The motivation for an open-source, microbiology focused LIMS was described as follows at the inception of the program:
"Surveillance is a cornerstone of global antimicrobial resistance (AMR) containment and control activities. High quality surveillance enables estimation of the extent of the AMR problem, trends over time and the impact of interventions. AMR surveillance data can be used to inform empiric treatment guidelines which, alongside confirmation of individual patient infection, is arguably the most important function of clinical microbiology data.
Unfortunately, it remains challenging for many countries to generate high quality data, whether for clinical microbiology liaison work, for analysis of the AMR burden based on locally produced data or to submit to international AMR surveillance systems. These challenges are often greatest in low and middle income countries (LMICs) where healthcare resources are limited. Several international initiatives are aimed at improving the number and technical capability of diagnostic microbiology laboratories in LMICs, e.g. the Fleming Fund. However, one area of laboratory strengthening that has consistently been neglected and remains under-resourced is that of systematic data capture and data management.
A round-table event at the Wellcome Trust (Oct 2019) agreed upon the need for a freely available Laboratory Information Management System (LIMS) to plug this gap by enabling laboratories to manage specimens linked to a patient database, support bench workflow within the laboratory and easily access and analyse their own data (https://sedric.org.uk/data-from-surveillance-in-health-dash-round-table-summary/). This would enable laboratories to use data at the individual patient level (to guide treatment), at an aggregate data level locally within the hospital (to guide outbreak investigation or write antibiotic guidelines) or to report to regional, national or international surveillance networks.
The potential ability to interface with local hospital systems, other existing Hospital Information Systems, WHONET and GLASS is also required. Current systems are flawed as they are too expensive, are designed primarily for haematology or biochemistry results (highly automated and single timepoint), require repeated data entry steps, are not user-friendly, do not permit laboratories to access their own data or some combination of these flaws. Specifically, the small number of existing locally-hosted open access options have not been designed with diagnostic microbiology in mind and are provided with minimal support and training materials, so are of limited utility in settings without access to significant IT support. The creation of a LIMS that is appropriate for the LMIC context would provide substantial benefits not only for global AMR data integration, but for emerging infectious diseases also.
A comprehensive review summarised the informatics requirements for diagnostic microbiology laboratories in general (Rhoads DD, Clin Microbiol Rev. 2014). The authors described the unique features required for a diagnostic microbiology laboratory LIMS as compared with the blood sciences and it is proposed that the new LIMS be aligned with these specifications, specifically addressing the following items:
- Linkage between different databases, i.e. linkage between a unique isolate number and a unique patient identifier
- Multiple derivative tracking, i.e. multiple culture media, multiple bacterial isolates and antimicrobial susceptibility test (AST) results, molecular results
- Complex results reporting (AST data with multiple reference ranges depending on bug-drug combination) and the difficulties around bacterial nomenclature standardisation
- Reporting of, and retention of data for, both preliminary and final results
- Periodic generation of antibiograms, i.e. institution-level summary resistance profiles for key bacterial species to aid empiric treatment decision-making
- Compatibility with ISO15189 (medical laboratory) accreditation"