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| [[File:Daily Operations in the Microbiology Lab Aboard USNS Comfort (49826560406).jpg|right|450px]]
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| '''Title''': ''What are the key elements of a LIMS for medical microbiology?''
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| '''Author for citation''': Shawn E. Douglas
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| '''License for content''': [https://creativecommons.org/licenses/by-sa/4.0/ Creative Commons Attribution-ShareAlike 4.0 International]
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| '''Publication date''': April 2024
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| ==Introduction==
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| The medical [[microbiology]] [[laboratory]] is much like other medical laboratories in many ways with its patient- or population-driven focus. However, it has a variety of workflow requirements that manage to separate its needs from most of its biomedical peers. From the necessary creation of derivative specimens to having unique public health reporting requirements, these labs' workflows have their own unique needs, further affected (and enhanced) by a rapidly changing technological and employment landscape.
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| This brief topical article will examine the [[Informatics (academic field)|informatics]] needs of the medical microbiology lab, specifically addressing the 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. (Going forward, for simplicity, this article will discuss these requirements largely in the scope of a LIMS; however, note that an LIS is equally viable here.) Additional unique requirements will also be briefly discussed.
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| '''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.
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| ==Base LIMS requirements for medical microbiology labs==
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| A medical microbiology laboratory helps examine and identify microorganisms for both patient treatment and disease prevention and control. Like other biomedical 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 for the isolation and characterization of microorganisms, which are in turn driven by regulations and accreditation requirements affecting this important societal role. This requires a pre-configured and future-configurable solution like a LIMS 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.
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| What follows is a list of fundamental LIMS 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><ref>{{Citation |last=Aller |first=Raymond D. |last2=Salazar |first2=Vincent |date=2016-05-30 |editor-last=Truant |editor-first=Allan L. |editor2-last=Tang |editor2-first=Yi‐Wei |editor3-last=Waites |editor3-first=Ken B. |editor4-last=Bébéar |editor4-first=Cécile |editor5-last=Rennie |editor5-first=Robert P. |title=Microbiology Laboratory Information Systems |url=https://onlinelibrary.wiley.com/doi/10.1002/9781119021872.ch20 |work=Manual of Commercial Methods in Clinical Microbiology |language=en |edition=1 |publisher=Wiley |pages=377–385 |doi=10.1002/9781119021872.ch20 |isbn=978-1-118-13112-1 |accessdate=}}</ref><ref>{{Cite journal |last=Carey |first=Roberta B. |last2=Bhattacharyya |first2=Sanjib |last3=Kehl |first3=Sue C. |last4=Matukas |first4=Larissa M. |last5=Pentella |first5=Michael A. |last6=Salfinger |first6=Max |last7=Schuetz |first7=Audrey N. |date=2018-07 |title=Practical Guidance for Clinical Microbiology Laboratories: Implementing a Quality Management System in the Medical Microbiology Laboratory |url=https://journals.asm.org/doi/10.1128/CMR.00062-17 |journal=Clinical Microbiology Reviews |language=en |volume=31 |issue=3 |pages=e00062–17 |doi=10.1128/CMR.00062-17 |issn=0893-8512 |pmc=PMC6056841 |pmid=29720490}}</ref><ref name="TurnerLabInfo20">{{Cite web |last=Turner, P.; Rupali, P.; Opintan, J.A. et al. |date=12 September 2020 |title=Laboratory informatics capacity is a neglected component of effective antimicrobial resistance surveillance in resource-limited settings |work=Oxford University Research Archive |url=https://ora.ox.ac.uk/objects/uuid:fd143935-d2c1-459c-bdd7-623001113037/files/rnv9353211 |publisher=Oxford University |accessdate=17 April 2024}}</ref><ref name=":0">{{Cite journal |last=Vandenberg |first=Olivier |last2=Durand |first2=Géraldine |last3=Hallin |first3=Marie |last4=Diefenbach |first4=Andreas |last5=Gant |first5=Vanya |last6=Murray |first6=Patrick |last7=Kozlakidis |first7=Zisis |last8=van Belkum |first8=Alex |date=2020-03-18 |title=Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies |url=https://journals.asm.org/doi/10.1128/CMR.00057-19 |journal=Clinical Microbiology Reviews |language=en |volume=33 |issue=2 |pages=e00057–19 |doi=10.1128/CMR.00057-19 |issn=0893-8512 |pmc=PMC7048017 |pmid=32102900}}</ref><ref name="SlclabVideos23">{{cite web |url=https://slclab.com/en/videos-en.aspx |title=Video tutorials - Microbiology Results (Antibiogram) |publisher=SLCLAB Informática SL |date=2023 |accessdate=17 April 2024}}</ref><ref name="BGASoftMolec23">{{cite web |url=https://www.limsabc.com/molecular-id/ |title=Molecular ID LIS Solution |publisher=BGASoft, Inc |date=2023 |accessdate=17 April 2024}}</ref><ref name="FutrellAddress23">{{cite web |url=https://www.orchardsoft.com/white_paper/automation-contributes-to-laboratory-efficiency/ |title=Address Lab Staffing Shortages with Integrated Automation Solutions - White Paper |author=Futrell, K. |publisher=Orchard Software |date=05 December 2023 |accessdate=17 April 2024}}</ref><ref name="CRMSData21">{{cite web |url=https://www.rapidmicrobiology.com/news/data-integrity-in-the-microbiology-lab |title=Data Integrity in the Microbiology Lab |author=Charles River Microbial Solutions |work=Rapid Microbiology |publisher=Rapid Test Methods Ltd |date=03 September 2021 |accessdate=17 April 2024}}</ref><ref name="ArctaSEDRI23">{{Cite web |last=Arcta Solutions |date=13 July 2023 |title=SEDRI LIMS - A Microbiology Focused Open-Source LIMS |url=https://www.paho.org/sites/default/files/2023-10/p15-20223-cde-relavra-d2-sesion-3-sedri-lims-experiencia-desarrollador-matthew-king.pdf |format=PDF |publisher=Arcta Solutions |accessdate=17 April 2024}}</ref><ref name="CorpexLeeuwenbook">{{cite web |url=https://www.corpex.info/leeuwenbook.html |title=Leeuwenbook - Portable Microbiology Laboratory Solution |publisher=Corpex |accessdate=17 April 2024}}</ref><ref name="TechnidataNexLabs18">{{cite web |url=https://www.lig-systems.ch/wp-content/uploads/2018/02/GB-MKT555_flyer_TDNexLabs_Microbiology_EN.pdf |format=PDF |title=TD NexLabs Microbiology |publisher=Technidata SAS |date=February 2018 |accessdate=17 April 2024}}</ref>
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| '''Test, specimen, and result management'''
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| *Specimen accessioning and management, with support for unique IDs
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| *Specimen batching
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| *[[Barcode]], RFID, and label support
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| *End-to-end specimen, aliquot, and other inventory tracking
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| *Pre-defined and configurable industry-specific test and method management for a variety of tests, including susceptibility, reflex, and molecular testing
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| *Pre-defined and configurable industry-specific workflows and worksheets
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| *Configurable screens and data fields
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| *Specimen collection, testing, instrument, etc. scheduling and assignment
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| *Test requesting
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| *Data import, export, and archiving
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| *Robust query tools
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| *Analytical tools, including [[data visualization]], statistical analysis, and [[data mining]] tools
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| *Document and image management
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| *Patient management, including infection history
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| *Facility and specimen collection site management
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| *Storage management and monitoring
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| '''Quality, security, and compliance'''
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| *[[Quality assurance]] / [[quality control]] mechanisms
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| *Mechanisms for compliance with ISO 15189, ASTM, A2LA, CLIA, good clinical practice (GCP), and other standards, requirements, and guidelines
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| *Result, method, and batch validation, review, and release
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| *Data validation
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| *Trend and control charting for statistical analysis and measurement of uncertainty
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| *User qualification, performance, and training management
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| *[[Audit trail]]s and [[chain of custody]] support
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| *Configurable and granular role-based security
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| *Configurable system access and use (i.e., authentication requirements, account usage rules, account locking, etc.)
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| *[[Electronic signature]] support
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| *Data [[encryption]] and secure communication protocols
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| *Archiving and [[Data retention|retention]] of data and information
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| *Configurable data [[backup]]s
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| *Status updates and alerts
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| *Incident and non-conformance notification, tracking, and management
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| '''Operations management and reporting'''
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| *Configurable dashboards for monitoring results and reporting
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| *Customizable rich-text reporting, with multiple supported output formats
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| *Custom and industry-specific reporting, including for specialized testing
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| *Email integration
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| *Bi-directional instrument interfacing and data management
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| *Third-party software interfacing (e.g., [[hospital information system]]s (HIS), other databases)
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| *Data import, export, and archiving
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| *Instrument calibration and maintenance tracking
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| *Inventory and supply management
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| *Supplier/vendor/customer management
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| *Patient/provider portal
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| ==Specialty LIMS requirements==
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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 medical microbiology 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. Some vendor solutions may have been tailored with the direct input of microbiologists who've been in the field for decades. In that regard, a medical microbiology LIMS vendor may also include specialized functionality that assists these labs with their unique tasks. This includes the provision of:
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| *'''Derivative asset management, linking, and tracking''': Unlike many other labs in the biomedical sciences, a medical microbiology lab will end up creating (e.g., via [[cell culture]]) 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" /> Having sufficient LIMS tools to improve management of cultures and other derivatives is thus quite useful. 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" />
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| *'''Support for notations on primary and derivative assets, as well as other entities''': Given the above about primary specimens and the culturing of derivatives, it's vital that careful note-taking is performed at the various stages of analysis and interpretation by microbiologists. This electronic note-taking—in the past performed on physical note cards<ref name="RhoadsClin14" />—in turn can improve quality and patient outcomes. As such, many informatics systems will provide note-taking functions at granular levels for a variety of entities in the system.<ref name="RhoadsClin14" />
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| *'''Robust support for interfacing with a vast variety of systems and instruments''': While system and instrument interfacing is largely ''de facto'' required out of most any LIMS, this interfacing is essential to and more complex for a majority of medical microbiology labs. Communication between the LIMS and any HIS, for example, must be unhindered and clear such that analytical and interpretive orders placed in the HIS make their way to the LIMS, and results from the lab are readily transferred back to the HIS in a standardized and readable format. This interfacing must be verified periodically to ensure high levels of quality and patient outcomes. As such, the microbiology LIMS must have robust interfacing support using standardized protocols that ensure clear and rapid bidirectional communication between other informatics systems and laboratory instruments.<ref name="RhoadsClin14" /> This includes total laboratory automation (TLA) instruments and systems, which have gradually become more viable for the microbiology lab.<ref name="RhoadsClin14" /><ref name=":0" /><ref name="FutrellAddress23" /><ref>{{Cite journal |last=Antonios |first=Kritikos |last2=Croxatto |first2=Antony |last3=Culbreath |first3=Karissa |date=2021-12-30 |title=Current State of Laboratory Automation in Clinical Microbiology Laboratory |url=https://academic.oup.com/clinchem/article/68/1/99/6490228 |journal=Clinical Chemistry |language=en |volume=68 |issue=1 |pages=99–114 |doi=10.1093/clinchem/hvab242 |issn=0009-9147}}</ref> Additionally, as the early promise of automated microbiology image analysis<ref name="RhoadsClin14" /> has progressed to full-fledged systems with [[artificial intelligence]] (AI) components<ref name=":0" /><ref name="SandleEnhanc21">{{cite web |url=https://www.europeanpharmaceuticalreview.com/article/166302/enhancing-rapid-microbiology-methods-how-ai-is-shaping-microbiology/ |title=Enhancing rapid microbiology methods: how AI is shaping microbiology |author=Sandle, T. |work=European Pharmaceutical Review |date=22 December 2021 |accessdate=17 April 2024}}</ref><ref name="GilesSciBiomicv3_24">{{cite web |url=https://www.biomic.com/biomic-v3.html |title=BIOMIC V3 |publisher=Giles Scientific, Inc |date=2024 |accessdate=17 April 2024}}</ref>, the modern microbiology LIMS need to effectively interface with these systems too. Finally, connections to a wide variety of third-party [[database]]s used for identification and surveillance of microorganisms and their resistances, including WHONET<ref name="TurnerLabInfo20" /><ref name="ArctaSEDRI23" />, are important and must be addressed by any microbiology LIMS.<ref name="RhoadsClin14" />
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| *'''More robust, standardized, optimized, and automated result entry and reporting''': Microbiology labs in particular have multiple requirements and methods for reporting analytical and interpretive results, compared to other clinical laboratory disciplines, which usually report in a largely quantitative way. The microbiology lab will need to report and interpret complex qualitative, semi-quantitative, and quantitative data and information, using long and repetitive text strings (e.g., ''Staphylococcus epidermidis'') in both preliminary and final results. Ensuring ease-of-use with keyboard shortcuts for long, repetitive text strings, while also ensuring succinct, standardized terminology (e.g., using a common internationally accepted data model<ref name="RinaldiTowards23">{{Cite journal |last=Rinaldi |first=Eugenia |last2=Drenkhahn |first2=Cora |last3=Gebel |first3=Benjamin |last4=Saleh |first4=Kutaiba |last5=Tönnies |first5=Hauke |last6=von Loewenich |first6=Friederike D. |last7=Thoma |first7=Norbert |last8=Baier |first8=Claas |last9=Boeker |first9=Martin |last10=Hinske |first10=Ludwig Christian |last11=Diaz |first11=Luis Alberto Peña |date=2023-09-23 |title=Towards interoperability in infection control: a standard data model for microbiology |url=https://www.nature.com/articles/s41597-023-02560-x |journal=Scientific Data |language=en |volume=10 |issue=1 |pages=654 |doi=10.1038/s41597-023-02560-x |issn=2052-4463 |pmc=PMC10517923 |pmid=37741862}}</ref>) and clear and accurate test results or interpretations is imperative. A LIMS can apply a more "synoptic" approach to reporting typically found with surgical pathology, supporting highly configurable layouts, the enforcement of standardized nomenclature, and appropriate result highlighting mechanisms to ensure more confident report interpretation by both microbiologists and treating physicians.<ref name="RhoadsClin14" />
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| *'''Analytical and reporting support for susceptibility testing and antibiograms''': An antibiogram is a cumulative summary or "overall profile of [''in vitro''] susceptibility testing results for a specific microorganism to an array of antimicrobial drugs," often given in a tabular form.<ref name="UnivMNHowTo20">{{cite web |url=https://arsi.umn.edu/sites/arsi.umn.edu/files/2020-02/How_to_Use_a_Clinical_Antibiogram_26Feb2020_Final.pdf |format=PDF |title=How to Use a Clinical Antibiogram |author=Antimicrobial Resistance and Stewardship Initiative, University of Minnesota |date=February 2020 |accessdate=17 April 2024}}</ref> There are multiple approaches to antibiograms for a wide variety of susceptibility testing, common to microbiology labs.<ref>{{Cite journal |last=Gajic |first=Ina |last2=Kabic |first2=Jovana |last3=Kekic |first3=Dusan |last4=Jovicevic |first4=Milos |last5=Milenkovic |first5=Marina |last6=Mitic Culafic |first6=Dragana |last7=Trudic |first7=Anika |last8=Ranin |first8=Lazar |last9=Opavski |first9=Natasa |date=2022-03-23 |title=Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods |url=https://www.mdpi.com/2079-6382/11/4/427 |journal=Antibiotics |language=en |volume=11 |issue=4 |pages=427 |doi=10.3390/antibiotics11040427 |issn=2079-6382 |pmc=PMC9024665 |pmid=35453179}}</ref> While it's not common for a LIMS or LIS to have extensive data analysis capabilities, some may support the sometimes complex work of generating antibiograms.<ref name="RhoadsClin14" /><ref name="SlclabVideos23" /><ref name="BGASoftMolec23" /> At a minimum, the LIMS should have robust reporting capabilities able to handle the nuances of susceptibility testing and antibiograms, particularly to the standard CLSI M39 ''Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data''.<ref name="RhoadsClin14" /><ref>{{Cite journal |last=Simner |first=Patricia J. |last2=Hindler |first2=Janet A. |last3=Bhowmick |first3=Tanaya |last4=Das |first4=Sanchita |last5=Johnson |first5=J. Kristie |last6=Lubers |first6=Brian V. |last7=Redell |first7=Mark A. |last8=Stelling |first8=John |last9=Erdman |first9=Sharon M. |date=2022-10-19 |editor-last=Humphries |editor-first=Romney M. |title=What’s New in Antibiograms? Updating CLSI M39 Guidance with Current Trends |url=https://journals.asm.org/doi/10.1128/jcm.02210-21 |journal=Journal of Clinical Microbiology |language=en |volume=60 |issue=10 |pages=e02210–21 |doi=10.1128/jcm.02210-21 |issn=0095-1137 |pmc=PMC9580356 |pmid=35916520}}</ref> Ideally, the LIMS can even run the analyses themselves, pulling data from the LIMS and HIS, but again this may not be common.
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| *'''Support for flexible public health reporting''': In addition to supporting susceptibility testing and antibiogram analysis and reporting, the medical microbiology LIMS will also need to provide flexible reporting capabilities to allow such labs to meet public health reporting requirements. As Rhoads ''et al.'' note, "the reportable findings are somewhat dynamic, often with annual modifications, so informatics support requires ongoing vigilance to keep up with expectations of public health authorities," including "efficiently communicating with public health agencies and rapidly identifying outbreaks."<ref name="RhoadsClin14" /> In the U.S., this means microbiology information systems like LIMS need to be National Notifiable Diseases Surveillance System (NNDSS)-compatible.<ref name="CDCIntegrated">{{cite web |url=https://www.cdc.gov/nndss/about/nedss.html |title=Integrated Surveillance Information Systems/NEDSS |publisher=Centers for Disease Control and Prevention |accessdate=17 April 2024}}</ref> The [[COVID-19]] [[pandemic]], however, highlighted that standards-based international collaboration from and interoperability with these and other systems is vital to public health scenarios beyond a country's borders. This means the LIMS must support internationally-recognized terminologies such as [[LOINC]], [[SNOMED CT]], and UCUM for reporting and sharing data within and beyond national borders.<ref name="RinaldiTowards23" />
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| *'''Decision support systems for medical microbiology''': Just as there are [[decision support system]]s (DSS) built into some LIMS that can guide pharmacogenomics (PGx) decisions made with the aid of [[molecular diagnostics]] testing<ref name="EmgenexLIS24">{{cite web |url=https://www.emgenex.com/lis |title=Redefining LIS |publisher=Emgenex, Inc |date=2024 |accessdate=17 April 2024}}</ref>, a handful of LIMS or HIS options may incorporate DSS to better guide microbiology-based decisions on antibiotic prescription.<ref name="RhoadsClin14" /><ref name="EgliDigital20">{{Cite journal |last=Egli |first=A. |last2=Schrenzel |first2=J. |last3=Greub |first3=G. |date=2020-10 |title=Digital microbiology |url=https://linkinghub.elsevier.com/retrieve/pii/S1198743X20303670 |journal=Clinical Microbiology and Infection |language=en |volume=26 |issue=10 |pages=1324–1331 |doi=10.1016/j.cmi.2020.06.023 |pmc=PMC7320868 |pmid=32603804}}</ref> (DSS has already been used for other purposes in LIMS.<ref>{{Cite journal |last=Díaz-Gimenez |first=Macarena |last2=Carratala Calvo |first2=Arturo |last3=Vinyals-Bellido |first3=Inmaculada |last4=Corchon-Peyrallo |first4=Africa |last5=Hervas-Romero |first5=Ausias |last6=Pozo-Giraldez |first6=Adela |last7=Rodriguez-Borja |first7=Enrique |date=2021-06-15 |title=Decision support system through automatic algorithms and electronic request in diagnosis of anaemia for primary care patients |url=https://www.biochemia-medica.com/en/journal/31/2/10.11613/BM.2021.020702 |journal=Biochemia medica |volume=31 |issue=2 |pages=250–257 |doi=10.11613/BM.2021.020702 |pmc=PMC8047786 |pmid=33927552}}</ref><ref>{{Cite web |date=2022 |title=Sanela LIMS (Lab Information Management System) |url=https://sanelahealth.com/lims-software.html |publisher=Sanela Health |accessdate=17 April 2024}}</ref>) Those DSS may be guided with the help of supervised [[machine learning]] (ML) algorithms or other AI components.<ref name="EgliDigital20" /> However, such systems have their own acquisition and implementation costs, and maintaining the DSS with relevant data at regular intervals to ensure the DSS' usefulness adds additional costs the microbiology lab must weigh.<ref name="RhoadsClin14" />
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| ==Conclusion==
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| The medical microbiology laboratory is similar to other clinical labs in its patient- and population-driven focus. However, the work of analyzing and identifying microorganisms in specimens is anything but straightforward. With its unique workflows and public health duties, we find this lab has a sometimes significantly different workflow than an ordinary clinical diagnostics laboratory. In a rapidly changing technological and microbiological environment, compounded by economic and employee realities, an informatics system like a LIMS or LIS can help do a lot of the heavy lifting and streamline medical microbiology operations. This article sought to identify the key elements of these software solutions as they relate to the medical microbiology lab, addressing both fundamental functionality and specialty functionality uniquely developed for such labs. This includes the important workflow management aspects of preparing and tracking derivative specimens like cell cultures, as well a variety of interfacing and reporting tools in high demand for microbiology operations.
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| ==References==
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| {{Reflist|colwidth=30em}}
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| <!---
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| [[Category:LIMS Q&A articles (added in 2024)]]
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| [[Category:LIMS Q&A articles (all)]]
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| [[Category:LIMS Q&A articles on materials testing]] Place all category tags here-->
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