Positive effects of audit and feedback on antimicrobial use in hospitalized patients limited to audited patients

Objective

Audit and feedback is an antimicrobial stewardship (AMS) strategy, with the potential to also optimize antimicrobial use in non-audited patients. This study aimed to determine whether audit and feedback reduce antimicrobial use in both audited and non-audited patients.

Design

Before-after trial with a 1-year intervention period and 2.5-year historical cohort.

Setting

750-bed community hospital in the Netherlands.

Patients

All patients admitted to the urology wards during the 3.5-year study period were observed. Patients were classified as using antimicrobials if any antimicrobial was used for therapeutic reasons. Patients using antimicrobials prophylactically were excluded from measurements.

Intervention

The AMS team provided audit and feedback on antimicrobial use for patients using antimicrobials for 2 days. Retrospectively, antimicrobial use and length of stay (LOS) were compared with the historical cohort.

Results

Audits modified antimicrobial treatment in 52.8% of the cases. De-escalating, stopping, and switching from intravenous to oral treatment accounted for 72% of these modifications. Compared to patients from the cohort, who also used antimicrobials for 2 days, antimicrobial use decreased from 14.21 DDD/patient (95% CI, 13.08-15.34) to 11.45 DDD/patient (95% CI, 8.26-14.64; P = .047) for audited patients. Furthermore, mean LOS decreased from 7.42 days (95% CI, 6.79-8.06) to 6.13 days (95% CI, 5.38-6.89; P = .031). However, looking at all patients admitted to the urology wards, the percentage of patients using antimicrobials and total antimicrobial use remained unchanged.

Conclusions

Audit and feedback reduce antimicrobial use and LOS, but only for audited patients. Positive effects are not automatically transferred to patients for whom no audits have been performed.

Automated multiclass segmentation, quantification, and visualization of the diseased aorta on hybrid PET/CT-SEQUOIA

BACKGROUND

Cardiovascular disease is the most common cause of death worldwide, including infection and inflammation related conditions. Multiple studies have demonstrated potential advantages of hybrid positron emission tomography combined with computed tomography (PET/CT) as an adjunct to current clinical inflammatory and infectious biochemical markers. To quantitatively analyze vascular diseases at PET/CT, robust segmentation of the aorta is necessary. However, manual segmentation is extremely time-consuming and labor-intensive.

PURPOSE

To investigate the feasibility and accuracy of an automated tool to segment and quantify multiple parts of the diseased aorta on unenhanced low-dose computed tomography (LDCT) as an anatomical reference for PET-assessed vascular disease.

METHODS

A software pipeline was developed including automated segmentation using a 3D U-Net, calcium scoring, PET uptake quantification, background measurement, radiomics feature extraction, and 2D surface visualization of vessel wall calcium and tracer uptake distribution. To train the 3D U-Net, 352 non-contrast LDCTs from (2-[18 F]FDG and Na[18 F]F) PET/CTs performed in patients with various vascular pathologies with manual segmentation of the ascending aorta, aortic arch, descending aorta, and abdominal aorta were used. The last 22 consecutive scans were used as a hold-out internal test set. The remaining dataset was randomly split into training (n = 264; 80%) and validation (n = 66; 20%) sets. Further evaluation was performed on an external test set of 49 PET/CTs. The dice similarity coefficient (DSC) and Hausdorff distance (HD) were used to assess segmentation performance. Automatically obtained calcium scores and uptake values were compared with manual scoring obtained using clinical softwares (syngo.via and Affinity Viewer) in six patient images. intraclass correlation coefficients (ICC) were calculated to validate calcium and uptake values.

RESULTS

Fully automated segmentation of the aorta using a 3D U-Net was feasible in LDCT obtained from PET/CT scans. The external test set yielded a DSC of 0.867 ± 0.030 and HD of 1.0 [0.6-1.4] mm, similar to an open-source model with a DSC of 0.864 ± 0.023 and HD of 1.4 [1.0-1.8] mm. Quantification of calcium and uptake values were in excellent agreement with clinical software (ICC: 1.00 [1.00-1.00] and 0.99 [0.93-1.00] for calcium and uptake values, respectively).

CONCLUSIONS

We present an automated pipeline to segment the ascending aorta, aortic arch, descending aorta, and abdominal aorta on LDCT from PET/CT and to accurately provide uptake values, calcium scores, background measurement, radiomics features, and a 2D visualization. We call this algorithm SEQUOIA (SEgmentation, QUantification, and visualizatiOn of the dIseased Aorta) and is available at https://github.com/UMCG-CVI/SEQUOIA. This model could augment the utility of aortic evaluation at PET/CT studies tremendously, irrespective of the tracer, and potentially provide fast and reliable quantification of cardiovascular diseases in clinical practice, both for primary diagnosis and disease monitoring.

Identifying the need for infection-related consultations in intensive care patients using machine learning models

Infection-related consultations on intensive care units (ICU) have a positive impact on quality of care and clinical outcome. However, timing of these consultations is essential and to date they are typically event-triggered and reactive. Here, we investigate a proactive approach to identify patients in need for infection-related consultations by machine learning models using routine electronic health records. Data was retrieved from a mixed ICU at a large academic tertiary care hospital including 9684 admissions. Infection-related consultations were predicted using logistic regression, random forest, gradient boosting machines, and long short-term memory neural networks (LSTM). Overall, 7.8% of admitted patients received an infection-related consultation. Time-sensitive modelling approaches performed better than static approaches. Using LSTM resulted in the prediction of infection-related consultations in the next clinical shift (up to eight hours in advance) with an area under the receiver operating curve (AUROC) of 0.921 and an area under the precision recall curve (AUPRC) of 0.541. The successful prediction of infection-related consultations for ICU patients was done without the use of classical triggers, such as (interim) microbiology reports. Predicting this key event can potentially streamline ICU and consultant workflows and improve care as well as outcome for critically ill patients with (suspected) infections.

Improved [18F]FDG PET/CT Diagnostic Accuracy for Infective Endocarditis Using Conventional Cardiac Gating or Combined Cardiac and Respiratory Motion Correction (CardioFreezeTM)

Infective endocarditis (IE) is a serious and diagnostically challenging condition. [18F]FDG PET/CT is valuable for evaluating suspected IE, but it is susceptible to motion-related artefacts. This study investigated the potential benefits of cardiac motion correction for [18F]FDG PET/CT. In this prospective study, patients underwent [18F]FDG PET/CT for suspected IE, combined with a conventional cardiac gating sequence, a data-driven cardiac and respiratory gating sequence (CardioFreezeTM), or both. Scans were performed in adherence to EANM guidelines and assessors were blinded to patients' clinical contexts. Final diagnosis of IE was established based on multidisciplinary consensus after a minimum of 4 months follow-up and surgical findings, whenever performed. Seven patients participated in the study, undergoing both an ungated [18F] FDG-PET/CT and a scan with either conventional cardiac gating, CardioFreezeTM, or both. Cardiac motion correction improved the interpretability of [18F]FDG PET/CT in four out of five patients with valvular IE lesions, regardless of the method of motion correction used, which was statistically significant by Wilcoxon's signed rank test: p = 0.046. In one patient the motion-corrected sequence confirmed the diagnosis of endocarditis, which had been missed on non-gated PET. The performance of the two gating sequences was comparable. In conclusion, in this exploratory study, cardiac motion correction of [18F]FDG PET/CT improved the interpretability of [18F]FDG PET/CT. This may improve the sensitivity of PET/CT for suspected IE. Further larger comparative studies are necessary to confirm the additive value of these cardiac motion correction methods.

Added value of semi-quantitative analysis of [18F]FDG PET/CT for the diagnosis of device-related infections in patients with a left ventricular assist device

AIMS

Left ventricular assist devices (LVADs) improve quality of life and survival in patients with advanced heart failure, but device-related infections (DRIs) remain cumbersome. We evaluated the diagnostic capability of [18F]FDG PET/CT, factors affecting its accuracy, and the additive value of semi-quantitative analysis for the diagnosis of DRI.

METHODS AND RESULTS

LVAD recipients undergoing [18F]FDG PET/CT between 2012 and 2020 for suspected DRI were retrospectively included. [18F]FDG PET/CT was performed and evaluated in accordance with EANM guidelines. The final diagnosis of DRI, based on multidisciplinary consensus and findings during surgery, whenever performed, was used as the reference for diagnosis. 41 patients were evaluated for 59 episodes of suspected DRI. The clinical evaluation established driveline infection in 32 (55%) episodes, central device infection in 6 (11%), and combined infection in 2 (4%). Visual analysis of [18F]FDG PET/CT achieved a sensitivity and specificity for driveline infections of 0.79 and 0.71, respectively, whereas semi-quantitative analysis achieved a sensitivity and specificity of 0.94 and 0.83, respectively. For central device component infection, visual analysis of [18F]FDG PET/CT achieved a sensitivity and specificity of 0.75 and 0.60, respectively. Semi-quantitative analysis using SUVratio achieved a sensitivity and specificity of 1.0 and 0.8, respectively. The increase of specificity for central component infection was statistically significant (P = 0.05).

CONCLUSIONS

[18F]FDG PET/CT reliably predicts the presence of DRI in LVAD recipients. Semi-quantitative analysis may increase the specificity of [18F]FDG PET/CT for the analysis of central device component infection and should be considered in equivocal cases after visual analysis.

Genomic-regions associated with cold stress tolerance in Asia-adapted tropical maize germplasm

Maize is gaining impetus in non-traditional and non-conventional seasons such as off-season, primarily due to higher demand and economic returns. Maize varieties directed for growing in the winter season of South Asia must have cold resilience as an important trait due to the low prevailing temperatures and frequent cold snaps observed during this season in most parts of the lowland tropics of Asia. The current study involved screening of a panel of advanced tropically adapted maize lines to cold stress during vegetative and flowering stage under field conditions. A suite of significant genomic loci (28) associated with grain yield along and agronomic traits such as flowering (15) and plant height (6) under cold stress environments. The haplotype regression revealed 6 significant haplotype blocks for grain yield under cold stress across the test environments. Haplotype blocks particularly on chromosomes 5 (bin5.07), 6 (bin6.02), and 9 (9.03) co-located to regions/bins that have been identified to contain candidate genes involved in membrane transport system that would provide essential tolerance to the plant. The regions on chromosome 1 (bin1.04), 2 (bin 2.07), 3 (bin 3.05-3.06), 5 (bin5.03), 8 (bin8.05-8.06) also harboured significant SNPs for the other agronomic traits. In addition, the study also looked at the plausibility of identifying tropically adapted maize lines from the working germplasm with cold resilience across growth stages and identified four lines that could be used as breeding starts in the tropical maize breeding pipelines.

Better antimicrobial resistance data analysis and reporting in less time

Objectives

Insights about local antimicrobial resistance (AMR) levels and epidemiology are essential to guide decision-making processes in antimicrobial use. However, dedicated tools for reliable and reproducible AMR data analysis and reporting are often lacking. We aimed to compare traditional data analysis and reporting versus a new approach for reliable and reproducible AMR data analysis in a clinical setting.

Methods

Ten professionals who routinely work with AMR data were provided with blood culture test results including antimicrobial susceptibility results. Participants were asked to perform a detailed AMR data analysis in a two-round process: first using their software of choice and next using our newly developed software tool. Accuracy of the results and time spent were compared between both rounds. Finally, participants rated the usability using the System Usability Scale (SUS).

Results

The mean time spent on creating the AMR report reduced from 93.7 to 22.4 min (P < 0.001). Average task completion per round changed from 56% to 96% (P < 0.05). The proportion of correct answers in the available results increased from 37.9% in the first to 97.9% in the second round (P < 0.001). Usability of the new tools was rated with a median of 83.8 (out of 100) on the SUS.

Conclusions

This study demonstrated the significant improvement in efficiency and accuracy in standard AMR data analysis and reporting workflows through open-source software. Integrating these tools in clinical settings can democratize the access to fast and reliable insights about local microbial epidemiology and associated AMR levels. Thereby, our approach can support evidence-based decision-making processes in the use of antimicrobials.

Host DNA depletion can increase the sensitivity of Mycobacterium spp. detection through shotgun metagenomics in sputum

Identification and phenotypic drug-susceptibility testing for mycobacteria are time-consuming and challenging but essential for managing mycobacterial infections. Next-generation sequencing (NGS) technologies can increase diagnostic speed and quality, but standardization is still lacking for many aspects (e.g., unbiased extraction, host depletion, bioinformatic analysis). Targeted PCR approaches directly on sample material are limited by the number of targets that can be included. Unbiased shotgun metagenomics on direct material is hampered by the massive amount of host DNA, which should be removed to improve the microbial detection sensitivity. For this reason, we developed a method for NGS-based diagnosis of mycobacteria directly from patient material. As a model, we used the non-tuberculous mycobacterium (NTM) Mycobacterium abscessus. We first compared the efficiency of three different DNA extraction kits for isolating DNA (quality and concentration). The two most efficient kits were then used in a follow-up study using artificial sputum. Finally, one extraction kit was selected and further evaluated for DNA isolation from a patients’ sputum mixture spiked with M. abscessus at three concentrations (final concentrations 108, 107, 106  CFU/ml). The spiked sputum samples were processed with and without saponin treatment (ST) in combination with DNAse treatment prior to bacterial DNA extraction to evaluate the recovery of bacteria and depletion of host DNA by PCR and Illumina sequencing.

While Ct values of the qPCR targeting mycobacterial ITS DNA remained rather stable, Ct values in the qPCR targeting the human β-actin gene increased by five Ct values in ST samples. In subsequent Illumina sequencing, a decrease of 89% of reads mapped to the human genome was observed in ST samples. The percentage of reads mapped to M. abscessus (108 CFU/ml) increased by 89%, and the sequencing depth increased two times when undergoing ST.

In conclusion, the sensitivity of M. abscessus detection in artificial sputum was increased using a saponin pre-treatment step. The saponin followed by the DNase I treatment approach could be efficiently applied to detect and characterize mycobacterial infections, including tuberculosis, directly from sputum.

Scientific advisory on nocturnal hypoglycemia in insulin-treated patients with diabetes: Recommendations from Indian experts

INTRODUCTION

Insulin is one of the commonly prescribed glucose lowering agents in diabetes. Hypoglycemia is the most common complication, and severe hypoglycemia is the most serious complication of insulin therapy. Almost half of all severe hypoglycemia episodes (HEs) occur at night. However, patients are often unaware of their nocturnal hypoglycaemia (NH) risk. Additionally, both healthcare professionals and patients find it difficult to manage NH. The purpose of this expert group meeting is to improve NH awareness and provide guidance for the physicians to recognize and manage NH.

METHOD

The panel of experts in an e-board deliberated extensively upon the available literature and guidelines on hypoglycemia and NH discussed the consensus on definition, detection, reporting, monitoring, treatment, and optimization of therapy in NH.

RESULT

& Conclusion: Though there are many guidelines on the management of HEs in patients with diabetes, very few touch the topic of NH. This scientific advisory on management of NH in insulin treated patients with diabetes is formulated to address this gap in understanding regarding management of NH. The experts provide recommendations for the nocturnal window, defining NH based on blood glucose values, recognition, prevention and management of NH.

Mapping twenty years of antimicrobial resistance research trends

OBJECTIVE

Antimicrobial resistance (AMR) is a global threat to health and healthcare. In response to the growing AMR burden, research funding also increased. However, a comprehensive overview of the research output, including conceptual, temporal, and geographical trends, is missing. Therefore, this study uses topic modelling, a machine learning approach, to reveal the scientific evolution of AMR research and its trends, and provides an interactive user interface for further analyses.

METHODS

Structural topic modelling (STM) was applied on a text corpus resulting from a PubMed query comprising AMR articles (1999-2018). A topic network was established and topic trends were analysed by frequency, proportion, and importance over time and space.

RESULTS

In total, 88 topics were identified in 158,616 articles from 166 countries. AMR publications increased by 450% between 1999 and 2018, emphasizing the vibrancy of the field. Prominent topics in 2018 were Strategies for emerging resistances and diseases, Nanoparticles, and Stewardship. Emerging topics included Water and environment, and Sequencing. Geographical trends showed prominence of Multidrug-resistant tuberculosis (MDR-TB) in the WHO African Region, corresponding with the MDR-TB burden. China and India were growing contributors in recent years, following the United States of America as overall lead contributor.

CONCLUSION

This study provides a comprehensive overview of the AMR research output thereby revealing the AMR research response to the increased AMR burden. Both the results and the publicly available interactive database serve as a base to inform and optimise future research.

Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis

Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) isolates can be used to get an accurate diagnosis, to guide clinical decision making, to control tuberculosis (TB) and for outbreak investigations. We evaluated the performance of long-read (LR) and/or short-read (SR) sequencing for anti-TB drug-resistance prediction using the TBProfiler and Mykrobe tools, the fraction of genome recovery, assembly accuracies and the robustness of two typing approaches based on core-genome SNP (cgSNP) typing and core-genome multi-locus sequence typing (cgMLST). Most of the discrepancies between phenotypic drug-susceptibility testing (DST) and drug-resistance prediction were observed for the first-line drugs rifampicin, isoniazid, pyrazinamide and ethambutol, mainly with LR sequence data. Resistance prediction to second-line drugs made by both TBProfiler and Mykrobe tools with SR- and LR-sequence data were in complete agreement with phenotypic DST except for one isolate. The SR assemblies were more accurate than the LR assemblies, having significantly (P <0.05) fewer indels and mismatches per 100 kbp. However, the hybrid and LR assemblies had slightly higher genome fractions. For LR assemblies, Canu followed by Racon, and Medaka polishing was the most accurate approach. The cgSNP approach, based on either reads or assemblies, was more robust than the cgMLST approach, especially for LR sequence data. In conclusion, anti-TB drug-resistance prediction, particularly with only LR sequence data, remains challenging, especially for first-line drugs. In addition, SR assemblies appear more accurate than LR ones, and reproducible phylogeny can be achieved using cgSNP approaches.

The Visual Dictionary of Antimicrobial Stewardship, Infection Control, and Institutional Surveillance Data

Objectives: Data and data visualization are integral parts of (clinical) decision-making in general and stewardship (antimicrobial stewardship, infection control, and institutional surveillance) in particular. However, systematic research on the use of data visualization in stewardship is lacking. This study aimed at filling this gap by creating a visual dictionary of stewardship through an assessment of data visualization (i.e., graphical representation of quantitative information) in stewardship research. Methods: A random sample of 150 data visualizations from published research articles on stewardship were assessed (excluding geographical maps and flowcharts). The visualization vocabulary (content) and design space (design elements) were combined to create a visual dictionary. Additionally, visualization errors, chart junk, and quality were assessed to identify problems in current visualizations and to provide improvement recommendations. Results: Despite a heterogeneous use of data visualization, distinct combinations of graphical elements to reflect stewardship data were identified. In general, bar (n = 54; 36.0%) and line charts (n = 42; 28.1%) were preferred visualization types. Visualization problems comprised color scheme mismatches, double y-axis, hidden data points through overlaps, and chart junk. Recommendations were derived that can help to clarify visual communication, improve color use for grouping/stratifying, improve the display of magnitude, and match visualizations to scientific standards. Conclusion: Results of this study can be used to guide data visualization creators in designing visualizations that fit the data and visual habits of the stewardship target audience. Additionally, the results can provide the basis to further expand the visual dictionary of stewardship toward more effective visualizations that improve data insights, knowledge, and clinical decision-making.

18F-FDG-Uptake in Mediastinal Lymph Nodes in Suspected Prosthetic Valve Endocarditis: Predictor or Confounder?

Introduction: Prosthetic valve endocarditis (PVE) is a serious disease affecting ~0.4% of prosthetic valve recipients per year. ¹⁸F-FDG-PET/CT has high sensitivity and specificity for PVE and is included as major criterion for the diagnosis in recent guidelines of the European Society of Cardiology. We addressed the question whether increased FDG-uptake in mediastinal lymph nodes could help to support the visual diagnostic assessment of PVE. Methods: In this sub-analysis of a previously published retrospective multicentre study, 160 unique patients were identified who underwent ¹⁸F-FDG-PET/CT for evaluation of suspected PVE. ¹⁸F-FDG-PET/CT was performed in adherence to the European Association of Nuclear Medicine guidelines of 2015 and scans were assessed for signs of mediastinal lymph node activity by 2 experienced nuclear medicine physicians who were blinded to clinical context. Clinical diagnosis of PVE had been established based on surgical findings or multidisciplinary consensus after a 1-year follow-up in 80 of 160 patients (50%). Results: In total, 52 patients showed increased mediastinal lymph node activity. Mediastinal lymph node activity on ¹⁸F-FDG-PET/CT did not increase diagnostic accuracy when added to the visual analysis of scans for signs of PVE: X ²: 0.118, p = 0.731). After excluding patients with known confounders for ¹⁸F-FDG-PET/CT, namely use of Bioglue® during prosthetic valve implantation and C-reactive protein levels below 40 mg/L, mediastinal lymph node activity was still not of additional diagnostic value compared to visual analysis alone (X²:0.129, p = 0.723). Discussion: Assessment of mediastinal lymph node activity did not improve ¹⁸F-FDG-PET/CT diagnostic accuracy for suspected PVE compared to visual assessment of the valve alone, as it seems to be a rather a specific finding, that might be caused by sternal wound or mediastinal infections or even by subclinical respiratory infections. Future studies might elucidate whether increased FDG active lymph nodes indicate a high-risk patient group and whether more detailed assessment of mediastinal lymph nodes could improve their additional diagnostic benefit.

18F-FDG PET/CT in Infective Endocarditis: Indications and Approaches for Standardization

Purpose of Review

Additional imaging modalities, such as FDG-PET/CT, have been included into the workup for patients with suspected infective endocarditis, according to major international guidelines published in 2015. The purpose of this review is to give an overview of FDG-PET/CT indications and standardized approaches in the setting of suspected infective endocarditis.

Recent Findings

There are two main indications for performing FDG-PET/CT in patients with suspected infective endocarditis: (i) detecting intracardiac infections and (ii) detection of (clinically silent) disseminated infectious disease. The diagnostic performance of FDG-PET/CT for intracardiac lesions depends on the presence of native valves, prosthetic valves, or implanted cardiac devices, with a sensitivity that is poor for native valve endocarditis and cardiac device-related lead infections, but much better for prosthetic valve endocarditis and cardiac device-related pocket infections. Specificity is high for all these indications. The detection of disseminated disease may also help establish the diagnosis and/or impact patient management.

Summary

Based on current evidence, FDG-PET/CT should be considered for detection of disseminated disease in suspected endocarditis. Absence of intracardiac lesions on FDG-PET/CT cannot rule out native valve endocarditis, but positive findings strongly support the diagnosis. For prosthetic valve endocarditis, standard use of FDG-PET/CT is recommended because of its high sensitivity and specificity. For implanted cardiac devices, FDG-PET/CT is also recommended, but should be evaluated with careful attention to clinical context, because its sensitivity is high for pocket infections, but low for lead infections. In patients with prosthetic valves with or without additional aortic prosthesis, combination with CTA should be considered. Optimal timing of FDG-PET/CT is important, both during clinical workup and technically (i.e., post tracer injection). In addition, procedural standardization is key and encompasses patient preparation, scan acquisition, reconstruction, subsequent analysis, and clinical interpretation. The recommendations discussed here will hopefully contribute to improved standardization and enhanced performance of FDG-PET/CT in the clinical management of patients with suspected infective endocarditis.

The value of 18F-FDG PET/CT for the diagnosis of device related infections in patients with a left ventricular assist device - a dual centre study

Funding Acknowledgements

Type of funding sources: Private company. Main funding source(s): Partnership UMCG Siemens for building the future of Health (PUSH)

Background

Left ventricular assist devices (LVADs) are increasingly used for the treatment of end-stage heart failure. LVADs improve quality of life and long-term survival, but device specific infections remain cumbersome. These infections can lead to life threatening complications and are difficult to diagnose with conventional radiological imaging. In this study, FDG-PET/CT accuracy for the diagnosis of LVAD specific infections was evaluated with specific focus on potential confounders and the additive value of semi-quantitative analysis.

Materials/methods

All LVAD recipients with an available FDG-PET/CT from September 2013 until August 2020 in two LVAD centres in the Netherlands, with a suspicion of driveline and/or central device infection were included. FDG-PET/CT was performed according to European Association of Nuclear Medicine (EANM) guidelines. Potential confounders were documented and assessors were blinded to the clinical context of included patients. Assessment of FDG-PET/CT was performed visually and semi-quantitatively with 6 regions of interest alongside the driveline and central device components. The final clinical diagnosis of either driveline infection or central device infection, based on findings during surgical intervention or multidisciplinary consensus, was used as the reference for diagnosis.

Results

In total 38 patients (average age 55 years, 84% males) were evaluated for a total of 55 episodes of suspected device-specific infection. Clinical evaluation established driveline infection in 28 cases, central device infection in 7 and combined infection in 4. Visual analysis obtained  a sensitivity and specificity of 0.83 and 0.75 respectively, in differentiation between infected and non-infected drivelines. Visual analysis of FDG-PET/CT of central device components showed excellent sensitivity: 1.0, but suffered from poor specificity: 0.23.  Semi-quantitative analysis using a SUVmax was comparable to visual analysis for establishing driveline infections, with a sensitivity and specificity of 0.80 and 0.84 respectively, while for central device infections, semi-quantitative analysis using a SUVratio outperformed visual analysis, with a sensitivity and specificity reaching 0.88 and 0.90 respectively.

Conclusions

FDG-PET/CT is a valuable tool for the assessment of device-specific infections in LVAD recipients. Semi-quantitative analysis can significantly increase diagnostic accuracy of FDG-PET/CT for the analysis of the central device components and should be considered in cases where the diagnosis cannot be rejected based on visual analysis.

Genome-wide association mapping in maize: status and prospects

Genome-wide association study (GWAS) provides a robust and potent tool to retrieve complex phenotypic traits back to their underlying genetics. Maize is an excellent crop for performing GWAS due to diverse genetic variability, rapid decay of linkage disequilibrium, availability of distinct sub-populations and abundant SNP information. The application of GWAS in maize has resulted in successful identification of thousands of genomic regions associated with many abiotic and biotic stresses. Many agronomic and quality traits of maize are severely affected by such stresses and, significantly affecting its growth and productivity. To improve productivity of maize crop in countries like India which contribute only 2% to the world's total production in 2019-2020, it is essential to understand genetic complexity of underlying traits. Various DNA markers and trait associations have been revealed using conventional linkage mapping methods. However, it has achieved limited success in improving polygenic complex traits due to lower resolution of trait mapping. The present review explores the prospects of GWAS in improving yield, quality and stress tolerance in maize besides, strengths and challenges of using GWAS for molecular breeding and genomic selection. The information gathered will facilitate elucidation of genetic mechanisms of complex traits and improve efficiency of marker-assisted selection in maize breeding.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02799-4.

The tripartite insurance model (TIM): a financial incentive to prevent outbreaks of infections due to multidrug-resistant microorganisms in hospitals

Healthcare-associated infections caused by multidrug-resistant organisms (MDROs) constitute a major challenge worldwide, but care providers are often not sufficiently incentivized to implement recommended infection prevention measures to prevent the spread of such infections. We propose a new approach which creates incentives for hospitals, external laboratories and insurers to collaborate on preventing MDRO outbreaks by testing more and implementing infection prevention measures. This tripartite insurance model (TIM) redistributes the costs of preventing and combating MDRO outbreaks in a way that all parties benefit from reducing the number of outbreaks.

Cropland trees need to be included for accurate model simulations of land-atmosphere heat fluxes, temperature, boundary layer height, and ozone

Trees significantly impact land-atmosphere feedbacks through evapotranspiration, photosynthesis and isoprene emissions. These processes influence the local microclimate, air quality and can mitigate temperature extremes and sequester carbon dioxide. Despite such importance, currently only 5 out of 15 atmospheric chemistry climate models even partially account for the presence of cropland trees. We first show that the tree cover over intensely farmed regions in Asia, Australia and South America is significantly underestimated (e.g. only 1-3% tree cover over north-India) in the Model of Emissions of Gases and Aerosol from Nature (MEGAN) and absent in Noah land-surface module of the Weather Research and Forecasting (WRF-Chem) Model. By including the actual tree cover (~10%) over the north-west Indo Gangetic Plain in the Noah land-surface module of the WRF-Chem and the MEGAN module, during the rice growing monsoon season in August, we find that the latent heat flux alone increases by 100%-300% while sensible heat flux reduces by 50%-100%, leading to a reduction in daytime boundary layer height by 200-400 m. This greatly improves agreement between the modelled and measured temperature, boundary layer height and surface ozone, which were earlier overestimated and isoprene and its oxidation products which were earlier underestimated. Mitigating peak daytime temperatures and ozone improves rice production by 10 to 20%. Our findings from north west Indo-Gangetic Plain establish that such plantations mitigate heat stress, and have beneficial effects on crop yields while also sequestering carbon. Expanding agroforestry practices to 50% of the cropland area could result in up to 40% yield gain regionally. Implementing such strategies globally could increase crop production and sequester 0.3-30 GtC per year, and therefore future climate mitigation and food security efforts should consider stakeholder participation for increased cropland agroforestry in view of its beneficial effects.

Relationship between 18F-FDG Uptake in the Oral Cavity, Recent Dental Treatments, and Oral Inflammation or Infection: A Retrospective Study of Patients with Suspected Endocarditis

[18F]-fluorodeoxyglucose positron emission tomography ([18F]FDG PET/CT) has proven to be a useful diagnostic tool in patients with suspected infective endocarditis (IE), but is conflicting in relation to dental procedures.

QUESTIONS

Is there a correlation between [18F]FDG PET/CT findings, recent dental treatment, and an affected oral cavity? (2) Is there a correlation between infective endocarditis (IE), oral health status, and (extra)cardiac findings on [18F]FDG PET/CT?

METHODS

This retrospective study included 52 patients. All [18F]FDG PET/CT scans were examined visually by pattern recognition using a three-point scale and semi-quantified within the volume of interest (VOI) using SUVmax.

RESULTS

19 patients were diagnosed with IE (group 1), 14 with possible IE (group 2), and 19 without IE based on the modified Duke criteria (group 3). No correlation was found between visual PET and SUVmax and sites of oral inflammation and infection. The visual PET scores and SUVmax were not significantly different between all groups. A significant difference in the SUVmax of the valve between all groups was observed.

CONCLUSIONS

This study suggests that no correlation exists between the PET findings in the oral cavity and dental treatments or inflammation/infection. No correlation between IE, actual oral health status, and extra-cardiac findings was demonstrated. Additional research is needed to conclude whether [18F]FDG PET/CT imaging is a reliable diagnostic modality for oral inflammation and infection sites.

The value of 18F-FDG PET/CT for the diagnosis of device-related infections in patients with a left ventricular assist device: a systematic review and meta-analysis

Background

Left ventricular assist devices (LVADs) are increasingly used for the treatment of advanced heart failure. LVADs improve quality of life and decrease mortality, but the driveline carries substantial risk for major infections. These device-related LVAD and driveline infections are difficult to diagnose with conventional imaging. We reviewed and analysed the current literature on the additive value of ¹⁸F-fluorodeoxyglucose positron emission tomography combined with computed tomography (FDG-PET/CT) imaging for the diagnosis of LVAD-related infections.”

Materials/methods

We performed a systematic literature review using several databases from their inception until the 31st of December, 2019. Studies investigating the diagnostic performance of FDG-PET/CT in patients with suspected LVAD infection were retrieved. After a bias risk assessment using QUADAS-2, a study-aggregate meta-analysis was performed on a per examination-based analysis.

Results

A total of 10 studies were included in the systematic review, eight of which were also eligible for study-aggregate meta-analysis. For the meta-analysis, a total of 256 FDG-PET/CT scans, examining pump/pocket and/or driveline infection, were acquired in 230 patients. Pooled sensitivity of FDG-PET/CT was 0.95 (95% confidence interval (CI) 0.89–0.97) and pooled specificity was 0.91 (95% CI 0.54–0.99) for the diagnosis of device-related infection. For pump/pocket infection, sensitivity and specificity of FDG-PET/CT were 0.97 (95%CI 0.69–1.00) and 0.93 (95%CI 0.64–0.99), respectively. For driveline infection, sensitivity and specificity were 0.96 (95%CI 0.88–0.99) and 0.99 (95%CI 0.13–1.00) respectively. Significant heterogeneity existed across studies for specificity, mostly caused by differences in scan procedures. Predefined criteria for suspicion of LVAD and/or driveline infection were lacking in all included studies.

Conclusions

FDG-PET/CT is a valuable tool for assessment of device-related infection in LVAD patients, with high sensitivity and high, albeit variable, specificity. Standardization of FDG-PET/CT procedures and criteria for suspected device-related LVAD infections are needed for consistent reporting of FDG-PET/CT scans.

Electronic supplementary material

The online version of this article (10.1007/s00259-020-04930-8) contains supplementary material, which is available to authorized users.

[Hydroxychloroquine and chloroquine for COVID-19: no evidence of effectiveness]

On 3 March 2020, the document 'Drug treatment options for patients with COVID-19 (infections with SARS-CoV-2)' was published on the website of the Dutch Working Party on Antibiotic Policy (StichtingWerkgroepAntibioticabeleid, SWAB). Based on a 7-step analysis of the literature, hydroxychloroquine (HCQ) and chloroquine (CQ) were initially included in the SWAB document as possible drug treatments for hospitalised adult COVID-19 patients. However, recent weeks have seen the publication of the results of various studies into the effectiveness of treatment with HCQ and CQ in patients with COVID-19. On the basis of these results, we conclude that there is insufficient evidence to consider HCQ and CQ as meaningful treatment options in patients with COVID-19. Clinically relevant QTc prolongation occurs in at least 1 in 10 COVID-19 patients treated with HCQ or HQ.

Imaging infective endocarditis: Adherence to a diagnostic flowchart and direct comparison of imaging techniques

BACKGROUND

Multimodality imaging is recommended to diagnose infective endocarditis. Value of additional imaging to echocardiography in patients selected by a previously proposed flowchart has not been evaluated.

METHODS

An observational single-center study was performed. Adult patients suspected of endocarditis/device infection were prospectively and consecutively enrolled from March 2016 to August 2017. Adherence to a diagnostic imaging-in-endocarditis-flowchart was evaluated in 176 patients. Imaging techniques were compared head-to-head in 46 patients receiving echocardiography (transthoracic plus transesophageal), multi-detector computed tomography angiography (MDCTA), and 18F-fluorodeoxyglucose positron emission tomography (FDG-PET/CT).

RESULTS

69% of patients (121/176) adhered to the flowchart. Sensitivity of echocardiography, MDCTA, FDG-PET/CT in patients without prosthesis was 71%, 57%, 29% (86% when combined), while specificity was 100%, 75%, 100%, respectively. Sensitivity in patients with prosthesis was 75%, 75%, 83%, respectively (100% when combined), while specificity was 86% for all three modalities. Echocardiography performed best in the assessment of vegetations, morphological valve abnormalities/dehiscence, septum defects, and fistula formation. MDCTA performed best in the assessment of abscesses and ventricular assist device infection. FDG-PET/CT performed best in the assessment of cardiac device infection, extracardiac infectious foci, and alternative diagnoses.

CONCLUSIONS

This study demonstrates that the evaluated imaging-in-endocarditis-flowchart is applicable in daily clinical practice. Echocardiography, MDCTA, and FDG-PET/CT provide relevant complementary diagnostic information, particularly in patients with intracardiac prosthetic material.

Machine learning in infection management using routine electronic health records: tools, techniques, and reporting of future technologies

BACKGROUND

Machine learning (ML) is increasingly being used in many areas of health care. Its use in infection management is catching up as identified in a recent review in this journal. We present here a complementary review to this work.

OBJECTIVES

To support clinicians and researchers in navigating through the methodological aspects of ML approaches in the field of infection management.

SOURCES

A Medline search was performed with the keywords artificial intelligence, machine learning, infection∗, and infectious disease∗ for the years 2014-2019. Studies using routinely available electronic hospital record data from an inpatient setting with a focus on bacterial and fungal infections were included.

CONTENT

Fifty-two studies were included and divided into six groups based on their focus. These studies covered detection/prediction of sepsis (n = 19), hospital-acquired infections (n = 11), surgical site infections and other postoperative infections (n = 11), microbiological test results (n = 4), infections in general (n = 2), musculoskeletal infections (n = 2), and other topics (urinary tract infections, deep fungal infections, antimicrobial prescriptions; n = 1 each). In total, 35 different ML techniques were used. Logistic regression was applied in 18 studies followed by random forest, support vector machines, and artificial neural networks in 18, 12, and seven studies, respectively. Overall, the studies were very heterogeneous in their approach and their reporting. Detailed information on data handling and software code was often missing. Validation on new datasets and/or in other institutions was rarely done. Clinical studies on the impact of ML in infection management were lacking.

IMPLICATIONS

Promising approaches for ML use in infectious diseases were identified. But building trust in these new technologies will require improved reporting. Explainability and interpretability of the models used were rarely addressed and should be further explored. Independent model validation and clinical studies evaluating the added value of ML approaches are needed.

Marked Changes in Gut Microbiota in Cardio-Surgical Intensive Care Patients: A Longitudinal Cohort Study

Background: Virtually no studies on the dynamics of the intestinal microbiota in patients admitted to the intensive care unit (ICU) are published, despite the increasingly recognized important role of microbiota on human physiology. Critical care patients undergo treatments that are known to influence the microbiota. However, dynamics and extent of such changes are not yet fully understood. To address this topic, we analyzed the microbiota before, during and after planned major cardio surgery that, for the first time, allowed us to follow the microbial dynamics of critical care patients. In this prospective, observational, longitudinal, single center study, we analyzed the fecal microbiota using 16S rRNA gene sequencing.

Results: Samples of 97 patients admitted between April 2015 and November 2016 were included. In 32 patients, data of all three time points (before, during and after admission) were available for analysis. We found a large intra-individual variation in composition of gut microbiota. During admission, a significant change in microbial composition occurred in most patients, with a significant increase in pathobionts combined with a decrease in strictly anaerobic gut bacteria, typically beneficial for health. A lower bacterial diversity during admission was associated with longer hospitalization. In most patients analyzed at all three time points, the change in microbiota during hospital stay reverted to the original composition post-discharge.

Conclusions: Our study shows that, even with a short ICU stay, patients present a significant change in microbial composition shortly after admission. The unique longitudinal setup of this study displayed a restoration of the microbiota in most patients to baseline composition post-discharge, which demonstrated its great restorative capacity. A relative decrease in benign or even beneficial bacteria and increase of pathobionts shifts the microbial balance in the gut, which could have clinical relevance. In future studies, the microbiota of ICU patients should be considered a good target for optimisation.

Volatile organic compound measurements point to fog-induced biomass burning feedback to air quality in the megacity of Delhi

We report the first ambient measurements of thirteen VOCs for investigations of emissions and air quality during fog and non-fog wintertime conditions at a tower site (28.57° N, 77.11° E, 220 m amsl) in the megacity of Delhi. Measurements of acetonitrile (biomass burning (BB) tracer), isoprene (biogenic emission tracer in daytime), toluene (a traffic exhaust tracer) and benzene (emitted from BB and traffic), together with soluble and reactive oxygenated VOCs such as methanol, acetone and acetaldehyde were performed during the winters of 2015-16 and 2016-17, using proton transfer reaction mass spectrometry. Remarkably, ambient VOC composition changes during fog were not governed by solubility. Acetaldehyde, toluene, sum of C8-aromatics (e.g. xylenes), sum of C9-aromatics (e.g. trimethyl benzenes) decreased by ≥30% (>95% confidence interval), whereas acetonitrile and benzene showed significant increases by 20% (>70% confidence interval), even after accounting for boundary layer dilution. During fog, the lower temperatures appeared to induce an emissions feedback from enhanced open BB within Delhi for warming, releasing both gaseous and aerosol pollutants with consequences for fog chemistry, sustenance and intensity. The potential feedback is important to consider for improving current emission parametrizations in models used for predicting air quality and fog in such atmospheric environments.

Improving the Diagnostic Performance of 18F-Fluorodeoxyglucose Positron-Emission Tomography/Computed Tomography in Prosthetic Heart Valve Endocarditis

BACKGROUND

¹⁸F-Fluorodeoxyglucose (FDG) positron-emission tomography/computed tomography (PET/CT) was recently introduced as a new tool for the diagnosis of prosthetic heart valve endocarditis (PVE). Previous studies reporting a modest diagnostic accuracy may have been hampered by unstandardized image acquisition and assessment, and several confounders, as well. The aim of this study was to improve the diagnostic performance of FDG PET/CT in patients in whom PVE was suspected by identifying and excluding possible confounders, using both visual and standardized quantitative assessments.

METHODS

In this multicenter study, 160 patients with a prosthetic heart valve (median age, 62 years [43-73]; 68% male; 82 mechanical valves; 62 biological; 9 transcatheter aortic valve replacements; 7 other) who underwent FDG PET/CT for suspicion of PVE, and 77 patients with a PV (median age, 73 years [65-77]; 71% male; 26 mechanical valves; 45 biological; 6 transcatheter aortic valve replacements) who underwent FDG PET/CT for other indications (negative control group), were retrospectively included. Their scans were reassessed by 2 independent observers blinded to all clinical data, both visually and quantitatively on available European Association of Nuclear Medicine Research Ltd-standardized reconstructions. Confounders were identified by use of a logistic regression model and subsequently excluded.

RESULTS

Visual assessment of FDG PET/CT had a sensitivity/specificity/positive predictive value/negative predictive value for PVE of 74%/91%/89%/78%, respectively. Low inflammatory activity (C-reactive protein <40 mg/L) at the time of imaging and use of surgical adhesives during prosthetic heart valve implantation were significant confounders, whereas recent valve implantation was not. After the exclusion of patients with significant confounders, diagnostic performance values of the visual assessment increased to 91%/95%/95%/91%. As a semiquantitative measure of FDG uptake, a European Association of Nuclear Medicine Research Ltd-standardized uptake value ratio of ≥2.0 was a 100% sensitive and 91% specific predictor of PVE.

CONCLUSIONS

Both visual and quantitative assessments of FDG PET/CT have a high diagnostic accuracy in patients in whom PVE is suspected. FDG PET/CT should be implemented early in the diagnostic workup to prevent the negative confounding effects of low inflammatory activity (eg, attributable to prolonged antibiotic therapy). Recent valve implantation was not a significant predictor of false-positive interpretations, but surgical adhesives used during implantation were.

An epidemiological profile of chronic obstructive pulmonary disease: A community-based study in Delhi

BACKGROUND

Different definitions used for chronic obstructive pulmonary disease (COPD) preclude getting reliable prevalence estimates. Study objective was to find the prevalence of COPD as per standard Global Initiative for Chronic Obstructive Lung Disease definition, risk factors associated, and treatment seeking in adults >30 years.

METHODOLOGY

Community-based cross-sectional study was conducted in Delhi, among 1200 adults, selected by systematic random sampling. Pretested questionnaire was used to interview all subjects and screen for symptoms of COPD. Postbronchodilator spirometry was done to confirm COPD.

STATISTICAL ANALYSIS

Adjusted odds ratio (aOR) was calculated by multivariable analysis to examine the association of risk factors with COPD. Receiver operating characteristic (ROC) curve was developed to assess predictability.

RESULTS

The prevalence of COPD was 10.1% (95% confidence interval [CI] 8.5, 11.9%). Tobacco smoking was the strongest risk factor associated (aOR 9.48; 95% CI 4.22, 14.13) followed by environmental tobacco smoke (ETS), occupational exposure, age, and biomass fuel. Each pack-year of smoking increased 15% risk of COPD. Ex-smokers had 63% lesser risk compared to current smokers. Clinical allergy seems to preclude COPD (aOR 0.06; 95% CI 0.02, 0.37). ROC analysis showed 94.38% of the COPD variability can be assessed by this model (sensitivity 57.4%; positive predictive value 93.3%). Only 48% patients were on treatment. Treatment continuation was impeded by its cost.

CONCLUSION

COPD prevalence in the region of Delhi, India, is high, and our case-finding population study identified a high rate of patients who were not on any treatment. Our study adds to creating awareness on the importance of smoking cessation, early diagnosis of COPD, and the need for regular treatment.

Clonal clusters and virulence factors of methicillin-resistant Staphylococcus Aureus: Evidence for community-acquired methicillin-resistant Staphylococcus Aureus infiltration into hospital settings in Chennai, South India

Background and Objective

Staphylococcus aureus is one of the major pathogens of nosocomial infections as wells as community-acquired (CA) infections worldwide. So far, large-scale comprehensive molecular and epidemiological characterisation of S. aureus from very diverse settings has not been carried out in India. The objective of this study is to evaluate the molecular, epidemiological and virulence characteristics of S. aureus in both community and hospital settings in Chennai, southern India.

Methods

S. aureus isolates were obtained from four different groups (a) healthy individuals from closed community settings, (b) inpatients from hospitals, (c) outpatients from hospitals, representing isolates of hospital-community interface and (d) HIV-infected patients to define isolates associated with the immunocompromised. Antibiotic susceptibility testing, multiplex polymerase chain reactions for detection of virulence and resistance determinants, molecular typing including Staphylococcal cassette chromosome mec (SCCmec) and agr typing, were carried out. Sequencing-based typing was done using spa and multilocus sequence typing (MLST) methods. Clonal complexes (CC) of hospital and CA methicillin-resistant S. aureus (MRSA) were identified and compared for virulence and resistance.

Results and Conclusion

A total of 769 isolates of S. aureus isolates were studied. The prevalence of MRSA was found to be 7.17%, 81.67%, 58.33% and 22.85% for groups a, b, c and d, respectively. Of the four SCCmec types (I, III, IV and V) detected, SCCmec V was found to be predominant. Panton-Valentine leucocidin toxin genes were detected among MRSA isolates harbouring SCCmec IV and V. A total of 78 spa types were detected, t657 being the most prevalent. 13 MLST types belonging to 9 CC were detected. CC1 (ST-772, ST-1) and CC8 (ST238, ST368 and ST1208) were found to be predominant among MRSA. CA-MRSA isolates with SCCmec IV and V were isolated from all study groups including hospitalised patients and were found to be similar by molecular tools. This shows that CA MRSA has probably infiltrated into the hospital settings.

Rapid Analysis of Diagnostic and Antimicrobial Patterns in R (RadaR): Interactive Open-Source Software App for Infection Management and Antimicrobial Stewardship

BACKGROUND

Analyzing process and outcome measures for all patients diagnosed with an infection in a hospital, including those suspected of having an infection, requires not only processing of large datasets but also accounting for numerous patient parameters and guidelines. Substantial technical expertise is required to conduct such rapid, reproducible, and adaptable analyses; however, such analyses can yield valuable insights for infection management and antimicrobial stewardship (AMS) teams.

OBJECTIVE

The aim of this study was to present the design, development, and testing of RadaR (Rapid analysis of diagnostic and antimicrobial patterns in R), a software app for infection management, and to ascertain whether RadaR can facilitate user-friendly, intuitive, and interactive analyses of large datasets in the absence of prior in-depth software or programming knowledge.

METHODS

RadaR was built in the open-source programming language R, using Shiny, an additional package to implement Web-app frameworks in R. It was developed in the context of a 1339-bed academic tertiary referral hospital to handle data of more than 180,000 admissions.

RESULTS

RadaR enabled visualization of analytical graphs and statistical summaries in a rapid and interactive manner. It allowed users to filter patient groups by 17 different criteria and investigate antimicrobial use, microbiological diagnostic use and results including antimicrobial resistance, and outcome in length of stay. Furthermore, with RadaR, results can be stratified and grouped to compare defined patient groups on the basis of individual patient features.

CONCLUSIONS

AMS teams can use RadaR to identify areas within their institutions that might benefit from increased support and targeted interventions. It can be used for the assessment of diagnostic and therapeutic procedures and for visualizing and communicating analyses. RadaR demonstrated the feasibility of developing software tools for use in infection management and for AMS teams in an open-source approach, thus making it free to use and adaptable to different settings.

A Comparison of Three Different Bioinformatics Analyses of the 16S-23S rRNA Encoding Region for Bacterial Identification

Rapid and reliable identification of bacterial pathogens directly from patient samples is required for optimizing antimicrobial therapy. Although Sanger sequencing of the 16S ribosomal RNA (rRNA) gene is used as a molecular method, species identification and discrimination is not always achievable for bacteria as their 16S rRNA genes have sometimes high sequence homology. Recently, next generation sequencing (NGS) of the 16S–23S rRNA encoding region has been proposed for reliable identification of pathogens directly from patient samples. However, data analysis is laborious and time-consuming and a database for the complete 16S–23S rRNA encoding region is not available. Therefore, a better, faster, and stronger approach is needed for NGS data analysis of the 16S–23S rRNA encoding region. We compared speed and diagnostic accuracy of different data analysis approaches: de novo assembly followed by Basic Local Alignment Search Tool (BLAST), operational taxonomic unit (OTU) clustering, or mapping using an in-house developed 16S–23S rRNA encoding region database for the identification of bacterial species. De novo assembly followed by BLAST using the in-house database was superior to the other methods, resulting in the shortest turnaround time (2 h and 5 min), approximately 2 h less than OTU clustering and 4.5 h less than mapping, and a sensitivity of 80%. Mapping was the slowest and most laborious data analysis approach with a sensitivity of 60%, whereas OTU clustering was the least laborious approach with 70% sensitivity. Although the in-house database requires more sequence entries to improve the sensitivity, the combination of de novo assembly and BLAST currently appears to be the optimal approach for data analysis.

Sonication of heart valves detects more bacteria in infective endocarditis

Optimal antimicrobial treatment of infective endocarditis requires identification and susceptibility patterns of pathogens. Sonication of explanted heart valves could increase the identification and culture of pathogens, as shown in prosthetic joint and pacemaker/ICD infections. We tested 26 explanted heart valves from 20 patients with active definite endocarditis for added diagnostic value of sonication to the standard microbiological workup in a prospective diagnostic proof of concept study. Two sonication protocols (broth enrichment vs. centrifugation) were compared in an additional 35 negative control valves for contamination rates. We selected sonication/centrifugation based on acceptable false positive rates (11.4%; 4/35). Sonication/enrichment yielded many false positive results in negative controls (28.6%; 10/35), mainly Propionibacterium acnes (next-generation sequencing excluded technical problems). Compared to direct culture only, adding sonication/centrifugation (including molecular testing) significantly increased the diagnostic yield from 6/26 to 17/26 valves (p = 0.003). Most importantly, culture positives almost doubled (from 6 to 10), providing unique quantitative information about antimicrobial susceptibility. Even if direct molecular testing was added to the standard workup, sonication/centrifugation provided additional diagnostic information in a significant number of valves (8/26; 31%; p = 0.013). We concluded that sonication/centrifugation added relevant diagnostic information in the workup of heart valves with infective endocarditis, with acceptable contamination rates.

Diagnosis of bloodstream infections from positive blood cultures and directly from blood samples: recent developments in molecular approaches

BACKGROUND

Bloodstream infections are a major cause of death with increasing incidence and severity. Blood cultures are still the reference standard for microbiological diagnosis, but are rather slow. Molecular methods can be used as add-on complementary assays. They can be useful to speed up microbial identification and to predict antimicrobial susceptibility, applied to direct blood samples or positive blood cultures.

AIM

To review recent developments in molecular-based diagnostic platforms used for the identification of bloodstream infections, with a focus on assays performed directly on blood samples and positive blood cultures.

SOURCES

Peer reviewed articles, conference abstracts, and manufacturers' websites.

CONTENT

We give an update on recent developments of molecular methods in diagnosing BSIs. We first describe the currently available molecular methods to be used for positive blood cultures including: a) in situ hybridization-based methods; b) DNA-microarray-based hybridization technology; c) nucleic acid amplification-based methods; and d) combined methods. Subsequently, molecular methods applied directly to whole blood samples are discussed, including the use of nucleic acid amplification-based methods, T2 magnetic resonance-based methods, and metagenomics for diagnosing BSIs.

IMPLICATIONS

Advances in molecular-based methods complementary to conventional blood culture diagnostics and antimicrobial stewardship programmes may optimize infection management by allowing rapid identification of pathogens and relevant antimicrobial resistance genes. Rapid diagnosis of the causing microorganism and relevant resistance determinants is important for early administration and modification of appropriate antimicrobial therapy. Ultimately, this may lead to improved quality and cost-effectiveness of health care, as well as reduced antimicrobial resistance selection.

Liraglutide and Dulaglutide therapy in addition to SGLT-2 inhibitor and metformin treatment in Indian type 2 diabetics: a real world retrospective observational study

Background

Therapy for Type 2 diabetes (T2D) has been transformed by the introduction of newer agents like Glucagon like Peptide Receptor Agonists (GLP-1RA) and Sodium-glucose linked transporter inhibitors (SGLT2i). However with co-initiation of SGLT2i and GLP-1RA in the DURATION 8 trial an improvement in HbA1c was noted but the beneficial effect was not equal to the sum of its parts. In view of this we proceeded to test the hypothesis that sequential addition of GLP-1RA therapy to metformin and SGLT-2i may be more beneficial.

Methods

A retrospective real world observational case note study conducted in two diabetes care centres in India analyzed the first 60 consecutive T2D patients who could afford this therapy and had not achieved their glycaemic target (HbA1c < 7%)on metformin and SGLT2i. All these patients were additionally treated with either Dulaglutide or Liraglutide and followed up for 13 weeks.

Results

Across the entire 13-week study period, both liraglutide and dulaglutide proved to be an excellent add on to metformin and SGLT-2 inhibitor. There was significant reduction in HbA1c and body weight. Liraglutide had an additional significant impact on systolic blood pressure reduction in contrast to the dulaglutide arm. Comparatively, liraglutide and dulaglutide achieved similar metabolic control. However, a larger proportion of patients achieved HbA1c below 7.0% in the liraglutide arm (63.3%) compared to the dulaglutide arm (30%) and this difference was statistically significant.

Conclusion

In this retrospective study in Indian type 2 diabetic patients poorly controlled with metformin and SGLT-2 inhibitor we found a meaningful impact of adding a GLP-1 RA on all metabolic parameters. There were additional advantages seen with liraglutide as far achieving target HbA1c of less than 7% and also on the quantum of weight loss and systolic blood pressure reduction.

A standardized approach to treat complex aortic valve endocarditis: a case series

Background

Surgical treatment of complicated aortic valve endocarditis often is challenging, even for experienced surgeons. We aim at demonstrating a standardized surgical approach by stentless bioprostheses for the treatment of aortic valve endocarditis complicated by paravalvular abscess formation.

Methods

Sixteen patients presenting with aortic valve endocarditis (4 native and 12 prosthetic valves) and paravalvular abscess formation at various localizations and to different extents were treated by a standardized approach using stentless bioprostheses. The procedure consisted of thorough debridement, root replacement with reimplantation of the coronary arteries and correction of accompanying pathologies (aortoventricular and aortomitral dehiscence, septum derangements, Gerbode defect, total atrioventricular conduction block, mitral and tricuspid valve involvement).

Results

All highly complex patients included (14 males and 2 females; median age 63 years [range 31–77]) could be successfully treated with stentless bioprostheses as aortic root replacement. Radical surgical debridement of infected tissue with anatomical recontruction was feasible. Although predicted operative mortality was high (median logarithmic EuroSCORE I of 40.7 [range 12.8–68.3]), in-hospital and 30-day mortality rates were favorable (18.8 and 12.5% respectively).

Conclusions

Repair of active aortic valve endocarditis complicated by paravalvular abscess formation and destruction of the left ventricular outflow tract with stentless bioprosthesis is a valuable option for both native and prosthetic valves. It presents a standardized approach with a high success rate for complete debridement, is readily available, and yields comparable clinical outcomes to the historical gold standard, repair by homografts. Additionally, use of one type of prosthesis reduces logistical issues and purchasing costs.

Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis

Outbreak management of extended spectrum β-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing Escherichia coli outbreak, 149 fecal samples and rectal eSwabs were collected by a cross-sectional survey in a Dutch nursing home. Samples were processed by routine diagnostic methods. Retrospectively, ESBL-producing bacteria and resistance genes were detected directly from eSwab medium by an accelerated workflow without prior enrichment cultures by an amplicon-based next-generation sequencing (NGS) method, and culture. A total of 27 (18.1%) samples were positive in either test. Sensitivity for CTX-M detection was 96.3% for the phenotypic method and 85.2% for the NGS method, and the specificity was 100% for both methods, as confirmed by micro-array. This resulted in a positive predictive value (PPV) of 100% for both methods, and a negative predictive value (NPV) of 99.2% and 96.8% for the phenotypic method and the NGS method, respectively. Time to result was four days and 14 h for the phenotypic method and the NGS method, respectively. In conclusion, the sensitivity without enrichment shows promising results for further use of amplicon-based NGS for screening during outbreaks.

Staphylococcal infections impair the mesothelial fibrinolytic system: The role of cell death and cytokine release

Bacterial peritonitis is a serious complication of peritoneal dialysis patients and of patients after abdominal surgery. Especially episodes due to Staphylococcus aureus can harm the peritoneum severely, resulting in peritoneal fibrosis. Human peritoneal mesothelial cells play a critical role in maintaining the integrity of the peritoneum, as they release components of the fibrinolytic system and regulate the influx of immune cells by expressing chemokines and adhesion molecules. Using cultured human peritoneal mesothelial cells (HMCs) and blood mononuclear cells,we analyzed the effect of different staphylococcal strains on mesothelial fibrinolysis and on inflammatory reactions and show that only S. aureus strains with an invasive and hemolytic phenotype decrease the production of fibrinolytic system components, most likely via cell death induction. Furthermore, HMCs react to invading staphylococci by enhanced expression of chemokines and adhesion molecules. Mononuclear cells were activated by all staphylococcal strains tested, and their culture supernatants impaired mesothelial fibrinolysis. Simvastatin, a 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitor, efficiently enhanced the mesothelial fibrinolytic capacity under these inflammatory conditions, but did not protect HMCs against S. aureus-induced cell death. We conclude that only selected S. aureus strains decrease the release of fibrinolytic system components and provoke a mesothelial inflammatory response. These factors most likely contribute to peritoneal fibrosis and might account for the severe clinical presentation of S. aureus peritonitis.

Fibronectin binding proteins contribute to the adherence of Staphylococcus aureus to intact endothelium in vivo

Staphylococcal adhesins mediate attachment to matrix proteins and endothelial cells in vitro, yet, their role in primary adherence to the physiologic vessel wall has not been studied in vivo, and complex endocarditis models yielded ambiguous results. Recently, we developed a hamster model to study interaction kinetics of S. aureus with intact microvasculature using intravital fluorescence microscopy (Laschke et al. J Infect Dis 2005; 191: 435-43) providing the basis for this study. S. aureus Cowan 1 wild type (WT) log phase cells adhered to postcapillary venules to a significantly larger extent compared to stationary phase staphylococci, a finding in congruence with the fact that the staphylococcal adhesin repertoire largely depends on the growth phase. In comparison, the adherence rate of the fnbA deleted mutant (DU5895) to the vessel wall was significantly reduced to approximately 40% of WT. These DU5895 attachment rates were similar to those of an S. carnosus strain (TM300). In contrast, upon heterologous complementation of TM300 with either fnbA and fnbB, adherence of these transformants to the microvasculature increased, an increase found to be significant for fnbA transformant single cocci and clusters at 30 and 60 min when compared to S. carnosus TM300 WT. In conclusion, these results demonstrate that staphylococcal FnBPs significantly contribute to primary interaction with intact endothelium under physiologic conditions. Accordingly, this attribution of staphylococcal FnBPs providea rationale for novel intervention strategies such as the use of anti-FnBP antibodies in endovascular S. aureus disease.

Arsenic load in rice ecosystem and its mitigation through deficit irrigation

Rice the staple food is a notable intake source of arsenic to the rural population of eastern India through food-chain. A field survey was carried out to study the variation of arsenic load in different parts of rice genotype Shatabdi (most popular genotype of the region) exposed to varying level of arsenic present in the irrigation water and soil. As irrigation is the primary source of arsenic contamination, a study was conducted to assess arsenic load in rice ecosystem under deficit irrigation practices like intermittent ponding (IP), saturation (SAT) and aerobic (AER) imposed during stress allowable stage (16-40 days after transplanting) of the crop (genotype Shatabdi). Present survey showed that arsenic content in water and soil influenced the arsenic load of rice grain. Variation in arsenic among different water and soil samples influenced grain arsenic load to the maximum extent followed by straw. Deviation in root arsenic load due to variation in water and soil arsenic content was lowest. Arsenic concentration of grain is strongly related to the arsenic content of both irrigation water and soil. However, water has 10% higher impact on grain arsenic load over soil. Translocation of arsenic from root to shoot decreased with the increase in arsenic content of water. Imposition of saturated and aerobic environment reduced both yield and grain arsenic load. In contrast under IP a marked decrease in grain arsenic content recorded with insignificant reduction in yield. Deficit irrigation resulted in significant reduction (17.6-25%) in arsenic content of polished rice and the values were lower than that of the toxic level (<0.2 mg kg^-1). In contrast the decrease in yield was to the tune of 0.9% under IP regime over CP.

Pharmacokinetic modeling of gentamicin in treatment of infective endocarditis: Model development and validation of existing models

Gentamicin shows large variations in half-life and volume of distribution (Vd) within and between individuals. Thus, monitoring and accurately predicting serum levels are required to optimize effectiveness and minimize toxicity. Currently, two population pharmacokinetic models are applied for predicting gentamicin doses in adults. For endocarditis patients the optimal model is unknown. We aimed at: 1) creating an optimal model for endocarditis patients; and 2) assessing whether the endocarditis and existing models can accurately predict serum levels. We performed a retrospective observational two-cohort study: one cohort to parameterize the endocarditis model by iterative two-stage Bayesian analysis, and a second cohort to validate and compare all three models. The Akaike Information Criterion and the weighted sum of squares of the residuals divided by the degrees of freedom were used to select the endocarditis model. Median Prediction Error (MDPE) and Median Absolute Prediction Error (MDAPE) were used to test all models with the validation dataset. We built the endocarditis model based on data from the modeling cohort (65 patients) with a fixed 0.277 L/h/70kg metabolic clearance, 0.698 (±0.358) renal clearance as fraction of creatinine clearance, and Vd 0.312 (±0.076) L/kg corrected lean body mass. External validation with data from 14 validation cohort patients showed a similar predictive power of the endocarditis model (MDPE -1.77%, MDAPE 4.68%) as compared to the intensive-care (MDPE -1.33%, MDAPE 4.37%) and standard (MDPE -0.90%, MDAPE 4.82%) models. All models acceptably predicted pharmacokinetic parameters for gentamicin in endocarditis patients. However, these patients appear to have an increased Vd, similar to intensive care patients. Vd mainly determines the height of peak serum levels, which in turn correlate with bactericidal activity. In order to maintain simplicity, we advise to use the existing intensive-care model in clinical practice to avoid potential underdosing of gentamicin in endocarditis patients.

Combating the Complex Global Challenge of Antimicrobial Resistance: What can Antimicrobial Stewardship Contribute?

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Challenges for a Sustainable Financial Foundation for Antimicrobial Stewardship

Antimicrobial resistance is a worldwide threat and a problem with large clinical and economic impact. Antimicrobial Stewardship Programs are a solution to curb resistance development. A problem of resistance is a separation of actions and consequences, financial and clinical. Such a separation makes it difficult to create support among stakeholders leading to a lack of sense of responsibility. To counteract the resistance development it is important to perform diagnostics and know how to interpret the results. One should see diagnostics, therapy and resistance as one single process. Within this process all involved stakeholders need to work together on a more institutional level. We suggest therefore a solution: combining diagnostics and therapy into one single financial product. Such a product should act as an incentive to perform correct diagnostics. It also makes it easier to cover the costs of an antimicrobial stewardship program, which is often overlooked. Finally, such a product involves all stakeholders in the process and does not lay the costs at one stakeholder and the benefits somewhere else, solving the misbalance that is present nowadays.

Strategies to enhance rational use of antibiotics in hospital: a guideline by the German Society for Infectious Diseases

Introduction

In the time of increasing resistance and paucity of new drug development there is a growing need for strategies to enhance rational use of antibiotics in German and Austrian hospitals. An evidence-based guideline on recommendations for implementation of antibiotic stewardship (ABS) programmes was developed by the German Society for Infectious Diseases in association with the following societies, associations and institutions: German Society of Hospital Pharmacists, German Society for Hygiene and Microbiology, Paul Ehrlich Society for Chemotherapy, The Austrian Association of Hospital Pharmacists, Austrian Society for Infectious Diseases and Tropical Medicine, Austrian Society for Antimicrobial Chemotherapy, Robert Koch Institute.

Materials and methods

A structured literature research was performed in the databases EMBASE, BIOSIS, MEDLINE and The Cochrane Library from January 2006 to November 2010 with an update to April 2012 (MEDLINE and The Cochrane Library). The grading of recommendations in relation to their evidence is according to the AWMF Guidance Manual and Rules for Guideline Development.

Conclusion

The guideline provides the grounds for rational use of antibiotics in hospital to counteract antimicrobial resistance and to improve the quality of care of patients with infections by maximising clinical outcomes while minimising toxicity. Requirements for a successful implementation of ABS programmes as well as core and supplemental ABS strategies are outlined. The German version of the guideline was published by the German Association of the Scientific Medical Societies (AWMF) in December 2013.

Real-life data on antibiotic prescription and sputum culture diagnostics in acute exacerbations of COPD in primary care

Background

Acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are generally treated with optimization of bronchodilation therapy and a course of oral corticosteroids, mostly without antibiotics. The Dutch guidelines recommend prudent use of antibiotics, with amoxicillin or doxycycline as first choice. Here we evaluate adherence to these guidelines with regard to antibiotic prescription in AECOPD in primary care and the use of sputum cultures.

Methods

We retrospectively analyzed a longitudinal cohort of patients in three primary care practices in the north-eastern region of the Netherlands from 2009 to 2013 (n=36,172 subjects) participating in the Registration Network Groningen. Antibiotics prescribed for AECOPD −10/+28 days from the start date of corticosteroid courses were evaluated. In addition, we assessed regional data on the susceptibility of respiratory pathogens from COPD patients.

Results

We identified 1,297 patients with COPD. Of these, 616 experienced one or more exacerbations, resulting in a total of 1,558 exacerbations, for which 1,594 antibiotic courses were prescribed. The recommended antibiotics doxycycline and amoxicillin accounted for 56% of the prescribed antibiotics overall and for 35% in subsequent antibiotic courses. The alternative choices were not based on culture results because only in 67 AECOPD events (2.9%) sputum samples were taken. Regional data including 3,638 sputum samples showed that pathogens relevant in AECOPD were detected in 19% of cultures.

Conclusion

Our study shows that guidelines regarding the prescription of antibiotics are poorly followed, particularly in recurrent exacerbations. Sputum cultures were performed in a small minority of cases. Performing sputum diagnostics in patients with early treatment failure or a repeated exacerbation when antibiotic treatment is started may further rationalize antibiotic treatment.

Diagnostic value of imaging in infective endocarditis: a systematic review

Sensitivity and specificity of the modified Duke criteria for native valve endocarditis are both suboptimal, at approximately 80%. Diagnostic accuracy for intracardiac prosthetic material-related infection is even lower. Non-invasive imaging modalities could potentially improve diagnosis of infective endocarditis; however, their diagnostic value is unclear. We did a systematic literature review to critically appraise the evidence for the diagnostic performance of these imaging modalities, according to PRISMA and GRADE criteria. We searched PubMed, Embase, and Cochrane databases. 31 studies were included that presented original data on the performance of electrocardiogram (ECG)-gated multidetector CT angiography (MDCTA), ECG-gated MRI, ¹⁸F-fluorodeoxyglucose (¹⁸F-FDG) PET/CT, and leucocyte scintigraphy in diagnosis of native valve endocarditis, intracardiac prosthetic material-related infection, and extracardiac foci in adults. We consistently found positive albeit weak evidence for the diagnostic benefit of ¹⁸F-FDG PET/CT and MDCTA. We conclude that additional imaging techniques should be considered if infective endocarditis is suspected. We propose an evidence-based diagnostic work-up for infective endocarditis including these non-invasive techniques.

Positive impact of infection prevention on the management of nosocomial outbreaks at an academic hospital

Aim: Infection prevention (IP) measures are vital to prevent (nosocomial) outbreaks. Financial evaluations of these are scarce. An incremental cost analysis for an academic IP unit was performed. Material & methods: On a yearly basis, we evaluated: IP measures; costs thereof; numbers of patients at risk for causing nosocomial outbreaks; predicted outbreak patients; and actual outbreak patients. Results: IP costs rose on average yearly with €150,000; however, more IP actions were undertaken. Numbers of patients colonized with high-risk microorganisms increased. The trend of actual outbreak patients remained stable. Predicted prevented outbreak patients saved costs, leading to a positive return on investment of 1.94. Conclusion: This study shows that investments in IP can prevent outbreak cases, thereby saving enough money to earn back these investments.

Preclinical studies and prospective clinical applications for bacteria-targeted imaging: the future is bright

Bacterial infections are a frequently occurring and major complication in human healthcare, in particular due to the rapid increase of antimicrobial resistance and the emergence of pan-drug-resistant microbes. Current anatomical and functional imaging modalities are insufficiently capable of distinguishing sites of bacterial infection from sterile inflammation. Therefore, definitive diagnosis of an infection can often only be obtained by tissue biopsy and subsequent culture and, occasionally, a definite diagnosis even appears to be impossible. To accurately diagnose bacterial infections early, novel imaging modalities are urgently needed. In this regard, bacteria-targeted imaging is an attractive option due to its specificity. Here, different bacteria-targeted imaging approaches are reviewed, and their promising future perspectives are discussed.