Comparison of various phenotypic methods in detection of extended-spectrum beta-lactamases

Genişlemiş spektrumlu beta-laktamaz (GSBL) enzimi bazı Gram negatif bakterilerde sefalosporinlere, geniş spektrumlu penisilinlere ve monobaktamlara karşı direnç sorununa neden olmaktadır. Tedavi başarısını arttırmak için bu enzimlerin varlığı çeşitli yöntemlerle araştırılmaktadır. Çalışmamızda Düzce Üniversitesi Araştırma ve Uygulama Hastanesi Klinik Mikrobiyoloji Laboratuvarında üretilen Escherichia coli ve Klebsiella suşlarında GSBL saptanmasında kullanılan fenotipik testlerin [disk difüzyon tarama testi (DDTT), çift disk sinerji testi (ÇDST), E-test] etkinliği karşılaştırılmıştır. Klebsiella spp. ve K.pneumoniae suşlarında, tarama testi ve E-test benzer sonuçlar vermiş iken ÇDST diğer testlerin saptayabildiği GSBL’lerin hepsini saptayamamıştır. Bu testin etkinliği, E-test ile karşılaştırıldığında Klebsiella spp. için p=0.002 ve K.pneumoniae için p=0.041 düzeyinde ve tarama testi ile karşılaştırıldığında Klebsiella spp. için p=0.001 ve K.pneumoniae için p=0.041 düzeyinde, anlamlı olarak düşük bulunmuştur. E.coli suşlarında ise farklı olarak; ÇDST ile E-test sonuçları benzer iken (p=0.187), tarama testi ÇDST’ne göre anlamlı derecede daha etkin bulunmuştur (p<0.05). Sonuç olarak, Gram negatif bakteri kaynaklı infeksiyonların tedavisinde antibiyotiklerin hastaya uygulanıp uygulanmaması konusunda karar verirken ÇDST’nin tek başına kullanılmaması gerektiği, DDTT yapılmasının çok önemli olduğu ve E-test ile doğrulanması gerektiği düşünülmüştür.Extended-spectrum beta-lactamase (ESBL) enzymes of some gram-negative bacteria cause resistance to cephalosporins, broad-spectrum penicillins and monobactams. The presence of these enzymes must be investigated by various methods for the success of the treatment. In this study, the effectiveness of various phenotypic methods for detection of extended-spectrum beta-lactamases [disk diffusion screening test (DDTT), double-disk synergy test (DDST), and E-test] in Escherichia coli and Klebsiella strains isolated in Clinical Microbiology Laboratory of Duzce University, Medical Faculty were compared. Similar results were obtained with screening test and E-test, whereas DDST was found insufficient in detecting ESBL&amp;#8217;s that were determined by other methods. The effectivity of this test was found significantly low, when compared with E-test, with results for Klebsiella spp. (p=0.002) and K.pneumoniae (p=0.041) and screening test, with results for the Klebsiella spp. (p=0.001) and K.pneumoniae (p=0.041). For E.coli strains, results obtained with DDST and E-test (p=0.187) were found similar but, screening test was significantly effective than DDST (p&lt;0.05). As a result, for the decision of the choice of antibiotics in the treatment of Gram-negative bacterial infections, DDST should not be used alone. Use of DDTT is very important and E-test should be used for verification

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

AbstractBackground: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

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

The Role of Meteorological Parameters in COVID-19 Infection

Objective: The SARS-CoV-2 infection outbreak was given the name CoronavirusDisease 2019 (COVID-19) by the World Health Organization. Meteorologicalparameters are one of the most important factors affecting infectious diseases. Theaim of this study is to analyze the correlation between meteorological parameters andthe COVID-19 pandemic.Methods: One hundred ninety-seven COVID-19 patients diagnosed and treated in theTurkish province of Duzce between 29.03.2020 and 04.05.2020 were included in thisstudy.Results: We found the relationship between air quality parameters and COVID-19case numbers revealed significant negative correlation between positive patientnumber and air temperature, relative humidity, and NO2, and significant positivecorrelation with air pressure, but no correlation with PM10, PM2.5, SO2, NO, or CO.Conclusions: Our findings are important as a preliminary study, since interactionsbetween air pollutants and meteorological factors may be involved in the transmissionand pathogenesis of COVID-19, and large-scale studies should now be designed for abetter understanding of these interactions.Amaç: SARS-CoV-2 enfeksiyonu salgınına Dünya Sağlık Örgütü tarafından Coronavirus Hastalığı 2019 (COVID-19) adı verildi. Meteorolojik parametreler bulaşıcı hastalıkları etkileyen en önemli faktörlerdendir. Bu çalışmanın amacı meteorolojik parametreler ile COVID-19 salgını arasındaki ilişkiyi incelemektir. Gereç ve Yöntem: Türkiye Düzce ilinde 29.03.2020 ve 04.05.2020 tarihleri arasında tanı ve tedavi edilen 197 COVID-19 hastası çalışmaya alındı. Bulgular: Hava kalitesi parametreleri ile COVID-19 olgu sayıları arasındaki ilişkinin, Pozitif hasta sayısı ile hava sıcaklığı, bağıl nem ve NO2 arasında anlamlı negatif korelasyon olduğu ve hava basıncı ile anlamlı pozitif korelasyon olduğu, ancak PM10, PM2.5 SO2, NO veya CO ile korelasyon olmadığı saptandı. Sonuç: Bulgularımız bir ön çalışma olarak önemlidir, çünkü hava kirleticileri ile meteorolojik faktörler arasındaki etkileşimler COVID-19'un bulaşması ve patogenezinde rol oynayabilir ve bu etkileşimlerin daha iyi anlaşılması için büyük ölçekli çalışmalar tasarlanmalıdırWOS:00061311550000

SCREENING OF WHEAT GERM PLASM FOR RESISTANCE TO MICRODOCHIUM NIVALE UNDER FIELD CONDITIONS

Pink snow mold, caused by Microdochium nivale, is a serious disease of winter wheat (Triticum aestivum) in the Northern Hemisphere. A field study with artificial inoculation was conducted using 38 winter wheat cultivars during the 2002-2003 at Erzurum, Turkey. Significant differences were detected among cultivars for reaction and yield components to the M. nivale. The most resistant winter wheat cultivars were Harmankaya and Pehlivan, and the most susceptible ones were Aytin-97, Kirgiz-95 and Bayraktar. Yield components decreased significantly in inoculated plants. Pink snow mold resulted in decreased number of spikes per m(2), the grain yield and the plant height of 71.1, 67.3 and 13.2% respectively

Metisiline Dirençli Stafilokoklarda Azalmış Vankomisin Duyarlılığının Araştırılması

Amaç: Son yıllarda metisilin dirençli stafilokoklarda glikopeptid grubu antibiyotiklere karşı azalmış duyarlılıktan sözedilmektedir. Hastanemiz mikrobiyoloji laboratuvarına gönderilen çeşitli klinik örneklerde vankomisine dirençli (VRS),azalmış duyarlı (VIS) ve heterojen dirençli (hVIS) stafilokok suşlarını araştırmayı amaçladık.Gereç ve Yöntemler: Toplam 341 stafilokok suşu incelemeye alındı. S. aureus izolatlarında metisilin direncinisaptamada, oksasilin agar tarama testi kullanıldı. Koagülaz negatif stafilokok izolatlarında metisilin direncininsaptanmasında oksasilin disk difüzyon testine göre duyarlılığı ve özgüllüğü daha yüksek olan sefoksitin disk difüzyon(30 µg) yöntemi kullanıldı. Metisiline karşı dirençli bulunan stafilokoklarda vankomisin direncini saptamada;vankomisin agar tarama, standart E-test, Makro E-test ve popülasyon analiz profili yöntemleri kullanıldı.Bulgular: S. aureus izolatlarının 115’i (%54,2) metisilin dirençli S. aureus (MRSA), koagülaz negatif stafilokokizolatlarının 66’sı (%51,2) metisilin dirençli koagülaz negatif stafilokok (MRKNS) olarak bulundu. 181 metisilindirençli stafilokok suşunun vankomisin agar tarama yöntemine göre ilk 24 saatte sadece ikisinde kuşkulu vankomisineduyarlılığı azalmış stafilokok suşu (VIS) üremesi saptandı. Üreme saptanan suşların her ikisi de S. aureus idi. Metisilindirençli S. aureus suşları standart E Test ve Makro E Test incelemelerinde vankomisine duyarlı olarak bulundu. PAPyöntemi ile hiçbir suşta vankomisin direnci saptanmadı.Sonuç: Çalışmamıza göre laboratuvarımızda izole edilen metisilin dirençli stafilokoklarda vankomisine karşı direnç(VRS), azalmış duyarlılık (VIS) ve heterojen direnç (hVIS) saptanmamıştır. Bu seçkin antibiyotiğin özenlikullanılmasının, gerek tedavi öncesi, gerekse tedavi sırasında hastaların mikrobiyolojik yönden yakın izleminin önemlive gerekli olduğu düşünüldü.Aim: In recent years, decreased susceptibility to glycopeptide group antibiotics has been reported in methicillin resistant staphylococci. We aimed to investigate vancomycin resistant (VRS), vancomycin intermediate (VIS) and heterogeneous resistant (hVIS) staphylococci strains in various clinical specimens sent to our hospital microbiology laboratory. Material and Methods: A total of 341 staphylococcus strains were examined. Oxacillin agar screening test was used to determine methicillin resistance in S. aureus isolates. In the determination of methicillin resistance in coagulase negative staphylococci isolates, disc diffusion (30 µg) method with higher sensitivity and specificity than oxacilin disc diffusion test was used. To determine vancomycin resistance in methicillin-resistant staphylococci; vancomycin agar screening, Standard E-test, Macro E-test and Population analysis profile methods were used. Results: 115 (54.2%) of S. aureus isolates were methicillin resistant S. aureus (MRSA), 66 (51.2%) of coagulase negative staphylococci isolates were found to be methicillin resistant coagulase negative staphylococci (MRCNS). Of the 181 methicillin-resistant staphylococcus strains, only two [strains of suspected vancomycin-susceptible staphylococcus strain (VIS)] were detected in the first 24 hours according to vancomycin agar screening method. Both strains were S. aureus. Methicillin-resistant S. aureus strains were found to be susceptible to vancomycin in standard E Test and Macro E Test examinations. No vancomycin resistance was detected by PAP method. Conclusion: According to our study, vancomycin resistance (VRS), vancomycin intermediate (VIS) and heterogeneous resistance (hVIS) were not detected in methicillin resistant staphylococci isolated in our laboratory. Careful use of this selective antibiotic and microbiological follow-up of the patients before and during treatment were considered important and necessary

Bağışıklığı Baskılanmış Bir Hastada Chryseobacterium indologenes Kaynaklı Trakeobronşit Olgusu

Chryseobacterium indologenes, önceki adıyla Flavobacterium indologenes, toprak, su, bitki ve yiyeceklerde doğal olarak bulunan, hastane ortamında ise su sistemleri ve ıslak yüzeylerde saptanabilen bir bakteridir. İnsan florasında yer almayan bakteri, enfeksiyon etkeni olarak nadiren izole edilmekle birlikte, son yıllarda Chryseobacterium indologenes kaynaklı enfeksiyonların sıklığında artış görülmektedir. Bu raporda, karaciğer transplantasyonundan ardından immünosüpresif tedavi gören bir hastada gelişen Chryseobacterium indologenes kaynaklı trakeobronşitin sunulması amaçlanmıştırFound in water systems and on damp surfaces in the hospital environment, Chryseobacterium indologenes is a naturally occurring bacterium which is rarely isolated in clinical samples. However, in recent years, Chryseobacterium indologenes has increasingly emerged as an agent of infection in patients with suppressed immune systems. This report presents the case of a patient receiving immunosuppressive treatment following a liver transplant who developed Chryseobacterium indologenes-related tracheobronchiti

Bir Üniversite Hastanesindeki Oksijen Tedavisi Nemlendiricilerinin Mikrobiyolojik Açıdan İncelenmesi

Amaç: Hastane enfeksiyonları tıp dünyasının çözüm bulmaya çalıştığı öncelikli sorunlar arasında yeralmaya devam etmektedir. Yatan hastalarda nozokomiyal pnömoniye sebep olabilecek kaynaklardanbiri de oksijen tedavisi sırasında kullanılan nemlendirme cihazlarıdır. Bu çalışmada Düzce Üniversitesi Araştırma ve Uygulama Hastanesi’nin çeşitli servislerinde bulunan oksijen tedavisi nemlendiricilerinimikrobiyolojik açıdan incelemek amaçlanmıştır.Gereç ve Yöntemler: 16.9.2016—20.3.2017 döneminde toplam 102 adet oksijen tedavisi nemlendiricisinden steril kaplara su örnekleri alınarak %5 koyun kanlı agar, eosin methylene blue agar, Sabourauddextrose agar ve Löwenstein–Jensen besiyerine ekim yapıldı. Üreyen koloniler konvansiyonel ve otomatize yöntemler kullanılarak tanımlandı.Bulgular: Yüz iki örneğin 69’unda (%68) toplam 98 adet mikroorganizma üremiştir. Bu organizmaların75’i (%77) bakteri, 23’ü (%23) mantar idi. Bakterilerin 56’sı (%75) nonfermentatif Gram-negatif bakteri(Chryseobacterium indologenes, Pseudomonas aeruginosa, Acinetobacter lwoffii, Acinetobacter baumannii, Acinetobacter ursingii, Acinetobacter haemolyticus, Sphingomonas paucimobilis, Stenotrophomonas maltophilia, Delftia acidovorans, Brevundimonas diminuta); 13’ü (%18) Corynebacterium spp.;2’si (%3) Rhizobium radiobacter; 1’i (%1) Bacillus spp.; 1’i (%1) Neisseria spp.; 1’i (%1) Staphylococcusepidermidis; 1’i ise (%1) Mycobacterium gordonae idi. Mantarların ise 21’i (%91) küf mantarı (Fusariumspp., Aspergillus spp., Penicillium spp., Exophiala spp., Cladosporium spp., Acremonium spp., Cladophialophora spp., Alternaria spp.); 2’si (%9) maya mantarı (Candida krusei, Candida albicans) idi.Tartışma ve Sonuç: Servislerde bulunan oksijen tedavisi nemlendiricilerinin kullanımı ve dezenfeksiyonuile ilgili kurallara yeterince uyulmadığı görülmüştür. Sağlık çalışanlarının bu kurallara riayet konusundaeğitilmesi ve denetlenmesi gerektiği düşünülmüştür.Aim: Hospital infections continue to be a primary problem for which the medical world seeks a solution. One potential cause of nosocomial pneumonia in hospitalized patients is the humidification devices used in oxygen therapy. In this study, we aimed to microbiologically examine the oxygen therapy humidifiers in use in various departments of the Düzce University Research and Training Hospital, Turkey. Materials and Methods: Between 16.9.2016 and 20.3.2017, water samples from a total of 102 oxygen therapy humidifiers were collected into sterile containers for culturing in 5% sheep blood agar, eosin methylene blue agar, Sabouraud dextrose agar, and the Löwenstein–Jensen medium. The colonies grown were identified using conventional and automated methods. Results: A total of 98 microorganisms were grown in 69 (68%) of the 102 samples obtained. Of these organisms, 75 (77%) were bacteria and 23 (23%) fungi. Of the bacteria, 56 (75%) were nonfermentative gram-negative bacteria (Chryseobacterium indologenes, Pseudomonas aeruginosa, Acinetobacter lwoffii, Acinetobacter baumannii, Acinetobacter ursingii, Acinetobacter haemolyticus, Sphingomonas paucimobilis, Stenotrophomonas maltophilia, Delftia acidovorans, Brevundimonas diminuta), 13 (18%) Corynebacterium spp., 2 (3%) Rhizobium radiobacter, 1 (1%) Bacillus spp., 1 (1%) Neisseria spp. 1 (1%) Staphylococcus epidermidis, and 1 (1%) Mycobacterium gordonae. Of the fungi, 21 (91%) were molds (Fusarium spp., Aspergillus spp., Penicillium spp., Exophiala spp., Cladosporium spp., Acremonium spp., Cladophialophora spp., Alternaria spp.) and 2 (9%) yeasts (Candida krusei, Candida albicans). Discussion and Conclusion: It was seen that the regulations for use and disinfection of oxygen therapy humidifiers were not adequately observed in the hospital departments. It was concluded that health professionals should be trained and supervised for compliance with the regulations

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

WOS: 000248245200003PubMed: 24683206Background: 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