Laboratory informatics capacity for effective antimicrobial resistance surveillance in resource-limited settings

A Situation Analysis of the Capacity of Laboratories in Faith-Based Hospitals in Zambia to Conduct Surveillance of Antimicrobial Resistance: Opportunities to Improve Diagnostic Stewardship

Antimicrobial resistance (AMR) is a public health problem exacerbated by the overuse and misuse of antibiotics and the inadequate capacity of laboratories to conduct AMR surveillance. This study assessed the capacity of laboratories in seven faith-based hospitals to conduct AMR testing and surveillance in Zambia. This multi-facility, cross-sectional exploratory study was conducted from February 2024 to April 2024. We collected and analysed data using the self-scoring Laboratory Assessment of Antibiotic Resistance Testing Capacity (LAARC) tool. This study found an average score of 39%, indicating a low capacity of laboratories to conduct AMR surveillance. The highest capacity score was 47%, while the lowest was 25%. Only one hospital had a full capacity (100%) to utilise a laboratory information system (LIS). Three hospitals had a satisfactory capacity to perform data management with scores of 83%, 85%, and 95%. Only one hospital had a full capacity (100%) to process specimens, and only one hospital had good safety requirements for a microbiology laboratory, with a score of 89%. This study demonstrates that all the assessed hospitals had a low capacity to conduct AMR surveillance, which could affect diagnostic stewardship. Therefore, there is an urgent need to strengthen the microbiology capacity of laboratories to enhance AMR surveillance in Zambia.

Laboratory Information Management Systems in Oral Pathology: A Comprehensive Review

Efficiency in oral pathological laboratory processes is paramount for timely and accurate diagnosis. This review explores various strategies and methodologies that help streamline oral pathological laboratory workflows to enhance productivity and reduce turnaround times. Key focus areas include specimen collection, handling, processing, and analysis. Optimization techniques such as automation, digitalization, and standardization are discussed in detail, emphasizing their role in minimizing errors and maximizing throughput. Additionally, the integration of advanced technologies such as artificial intelligence and machine learning is examined for their potential to improve laboratory operations. Moreover, the importance of quality control measures and compliance with regulatory standards is underscored as essential components of any successful laboratory streamlining initiative. By implementing a comprehensive approach that addresses the entire diagnostic pathway, oral pathological laboratories can achieve significant efficiency, ultimately leading to better patient care and outcomes.

Evaluation of three protocols for direct susceptibility testing for gram negative-Enterobacteriaceae from patient samples in Uganda with SMS reporting

In Uganda, the challenge of generating and timely reporting essential antimicrobial resistance (AMR) data has led to overreliance on empirical antibiotic therapy, exacerbating the AMR crisis. To address this issue, this study aimed to adapt a one-step AMR testing protocol alongside an SMS (Short Message Service) result relay system (SRRS), with the potential to reduce the turnaround time for AMR testing and result communication from 4 days or more to 1 day in Ugandan clinical microbiology laboratories. Out of the 377 samples examined, 54 isolates were obtained. Notably, E. coli (61%) and K. pneumoniae (33%) were the most frequently identified, majority testing positive for ESBL. Evaluation of three AMR testing protocols revealed varying sensitivity and specificity, with Protocol A (ChromID ESBL-based) demonstrating high sensitivity (100%) but no calculable specificity, Protocol B (ceftazidime-based) showing high sensitivity (100%) and relatively low specificity (7.1%), and Protocol C (cefotaxime-based) exhibiting high sensitivity (97.8%) but no calculable specificity. ESBL positivity strongly correlated with resistance to specific antibiotics, including cefotaxime, ampicillin, and aztreonam (100%), cefuroxime (96%), ceftriaxone (93%), and trimethoprim sulfamethoxazole (87%). The potential of integrating an SRRS underscored the crucial role this could have in enabling efficient healthcare communication in AMR management. This study underscores the substantial potential of the tested protocols for accurately detecting ESBL production in clinical samples, potentially, providing a critical foundation for predicting and reporting AMR patterns. Although considerations related to specificity warrant careful assessment before widespread clinical adoption.

Microfoundations of Data-Driven Antimicrobial Stewardship Policy (ASP)

This paper introduces a comprehensive framework that elucidates the microfoundations of data-driven antimicrobial stewardship programs (ASPs), specifically focusing on resource-constrained settings. Such settings necessitate the utilization of available resources and engagement among multiple stakeholders. The microfoundations are conceptualized as interlinked components: input, process, output, and outcome. Collectively, these components provide a comprehensive framework for understanding the development and implementation of data-driven ASPs in resource-constrained settings. It underscores the importance of considering both the social and material dimensions when evaluating microbiological, clinical, and social impacts. By harmonizing technology, practices, values, and behaviors, this framework offers valuable insights for the development, implementation, and assessment of ASPs tailored to resource-constrained environments.

Capturing Data on Antimicrobial Resistance Patterns and Trends in Use in Regions of Asia (CAPTURA)

BACKGROUND

In 2015, the UK government established the Fleming Fund with the aim to address critical gaps in surveillance of antimicrobial resistance (AMR) in low- and middle-income countries in Asia and Africa. Among a large portfolio of grants, the Capturing Data on Antimicrobial Resistance Patterns and Trends in Use in Regions of Asia (CAPTURA) project was awarded with the specific objective of expanding the volume of historical data on AMR, consumption (AMC), and use (AMU) in the human healthcare sector across 12 countries in South and Southeast Asia.

METHODS

Starting in early 2019, the CAPTURA consortium began working with local governments and >100 relevant data-holding facilities across the region to identify, assess for quality, prioritize, and subsequently retrieve data on AMR, AMC, and AMU. Relevant and shared data were collated and analyzed to provide local overviews for national stakeholders as well as regional context, wherever possible.

RESULTS

From the vast information resource generated on current surveillance capacity and data availability, the project has highlighted gaps and areas for quality improvement and supported comprehensive capacity-building activities to optimize local data-collection and -management practices.

CONCLUSIONS

The project has paved the way for expansion of surveillance networks to include both the academic and private sector in several countries and has actively engaged in discussions to promote data sharing at the local, national, and regional levels. This paper describes the overarching approach to, and emerging lessons from, the CAPTURA project, and how it contributes to other ongoing efforts to strengthen national AMR surveillance in the region and globally.

Blood culture versus antibiotic use for neonatal inpatients in 61 hospitals implementing with the NEST360 Alliance in Kenya, Malawi, Nigeria, and Tanzania: a cross-sectional study

BACKGROUND

Thirty million small and sick newborns worldwide require inpatient care each year. Many receive antibiotics for clinically diagnosed infections without blood cultures, the current 'gold standard' for neonatal infection detection. Low neonatal blood culture use hampers appropriate antibiotic use, fuelling antimicrobial resistance (AMR) which threatens newborn survival. This study analysed the gap between blood culture use and antibiotic prescribing in hospitals implementing with Newborn Essential Solutions and Technologies (NEST360) in Kenya, Malawi, Nigeria, and Tanzania.

METHODS

Inpatient data from every newborn admission record (July 2019-August 2022) were included to describe hospital-level blood culture use and antibiotic prescription. Health Facility Assessment data informed performance categorisation of hospitals into four tiers: (Tier 1) no laboratory, (Tier 2) laboratory but no microbiology, (Tier 3) neonatal blood culture use < 50% of newborns receiving antibiotics, and (Tier 4) neonatal blood culture use > 50%.

RESULTS

A total of 144,146 newborn records from 61 hospitals were analysed. Mean hospital antibiotic prescription was 70% (range = 25-100%), with 6% mean blood culture use (range = 0-56%). Of the 10,575 blood cultures performed, only 24% (95%CI 23-25) had results, with 10% (10-11) positivity. Overall, 40% (24/61) of hospitals performed no blood cultures for newborns. No hospitals were categorised as Tier 1 because all had laboratories. Of Tier 2 hospitals, 87% (20/23) were District hospitals. Most hospitals could do blood cultures (38/61), yet the majority were categorised as Tier 3 (36/61). Only two hospitals performed > 50% blood cultures for newborns on antibiotics (Tier 4).

CONCLUSIONS

The two Tier 4 hospitals, with higher use of blood cultures for newborns, underline potential for higher blood culture coverage in other similar hospitals. Understanding why these hospitals are positive outliers requires more research into local barriers and enablers to performing blood cultures. Tier 3 facilities are missing opportunities for infection detection, and quality improvement strategies in neonatal units could increase coverage rapidly. Tier 2 facilities could close coverage gaps, but further laboratory strengthening is required. Closing this culture gap is doable and a priority for advancing locally-driven antibiotic stewardship programmes, preventing AMR, and reducing infection-related newborn deaths.

Has Data Quality of an Antimicrobial Resistance Surveillance System in a Province of Nepal Improved between 2019 and 2022?

An operational research study was conducted in 2019 to assess the quality of data submitted by antimicrobial resistance (AMR) surveillance sites in the Bagmati Province of Nepal to the National Public Health Laboratory for Global Antimicrobial Resistance and Use Surveillance System (GLASS). Measures were implemented to enhance the quality of AMR surveillance by strengthening capacity, improving infrastructure, implementing data sharing guidelines, and supervision. The current study examined reports submitted by surveillance sites in the same province in 2022 to assess whether the data quality had improved since 2019. The availability of infrastructure at the sites was assessed. Of the nine surveillance sites in the province, seven submitted reports in 2022 versus five in 2019. Completeness in reporting improved significantly from 19% in 2019 to 100% in 2022 (p < 0.001). Timely reports were received from two sites in 2019 and only one site in 2022. Specimen-pathogen consistency in accordance with the GLASS guidelines for urine, feces, and genital swab specimens improved, with ≥90% consistency at all sites. Overall, the pathogen-antibacterial consistency improved significantly for each GLASS priority pathogen. The study highlights the importance of dedicated infrastructure and institutional arrangements for AMR surveillance. Similar assessments covering all provinces of the country can provide a more complete country-wide picture.

Antimicrobial Resistance (AMR)

Antimicrobial resistance (AMR) has now emerged as a chronic public health problem globally, with the forecast of 10 million deaths per year globally by 2050. AMR occurs when viruses, bacteria, fungi and parasites do not respond to antimicrobial treatments in humans and animals, thus allowing the survival of the microorganism within the host. The prominent cause contributing to the current crisis remains to be the overuse and misuse of antimicrobials, particularly the inappropriate usage of antibiotics, increasing the global burden of antimicrobial resistance. The global consumption and usage of antibiotics are therefore closely monitored at all times. This review provides a current overview of the implications of strategies used by international governmental organisations, including the UN's 17 Sustainable Development Goals (SDGs), to address the problem of antibiotic resistance, as well as the "One Health Approach," a system incorporating a multidisciplinary effort to achieve the best possible health outcome by acknowledging the clear connections between humans, animals and their shared environment. The importance of public awareness and health literacy of lay audiences still needs to be further emphasised as part of global and local action plans. Antimicrobial resistance continues to be a major global public health dilemma of the 21st century. Already this topic is receiving substantial political input from the G7 countries and continues to be on the agenda of numerous political conferences. The consequences of failure to adequately address AMR are profound, with estimations of a return to the pre-antibiotic era, where everyday infections relating to childbirth, surgery and open fractured limbs could be potentially life-threatening. AMR itself represents a microcosm of factors, including social anthropology, civil unrest/war, diasporas, ethnic displacement, political systems, healthcare, economics, societal behaviour both at a population and individual level, health literacy, geoclimatic events, global travel and pharmaceutical innovation and investment, thus finding a solution that adequately addresses AMR and which helps stem further AMR emergence is complicated. Success will involve individuals, communities and nations all working together to ensure that the world continues to possess a sufficient armamentarium of effective antimicrobials that will sustain human and animal health, both now and in the future.

Surveillance of antimicrobial resistance in human health in Tanzania: 2016-2021

Background

Antimicrobial resistance (AMR) surveillance plays an important role in early detection of resistant strains of pathogens and informs treatments decisions at local, regional and national levels. In 2017, Tanzania developed a One Health AMR Surveillance Framework to guide establishment of AMR surveillance systems in the human and animal sectors.

Aim

We reviewed AMR surveillance studies in Tanzania to document progress towards establishing an AMR surveillance system and determine effective strengthening strategies.

Methods

We conducted a literature review on AMR studies conducted in Tanzania by searching Google Scholar, PubMed, and the websites of the Tanzania Ministry of Health and the World Health Organization for articles written in English and published from January 2012 to March 2021 using relevant search terms. Additionally, we reviewed applicable guidelines, plans, and reports from the Tanzanian Ministry of Health.

Results

We reviewed 10 articles on AMR in Tanzania, where studies were conducted at hospitals in seven of Tanzania's 26 regions between 2012 and 2019. Nine AMR sentinel sites had been established, and there was suitable and clear coordination under 'One Health'. However, sharing of surveillance data between sectors had yet to be strengthened. Most studies documented high resistance rates of Gram-negative bacteria to third-generation cephalosporins. There were few laboratory staff who were well trained on AMR.

Conclusion

Important progress has been made in establishing a useful, reliable AMR surveillance system. Challenges include a need to develop, implement and build investment case studies for the sustainability of AMR surveillance in Tanzania and ensure proper use of third-generation cephalosporins.

What this study adds

This article adds to the knowledge base of AMR trends in Tanzania and progress made in the implementation of AMR surveillance in human health sector as a contribution to the global AMR initiatives to reduce AMR burden worldwide. It has highlighted key gaps that need policy and implementation level attention.

Assessment of laboratory capacity in conflict-affected low-resource settings using two World Health Organization laboratory assessment tools

OBJECTIVES

Laboratory diagnostic services are essential to drive evidence-based treatment decisions, manage outbreaks, and provide population-level data. Many low- and middle-income countries (LMICs) lack sufficient diagnostic capacity, often further exacerbated in conflict-affected areas. This project assessed laboratory services in conflict-affected LMICs to understand gaps and opportunities for improving laboratory capacity.

METHODS

The World Health Organization Laboratory Assessment Tool Facility Questionnaire (WHO Laboratory Tool) and Stepwise Laboratory Improvement Process Towards Accreditation (SLIPTA) checklist were used to assess five laboratories in Eastern Democratic Republic of the Congo (DRC) and five in Gaza, Palestine. Total scores and percentage outcomes by indicator were calculated.

RESULTS

Average WHO Laboratory Tool score across all facilities was 41% (range 32-50%) in DRC and 78% (range 72-84%) in Gaza. Lowest scoring indicators in DRC were Biorisk management (13%, range 8-21%), Documentation (14%, range 6-21%), and in Gaza, were Facilities (59%, range 46-75%) and Documentation (60%, range 44-76%). Highest scoring indicators in DRC were Facilities (70%, range 45-83%) and Data and Information Management (61%, range 38-80%), and in Gaza were Data Information and Management (96%) and Public Health Function (91%, range 88-94%). In DRC, no laboratory achieved a SLIPTA star rating. In Gaza, two laboratories had a 3-star SLIPTA rating, one had a 2-star rating and two had a 1-star rating.

CONCLUSIONS

Laboratory systems in conflict-affected LMICs have significant gaps. Implementating improvement strategies in such settings may be especially challenging.

Innovation for infection prevention and control-revisiting Pasteur's vision

Louis Pasteur has long been heralded as one of the fathers of microbiology and immunology. Less known is Pasteur's vision on infection prevention and control (IPC) that drove current infection control, public health, and much of modern medicine and surgery. In this Review, we revisited Pasteur's pioneering works to assess progress and challenges in the process and technological innovation of IPC. We focused on Pasteur's far-sighted conceptualisation of the hospital as a reservoir of microorganisms and amplifier of transmission, aseptic technique in surgery, public health education, interdisciplinary working, and the protection of health services and patients. Examples from across the globe help inform future thinking for IPC innovation, adoption, scale up and sustained use.

Establishing a national reference laboratory for antimicrobial resistance using a whole-genome sequencing framework: Nigeria's experience

Whole-genome sequencing (WGS) is finding important applications in the surveillance of antimicrobial resistance (AMR), providing the most granular data and broadening the scope of niches and locations that can be surveilled. A common but often overlooked application of WGS is to replace or augment reference laboratory services for AMR surveillance. WGS has supplanted traditional strain subtyping in many comprehensive reference laboratories and is now the gold standard for rapidly ruling isolates into or out of suspected outbreak clusters. These and other properties give WGS the potential to serve in AMR reference functioning where a reference laboratory did not hitherto exist. In this perspective, we describe how we have employed a WGS approach, and an academic-public health system collaboration, to provide AMR reference laboratory services in Nigeria, as a model for leapfrogging to national AMR surveillance.

Global and Regional Burden of Bacterial Antimicrobial Resistance in Urinary Tract Infections in 2019

BACKGROUND

There are still no detailed data about the burden of bacterial antimicrobial resistance (AMR) in urinary tract infections (UTI). Concrete knowledge of global and regional bacterial AMR data is crucial for developing informed programs and policies to control bacterial AMR and for prudent use of antibiotics to optimize antibiotic therapy in patients with UTI. This study aimed to provide comprehensive global and regional estimates for the AMR burden of UTI in 2019.

METHODS

Data were obtained from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD), including death, disability-adjusted life-years (DALYs), year lived with disability (YLD), and years of life lost (YLL) for bacterial AMR in UTI for 7 GBD super-regions, 21 regions, 14 pathogens, 13 antibiotic classes, and 66 pathogen-antibiotic combinations in 2019. The estimates were based on two counterfactual scenarios: drug-susceptible infection and no infection.

RESULTS

Globally, there were 64.89 thousand deaths (95% uncertainty interval [UI]: 45.86-93.35) attributed to and 0.26 million deaths (95% UI: 0.18-0.36) associated with bacterial AMR in UTI in 2019. Among regions, the all-age death rates were higher in southern Latin America, tropical Latin America, and Europe and lower in sub-Saharan Africa. Escherichia coli and Klebsiella pneumoniae accounted for more than 50% of deaths attributable to and associated with AMR, and resistance was high among multiple types of antibiotic class, including fluoroquinolones, carbapenems, and third-generation cephalosporins. There were 2 pathogen-drug combinations that caused more than 6000 resistance-attributable deaths: third-generation cephalosporin-resistant Escherichia coli and fluoroquinolone-resistant Escherichia coli.

CONCLUSIONS

AMR in UTI is an unignorable health problem, both for the management of urology disease and for global antibiotic resistance. Special tailored strategies, including enhanced surveillance and rational use of antibiotics, should be developed for different regions according to the region-specific pathogen-antibiotic situations and resources.

Electronic information systems for One Health surveillance of antimicrobial resistance: a systematic scoping review

INTRODUCTION

Electronic information systems (EIS) that implement a 'One Health' approach by integrating antimicrobial resistance (AMR) data across the human, animal and environmental health sectors, have been identified as a global priority. However, evidence on the availability, technical capacities and effectiveness of such EIS is scarce.

METHODS

Through a qualitative synthesis of evidence, this systematic scoping review aims to: identify EIS for AMR surveillance that operate across human, animal and environmental health sectors; describe their technical characteristics and capabilities; and assess whether there is evidence for the effectiveness of the various EIS for AMR surveillance. Studies and reports between 1 January 2000 and 21 July 2021 from peer-reviewed and grey literature in the English language were included.

RESULTS

26 studies and reports were included in the final review, of which 27 EIS were described. None of the EIS integrated AMR data in a One Health approach across all three sectors. While there was a lack of evidence of thorough evaluations of the effectiveness of the identified EIS, several surveillance system effectiveness indicators were reported for most EIS. Standardised reporting of the effectiveness of EIS is recommended for future publications. The capabilities of the EIS varied in their technical design features, in terms of usability, data display tools and desired outputs. EIS that included interactive features, and geospatial maps are increasingly relevant for future trends in AMR data analytics.

CONCLUSION

No EIS for AMR surveillance was identified that was designed to integrate a broad range of AMR data from humans, animals and the environment, representing a major gap in global efforts to implement One Health approaches to address AMR.