassay (CMIA) tests were performed on each serum sample. In case of discordance between results, TPHA was applied as a second treponemal test. Overall, 207 patients were serodiagnosed with syphilis. Among the 4,789 samples tested, 125 (2.6%) and 206 (4.3%) were positive using the traditional and reverse algorithms, respectively. The missed diagnosis rate of the traditional algorithm was 42.5%. The reverse algorithm had a higher sensitivity than that of the traditional algorithm. The sensitivity levels of the traditional and reverse algorithms were 57.49% and 99.85% respectively. The false positivity rate of the reverse algorithm was 0.02%.

[Evaluation of EUCAST Direct Rapid Antimicrobial Susceptibility Test Method in Blood Culture Bottles with Positive Signal]. / Pozitif Sinyal Veren Kan Kültürü Siselerinde EUCAST Dogrudan Hizli Antimikrobiyal Duyarlilik Testi Yönteminin Degerlendirilmesi.

Early reporting of the antibiotic susceptibility testing (AST) results is essential for the survival of sepsis patients. In 2019, European Committee on Antimicrobial Susceptibility Testing (EUCAST) published a proposal to detect antimicrobial susceptibility from positive blood culture bottles with a rapid antimicrobial susceptibility test (RAST) method in a maximum of eight hours. In this study, it was aimed to evaluate the EUCAST RAST method in blood culture bottles that resulted with positive signal in BacT/ALERT (bioMérieux, France) blood culture system and that showed gram-negative bacteria with single morphology with Gram stain. The study was conducted prospectively between April 2019 and November 2019. Ninety blood culture bottles that we detected single gram negative bacteria morphology by Gram stain were tested according to the EUCAST RAST method, The isolates obtained from the blood culture bottles were studied with the EUCAST disk diffusion method and the Vitek 2 Compact (bioMerieux, France) automated system. The results obtained with RAST were compared with the results of these methods. The turn around time of the RAST method was recorded. Categorical agreement of the RAST method with conventional methods and the very major error rates were determined. Of the 14 isolates not yet covered by the EUCAST HADT method, 12 were determined to be other Enterobacterales members and two as other non-fermentatives. Two isolates were detected with the same morphological characteristics in Gram stain of the blood culture bottle and the same antibiotic susceptibility profile, but with different identification results. These sixteen isolates were excluded from the study. In this study the susceptibility of 74 isolates were determined according to the EUCAST breakpoint tables, of which 31 were Klebsiella pneumoniae, 35 were Escherichia coli, four were Acinetobacter baumannii and four were Pseudomonas aeruginosa. According to the evaluation periods of EUCAST RAST; the susceptibility profile was reported for nine (12%) of E.coli at four hours, eight (11%) at six hours, 18 (24%) at eight hours; three (4%) of K.pneumoniae at four hours, 16 (21%) at six hours, 12 (16%) at eight hours; three of P.aeruginosa (4%) at six hours, one (1%) at eight hours; two of A.baumannii (2%) at six hours and two (2%) at eight hours. The categorical aggrement of the RAST method was 91.8% with the automated system and 96.8% with the disc diffusion method. Very major errors of RAST method compared to the automated system were detected for piperacillin-tazobactam (17.7%), ceftazidime (11.6%) and meropenem (5.6%); and when compared to the disc diffusion method, for cefotaxime (5.7%) and meropenem (6.7%). Our results have shown that EUCAST RAST method can practicaly be performed in routine laboratories to report early results with a low cost. Because of the very major errors it is necessary to confirm the results with the standard methods.

[A case of Peritonitis Caused by Wickerhamomyces anomalus (Candida pelliculosa) Related to Peritoneal Dialysis]. / Wickerhamomyces anomalus (Candida pelliculosa)'un Etken Oldugu Periton Diyalizi Iliskili Bir Peritonit Olgusu.

Fungal peritonitis is less commonly seen than bacterial peritonitis in patients undergoing peritoneal dialysis (PD), but it is a serious complication with high morbidity and mortality. It often results in catheter loss and modifying therapy from PD to hemodialysis. The causative organisms are often Candida species. In this report, a PD-associated peritonitis caused by Wickerhamomyces anomalus (Candida pelliculosa), a rare fungal infection agent with increasing clinical importance by causing different clinical pictures was presented. An outpatient peritoneal fluid culture was sent from a 48-yearold male patient, who had been undergoing continuous peritoneal dialysis (CAPD) for 9 years, due to abdominal pain and blur in peritoneal fluid during dialysis. The patient admitted to the emergency department four days later due to the persistence of his complaints. A sample of peritoneal fluid was taken in the emergency department and sent to the laboratory for microbiological analysis. In the direct microscopical examination of the peritoneal fluid; cell number was determined as 210/mm3, and no microorganisms were seen in the Gram and methylene blue staining. The patient was admitted to the nephrology service with a pre-diagnosis of PD-associated peritonitis. Enterobacter aerogenes was grown in the peritoneal fluid culture which was sent from the dialysis outpatient clinic four days ago. The peritoneal fluid sample sent from the emergency department was inoculated on 5% sheep blood , EMB and chocolate agars and no growth was detected. As the patient's complaints and peritoneal fluid leukocyte count continued to increase, peritoneal fluid cultures were repeated and recurrent growth of yeast was detected in cultures. The yeast was identified as Candida pelliculosa by matrix assisted laser desorption ionization time-of-flight mass spectrofotometry (MALDI-TOF) VITEK®MS (bioMerieux, France). The species identification was confirmed by sequencing the target ITS gene regions on the rRNA and the isolate was identified as 100% Wickerhamomyces anomalus (sexual reproduction form of Candida pelliculosa, teleomorph). The reference microdilution method was performed according to the recommendations of the Clinical and Laboratory Standards Institute (CLSI) in order to test the antifungal susceptibility. After 24 hour incubation, the minimal inhibitory concentrations (MIC) were determined as 0.03 µg/ml for amphotericin B, 0.125 µg/ml for caspofungin 0.125 µg/ml for voriconazole, 0.03 µg/ ml for itraconazole and 4 µg/ml for fluconazole. Fluconazole and anidulafungin were started for the treatment of fungal peritonitis. The patient's peritoneal dialysis catheter was removed and hemodialysis was applied to the patient. Clinical and laboratory symptoms regressed with antifungal therapy and the patient's anidulafungin treatment was discontinued for 14 days after the catheter removal. In conclusion, in patients undergoing CAPD, as in our case, fungal pathogens should also be considered although it is rare, when there is no laboratory and clinical improvement, and the response to treatment is not complete in PD-associated peritonitis to prevent delays in diagnosis and treatment.

Pneumococcal carriage in children with COVID-19.

Background: SARS-CoV-2 is the new virus, and Streptococcus pneumoniae is one of the most important pathogens affecting humans. However, we do not yet know whether these microorganisms interact. Thus, we aimed to evaluate the relationship between Streptococcus pneumoniae and SARS-CoV-2 in pediatric patients.Methods: This study was conducted retrospectively by means of medical records of pediatric patients who were tested for SARS-CoV-2 between March 11 and June 04, 2020, in the University of Health Sciences, Ankara Educating and Training Hospital and Hacettepe University Faculty of Medicine.Results: We evaluated 829 pediatric patients for S. pneumoniae and SARS-CoV-2 from their nasopharyngeal specimen. Of 115 children positive for SARS-CoV-2, 32.2% had a positive S. pneumoniae test, whereas of 714 children negative for SARS-CoV-2, 14.1% had a positive S. pneumoniae test (p < .01). We compared patients with positive vs. negative SARS-CoV-2 tests according to S. pneumoniae positivity There were no statistically significant differences in terms of gender, underlying disease, fever, cough, leukocytosis, lymphopenia, increased CRP, increased procalcitonin, findings of chest x-ray, severity of disease, and treatment.Conclusion: The nasopharyngeal S. pneumoniae carriage rate in patients with COVID-19 was higher than in non-infected children, while S. pneumoniae carriage did not affect the course of COVID-19 disease. Pneumococcal vaccination is significant, such that we do not know the outcomes of increased pneumococcal carriage for the upcoming months of pandemic.

Comparison of non-invasive tests with invasive tests in the diagnosis of celiac disease.

BACKGROUND/AIMS: Today, invasive diagnostic tests are necessary for definite diagnosis of adult celiac disease (CD). However, in selected children patients, the need for invasive tests is ceased. In this study, we evaluated adult patients according to the ESPGHAN (European Pediatric Gastroenterology Hepatology and Nutrition Society) criteria. METHODS: Thirty-nine patients (aged 17-66) with symptoms of CD were included. Serum samples were tested for total IgA, tTG-IgA (antitissue transglutaminase), tTG-IgG, DGP-IgA (antideamidated gliadin peptide), DGP-IgG, and EMA (endomysial antibodies). HLA-DQ typing was studied with PCR-SSP (sequence-specific primers) method. Biopsy samples were evaluated according to Marsh scoring. RESULTS: In CD patients, 71.4% (15/21) of the patients were diagnosed without biopsy according to the EPSGHAN criteria but when ESPGHAN's IgA tTG threshold value for children was taken into consideration (>200 IU/mL), the sensitivity decreased to 81%. Celiac disease diagnosed and control groups were compared in terms of HLA tissue types. DQ2.5 homozygous or DQ2.5/DQ2.2 was significantly higher in CD group, and DQ2- or DQ8-negative HLA tissue type was significantly higher in control group. CONCLUSION: When serological tests, HLA typing, and clinical symptoms are all in favor of CD, biopsy may not be performed in selected adult CD patients.

Evaluation of Invasive and Noninvasive Methods for the Diagnosis of Helicobacter Pylori Infection

Objective: The present study was conducted to evaluate invasive and noninvasive diagnostic methods for detection of Helicobacter pylori (H. pylori) in patients admitted with dyspeptic complaints and to compare sensitivities and specificities. Method: Sets of four gastric biopsy specimens were obtained from a total of 126 patients included in the study. The presence of H. pylori was determined by invasive tests including culture, rapid urease test, polymerase chain reaction (PCR) and histopathology. Among noninvasive tests, urea breath test, serological tests and enzyme-linked immunosorbent assay (ELISA) were performed. Results: H. pylori was isolated in 79 (62.7%) gastric biopsy cultures, whereas positivity was concluded for 105 (83.3%) patients by rapid urease test, for 106 (84.1%) by PCR, for 110 (87.3%) by histopathology, for 119 (94.4%) by urea breath test, and for 107 (84.9%) by ELISA. In the present study, the culture findings and histopathological examination findings were accepted as gold standard. According to the gold standard, urea breath test had the highest sensitivity (96.5%) and the lowest specificity (30%), whereas culture and histopathology had the highest specificities (100%). Conclusion: The use of PCR invasively with gastric biopsy samples yielded parallel results with the gold standard. PCR can be recommended for routine use in the diagnosis of H. pylori.

Does Helicobacter pylori exist in vocal fold pathologies and in the interarytenoid region?

The aim of this study was to investigate the existence of Helicobacter pylori (HP) in patients with benign and malignant vocal fold pathologies. This was a prospective clinical study conducted at a tertiary-care academic medical center. Fifty consecutive patients who had undergone microlaryngoscopy between August 2007 and July 2009 were included in the study. The patients with a reflux symptom index (RSI) above 12 and a reflux finding score (RFS) above 6 were accepted as having laryngopharyngeal reflux. Patients with urea breath test (UBT), HP-IgG, and HP cytotoxin-associated gene A (CagA)-IgG positivity were diagnosed as HP positive. During laryngoscopy, two surgical specimens were obtained, one from the primary vocal fold pathology and one from the interarytenoid region. The interarytenoid biopsy specimen was used for HP culture and PCR. The specimen from the vocal fold pathology was used to investigate the presence of HP. RSI was positive in 23 (46%) patients. The RFS positivity was 56%. The presence of HP was confirmed by UBT in 35 (70%), HP-IgG in 37 (74%), and HP CagA-IgG in 38 (76%) patients. There was no difference between RFS-positive and RFS-negative patients in terms of HP-IgG and UBT. None of the interarytenoid or vocal fold specimens showed the presence of HP. HP was not found in the histological specimens of vocal fold pathologies and the interarytenoid region. The presence of HP in the gastric mucosa does not have an effect on the RFS and RSI.

Concurrent assay for four bacterial species including alloiococcus otitidis in middle ear, nasopharynx and tonsils of children with otitis media with effusion: a preliminary report.

OBJECTIVES: To detect the prevalences of Alloiococcus otitidis, as well as Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis in children with chronic otitis media with effusion (OME) and to simultaneously investigate the colonization of these bacteria in the nasopharynx and palatine tonsils of these patients. METHODS: The study included 34 pediatric patients with OME, and 15 controls without OME. In the study group, A. otitidis, H. influenzae, S. pneumoniae, and M. catarrhalis were investigated in the samples obtained from middle ear effusions (MEE), nasopharyngeal swabs (NPS) and tonsillar swabs (TS), using multiplex polymerase chain reaction (PCR) and conventional culture methods. Only the samples obtained from NPS and TS were studied with the same techniques in the control group. RESULTS: A. otitidis was isolated only in MEE and only with multiplex PCR method. A. otitidis, S. pneumoniae, M. catarrhalis, H. influenzae were identified in 35%, 8.8%, 8.8%, and 2.9%, respectively, in 34 MEE. A. otitidis was not isolated in NPS or TS of the study and the control groups. CONCLUSION: The prevalence of A.otitidis is high in children with OME and A.otitidis doesn't colonize in the nasopharynx or tonsil.

Determination of Helicobacter pylori in patients with chronic nonspecific pharyngitis.

OBJECTIVES/HYPOTHESIS: To determine if there is a relationship between Helicobacter pylori colonization in the pharynx mucous membrane and chronic nonspecific pharyngitis. STUDY DESIGN: A prospective clinical study. METHODS: Seventy patients with chronic pharyngitis and 20 healthy control subjects were examined with polymerase chain reaction (PCR) and culture for H. pylori colonization in the pharynx mucous membrane between March 2008 and October 2008. Patients with pharyngitis were seperated into two groups (35 patients in each) by using C-14 urea breath test, according to the presence of gastric H. pylori infection. RESULTS: In the control group, none of the patients had H. pylori in the pharynx. In the chronic pharyngitis group, in 12 patients (34.3%) with gastric H. pylori infection and in seven patients (20%) without gastric infection, H. pylori colonization in pharynx mucosa was determined with the PCR method. In only two of chronic pharyngitis patients (5.8%), H. pylori infection was detected with culture. In the pharynx mucosa, the H. pylori infection rate was significantly higher in the chronic pharyngitis groups than in the control group (P = .002 between C-14 positive and control groups, P = .040 between C-14 negative and control groups). There was not a significant difference in H. pylori colonization in the pharynx of patients who had chronic pharyngitis with or without gastric ailments and H. pylori infection (P = .179). CONCLUSIONS: Chronic nonspecific pharyngitis without gastric H. pylori infection is significantly related to H. pylori colonization in the pharynx, and gastric involvement increases the rate of this spread. The gold standart for detection of H. pylori infection is the PCR method.

A pilot study to evaluate the adhesion of oral microorganisms to temporary soft lining materials.

The aim of the study was to compare the adhesion of oral microorganisms to different types of soft liner and acrylic resin surfaces. Three different soft lining materials were applied to cavities formed on the fitting surfaces of prostheses in 17 patients. On days 1, 7 and 14, the specimens were taken out and immediately processed for bacteriological evaluation. The numbers of adhering microorganisms were calculated and the specimens were compared among each other and also with a control group (acrylic resin). Data were analyzed by two-way ANOVA and least squares differences at a significance level of P < 0.05. Among the four materials tested the total number of oral microorganisms adhering to Softliner material was the greatest after each of the time periods tested. Higher numbers of oral bacteria and Candida were shown to adhere to soft lining materials than to acrylic resin. Microbial coverage increased continuously with time and the differences between days 1 and 14 were statistically significant (P < 0.05). Temporary soft lining materials are not resistant to adhesion and possible surface damage caused by oral bacteria, and therefore their use should be limited to short-term periods.

Prevalence of Helicobacter pylori in symptomatic patients and detection of clarithromycin resistance using melting curve analysis.

UNLABELLED: Abstract. BACKGROUND: Clarithromycin is often a component of combination therapies for Helicobacter pylori eradication; however, increases in resistance rates have decreased the success of the treatment. OBJECTIVE: This study was designed to determine the prevalence of H pylori infection in symptomatic patients and to detect clarithromycin resistance rates using melting curve analysis. METHODS: Patients scheduled for upper endoscopy at the Endoscopy Unit of the Department of Gastroenterology, Duzce University, Medical Faculty Hospital, Konuralp/Duzce, Turkey, were assessed for enrollment in the study. Two pairs of gastric biopsy specimens (antrum and corpus) were obtained from each study patient. Histopathologic examination, rapid urease test, culture, and polymerase chain reaction (PCR) of the specimens were used to identify H pylori infection. Clarithromycin resistance was detected using melting curve analysis. RESULTS: Seventy-five patients (41 women, 34 men; mean [SD]age, 42.6 [14.5] years [range, 17-70 years]) were included in the study. Using histopathology and rapid urease test, H pylori was detected in 40 (53.3%) of the 75 specimens. H pylori was detected using PCR in 40 (53.3%) specimens and by culture in 10 (13.3%) specimens. The specificity and sensitivity of PCR and culture were interpreted by comparing them with the results of histopathologic examination and urease tests. The specificity and sensitivity of PCR were 68.6% and 72.5%, respectively, and the specificity and sensitivity of culture were 97.1% and 22.5%, respectively. Of the 40 isolates, 21 (52.5%) were susceptible to clarithromycin, 12 (30.0%) were resistant, and a mixed susceptibility pattern was detected in 7 (17.5%) specimens. H pylori isolates from 19 (79.2%) of the 24 patients who had formerly used clarithromycin showed clarithromycin resistance. CONCLUSIONS: The prevalence of H pylori infection was 53.3% for the symptomatic patients in this study, and 47.5% of the isolates showed clarithromycin resistance using melting curve analysis. The PCR-based system used in this study was accurate for the detection of H pylori infection as well as clarithromycin susceptibility testing directly in biopsy specimens.

[Investigation of erythromycin resistance and resistance phenotypes in group A beta hemolytic streptococci]. / A grubu beta-hemolitik streptokoklarda eritromisin direnç oranlarinin ve direnc fenotipinin arastirilmasi.

Although penicillin resistance has not been determined in group A beta haemolytic streptococci (GABHS) yet, resistance to erythromycin and other macrolids is being reported frequently in the last years. In this study we investigated erythromycin resistance by using agar dilution method in 282 GABHS strains which were isolated from throat cultures that had been evaluated in the Ministry of Health, Ankara Training and Research Hospital's, Microbiology Laboratory. We also determined resistance phenotypes of resistant strains by double disc synergy method using erythromycin and clindamycin discs. Twelve of 282 strains (4.3%) were found resistant to erythromycin; five (41.7%) of which were M phenotype, four (33.3%) of which were constitutive type MLSB phenotype and three (25%) of which were inducible type MLSB phenotype. Investigation of resistance to macrolides that are alternatives to penicillin therapy in GABHS, is very important for the determination of the therapy and also to provide epidemiological data.