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Abstract The spread of multidrug resistant organisms (MDRO) is a global healthcare challenge. Nosocomial outbreaks caused by MDRO are an important contributor to this threat. Computer-based applications facilitating outbreak detection can be essential to address this issue. To allow application reusability across institutions, the various heterogeneous microbiology data representations needs to be transformed into standardised, unambiguous data models. In this work, we present a multi-centric standardisation approach by using openEHR as modelling standard. Data models have been consented in a multicentre and international approach. Participating sites integrated microbiology reports from primary source systems into an openEHR-based data platform. For evaluation, we implemented a prototypical application, compared the transformed data with original reports and conducted automated data quality checks. We were able to develop standardised and interoperable microbiology data models. The publicly available data models can be used across institutions to transform real-life microbiology reports into standardised representations. The implementation of a proof-of-principle and quality control application demonstrated that the new formats as well as the integration processes are feasible. Holistic transformation of microbiological data into standardised openEHR based formats is feasible in a real-life multicentre setting and lays the foundation for developing cross-institutional, automated outbreak detection systems.

The spread of multidrug resistant organisms (MDRO) is a global healthcare challenge. Nosocomial outbreaks caused by MDRO are an important contributor to this threat. Computer-based applications facilitating outbreak detection can be essential to address this issue. To allow application reusability across institutions, the various heterogeneous microbiology data representations needs to be transformed into standardised, unambiguous data models. In this work, we present a multi-centric standardisation approach by using openEHR as modelling standard. Data models have been consented in a multicentre and international approach. Participating sites integrated microbiology reports from primary source systems into an openEHR-based data platform. For evaluation, we implemented a prototypical application, compared the transformed data with original reports and conducted automated data quality checks. We were able to develop standardised and interoperable microbiology data models. The publicly available data models can be used across institutions to transform real-life microbiology reports into standardised representations. The implementation of a proof-of-principle and quality control application demonstrated that the new formats as well as the integration processes are feasible. Holistic transformation of microbiological data into standardised openEHR based formats is feasible in a real-life multicentre setting and lays the foundation for developing cross-institutional, automated outbreak detection systems. [ABSTRACT FROM AUTHOR]

Introduction: The objective of this study was to compare the numeric cut-off index (COI) of automated antigen tests with the cycle-threshold (Ct) value., Materials and Methods: COI values of all samples processed with the Elecsys® SARS-CoV-2 Antigen (Roche, Switzerland) from January to February 2022 were retrieved and the positive were compared to RdRP Cts of Allplex Variants I (Seegene, Korea). COI between 0.6 and 1 were considered indeterminate and overproved by RT-PCR., Results: From 13,937 samples 7944(57%) were positive and 189(1.35%) indeterminate. There was a strong correlation between Cts and COI values at the positive samples, but that was not the case for indeterminates., Conclusions: COI values of the positive samples (COI >1) are comparable to Ct values and may therefore be used as proxy viral loads, however this is not the case for indeterminate samples., Competing Interests: Declaration of competing interest The authors report no conflicts of interest relevant to this article., (Copyright © 2022 Elsevier Inc. All rights reserved.)

From the very beginning of the SARS-CoV-2 pandemic, one of the very few common opinions was that to control the expansion of the virus as many as the possible test had to be done. Antigen tests, being affordable and easy and fast to use, represented a great opportunity to expand the testing capacities of many healthcare systems. However, in 2021 with the appearance of the new SARS-CoV-2 variants, variant tracking strategies had to be implemented, which often included needing a second test to determine the variant of the patients diagnosed with antigen tests or not taking these samples into consideration at all. Therefore, we proposed recovering the positive antigen test devices to include them in our routine variant tracking strategy. The recovered positive antigen test devices obtained from 1st April 2021 to 15the January 2022 were analysed following the variant tracking protocol in force. The results obtained were compared to the positive samples detected by RT-PCR which were processed for variant tracking during the same period. 21,304 samples were processed, 6297 from the recovered positive antigen devices and 15,007 from the standard nasopharyngeal swabs. Only 773 (3.63%) samples were no conclusive, 104 (1.65%) from the recovered antigen devices and 669 (4.46%) from the RT-PCR positive group. This difference was statistically significant (p < 0.01). Taking this into account the proposed method is suitable and very recommendable, as it is an important measure to have a better and immediate picture of the circulating variants in every community., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Purpose: With the rise of the different Variants of Concern (VOC) and Variants of Interest (VOI) in order to control the SARS-CoV-2 pandemic, strategies for accurately tracking these different variants have been developed. While most of these strategies rely heavily on specific PCRs targeting the characteristic mutations of some lineages, several approaches using the alterations at the cycle threshold (Ct) of different commercial PCR diagnostic tests have been described. The objective of this study is to analyse the use of the Ct difference at the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay (Seegene, Korea) between the Nucleocapside (N) and the Spike (S) or RNA-dependent RNA polymerase (RdRP) genes as a preliminary screening for variant tracking., Methods: The samples analysed with the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay from 1 st of March 2021 to 26 th of December 2021 were selected. The Ct values for N, S, RdRP were collected, and the differences between N and S (ΔS) and N and RdRP (ΔRdRP) were calculated. Using ΔS and ΔRdRP a diagnostic test was designed and these results were compared to the routine Variant assessment., Results: The mean ΔS and ΔRdRP were characteristic for Alpha and Delta. This difference was statistically significant. For Every analysed Variant the diagnostic test achieved a higher than 90% sensitivity with a noteworthy performance with the Omicron variant (97% sensitivity and 90% specificity)., Conclusions: The analysis of the Ct alterations at the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay may be a suitable method for an early approach to SARS-CoV-2 variant assessment., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The aim of this study was to investigate the association between vancomycin trough level and clinical outcomes (mortality and nephrotoxicity) among infected paediatric patients with Gram-positive pathogens. We systematically searched the Scopus, EMBASE, Cochrane Central Register of Controlled Trials, PubMed and CINAHL databases up to March 2020. A total of seven retrospective cohort or case-control studies were included to compare clinical effects and safety: three studies set the threshold of vancomycin trough level at 10 mg/L and the others set it at 15 mg/L. Our analysis showed that vancomycin trough level of 10-15 mg/L was associated with significantly lower mortality [<10 mg/L vs. ≥10 mg/L, odds ratio (OR) = 3.21, 95% confidence interval (CI) 1.74-5.91; and <15 mg/L vs. ≥15 mg/L, OR = 0.31, 95% CI 0.10-0.95). The high vancomycin trough group (≥10 mg/L or ≥15 mg/L) showed a higher incidence of nephrotoxicity (<10 mg/L vs. ≥10 mg/L, OR = 0.06, 95% CI 0.03-0.12; and <15 mg/L vs. ≥15 mg/L, OR = 0.28, 95% CI 0.12-0.65). This is the first meta-analysis to reveal the optimal therapeutic range of vancomycin trough level in children. Our findings strongly suggest a superior benefit of vancomycin trough of 10-15 mg/L for paediatric patients., (Copyright © 2021 Elsevier Ltd. All rights reserved.)