[Evaluation of the Rapid Antigen Detection Kit with the Polymerase Chain Reaction for Detection of SARS-CoV-2 in Respiratory Samples]. / Solunum Yolu Örneklerinde SARS-CoV-2 Tespiti için Hizli Antijen Tespit Kitinin Polimeraz Zincir Reaksiyonu ile Birlikte Degerlendirilmesi.

The disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was named as coronavirus disease-2019 (COVID-19) by the World Health Organization (WHO) in February 11, 2020. The rapid diagnosis of COVID-19 patients is essential to reduce the disease spread. The reverse-transcription polymerase chain reaction (RT-PCR) is the gold standard test to diagnose SARS-CoV-2 acute infection. The rapid antigen test which can detect the presence of viral protein antigens in respiratory tract samples is being investigated as an alternative option, especially in cases where RT-PCR is not available or the test capacity is exceeded, due to its faster results, ease of application, low cost and lack of special equipment and personnel. In this study, it was aimed to evaluate the performance of a commercial rapid antigen test using nasopharyngeal samples of COVID-19 patients confirmed with RT-PCR. From the first day of the research, the first 80 consecutively SARS-CoV-2 RT-PCR positive and 40 RT-PCR negative respiratory samples sent to the Medical Microbiology Laboratory for routine SARS-CoV-2 RT-PCR testing were included in the study. RT-PCR tests of the samples were performed in routine studies with the BioSpeedy SARS-CoV-2 RT-PCR kit (Bioeksen, Turkey). Rapid antigen tests were performed with the Wesail COVID-19 antigen test kit (Guangdong, China) simultaneously with RT-PCR tests. Amongst the 80 positive RT-PCR samples, 56 were detected by the rapid antigen test. All the samples detected as positive with the rapid antigen tests were also positive with RT-PCR. There was a moderate agreement between the qualitative results of both tests (Kappa= 0.609, p<0.001). According to the PCR test, the sensitivity, specificity, positive predictive value (PPV), negative predictive value, and accuracy of the rapid antigen test were; 70%, 100%, 100%, 62.5%, and 80% (96/120), respectively. The sensitivities of the rapid antigen test were calculated as 92.6% in 54 samples with a cycle threshold (Ct) value of <17, 88.7% in 62 samples with a Ct value of <20, 77.8% in 72 samples with a Ct value of <22, and 74.7% in 75 samples with a Ct value of <25. According to our study data; the rapid antigen test was found less sensitive than the RT-PCR test. Negative results obtained with rapid antigen testing cannot exclude SARS-CoV-2 infection and must be confirmed by RT-PCR. In addition, according to the ROC analysis of rapid antigen test positivity obtained according to RT-PCR Ct values, the clinical performance of the rapid antigen test is good in samples with Ct values <20. The rapid antigen test should be evaluated as a reliable screening test in patients with high viral load. To the best of our knowledge, there is no other study in the literature performed with the Wesail COVID-19 rapid antigen test kit (Guangdong, China) used in our study. The fact that PPV was found to be 100% even at a low prevalence period of the pandemic will enable positive patients to be screened quickly and effectively with rapid antigen tests in the first step during the high prevalence period of the pandemic. In the light of these data and our results, it can be predicted that using the rapid antigen test as a screening test in the first step and confirming only negative patients with RT-PCR will contribute to the effective management of the pandemic process in terms of both time and cost. As a result of the study, the rapid antigen test with low sensitivity but high PPD can be included as a facilitating test in the first step of the diagnostic algorithm in terms of rapid identification of the patients with high viral load, initiation of treatment and providing filiation.

Prevalence of Sexually Transmitted Diseases in Asymptomatic Renal Transplant Recipients.

OBJECTIVES: Sexually transmitted diseases, which may be asymptomatic, have the potential to cause serious health problems in renal transplant recipients. The aim of this study was to determine the prevalence of sexually transmitted diseases in sexually active asymptomatic renal transplant patients by using real-time multiplex polymerase chain reaction assays. MATERIALS AND METHODS: This prospective controlled study was conducted between November 2016 and January 2017 in our hospital. Our study group included 80 consecutive, sexually active asymptomatic patients (40 men and 40 women) who had undergone renal transplant in our hospital and who presented to our outpatient clinic for routine follow-up. We also included a control group of 80 consecutive, sexually active nontransplant patients (40 men and 40 women). All patient samples were tested for Gardnerella vaginalis and obligate anaerobes (Prevotella bivia, Porphyromonas species), Candida species, Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma species, Trichomonas vaginalis, Neisseria gonorrhoeae, Chlamydia trachomatis, herpes simplex virus 1 and 2, and Cytomegalovirus by real-time multiplex polymerase chain reaction. RESULTS: The prevalences of infection with Gardnerella vaginalis and obligate anaerobes (P = .043), Ureaplasma species (P = .02), and Cytomegalovirus (P = .016) were found to be significantly higher in the study group versus the control group. However, there was no difference between the 2 groups regarding the prevalence of Mycoplasma infection (P = .70). CONCLUSIONS: Sexually transmitted diseases may occur more frequently in sexually active asymptomatic renal transplant recipients than in nontransplanted individuals. Real-time multiplex polymerase chain reaction analysis may be a suitable method for determining these pathogens.

Exploring the Legionella pneumophila positivity rate in hotel water samples from Antalya, Turkey.

The genus Legionella is a fastidious Gram-negative bacteria widely distributed in natural waters and man made water supply systems. Legionella pneumophila is the aetiological agent of approximately 90% of reported Legionellosis cases, and serogroup 1 is the most frequent cause of infections. Legionnaires' disease is often associated with travel and continues to be a public health concern at present. The correct water management quality practices and rapid methods for analyzing Legionella species in environmental water is a key point for the prevention of Legionnaires' disease outbreaks. This study aimed to evaluate the positivity rates and serotyping of Legionella species from water samples in the region of Antalya, Turkey, which is an important tourism center. During January-December 2010, a total of 1403 samples of water that were collected from various hotels (n = 56) located in Antalya were investigated for Legionella pneumophila. All samples were screened for L. pneumophila by culture method according to "ISO 11731-2" criteria. The culture positive Legionella strains were serologically identified by latex agglutination test. A total of 142 Legionella pneumophila isolates were recovered from 21 (37.5%) of 56 hotels. The total frequency of L. pneumophila isolation from water samples was found as 10.1%. Serological typing of 142 Legionella isolates by latex agglutination test revealed that strains belonging to L. pneumophila serogroups 2-14 predominated in the examined samples (85%), while strains of L. pneumophila serogroup 1 were less numerous (15%). According to our knowledge, our study with the greatest number of water samples from Turkey demonstrates that L. pneumophila serogroups 2-14 is the most common isolate. Rapid isolation of L. pneumophila from environmental water samples is essential for the investigation of travel related outbreaks and the possible resources. Further studies are needed to have epidemiological data and to determine the types of L. pneumophila isolates from Turkey.

Successful use of tigecycline for treatment of culture-negative pyogenic vertebral osteomyelitis.

BACKGROUND: Pyogenic vertebral osteomyelitis (PVO) is a severe infection that requires prolonged antimicrobial therapy and/or surgical interventions. Limited data are available on the safety and clinical efficacy of tigecycline in PVO. The objective of this study was to describe the clinical outcomes of patients treated with tigecycline for culture-negative PVO that was unresponsive to empirical antibiotic therapy including intravenous ampicillin-sulbactam plus ciprofloxacin or ampicillin-sulbactam alone. METHODS: We retrospectively reviewed 15 patients with culture-negative PVO from 2009 through 2014. The patients received tigecycline as secondary empirical therapy, after not responding to the first empirical therapy. Clinical success was defined as recovery from symptoms and normalization of laboratory parameters at the end of therapy. Continued clinical success at 24 weeks after the end of the therapy was defined as sustained clinical success. RESULTS: Tigecycline treatment was completed in 14 patients and discontinued in 1 due to severe nausea and vomiting. The mean age of the patients was 67.7 years (range 58-77 years), and 57.1% (8/14) were women. In all, 78.6% (11/14) of patients had risk factors for probable resistant staphylococcal and gram-negative infections such as diabetes mellitus, presence of hemodialysis catheters, and prior antibiotic usage. The average duration of tigecycline treatment was 8.3 weeks (range 6-11 weeks). Sustained clinical success was obtained in all patients. CONCLUSIONS: Tigecycline should be considered as an alternative agent for the treatment of PVO in selected patients due to microbiological activity against resistant gram-positive and gram-negative bacteria.

An outbreak of Pseudomonas aeruginosa infective endocarditis subsequent to coronary angiography.

OBJECTIVES: To describe an endocarditis outbreak affecting three patients due to Pseudomonas aeruginosa infection post coronary angiography performed in the Cardiovascular Surgery and Cardiology Medical Center of a private hospital. METHODS: After recognition of an infection cluster within a onemonth period, the outbreak was reported to Antalya Department of Health and a broad investigation was initiated in order to determine the most probable cause and/or source of nosocomial pseudomonal endocarditis. Patient data were obtained by medical record review as well as interviews with patients or their next of kin. Thirty-six surveillance samples for P. aeruginosa were collected from various locations within the coronary angiography unit. The outbreak research team reviewed the private hospital's Cardiovascular Surgery and Cardiology Medical Center's infection control procedures. The epidemiology of P. aeruginosa was studied through analysis of phenotypic markers, including antimicrobial sensitivity profiles. RESULTS: The infection control audit revealed multiple breaches of infection control procedures. Only 1/36 environmental samples yielded, which was isolated from a radio-opaque solution within an angiography injector pump. P. aeruginosa from the radio-opaque solution had an identical antimicrobial susceptibility pattern to the strain isolated from patients. Both samples were susceptible to all antipseudomonal agents. This outbreak could have been successfully controlled by instituting combined infection control measures. CONCLUSIONS: This outbreak emphasizes the important of adherence to infection control standards and practices for cardiac catheterization, as well as the need for closer collaboration between the Infection Control Committee and coronary angiography personnel.

Un brote epidémico de endocarditis por Pseudomonas aeruginosa secundario a angiografía coronaria / An outbreak of Pseudomonas aeruginosa infective endocarditis subsequent to coronary angiography

Objectives: To describe an endocarditis outbreak affecting three patients due to Pseudomonas aeruginosa infection post coronary angiography performed in the Cardiovascular Surgery and Cardiology Medical Center of a private hospital. Methods: After recognition of an infection cluster within a onemonth period, the outbreak was reported to Antalya Department of Health and a broad investigation was initiated in order to determine the most probable cause and/or source of nosocomial pseudomonal endocarditis. Patient data were obtained by medical record review as well as interviews with patients or their next of kin. Thirty-six surveillance samples for P. aeruginosa were collected from various locations within the coronary angiography unit. The outbreak research team reviewed the private hospital's Cardiovascular Surgery and Cardiology Medical Center's infection control procedures. The epidemiology of P. aeruginosa was studied through analysis of phenotypic markers, including antimicrobial sensitivity profiles. Results: The infection control audit revealed multiple breaches of infection control procedures. Only 1/36 environmental samples yielded, which was isolated from a radio-opaque solution within an angiography injector pump. P. aeruginosa from the radio-opaque solution had an identical antimicrobial susceptibility pattern to the strain isolated from patients. Both samples were susceptible to all antipseudomonal agents. This outbreak could have been successfully controlled by instituting combined infection control measures. Conclusions: This outbreak emphasizes the important of adherence to infection control standards and practices for cardiac catheterization, as well as the need for closer collaboration between the Infection Control Committee and coronary angiography personnel.

Objetivos: Describir un brote de endocarditis por Pseudomonas aeruginosa que afectó a tres pacientes tras habérseles efectuado una coronariografía en el Centro Médico de Cardiología y de Cirugía Cardiovascular (CMC-CCV) de un hospital privado. Métodos: Después de reconocer la aparición de un brote en un periodo de un mes, este hecho fue comunicado al Departamento de Salud de Antalya, iniciándose una exhaustiva investigación para precisar la más probable causa y/o fuente de las endocarditis nosocomiales. Se extrajo de los registros médicos los datos clínicos de los pacientes y se efectuaron entrevistas a los pacientes o sus familiares. Se extrajo 36 muestras medioambientales de vigilancia en busca de P. aeruginosa de diversos sitios dentro de la unidad de coronariografía. Un team que investigó el brote revisó los procedimientos en uso para la prevención de infecciones en el CMC-CCV. Se estudió la epidemiología de la P. aeruginosa mediante análisis de su fenotipos, incluyendo el perfil de susceptibilidad in vitro a antimicrobianos. Resultados: La auditoria comprobó el quiebre de diversas normas de control de infecciones. Sólo 1/36 de las muestras ambientales arrojó el cultivo de P. aeruginosa, a partir de una solución de medio radio-opaco dentro de una bomba inyectora empleada en las angiografías. Los aislados de P. aeruginosa desde la solución del medio radio-opaco tenían idéntico patrón de susceptibilidad antimicrobiana que las cepas recuperadas de los pacientes. Ambos tipos de muestras eran susceptibles a todos los antimicrobianos con actividad anti-pseudomonas. El brote pudo evitarse si se hubieran instaurado una serie de medidas de control de infecciones. Conclusiones: Este brote enfatiza la importancia de adherir a los estándares y prácticas de control de infecciones para la cateterización cardiaca, así como la necesidad de una estrecha colaboración entre el Comité de Control de Infecciones y el personal involucrado en el procedimiento de coronariografía.

[Comparison of Phoenix Automated System, API ID 32 Strep System and LightCycler Enterococcus MGRADE System in the Identification of Clinical Enterococcus Isolates]. / Klinik Enterokok Izolatlarinin Tanimlanmasinda Phoenix Otomatize Sistemi, API ID 32 Strep Sistemi ve Light Cycler Enterococcus MGRADE Sisteminin Karsilastirilmasi

Enterococci which are part of the commensal flora of the human gastrointestinal and genitourinary tracts, are increasing in importance as the cause of hospital-acquired infections. Identification of Enterococcus spp. at the species level is of great importance, for appropriate treatment of patients, infection control and to supply epidemiological data. Conventional methods for the identification of enterococcus isolates at species level is difficult and time consuming. Correct identification of enterococcus isolates in clinical microbiology laboratory by conventional methods is replaced by semi-automated or automated identification and molecular methods. The aim of this study was to evaluate the performance of Phoenix automated system (BD Diagnostic Systems, USA), API Rapid ID 32 Strep System (bioMerieux, France) and Enterococcus MGRADE LightCycler kit (Roche Molecular Biochemicals, Germany) used in real-time polymerase chain reaction (Rt-PCR), for the species level identification of enterococcus strains isolated from clinical specimens. A total of 90 vancomycin susceptible enterococci isolated from different patients were identified by all of the three commercial systems, together with conventional methods. Of the strains, 59 were identified as E.faecalis, 28 were E.faecium, and one of each as E.raffinosus, E.hirae and E.casseliflavus with conventional methods. One E.faecalis strain identified by the conventional system was identified as E.faecium by Phoenix system and one E.faecium strain as E.durans. One E.raffinosus strain identifed by the conventional method was identified as E.avium by API. Conventionally identified four E.faecalis strains were determined to be E.faecium by Rt-PCR and one E.faecium, one E.raffinosus and one E.casseliflavus as E.faecalis. Accordingly, the consistency of Phoenix, API Rapid ID 32 Strep and LightCycler Enterococcus MGRADE systems with the conventional methods were detected as 97.8% (88/90), 98.9% (89/90), and 92.2% (83/90), respectively. In conclusion, all of those three commercial assays are appropriate methods to be used for the identification of enterococci at the species level in the routine clinical microbiology laboratories, due to their high compliance with the conventional method, and their ability to yield the results at the same day.

[Investigation of ESBL types in community acquired urinary Escherichia coli isolates by isoelectric focusing and polymerase chain reaction]. / Toplum kaynakli üriner sistem enfeksiyonu etkeni Escherichia coli suslarinda GSBL enzim tiplerinin izoelektrik odaklama ve polimeraz zincir reaksiyonu yöntemleri ile arastirilmasi

The aim of this study was to determine the extended-spectrum beta-lactamase (ESBL) types by isoelectric focusing (IEF) and polymerase chain reaction (PCR) methods in 56 Escherichia coli strains isolated from urine samples of patients with community-acquired urinary tract infection and determined as ESBL positive with the phenotypic screening tests (E test and combined disk method). IEF revealed that most of the strains produced 1 to 3 different bands, mostly at the isoelectric points 8.2 (n= 44, 79%) compatible with CTX-M. Twenty four (43%) isolates had CTX-M and TEM enzyme bands together, 16 (29%) isolates had only CTX-M enzyme bands, 3 (5%) isolates had CTX-M, TEM, SHV bands, one had CTX-M and SHV enzyme bands together, and one had only TEM band. Eleven E.coli strains did not yield any enzyme bands. PCR analysis revealed that 93% (n= 52) of the isolates had CTX-M, 64% (n= 36) had TEM and 11% (n= 6) had SHV, while 29 (52%) had CTX-M + TEM, three had CTX-M + SHV, and three had CTX-M + TEM + SHV genes together. PER-1 type beta-lactamases were not detected by PCR method. PCR analysis of the eleven strains that yielded no band in IEF showed that 5 strains had CTX-M + TEM, 3 had CTX-M and 3 had TEM enzyme genes. The consistency between IEF and PCR methods for the determination of CTX-M, TEM and SHV enzymes was 85%, 78% and 67%, respectively. Genes encoding ESBL's are usually located on transferrable plasmids that may also carry other resistance determinants. Thus detection of beta-lactamase enzyme types in ESBL positive bacteria is important for the choice of appropriate antimicrobial agents for treatment.

Evaluation of in vitro activities of tigecycline and various antibiotics against Brucella spp.

Brucellosis is a zoonosis with a worldwide distribution and remains a significant public health problem mainly in the developing world. In this study we evaluated the in vitro activities and synergistic effects of antibiotic combinations against blood culture isolates of Brucella spp. In vitro susceptibilities of 76 blood culture isolates of Brucella melitensis and one blood culture isolate of Brucella abortus to doxycycline, streptomycin, gentamicin, trimethoprim-sulfamethoxazole, moxifloxacin, rifampin, ciprofloxacin, and tigecycline were examined by Etest method. For 37 patients with Brucella spp. isolates (36 B. melitensis, 1 B. abortus), antibiotic combinations used for treatment were identified with those tested in vitro for synergy using Etest method. Trimethoprim-sulfamethoxazole and tigecycline were the most active of the compounds tested with MIC90 value of 0.094 mg/l. Among antibiotic combinations only streptomycin-rifampin combination was synergistic for one Brucella spp. isolate. The other antibiotic combinations revealed antagonistic or indifferent activity. Complete clinical response was achieved in all patients. Further studies are required to determine the correlation between the antimicrobial susceptibility and synergy test results with the clinical course of patients. Brucellosis can be adequately treated with existing regimens in our region.