Pathogenicity determinants and antibiotic resistance profiles of enterococci from foods of animal origin in Turkey

In this study, the presence of genes responsible for the pathogenicity and antibiotic resistance profile of enterococci isolated from various foodstuffs of animal origin was investigated. The percentage prevalence of enterococci was 54.1% (203/375) and the average count was found to be 3.81 log cfu/ml-g. Species-specific primers revealed Enterococcus faecalis as the predominant species carrying one or more virulence-associated traits of efa, gelE, ace, esp and agg genetic markers. Only one E. faecium isolate (from milk) was positive for the esp gene. Regarding antibiotic resistance, the highest frequency of resistance was observed for tetracycline (21.7%), followed by quinupristin/dalfopristin (13.3%), ciprofloxacin (2.0%), penicillin (2.0%), linezolid (1.0%), ampicillin (1.0%), streptomycin (1.0%), and gentamicin (0.5%). Enterococcus faecalis showed a higher prevalence of antibiotic resistance than other enterococci. The percentage of multidrug resistance among the isolates was 3.4%. Twenty-nine E. faecalis isolates (26.6%) carrying one of the virulence-associated traits were at the same time resistant to at least one antibiotic. Our results show that foods of animal origin, including ready-to-eat products, may be reservoirs of antibiotic-resistant and potentially virulent enterococci

Evaluation of 86 Patients Whom Death While Being Followed up with Pre-Diagnosis of Covid-19

The Coronavirus-19 pandemic continues at full speed, and the number of patients who die from Covıd-19 is increasing. It was aimed to evaluate the demographic information and laboratory findings of 86 patients who died while being followed up in our hospital with a pre-diagnosis of Covıd-19. Identifying these characteristics of deceased patients will be essential to guide clinicians in identifying critically ill patients. Data on demographic information, comorbidities, time from hospitalization to death, molecular test results, thorax CT findings, biochemical findings, culture, antibiotic susceptibility, and the given treatments of the cases were collected from the electronic system Kastamonu Training and Research Hospital. While the RT-PCR test of 21 of the cases was positive, in 9 of the cases, control PCR tests were negative after a while. The CT results of 18 of the 21 initially RT-PCR positive cases were compatible with Covid-19, and the CT result of 3 could not be reached. When the blood test results of the cases were examined, neutrophil increase, white blood cell increase, lymphocyte reduction, and inflammatory markers increase were determined. A total of 43 bacterial growths were found in 21 cases. It has been observed that deaths in patients who were followed up with the pre-diagnosis of Covıd-19 generally occur in older people, males, and those with underlying diseases. It was thought that the cause of death could be underlying diseases, pathologies caused by inflammation, and secondary bacterial infections in addition to viral infection. Clinicians should be more careful about elderly patients, patients with secondary bacterial infections, or patients with neutrophilia, lymphopenia

The evaluation of antibiotic resistance in urinary tract ınfection agent enterobacteriaceae spp. for two years

Amaç: Üriner sistem infeksiyonu (ÜSİ) etkeni Enterobacteriaceae türlerinin iki yıllık antibiyotik direnç oranlarının saptanması amaçlanmıştır. Gereç ve Yöntem: Laboratuvarımıza, 2001-2003 tarihleri arasında ayaktan başvuran hastaların 533’ünde üriner sistem infeksiyonu etkeni izole edilmiş olup, 469’unda Enterobacteriaceae türleri tanımlanmıştır. Enterobacteriaceae izolatlarında antibiyotik duyarlılık testleri CLSI kriterlerine göre Kirby-Bauer disk difüzyon yöntemi ile çalışılmış, A ve U grubu antibiyotiklerden ampisilin, sefazolin, sefalotin, gentamisin, karbenisilin, norfloksasin/ofloksasin, lorakarbef ve nitrofurantoinin sonuçları irdelenmiştir. Bulgular: Hastaların %71.9’u kadın, %28.1’i erkekdir. Hastaların yaş grupları 0-2; 3-15; 16-45; >45 şeklinde sı- nıflandırılmış olup, ÜSİ görülme sıklığının dağılımı sırasıyla %25.3; %28.0; %26.5; %20.3 olarak bulunmuştur. Yaş grupları içerisinde yine kadınların oranlarının daha yüksek bulunduğu, ancak 0-2 yaş grubunda erkelerin oranının (%64,4) daha yüksek olduğu gözlenmiştir. En sık izole edilen tür E.coli (%78)’dir. Diğer türler sırasıyla K.pneumonia, P.mirabilis, K.oxytoca olup sıklıkları sırasıyla %8,7; %5,1 ve %3,1 şeklindedir. P.vulgaris, C.freundii, E.cloaca, M.morgagni ise toplam %3,8 sıklık göstermiştir. Tüm Enterobacteriaceae suşları için direnç oranları ampisilin, karbenisilin ve sefalotine karşı sırasıyla %69,0; %63,8 ve %55,3 olduğu, diğer antibiyotiklere karşı direncin ise %40’nin altında kaldığı gözlenmiştir. Sonuç: Bu çalışmanın bulgularına göre, ÜSİ ampirik tedavisinde sefazolin, gentamisin, norfloksasin/ofloksasin, lorakarbef ve nitrofurantoinin kullanılabilir durumda olduğu gözlenmiştir. Ancak yerel çalışmaların ülkenin bütü-nünü yansıtmakta yetersiz kalacağı düşünülerek, ulusal antibiyotik direnç surveyans sisteminin kurulmasının gerekli olduğu düşünülmektedir. Ayrıca, genel olarak infeksiyon hastalıklarının tedavisinde olduğu gibi ÜSİ vakalarında da antibiyotik duyarlılık testlerinin önemi bir kez daha vurgulanmaktadır

Investigation of the Change in Antibody Levels of COVID-19 RT-PCR Positive Patients Over Time

Introduction: Our aim was to determine the change in antibody response against COVID-19 over time and estimate the duration required for it to decrease to the threshold of the ELISA test in patients with a positive COVID-19 RT-PCR test. The purpose was to present data for epidemiological measures related to the risk of reinfection or the need for booster doses of the vaccine. Materials and Methods: The real-time RT-PCR method was used for diagnosing patients. Serum samples were collected from 177 patients 2-60 days after their COVID-19 RT-PCR test, and a second serum was taken from 35 patients from the first group 94-139 days after the initial sampling. A total of 212 serum samples were included in the study, and the Euroimmun ELISA (Lübeck, Germany) assay was used. Statistical analyses were performed using IBM SPSS Statistics software (version 22.0, IBM Corporation, Chicago, IL) for Windows. Results: The estimated time taken for antibodies to reach the threshold value varied according to immunoglobulin classes, targeted antigen, and disease severity. The longest durations were detected in the group that provided two serum samples, for anti-S IgG antibodies, and for patients with a severe clinical course. In the overall group, the durations were 62, 129, 72, and 41 days after the PCR test for anti-S IgG, anti-NCP IgG, and anti-NCP IgM, respectively. In the group that provided two serum samples, the durations were 197, 252, and 218 days for the same antibodies, respectively. Additionally, it was observed that even the first serum samples were below the threshold values for anti-NCP IgM. In terms of the clinical course, the longest durations were observed in patients with severe illness: 70, 158, 83, and 45 days for the aforementioned immunoglobulins, respectively. Additionally, 32% of patients did not have detectable antibodies. Conclusion: These results indicate that humoral immunity, as measured by anti-S IgG which has the longest duration and is most compatible with protective neutralizing antibodies, may remain protective for over four months and even up to eight months

National Antimicrobial Resistance Surveillance System (NAMRSS) External Quality Assessment Studies: 2011-2016

Establishment of sustainable and evidence-based surveillance systems are recommended for prevention of microbial resistance by the World Health Organization (WHO). As a necessity of these surveillance systems, participants are recommended to implement an external quality assessment (EQA) program. In this scope, National Antimicrobial Resistance Surveillance System (NARSS) has been established within the Public Health Institute of Turkey (PHIT) in our country since 2011. In the scope of this surveillance, NARSS EQA program has been implemented in a cycle per year and four isolates were sent to participants per cycle every year since 2011. In this study, it was aimed to evaluate the six years results of the EQA programs being implemented on NARSS participants between 2011 and 2016. The surveillance system consisted of 118 laboratories. Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumoniae, Enterococcus faecium/faecalis and Acinetobacter baumannii bacteria included in scope of the surveillance were sent to participants.Identification of bacteria to the species level, verification of the antibiotic susceptibility test results and existence of specified resistance of the isolates performed with valid test methods required from the participants. Identified isolates were cultured with routine microbiological methods and sent to participants in ambient temperature in triple carrying pouches inside suitable carrying media via PTT Cargo. The results were entered by means of passwords prepared by PHIT and sent to the web based system. The analysis of results were made with SPSS program. A total of twenty-three isolates were sent to participants between 2011 and 2016. It was determined that participants commonly preferred automated systems for bacterial identification and antibiotic sensitivity test results. The use of MALDI TOF MS system was determined to be raised up to 15.65% in 2016. It has been determined that usually little mistakes were done in bacterial identification but the error rate was high especially in antimicrobial susceptibility test results with close clinical threshold values. Although not required for antibiotic susceptibility test results, it was determined that phenotypic tests have been used more widely in determining the specific resistance mechanisms that are important for epidemiological data. It was determined that 80% of participants have used EUCAST standards in 2016. As a result of this research, we have observed that EQA studies of NARSS EQA are a good performance tool for sustainable and evidence based surveillance studies, that the national antimicrobial resistance data quality is sufficiently good and that the data can be shared on international platforms. In addition, the regular maintenance of national surveillance studies shown that laboratories have positive reflections on self improvement in achieving up to date and accurate results

Haemophilus influenzae in Cystic Fibrosis Cases: A Lower Respiratory Tract Infection Agent

In 288 sputum samples collected from children with cystic fibrosis (CF), Haemophilus influenzae was examined by enriched Columbia agar which is a selective media for routine practice. H. influenzae was the most frequent pathogen (11.4%) with 33 strains, the following one was Pseudomonas aeruginosa (11.1%) with 32 strains. After typing procedures, most of the isolates were found as non-typable strains (33.3%) and among the Biotype-1 (54.5%). The strains were studied for antibiotic susceptibility by Kirby-Bauer disk diffussion method; for ampicillin, as an empiric therapeutic agent, it was found 75.7%. The susceptibility ratios were 100% for imipenem and 51.5% for cephalotin. In CF cases, H. influenzae as a pathogen affecting the prognosis, seems to be an agent that must be investigated

The seropositivity and risk factors for rickettsial infections in selected areas from Black Sea Region of Turkey

Objectives: The aim of this study was to evaluate the seropositivity of rickettsial infections (rickettsioses) and to as-sess risky behaviors for rickettsioses in North Anatolia, which have dense tick population. Materials and methods: Blood samples of 409 voluntary participants were collected in a cross-sectional seropreva-lence research in Samsun-Tekkeköy and 171 from Samsun Regional Laboratory, KTÜ Medical Faculty/Clinic of Infec-tion Diseases and Tokat State Hospital to determine regional characteristics and risk factors of rickettsial infections. The total sample size was 580 persons. A standard questionnaire was performed by a face to face interview with par-ticipants. The 0-4 age group children were not included. The presence of anti-Rickettsia IgG antibodies was tested in blood samples with Indirect Immunoflourescein Antibody (IFA) method.Results: Spotted fever group anti-Rickettsia IgG antibody seropositivity was detected in 68 (11.7%) blood samples. Contrarily, typhus group anti-Rickettsia IgG antibody seropositivity was not found in any participant. With bivariate analyses following variables were found to be significantly correlated with rickettsia seropositivity: education status (p=0.015), age (p=0.001), working in farm (p=0.008), working in garden (p=0.022), agricultural activities (p=0.001), being interested in relaxation activity (p=0.009), animal breeding (p=0.007), milking (p=0.001) and exposure to wild animals (p=0.004). With logistic regression analysis; age [Risk Odds Ratio ‘ROR’=1.03 (95% GA=1.02-1.05)] and ex-posure to wild animals [ROR=1.97 (95% GA=1.12-3.46)] were found to be associated with increased seropositivity.Conclusions: Our results supported the existence of rickettsial diseases in Turkey. Further seroepidemiological in-vestigations are needed to detect incidence/prevalences of rickettsioses and related risky behaviors in our country

The first external quality assurance laboratory proficiencyassessment study of national antimicrobial resistancesurveillance system in Turkey

© 2018, Refik Saydam National Public Health Agency (RSNPHA).Objective: National Antimicrobial Resistance Surveillance System (NAMRSS) was established aiming to determine and track the percentage of antimicrobial resistance in Turkey, and in order to assure the reliability of the system, an external quality assurance laboratory proficiency assessment was performed in September 2011, for the first time. Methods: Four bacterial strains were sent to 77 participating laboratories. The laboratories were asked to perform the bacterial identification and antimicrobial susceptibility tests (AST) according to standard operating procedures of NAMRSS and Clinical and Laboratory Standards Institute. The results were collected using a web-based questionnaire and the data were analysed using SPSS 15.00. Bacterial identification scoring was defined as ten points when genus and species were accurately defined, eight points when genus was accurate but species was wrong, and zero point when it was misdiagnosed or not reported or contaminated. AST scoring included ten points per antibiotic when the result was correct. Two points were subtracted in case of a minor error (reported as susceptible or resistant when intermediate) and ten points in the case of a major or very major error (reported resistant when susceptable or as susceptible when resistant, respectively) during AST. The threshold value was determined as 70%. Results: From the system, 68 laboratories had sent data and analysed. For Klebsiella pneumoniae, Streptococcus pneumoniae, Enterococcus faecium and Pseudomonas aeruginosa the success percentage for the identification of were 92.6%; 91.2%; 89.7% and 98.5%, respectively; and for AST the median/maximum score that could be achieved were 50/80; 28/50; 40/40 and 60/60, respectively. When the success percentages were classified as ≤69.99%; 70.00%-89.99% and ≥ 90.00%, the distribution of the number of the laboratories were 10; 48; and 10 for the success percentage classes, respectively. Conclusion: In this study, the system was considered reliable