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Like other labs, medical microbiology labs increasingly require an informatics solution that meets all or most of its workflow requirements. These requirements are often driven by standardized test methods, in turn driven by regulations and accreditation requirements. This requires a pre-configured and future-configurable solution that enables medical microbiology personnel to quickly select and use standardized test methods and forms, and make the changes they need to those methods and forms if those changes make sense within the overall data structure of the LIMS or LIS. | Like other labs, medical microbiology labs increasingly require an informatics solution that meets all or most of its workflow requirements. These requirements are often driven by standardized test methods, in turn driven by regulations and accreditation requirements. This requires a pre-configured and future-configurable solution that enables medical microbiology personnel to quickly select and use standardized test methods and forms, and make the changes they need to those methods and forms if those changes make sense within the overall data structure of the LIMS or LIS. | ||
What follows is a list of fundamental LIMS or LIS functionality important to most any medical microbiology laboratory, with a majority of that functionality found in many vendor software solutions. | What follows is a list of fundamental LIMS or LIS functionality important to most any medical microbiology laboratory, with a majority of that functionality found in many vendor software solutions.<ref name="RhoadsClin14">{{Cite journal |last=Rhoads |first=Daniel D. |last2=Sintchenko |first2=Vitali |last3=Rauch |first3=Carol A. |last4=Pantanowitz |first4=Liron |date=2014-10 |title=Clinical Microbiology Informatics |url=https://journals.asm.org/doi/10.1128/CMR.00049-14 |journal=Clinical Microbiology Reviews |language=en |volume=27 |issue=4 |pages=1025–1047 |doi=10.1128/CMR.00049-14 |issn=0893-8512 |pmc=PMC4187636 |pmid=25278581}}</ref> | ||
'''Test, sample, and result management''' | '''Test, sample, and result management''' | ||
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Some laboratory informatics software vendors are addressing medical microbiology laboratories' needs beyond the features of a basic all-purpose LIMS. A standard LIMS tailored for materials testing may already contribute to some of these wider organizational functions, as well as more advanced laboratory workflow requirements, but many may not, or may vary in what additional functionality they provide. In that regard, a materials testing LIMS vendor may also include specialized functionality that assists these labs. This includes the provision of: | Some laboratory informatics software vendors are addressing medical microbiology laboratories' needs beyond the features of a basic all-purpose LIMS. A standard LIMS tailored for materials testing may already contribute to some of these wider organizational functions, as well as more advanced laboratory workflow requirements, but many may not, or may vary in what additional functionality they provide. In that regard, a materials testing LIMS vendor may also include specialized functionality that assists these labs. This includes the provision of: | ||
*''' | *'''Derivative asset linking and tracking''': Unlike many other labs in the biomedical sciences, a medical microbiology lab will end up creating multiple derivative assets from a single accessioned specimen. For example, a specimen suspected of polymicrobial infection may require derivative specimens representing "aerobic bacteria, anaerobic bacteria, mycobacteria, and/or fungi, and all of these need to be linked to the original accession number."<ref name="RhoadsClin14" /> As Rhoads ''et al.'' note, "properly handling the electronic information associated with a sample, such as tracking its derivatives, modifying descriptions of its derivatives, and linking its derivatives with their accession number, is a unique and essential aspect of the microbiology LIS."<ref name="RhoadsClin14" /> | ||
==Conclusion== | ==Conclusion== | ||
Revision as of 18:33, 17 April 2024
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Title: What are the key elements of a LIMS or LIS for medical microbiology?
Author for citation: Shawn E. Douglas
License for content: Creative Commons Attribution-ShareAlike 4.0 International
Publication date: April 2024
Introduction
This brief topical article will examine the informatics needs of the medical microbiology lab, including a base set of laboratory information management system (LIMS) or laboratory information system (LIS) functionality (i.e., system requirements) that is critical to fulfilling the information management and workflow requirements of this type of lab. Additional unique requirements will also be briefly discussed.
Note: Any citation leading to a software vendor's site is not to be considered a recommendation for that vendor. The citation should however still stand as a representational example of what vendors are implementing in their systems.
Base LIMS or LIS requirements for medical microbiology labs
Like other labs, medical microbiology labs increasingly require an informatics solution that meets all or most of its workflow requirements. These requirements are often driven by standardized test methods, in turn driven by regulations and accreditation requirements. This requires a pre-configured and future-configurable solution that enables medical microbiology personnel to quickly select and use standardized test methods and forms, and make the changes they need to those methods and forms if those changes make sense within the overall data structure of the LIMS or LIS.
What follows is a list of fundamental LIMS or LIS functionality important to most any medical microbiology laboratory, with a majority of that functionality found in many vendor software solutions.[1]
Test, sample, and result management
- Sample log-in and management, with support for unique IDs
- Sample batching
- Barcode and RFID support
- End-to-end sample and inventory tracking
- Pre-defined and configurable industry-specific test and method management for a variety of physical, mechanical, and chemical analyses
- Pre-defined and configurable industry-specific workflows
- Configurable screens and data fields
- Specification management
- Test, sampling, instrument, etc. scheduling and assignment
- Test requesting
- Data import, export, and archiving
- Robust query tools
- Analytical tools, including data visualization, statistical analysis, and data mining tools
- Document and image management
- Project management
- Facility and sampling site management
- Storage management and monitoring
Quality, security, and compliance
- Quality assurance / quality control mechanisms
- Mechanisms for compliance with ISO/IEC 17025, ISO 9000, ASTM, A2LA, ANAB, and other requirements
- Result, method, protocol, batch, and material validation, review, and release
- Data validation
- Trend and control charting for statistical analysis and measurement of uncertainty
- User qualification, performance, and training management
- Audit trails and chain of custody support
- Configurable and granular role-based security
- Configurable system access and use (i.e., authentication requirements, account usage rules, account locking, etc.)
- Electronic signature support
- Data encryption and secure communication protocols
- Archiving and retention of data and information
- Configurable data backups
- Status updates and alerts
- Incident and non-conformance notification, tracking, and management
Operations management and reporting
- Configurable dashboards for monitoring, by material, process, facility, etc.
- Customizable rich-text reporting, with multiple supported output formats
- Custom and industry-specific reporting, including certificates of analysis (CoAs)
- Email integration
- Bi-directional instrument interfacing and data management
- Third-party software interfacing (e.g., scientific data management system [SDMS], other databases)
- Data import, export, and archiving
- Instrument calibration and maintenance tracking
- Inventory and material management
- Supplier/vendor/customer management
- Customer portal
Specialty LIMS requirements
Some laboratory informatics software vendors are addressing medical microbiology laboratories' needs beyond the features of a basic all-purpose LIMS. A standard LIMS tailored for materials testing may already contribute to some of these wider organizational functions, as well as more advanced laboratory workflow requirements, but many may not, or may vary in what additional functionality they provide. In that regard, a materials testing LIMS vendor may also include specialized functionality that assists these labs. This includes the provision of:
- Derivative asset linking and tracking: Unlike many other labs in the biomedical sciences, a medical microbiology lab will end up creating multiple derivative assets from a single accessioned specimen. For example, a specimen suspected of polymicrobial infection may require derivative specimens representing "aerobic bacteria, anaerobic bacteria, mycobacteria, and/or fungi, and all of these need to be linked to the original accession number."[1] As Rhoads et al. note, "properly handling the electronic information associated with a sample, such as tracking its derivatives, modifying descriptions of its derivatives, and linking its derivatives with their accession number, is a unique and essential aspect of the microbiology LIS."[1]
Conclusion
References
- ↑ 1.0 1.1 1.2 Rhoads, Daniel D.; Sintchenko, Vitali; Rauch, Carol A.; Pantanowitz, Liron (1 October 2014). "Clinical Microbiology Informatics" (in en). Clinical Microbiology Reviews 27 (4): 1025–1047. doi:10.1128/CMR.00049-14. ISSN 0893-8512. PMC PMC4187636. PMID 25278581. https://journals.asm.org/doi/10.1128/CMR.00049-14.
