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Emerging research suggests gut microbiome may play a role in pancreatic cancer initiation and progression, but cultivation of the cancer microbiome remains challenging. This pilot study aims to investigate the possibility to cultivate pancreatic microbiome from pancreatic cystic lesions associated with invasive cancer. Intra-operatively acquired pancreatic cyst fluid samples showed culture-positivity mainly in the intraductal papillary mucinous neoplasm (IPMN) group of lesions. MALDI-TOF MS profiling analysis shows Gammaproteobacteria and Bacilli dominate among individual bacteria isolates. Among cultivated bacteria, Gammaproteobacteria, particularly Klebsiella pneumoniae, but also Granulicatella adiacens and Enterococcus faecalis, demonstrate consistent pathogenic properties in pancreatic cell lines tested in ex vivo co-culture models. Pathogenic properties include intracellular survival capability, cell death induction, or causing DNA double-strand breaks in the surviving cells resembling genotoxic effects. This study provides new insights into the role of the pancreatic microbiota in the intriguing link between pancreatic cystic lesions and cancer.

Amaç: Kan dolaşımı enfeksiyonu olan hastalarda; etkenin kısa sürede tanımlanması ve uygun antimikrobiyal tedavi uygulanması, morbidite ve mortalitenin azaltılması bakımından oldukça önemlidir. Bu çalışmada, kan kültüründen doğrudan tanımlama ve antibiyotik duyarlılık testlerinin yapılması için geliştirilen yeni bir yöntemin değerlendirilmesi amaçlanmıştır.Gereç ve Yöntem: BacT/Alert 3D sisteminde pozitif sinyal veren kan kültürü örneklerinden yıkama ve santrifüj işlemleri ile bakteriyel çökelti elde edildi. Bu çökeltiden Vitek MS kullanılarak tanımlama yapıldı, ardından VITEK 2 otomatize sisteminde doğrudan antibiyotik duyarlılık testi çalışıldı. Sonuçlar standart yöntem ile karşılaştırıldı.Bulgular: Tanımlama işlemi 80 kan kültürü örneğinde gerçekleştirildi. Doğrudan tanımlama işleminde 73 örnek tanımlandı ve bunlardan 72’si (%90) standart yöntemle uyumlu olarak sonuçlandı. Doğrudan antibiyotik duyarlılık testlerinin %97,9 oranında uyumlu olduğu saptandı. Değerlendirilen 635 antibiyotik duyarlılık sonucu içinde; 10’unda büyük hata, 3’ünde küçük hata olduğu görüldü.Sonuç: Kan kültürü örneklerinden çalışmada uygulanan prosedürler kullanılarak 24 saat içinde, maliyetli reaktifler ya da uzun işlem süresine gereksinim olmadan, standart uygulama sonuçlarına benzer bir şekilde tanımlama ve antibiyotik duyarlılık sonucu elde edilebileceği görülmüştür, Aim: In patients with bloodstream infection; identifying the causative agent in a short time and applying appropriate antimicrobial therapy is very important in terms of reducing morbidity and mortality. In this study, it was aimed to evaluate a new method developed for direct identification and antibiotic susceptibility testing from blood culture.Materials and Methods: Bacterial pellet was obtained from blood culture samples that showed positive signals in the BacT/Alert 3D system by washing and centrifugation. Identification was made from this pellet using Vitek MS, followed by direct antibiotic susceptibility testing in the VITEK 2 automated system. The results were compared with the standard method.Results: Identification was performed on 80 blood culture samples. In the direct identification process, 73 samples were identified, of which 72 (90%) resulted in agreement with the standard method. Direct antibiotic susceptibility tests were found to be compatible with a rate of 97.9%. Among the evaluated 635 antibiotic susceptibility results; it was observed that 10 of them had major errors and 3 of them had minor errors.Conclusions: Using the procedures applied in the study from blood culture samples, without the need for costly reagents or long processing time, it has been observed that identification and antibiotic susceptibility results can be obtained within 24 hours, similar to standard results.

Additional file 1: Table S1. Media used and incubation times according to sample types.

Streptococcus pneumoniae urinary antigen tests (UATs) may be interpreted using automatic readers to potentially automate sample incubation and provide standardized results reading. Here, we evaluated four UATs the BinaxNOW S. pneumoniae Antigen Card (Abbott, Chicago, USA), ImmuView S. pneumoniae and Legionella (SSI Diagnostica, Hillerød, Denmark), STANDARD F S. pneumoniae Ag FIA (SD Biosensor, Gyeonggi, South Korea), and Sofia S. pneumoniae FIA (Quidel Corporation, San Diego, USA) with their respective benchtop readers for their ability to detect S. pneumoniae urinary antigen. We found that these assays had a sensitivity of 76.9–86.5%, and specificity of 84.2–89.7%, with no significant difference found among the four UATs. The assays had a high level of agreement with each other, with 84.5% of samples testing consistently across all four assays. The automatically and visually read test results from the two immunochromatographic assays, BinaxNOW and ImmuView, were compared and showed excellent agreement between the two types of reading. Immunofluorescent-based assays, Sofia and STANDARD F, had significantly less time to detect compared to the two immunochromatographic assays due to having less assay setup procedures and shorter sample incubation times. In conclusion, the four UATs performed similarly in the detection of S. pneumoniae urinary antigen, and readers can bring increased flexibility to running UATs in the clinical routine.

Additional file 3: Table S1. Detailed information on microorganisms and focus of infection isolated from patients with COVID-19.

Additional file 2. Antimicrobial susceptibility patterns.

Background Optimal sampling is critical for the performance of blood cultures (BCs). Most guidelines recommend collecting 40 ml of blood, divided between two venipuncture sites, i.e., multi-sampling strategy (MSS). Sampling through a single venipuncture site, i.e., single-sampling strategy (SSS) is easier; however, the diagnostic performance of SSS compared to MSS remains unknown. Thus, we aimed to study if SSS is non-inferior to MSS for detection of pathogenic microorganisms. Methods A prospective, paired, non-inferiority design was used. Patients with clinically suspected sepsis admitted to an Emergency Department were included. Six BC bottles were simultaneously collected, consisting of four BC bottles from the first arm and two from the other arm. SSS consisted of BC bottles 1, 2, 3, and 4, and MSS consisted of BC bottles 1, 2, 5, and 6. Samples were incubated in a BacT/ALERT BC system. Results The final analysis included 549 episodes. Pathogenic microorganisms were detected in 162 cases (29.5%) with MSS and 160 cases (29.1%) with SSS, yielding an absolute difference of 0.36%, with a 95% confidence interval of -1.33 to 2.06%, which did not exceed the predefined non-inferiority margin of 5%. MSS tended to produce more contaminant growth (7.3% of cases) than SSS (5.3% of cases; p = 0.072). Conclusion The study showed that SSS was non-inferior to MSS in detecting pathogenic microorganisms and supports the use of SSS as a routine method.

BackgroundRecent outbreaks of Candida auris further exemplify that invasive Candida infections are a substantial threat to patients and healthcare systems. Even short treatment delays are associated with higher mortality rates. Epidemiological shifts towards more resistant Candida spp. require careful surveillance.ObjectivesTriggered by the emergence of C auris and by increasing antifungal resistance rates the European Confederation of Medical Mycology developed an international Candida Registry (FungiScope™ CandiReg) to allow contemporary multinational surveillance.MethodsCandiReg serves as platform for international cooperation to enhance research regarding invasive Candida infections. CandiReg uses the General Data Protection Regulation compliant data platform ClinicalSurveys.net that holds the electronic case report forms (eCRF). Data entry is supported via an interactive macro created by the software that can be accessed via any Internet browser.ResultsCandiReg provides an eCRF for invasive Candida infections that can be used for a variety of studies from cohort studies on attributable mortality to evaluations of guideline adherence, offering to the investigators of the 28 ECMM member countries the opportunity to document their cases of invasive Candida infection. CandiReg allows the monitoring of epidemiology of invasive Candida infections, including monitoring of multinational outbreaks. Here, we describe the structure and management of the CandiReg platform.ConclusionCandiReg supports the collection of clinical information and isolates to improve the knowledge on epidemiology and eventually to improve management of invasive Candida infections. CandiReg promotes international collaboration, improving the availability and quality of evidence on invasive Candida infection and contributes to improved patient management.