Laboratory Information Management System (LIMS) Analysis: A Lucrative Tool to Support the Control of Antimicrobial Resistance (AMR)

Abstract

Globally, antimicrobial resistance (AMR) poses a real risk to people’s health. To ascertain the burden, implications, and trends of AMR and to track the results of interventions, surveillance is a crucial activity. High-quality laboratory data must be efficiently collected and shared with surveillance systems. Particularly in LMICs with high disease loads, the capacity of laboratories is being dramatically increased. Building capacity for effective laboratory data administration is still a resource-constrained issue that, if left unresolved, may hamper development toward comprehensive AMR surveillance in LMICs. The absence of an open-source, useful lab tests database is particularly concerning. In this Personal View, we present an overview of the laboratory data management practices in Lower Middle Income Countries (LMIC) laboratories, a snapshot of the technological requirements for microbiological lab data management, and a description of the critical remedial measures. Current efforts to boost capability for AMR surveillance in LMICs would not be entirely successful without strategies for upgrading information technology equipment and information management systems in microbial labs.

1. Introduction

Worldwide, antibiotic use has spared millions of souls. However, overuse of antibiotics over the past 60 years has resulted in the evolution of antibiotic-resistant bacteria, hastening the spread of fatal infectious diseases and burdening society with financial costs. Even though this issue is frequently thought of as a worldwide one, some parts of the world are ignorant of its true extent [1]. AMR, an evolving danger to the general population, is caused by resistant strains of antibiotics. is making it harder to treat and prevent bacterial infections with today’s drugs.

Antibiotic-resistant organisms have emerged due to widespread antibiotic use during the past 60 years, accelerating the spread of fatal diseases and adding to the financial burden on society. There is no denying that this problem exists on a worldwide scale, yet in some regions of the world its scope is not quite evident [1].

The tendency of microorganisms to resist treatment or control via antimicrobial drugs adopted to do so is known as antibiotic resistance. Antimicrobial resistance (AMR) could pose a serious worldwide issue. Information on the rate of bacteria immune to antibiotics in countries of low- and middle socioeconomic status is scarce. Antibiotic resistance, however, is a significant international and domestic problem in West Pakistan, one of South Asia’s growing nations [2]. Recent discoveries of MDR (multi-drug resistant) and highly drug resistant microbes have both been made in Pakistan. The enterobacteriaceae family has developed quinolone resistance in Pakistan [3]. In addition, 93.7% of strains were found to be resistant to third-generation cephalosporins in a research on blood stream infections (BSI) [4]. The theory, which is commonly backed by a number of studies, contends that patients’ inaccurate indefinite consumption is to fault, along with irrational advice, incentives for overprescribing, self-treatment, less trained personnel, and a lack of professional training and standard examinations.

Suboptimal antimicrobial use can be caused by a number of things, including a general overreliance on empirical antimicrobial therapy with a concomitant disregard for microbiological outcomes, errors in testing at the lab, inability to bring in suitable samples for culture, unauthorized use of microbes in order assets and the absence of a microbiologically verified evaluation.

1.1 What is an antimicrobial stewardship program?

The Infectious Diseases Society of America (IDSA), the Society for Healthcare Epidemiology of America (SHEA), and the pediatric Infectious Diseases Society (PIDS), all agree that antibiotic stewardship involves collaborative efforts to encourage the selection of the best medication regimen, including the administration, time span, and route of administration. The purpose of these interventions is to measure and enhance the proper use of antibiotics [5].

The implementation of evidence-based treatments that maximize the use of antibiotics while limiting the emergence of resistance is the focus of ASPs. These programs include the creation of guidelines as well as regulatory and policy measures. Practically speaking, ASPs could be considered as the right course of action for employing antibiotics in a way that provides ongoing access to efficient treatment while minimizing side effects [5].

1.2 What is needed to set up an AMR surveillance system?

AMR surveillance typically requires a supportive environment and a commitment to delivering high-quality care in order for specialists from various facets of the medical field to follow good clinical practice, connect effectively, coordinate customs, and complete projects in the shortest possible time. Based on an effective infectious disease diagnostic cycle, this multifaceted or collaborative strategy includes clinicians who collect clinical samples for the microbiology lab and submit them there, a bacteriology lab that can perform species recognition and AST, as well as a system to report, collect, analyze, and analyze facts so that those who must take action are informed [6]. The uniform and verified information gathered from an effective AMR surveillance system can help countries create practical therapy recommendations, based on research public health policies, and other actions. There are a few key components for creating an AMR surveillance system. The system can grow gradually once these foundational pieces are in place [6].

1.3 Justification for surveillance of antimicrobial resistance

Data from AMR surveillance programs are used to track how bacteria respond to various antibiotic agents. Regular data distribution can aid in the revision of case management guidelines for healthcare facilities and aid in the methodical eradication of AMR. Additionally, this information can be utilized to educate the public, regulators, pharmacists, and medical professionals. To prove the effectiveness of treatment when treating communities during outbreaks, AMR surveillance is essential. It is crucial for both identifying the formation of novel resistance patterns and tracking the effectiveness of measures meant to reduce the burden and spread of AMR. It is obvious that in order to lower infectious disease-related mortality and morbidity, an effective surveillance system for AMR, which is a component of IDSR implementation and health systems improvement, is required [7].

In a national bacteriology reference laboratory, WHO handbook seeks to give background knowledge and outline the essential stages for countries conducting AMR surveillance for meningitis, bacteremia, and common enteric epidemic-prone Diseases. The adaptation of this guide to the national context and its acceptance would help to reduce the spread of AMR among these microorganisms, even though it encourages the sharing of laboratory data on AMR for high priority bacterial infections as meningitis, cholera, salmonellosis, and shigellosis [7].

1.4 Purpose and benefits of antimicrobial stewardship programs

The goal of ASPs is aimed at improving the clinical use of prescription antibiotics, which includes proper drug choice, a sufficient/balanced range, and use at the optimal moment, in the ideal amount, using the proper technique, and at appropriate periods [5]. There is growing evidence that ASPs improve the handling of disease, reduce complications linked to the use of antimicrobial agents, and enhance patient safety and quality of care [5].

1.5 Antimicrobial stewardship programs in different parts of the world

The Infectious Diseases Study Group for Antimicrobial Stewardship (ESCMID/ESGAP) and the Antimicrobial Stewardship Working Group of the International Society of Antimicrobial Chemotherapy (ISC) collaborated to conduct a global survey on antimicrobial stewardship in hospitals between March and September 2012. There were 67 participating nations from six different continents. 103 replies out of 660 came from Central and South America. Hospital AMS requirements differed from nation to nation. A total of 46% of hospitals already have an ASP, compared to 58% of hospitals worldwide, 66% of hospitals in Europe, and 67% of hospitals in North America [5].

At the local level, some initiatives have been created, such as mandated prescriptions for the purchase of antibiotics at pharmacies. Brazil and Mexico enacted laws in 2010, Chile in 1999, Colombia in 2005, and Chile in 1999, all of which were successful in lowering antibiotic consumption. A 12% decline in penicillin consumption was realized in Mexico. Following the implementation of the legislation, the large seasonal variation in penicillin consumption also decreased, indicating that antibiotics were previously not used appropriately for the treatment of transmissible infections of the respiratory system, a common example of antimicrobials abuse. Antimicrobial resistance reduction or stabilization (87%), a decrease in the amount of antibiotic prescriptions (53%), and clinical outcome improvement (49%) were the three main goals of ASPs across all nations [5].

1.6 Antimicrobial stewardship programs and WHO Global Action Plan

The WHO Global Action Plan on Antimicrobial Resistance and the PAHO Regional Action Plan both include antimicrobial stewardship programs [5]. In fact, suggestions for maximizing the use of antimicrobial medications in human and animal health are included in Objective 4 of the WHO Global Action Plan. The same goal specifically mentions that Member States must set up stewardship programs “that monitor and promote optimization of antimicrobial use at national and local levels in accordance with international standards to ensure the correct choice of antimicrobials at the right dose, based on evidence” [5].

2. Laboratory data management system

Systems for managing and evaluating large volumes of data from antimicrobial resistance (AMR) monitoring systems are called laboratory information management systems (LIMS). A crucial tool for informing policies and infection prevention and control measures is surveillance. A Laboratory Information Management System (LIMS) is used by the majority of labs. Laboratory information management systems (LIMS) are used in real time to monitor sample flow, automatically enter laboratory results, manage quality (for as by keeping an eye on reporting times), or highlight unexpected results. To investigate AMR patterns and trends, information should even be questioned at the regional, national, and international levels. To ensure that laboratory results are directly linked to other patient data, such as admission date and outcome data, laboratory information management systems (LIMS) should ideally be able to exchange data with hospital and patient data systems [8]. The majority of labs utilize a single LIMS for all types of samples. A single sample may yield multiple results in bacteriology (positive or negative, identification of the organism or organisms, multiple AST results, and additional testing like minimum inhibitory concentration (MIC)), and the workflows are more complicated (one sample may need to be handled over the course of several days). These are frequently not the best for bacteriology because they were created for hematology and biochemistry. The actual data from potential testing, such as zone widths or MIC values, are frequently not retained by many LIMS; rather, they can only retain the interpretations, such as resilient, intermediate, or prone. It is challenging to analyze data over time and look for trends because break-points and recommendations are frequently modified [9].

2.1 Laboratory capacity and quality management

Quite frequently, the limitation in AMR surveillance is laboratory full capacity. To build this capacity and ensure quality, it is crucial to implement internal quality assurance, take part in external quality assessment (EQA) programs in research facilities, develop and keep up with national standards of operation (SOPs) to guarantee consistency and integration of lab practices, and regularly train and inspire personnel [6]. In order to perform and/or regulate the aforementioned tasks, countries should establish a central coordinating laboratory. Assuring uniformity in picking out of samples, living things, and drugs to be tested is another benefit of using monitoring criteria [6].

Working with sponsored locations to make sure they have a functional LIMS is a fundamental responsibility of the Fleming Fund Country Grants. Country Grantees must also make sure that procedures are in place that can collect data and submit it to Global Antimicrobial Resistance and Use Surveillance System (GLASS) and national surveillance systems [6].

Antimicrobial resistance (AMR) still exists in Pakistan despite the country’s creation of a national action plan (NAP) to address inappropriate antimicrobial use and high antimicrobial resistance (AMR) rates there. The NAP was made public from the Department of National Health Services in May 2017. As a result, patient and LIMS are very necessary that will shape and strengthen the collection, management, and sharing of biological science information in lower middle income countries (LMICs) and boost screening of illnesses with public health significance such as antibiotic resistance (AMR). This can change how information is used to direct patient care, support information accessibility and usage for decision-making, and enable trend comparison on a regional and international level [6].

2.2 Elements of a laboratory-based surveillance system for AMR

The main method of identifying new drug resistance in the populace is surveillance, which enables prompt and effective response. Therefore, nations should improve their capability for the early detection and identification of resistant organisms that cause fetal diseases for public health [7].

Drug resistance monitoring national laboratories must staff qualified technologists, scientists, and pathologists. They should have the necessary tools and supplies to generate accurate results that will enable medication resistance surveillance. For informed decision-making, the information produced should be routinely shared with stakeholders and national authorities. Additionally, a laboratory must continually invest in purchasing supplies, media, and reagents, ensuring quality control, along with providing regular training for staff members and carrying out external quality assessment or proficiency testing, in order to successfully carry out the duties of isolation, identification, and antimicrobial susceptibility testing. A summary of the key findings from the national surveillance as well as clinical information from sentinel locations should be included in the AMR surveillance report [7]. Without requesting further information from hospitals, a nation with limited resources may carry out laboratory-based monitoring first, collecting data on susceptibility for widespread or epidemic-prone bacterial infections. Additional data may be prospectively collected if appropriate resources are available and the laboratory has experience tracking medication resistance, which should aid in enhancing AMR documentation [7].

2.3 Laboratory-based surveillance has several requirements

1. Prioritization of organisms to be observed, taking into mind the severity of the disease in the nation;

2. The selection of antibiotics to be tested for each isolate, taking into account the list of necessary medications and treatment recommendations;

3. Creating or modifying standard operating procedures (SOPs) for isolating, identifying, and testing the selected microorganisms’ susceptibility to various antibiotics;

4. Implementing or improving laboratory quality systems;

5. Establishing a database for information gathering and sharing with stakeholders via already-existing systems like IDSR.

2.4 Core components of LIMS

The specimen evaluation, custom executions, and storage space group make up the three main parts of an ideal LIMS. Think of a lab where different researchers track measurements in a variety of ways, from pen and paper to a sizable spreadsheet. It would be very challenging to guarantee that human error has not tainted your data; missing data, mistakes, and discrepancies in the data collected can all exacerbate any error. Let us examine the three parts of a LIMS in greater detail and discuss how they complement one another to help study participants and lab executives (Figure 1) [10].

Figure 1.

Core components of LIMS.

2.4.1 Recording samples using a LIMS software

The primary function of a LIMS is to record an item from the point that it arrives the laboratory by means of evaluation & preservation. In order to achieve this, all relevant evidence about the samples must be recorded at the time of first annexation, including the sample’s ID, origin, collect date, and estimating information (such as concentration, volume, and particle quantity). As the laboratory item progresses over its process, further data is noted, and this data is likewise preserved in the LIMS. This comprises test results, produced data samples, and statistics for immediate research [10].

Each lab study’s specific data is recorded by a LIMS, together with details on the people involved and the environment it has been in throughout its existence. Adding a sample to a section or combining it with different materials under scrutiny in the lab are also possible. This necessitates the employment of both an exterior barcode label on the test tube and a chemical “index” in addition to it. It can therefore be differentiated from the other specimens in the pool. All of this significant sample monitoring data is kept in the LIMS technique [10].

2.4.2 Protocol execution with a LIMS

The centralization of lab’s process flows and fundamental guidelines, methods, and phases is yet another key role of LIMS software. Despite of the truth, who holds the material or doing the analysis and in order to get a precise and consistent outcome, it is of the utmost importance to make sure every research individual adheres to the particulars of a given SOP (standard operating procedure). By scanning every phase in methods and standards, a LIMS supports standardization among the research group. That makes certain all of the laboratory’s personnel does the right actions, in the correct order, while subject is placed accurately by means of an exam [10].

The adoption of LIMS software, which can manage trial allocations, enables an object to be assigned the appropriate procedure as soon as it reaches a testing facility. A LIMS may also provide a lab stronger code implementation restrictions, granting access to study or clinical groups, depending on who is authorized to carry out the activity. Lab test results may be taken down, transmitted through the appropriate authorization line, and then followed by relevant collaborators [10].

2.4.3 Storage organization with a LIMS

The 3rd vital part of a LIMS is to keep a record of a specimen’s movements throughout its study career. The LIMS registers the location of the tube with the specimen or a container in a particular box (for example, slot A1 or B5) for each and every lab specimen. The system then keeps track of the shelf and slot that each package is on. The system also monitors the region and tier in which the chiller is located.

In busy labs, finding data fast depends on this “storage hierarchy” (Sample > Position > Box > Drawer > Rack > Shelf > Freezer > Room). Teams of researchers that are conscious of the precise location of lab samples remain useful, structured, and effective [10].

2.5 How laboratory information management system control antimicrobial resistance

LIMS can help control antimicrobial resistance in several ways:

1. Data management: LIMS can store and manage large amounts of data related to AMR, such as patient information, antibiotic usage, and susceptibility testing results. This allows for easy access, analysis, and interpretation of the data, which can help identify trends, patterns, and potential resistance patterns.

2. Antibiotic stewardship: LIMS can be integrated with antibiotic stewardship programs to help ensure proper and judicious use of antibiotics. For example, it can provide alerts or warnings when certain drugs are being overprescribed or when there are prescribing errors. This aids in stopping the emergence and expansion of resilience.

3. Susceptibility testing: LIMS can automate and streamline the process of susceptibility testing, which determines the effectiveness of antibiotics against specific pathogens. By standardizing and automating this process, LIMS reduces the chances of human error and improves the accuracy and consistency of test results. This ensures appropriate treatment and helps prevent the misuse or overuse of antibiotics.

4. Surveillance and tracking: LIMS can facilitate the surveillance and tracking of AMR patterns within a laboratory or across multiple laboratories. It can generate reports and dashboards that provide real-time insights into resistance trends, enabling timely interventions and control measures. LIMS can also integrate with regional or national surveillance systems to enable broader data sharing and analysis for better AMR control.

5. Data sharing and collaboration: LIMS can facilitate data sharing and collaboration between different laboratories, healthcare facilities, and regulatory agencies. This allows for the exchange of information and experiences regarding resistance patterns, treatment protocols, and prevention strategies. By sharing data and collaborating, stakeholders can collectively work toward tackling AMR.

3. Conclusion

Think about combining a variety of complementary programs and technologies to increase a Laboratory Information Management Systems (LIMS) capacity for addressing issues related to antibiotic resistance and enhancing patient care. Additional software can improve data administration and analysis in addition to the drawbacks mentioned by Sayed and colleagues. These include powerful Database Management Systems (DBMS) like MySQL or PostgreSQL, machine learning and AI algorithms for predictive analytics, and data analysis and visualization tools like R or Python. While laboratory automation software improves workflow efficiency, electronic health record (EHR) integration software guarantees smooth data transmission between clinical and laboratory records. Tools for encryption and cybersecurity are necessary to protect sensitive healthcare data. While cloud computing platforms provide scalability and cost-effectiveness, geographic information system (GIS) software aids in the identification of spatial patterns. A full LIMS ecosystem includes collaboration and communication tools, regulatory compliance software, quality control and assurance tools, mobile data gathering apps, and middleware for data integration and interoperability. Solutions for data backup, user education, and documentation guarantee data integrity and user competence. The combination of these software elements enables a comprehensive strategy to tackle antibiotic resistance and improve patient care.

Conflict of interest

None of the author’s interests are in conflict.