Control of Infectious Diseases in the Era of European Clinical Microbiology Laboratory Consolidation: New Challenges and Opportunities for the Patient and for Public Health Surveillance

Challenges and opportunities for incentivising antibiotic research and development in Europe

Antimicrobial, and particularly antibiotic resistance are one of the world's biggest challenges today, and urgent action is needed to reinvigorate the antibiotic development pipeline. To inform policy discussions during and after the 2023 Swedish Presidency of the Council of the European Union, we critically appraise incentive options recently proposed by the European Commission, and member states, and consider what has been achieved over the last two decades in relation to antibiotic research and development. While several new antibiotics have achieved regulatory approval in recent years, almost none have innovative characteristics such as new chemical classes or novel mechanisms of action. We consider four incentive options to incentivise research and development of new antibiotics, including subscription payments, market entry rewards, transferable exclusivity extensions, and milestone payments. While each option has advantages and drawbacks, a combination of incentives may be required and continued investment is needed by the EU in push incentives, such as direct funding and grants, to incentivise drug discovery and preclinical stages of development. The EU must also coordinate with international initiatives and support access to new and pre-existing antibiotics in LMICs through platforms such as the WHO, and G7 and G20 group of countries.

Successfully Implementing Digital Health to Ensure Future Global Health Security During Pandemics: A Consensus Statement

Importance

COVID-19 has highlighted widespread chronic underinvestment in digital health that hampered public health responses to the pandemic. Recognizing this, the Riyadh Declaration on Digital Health, formulated by an international interdisciplinary team of medical, academic, and industry experts at the Riyadh Global Digital Health Summit in August 2020, provided a set of digital health recommendations for the global health community to address the challenges of current and future pandemics. However, guidance is needed on how to implement these recommendations in practice.

Objective

To develop guidance for stakeholders on how best to deploy digital health and data and support public health in an integrated manner to overcome the COVID-19 pandemic and future pandemics.

Evidence Review

Themes were determined by first reviewing the literature and Riyadh Global Digital Health Summit conference proceedings, with experts independently contributing ideas. Then, 2 rounds of review were conducted until all experts agreed on the themes and main issues arising using a nominal group technique to reach consensus. Prioritization was based on how useful the consensus recommendation might be to a policy maker.

Findings

A diverse stakeholder group of 13 leaders in the fields of public health, digital health, and health care were engaged to reach a consensus on how to implement digital health recommendations to address the challenges of current and future pandemics. Participants reached a consensus on high-priority issues identified within 5 themes: team, transparency and trust, technology, techquity (the strategic development and deployment of technology in health care and health to achieve health equity), and transformation. Each theme contains concrete points of consensus to guide the local, national, and international adoption of digital health to address challenges of current and future pandemics.

Conclusions and Relevance

The consensus points described for these themes provide a roadmap for the implementation of digital health policy by all stakeholders, including governments. Implementation of these recommendations could have a significant impact by reducing fatalities and uniting countries on current and future battles against pandemics.

Effect of delayed entry of blood culture bottles in BACTEC automated blood culture system in the context of laboratory consolidation

Delayed entry of blood culture bottles is frequent in consolidated laboratories. A retrospective study evaluated time from insertion to detection and total detection time as a function of preincubation time, and we prospectively looked for false negative results. 69,604 blood culture bottles were reviewed for preincubation time, incubation time and total detection time. Positive cultures for specific bacterial subtypes were reviewed to assess the effect of preincubation time on likelihood of detection. 492 negative blood cultures were prospectively tested by 16S RNA PCR and Staphylococcus-specific PCR for the presence of bacterial DNA. Mean preincubation time for samples collected within the city-limits was 3.94 h versus 9.49–18.89 h for other client sites. Higher preincubation times were partially mitigated by a lower incubation time, with an overall increase in total detection time. A lower odds ratio of recovery of Staphylococcus spp was identified, but not confirmed by terminal subcultures and molecular assays. Prolonged preincubation of blood cultures affects total detection time despite a reduction in incubation time. Successful centralization of microbiological services may depend upon optimization of courier routes for inoculated blood culture bottles. Our data supports consideration for an increase in suggested maximum preincubation times.

Leveraging of SARS-CoV-2 PCR Cycle Thresholds Values to Forecast COVID-19 Trends

Introduction: We assessed the usefulness of SARS-CoV-2 RT-PCR cycle thresholds (Ct) values trends produced by the LHUB-ULB (a consolidated microbiology laboratory located in Brussels, Belgium) for monitoring the epidemic's dynamics at local and national levels and for improving forecasting models.

Methods: SARS-CoV-2 RT-PCR Ct values produced from April 1, 2020, to May 15, 2021, were compared with national COVID-19 confirmed cases notifications according to their geographical and time distribution. These Ct values were evaluated against both a phase diagram predicting the number of COVID-19 patients requiring intensive care and an age-structured model estimating COVID-19 prevalence in Belgium.

Results: Over 155,811 RT-PCR performed, 12,799 were positive and 7,910 Ct values were available for analysis. The 14-day median Ct values were negatively correlated with the 14-day mean daily positive tests with a lag of 17 days. In addition, the 14-day mean daily positive tests in LHUB-ULB were strongly correlated with the 14-day mean confirmed cases in the Brussels-Capital and in Belgium with coinciding start, peak, and end of the different waves of the epidemic. Ct values decreased concurrently with the forecasted phase-shifts of the diagram. Similarly, the evolution of 14-day median Ct values was negatively correlated with daily estimated prevalence for all age-classes.

Conclusion: We provide preliminary evidence that trends of Ct values can help to both follow and predict the epidemic's trajectory at local and national levels, underlining that consolidated microbiology laboratories can act as epidemic sensors as they gather data that are representative of the geographical area they serve.

Mini Review: Clinical Routine Microbiology in the Era of Automation and Digital Health

Clinical microbiology laboratories are the first line to combat and handle infectious diseases and antibiotic resistance, including newly emerging ones. Although most clinical laboratories still rely on conventional methods, a cascade of technological changes, driven by digital imaging and high-throughput sequencing, will revolutionize the management of clinical diagnostics for direct detection of bacteria and swift antimicrobial susceptibility testing. Importantly, such technological advancements occur in the golden age of machine learning where computers are no longer acting passively in data mining, but once trained, can also help physicians in making decisions for diagnostics and optimal treatment administration. The further potential of physically integrating new technologies in an automation chain, combined to machine-learning-based software for data analyses, is seducing and would indeed lead to a faster management in infectious diseases. However, if, from one side, technological advancement would achieve a better performance than conventional methods, on the other side, this evolution challenges clinicians in terms of data interpretation and impacts the entire hospital personnel organization and management. In this mini review, we discuss such technological achievements offering practical examples of their operability but also their limitations and potential issues that their implementation could rise in clinical microbiology laboratories.

Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap

The global spread of antimicrobial resistance (AMR) and lack of novel alternative treatments have been declared a global public health emergency by WHO. The greatest impact of AMR is experienced in resource-poor settings, because of lack of access to alternative antibiotics and because the prevalence of multidrug-resistant bacterial strains may be higher in low-income and middle-income countries (LMICs). Intelligent surveillance of AMR infections is key to informed policy decisions and public health interventions to counter AMR. Molecular surveillance using whole-genome sequencing (WGS) can be a valuable addition to phenotypic surveillance of AMR. WGS provides insights into the genetic basis of resistance mechanisms, as well as pathogen evolution and population dynamics at different spatial and temporal scales. Due to its high cost and complexity, WGS is currently mainly carried out in high-income countries. However, given its potential to inform national and international action plans against AMR, establishing WGS as a surveillance tool in LMICs will be important in order to produce a truly global picture. Here, we describe a roadmap for incorporating WGS into existing AMR surveillance frameworks, including WHO Global Antimicrobial Resistance Surveillance System, informed by our ongoing, practical experiences developing WGS surveillance systems in national reference laboratories in Colombia, India, Nigeria and the Philippines. Challenges and barriers to WGS in LMICs will be discussed together with a roadmap to possible solutions.

Recent Advances in Mouse Models of Sjögren's Syndrome

Sjögren's syndrome (SS) is a complex rheumatoid disease that mainly affects exocrine glands, resulting in xerostomia (dry mouth) and xerophthalmia (dry eye). SS is characterized by autoantibodies, infiltration into exocrine glands, and ectopic expression of MHC II molecules on glandular epithelial cells. In contrast to the well-characterized clinical and immunological features, the etiology and pathogenesis of SS remain largely unknown. Animal models are powerful research tools for elucidating the pathogenesis of human diseases. To date, many mouse models of SS, including induced models, in which disease is induced in mice, and genetic models, in which mice spontaneously develop SS-like disease, have been established. These mouse models have provided new insight into the pathogenesis of SS. In this review, we aim to provide a comprehensive overview of recent advances in the field of experimental SS.

Impact of Changes in Clinical Microbiology Laboratory Location and Ownership on the Practice of Infectious Diseases

The number of onsite clinical microbiology laboratories in hospitals is decreasing, likely related to the business model for laboratory consolidation and labor shortages, and this impacts a variety of clinical practices, including that of banking isolates for clinical or epidemiologic purposes. To determine the impact of these trends, infectious disease (ID) physicians were surveyed regarding their perceptions of offsite services. Clinical microbiology practices for retention of clinical isolates for future use were also determined. Surveys were sent to members of the Infectious Diseases Society of America's (IDSA) Emerging Infections Network (EIN). The EIN is a sentinel network of ID physicians who care for adult and/or pediatric patients in North America and who are members of IDSA. The response rate was 763 (45%) of 1,680 potential respondents. Five hundred forty (81%) respondents reported interacting with the clinical microbiology laboratory. Eighty-six percent of respondents thought an onsite laboratory very important for timely diagnostic reporting and ongoing communication with the clinical microbiologist. Thirty-five percent practiced in institutions where the core microbiology laboratory has been moved offsite, and an additional 7% (n = 38) reported that movement of core laboratory functions offsite was being considered. The respondents reported that only 24% of laboratories banked all isolates, with the majority saving isolates for less than 30 days. Based on these results, the trend toward centralized core laboratories negatively impacts the practice of ID physicians, potentially delays effective implementation of prompt and targeted care for patients with serious infections, and similarly adversely impacts infection control epidemiologic investigations.

Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies

Clinical microbiology is experiencing revolutionary advances in the deployment of molecular, genome sequencing-based, and mass spectrometry-driven detection, identification, and characterization assays. Laboratory automation and the linkage of information systems for big(ger) data management, including artificial intelligence (AI) approaches, also are being introduced. The initial optimism associated with these developments has now entered a more reality-driven phase of reflection on the significant challenges, complexities, and health care benefits posed by these innovations. With this in mind, the ongoing process of clinical laboratory consolidation, covering large geographical regions, represents an opportunity for the efficient and cost-effective introduction of new laboratory technologies and improvements in translational research and development. This will further define and generate the mandatory infrastructure used in validation and implementation of newer high-throughput diagnostic approaches. Effective, structured access to large numbers of well-documented biobanked biological materials from networked laboratories will release countless opportunities for clinical and scientific infectious disease research and will generate positive health care impacts. We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunities as key results.

A proposal for a comprehensive approach to infections across the surgical pathway

Despite evidence supporting the effectiveness of best practices in infection prevention and management, many healthcare workers fail to implement them and evidence-based practices tend to be underused in routine practice. Prevention and management of infections across the surgical pathway should always focus on collaboration among all healthcare workers sharing knowledge of best practices. To clarify key issues in the prevention and management of infections across the surgical pathway, a multidisciplinary task force of experts convened in Ancona, Italy, on May 31, 2019, for a national meeting. This document represents the executive summary of the final statements approved by the expert panel.

Bigger and Better? Representativeness of the Influenza A Surveillance Using One Consolidated Clinical Microbiology Laboratory Data Set as Compared to the Belgian Sentinel Network of Laboratories

Infectious diseases remain a serious public health concern globally, while the need for reliable and representative surveillance systems remains as acute as ever. The public health surveillance of infectious diseases uses reported positive results from sentinel clinical laboratories or laboratory networks, to survey the presence of specific microbial agents known to constitute a threat to public health in a given population. This monitoring activity is commonly based on a representative fraction of the microbiology laboratories nationally reporting to a single central reference point. However, in recent years a number of clinical microbiology laboratories (CML) have undergone a process of consolidation involving a shift toward laboratory amalgamation and closer real-time informational linkage. This report aims to investigate whether such merging activities might have a potential impact on infectious diseases surveillance. Influenza data was used from Belgian public health surveillance 2014–2017, to evaluate whether national infection trends could be estimated equally as effectively from only just one centralized CML serving the wider Brussels area (LHUB-ULB). The overall comparison reveals that there is a close correlation and representativeness of the LHUB-ULB data to the national and international data for the same time periods, both on epidemiological and molecular grounds. Notably, the effectiveness of the LHUB-ULB surveillance remains partially subject to local regional variations. A subset of the Influenza samples had their whole genome sequenced so that the observed epidemiological trends could be correlated to molecular observations from the same period, as an added-value proposition. These results illustrate that the real-time integration of high-throughput whole genome sequencing platforms available in consolidated CMLs into the public health surveillance system is not only credible but also advantageous to use for future surveillance and prediction purposes. This can be most effective when implemented for automatic detection systems that might include multiple layers of information and timely implementation of control strategies.

Valuing Health Surveillance as an Information System: Interdisciplinary Insights

The economic evaluation of health surveillance systems and of health information is a methodological challenge, as for information systems in general. Main present threads are considering cost-effectiveness solutions, minimizing costs for a given technically required output, or cost-benefit analysis, balancing costs with economic benefits of duly informed public interventions. The latter option, following a linear command-and-control perspective, implies considering a main causal link between information, decision, action, and health benefits. Yet, valuing information, taking into account its nature and multiple sources, the modalities of its processing cycle, from production to diffusion, decentralized use and gradual building of a shared information capital, constitutes a promising challenge. This work proposes an interdisciplinary insight on the value of health surveillance to get a renewed theoretical framework integrating information and informatics theory and information economics. The reflection is based on a typological approach of value, basically distinguishing between use and non-use values. Through this structured discussion, the main idea is to expand the boundaries of surveillance evaluation, to focus on changes and trends, on the dynamic and networked structure of information systems, on the contribution of diverse data, and on the added value of combining qualitative and quantitative information. Distancing itself from the command-and-control model, this reflection considers the behavioral fundaments of many health risks, as well as the decentralized, progressive and deliberative dimension of decision-making in risk management. The framework also draws on lessons learnt from recent applications within and outside of health sector, as in surveillance of antimicrobial resistance, inter-laboratory networks, the use of big data or web sources, the diffusion of technological products and large-scale financial risks. Finally, the paper poses the bases to think the challenge of a workable approach to economic evaluation of health surveillance through a better understanding of health information value. It aims to avoid over-simplifying the range of health information benefits across society while keeping evaluation within the boundaries of what may be ascribed to the assessed information system.