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==Sandbox begins below==
==Sandbox begins below==
<div class="nonumtoc">__TOC__</div>
<div class="nonumtoc">__TOC__</div>
[[File:PCR machine.jpg|thumb|right|A Bio-Rad thermal cycler as an example of a [[laboratory]] device that measures, processes, and sends information]]'''Laboratory informatics''' is the specialized application of information through a platform of instruments, software, and data management tools that allow scientific data to be captured, migrated, processed, and interpreted for immediate use, as well as stored, managed, and shared to support future research, development, and lab testing efforts while maximizing the efficiency of [[laboratory]] operations.<ref name="LM08Informatics">{{cite web |url=https://www.labmanager.com/computing-and-automation/laboratory-informatics-20964 |title=Informatics Are Really, Really, Really Important |author=Metrick, G. |work=Lab Manager Magazine |date=21 July 2008 |accessdate=19 March 2020}}</ref><ref name="CLIPaper">{{cite web |url=https://www.it.uu.se/edu/course/homepage/lims/vt12/ComprehensiveLaboratoryInformatics.pdf |archiveurl=https://web.archive.org/web/20170825181932/https://www.it.uu.se/edu/course/homepage/lims/vt12/ComprehensiveLaboratoryInformatics.pdf |format=PDF |title=Comprehensive Laboratory Informatics: A Multilayer Approach |author=Wood, S. |work=American Laboratory |date=September 2007 |pages=3 |archivedate=25 August 2017 |accessdate=25 August 2017}}</ref>
[[File:US Navy 070905-N-0194K-029 Lt. Paul Graf, a microbiology officer aboard Military Sealift Command hospital ship USNS Comfort (T-AH 20), examines wound cultures in the ship's microbiology laboratory.jpg|right|380px]]
'''Title''': ''What types of testing occur within a medical microbiology laboratory?''


==History==
'''Author for citation''': Shawn E. Douglas


The term "laboratory [[Informatics (academic field)|informatics]]" has been in use at least since the early 1980s<ref name="ExcerptaMedica">{{cite journal |url=https://books.google.com/books?id=z4GaAAAAIAAJ&q=%22laboratory+informatics%22&dq=%22laboratory+informatics%22&hl=en |journal=Excerpta Medica |title=Section 36: Health Economics and Hospital Management |volume=19 |issue=1 |year=1983 |page=72, 534}}</ref><ref name="NewSciLI">{{cite journal |url=https://books.google.com/books?id=uyceAQAAMAAJ&q=%22laboratory+informatics%22&dq=%22laboratory+informatics%22&hl=en |work=New Scientist |title=Research |publisher=New Science Publications |volume=109 |year=1986 |page=66}}</ref><ref name="InfoPath">{{cite journal |url=https://books.google.com/books?id=PbNYAAAAYAAJ&q=%22laboratory+informatics%22&dq=%22laboratory+informatics%22&hl=en |work=Informatics in Pathology |title=Introduction |publisher=Grune & Stratton |volume=1 |issue=1 |year=1986 |page=1}}</ref> and has expanded in meaning since then. Before the advent of computer technology, information management played an important role in laboratories and research efforts of all sorts. And while today the process of [[information management]] continues to be important, laboratory informatics tends to focus more on the technology associated with that information management process.<ref name="InfoClinLab">{{cite book |url=https://books.google.com/books?id=OKqGfr6xgFkC&pg=PA9 |title=Informatics for the Clinical Laboratory: A Practical Guide |editor=Cowan, D. |year=2002 |pages=9 |edition=1st |publisher=Springer |isbn=9780387244495}}</ref>
'''License for content''': [https://creativecommons.org/licenses/by-sa/4.0/ Creative Commons Attribution-ShareAlike 4.0 International]


The field itself is one which has seen significant growth as demand for fast and efficient electronic data exchange has boomed. A rapid series of technological developments have made laboratory equipment less static and more interactive, allowing large networks of integrated lab devices, computers, and telecommunications equipment to log, analyze, and distribute data. This has progressively enabled scientific research projects to move from a localized model to a more global model, one that allows "involved researchers to spend less time collecting data or waiting for information to arrive from another location, which in turn allows them to focus more on the work at hand and makes their research both faster and more efficient."<ref name="VI">{{cite web |url=http://www.virtualinformatics.com/content/Laboratory_informatics.htm |archiveurl=http://web.archive.org/web/20150425070143/http://virtualinformatics.com/content/Laboratory_informatics.htm |title=Laboratory Informatics |publisher=virtualinformatics.com |date=09 April 2011 |archivedate=25 April 2015 |accessdate=17 February 2017}}</ref> Tangentially, more robust and scalable data management systems have been developed to help laboratories stay competitive. Today, this often means adopting laboratory automation solutions that are capable of being developed and deployed in an agile fashion.<ref name="KrasovecLIMS09">{{cite journal |title=LIMS Get Agile |journal=International Clinical Trials |author=Krasovec, E. |volume=Spring 2009 |pages=32, 34 |year=2009 |url=https://www.informatics.abbott/shared/lims-get-agile.pdf |format=PDF}}</ref><ref name="CSolsAgile19">{{cite web |url=https://www.csolsinc.com/blog/agile-development-in-laboratory-informatics/ |title=Agile Development in Laboratory Informatics |publisher=CSols, Inc. |date=05 December 2019 |accessdate=19 March 2020}}</ref> Additionally, the rapid rate of change in the technological (e.g., cloud-computing, big data) and environmental needs (e.g., more automated workflows) of researchers—coupled with growing competition—has led to a variety of related efforts, such as conferences and trade shows, to assist directors, managers, and researchers in better keeping up with the industry.<ref name="MetrickTrends10">{{cite web |url=https://www.labmanager.com/laboratory-technology/trends-in-laboratory-informatics-19119 |title=Trends in Laboratory Informatics |author=Metrick, G. |work=Lab Manager Magazine |date=08 December 2010 |accessdate=19 March 2020}}</ref>
'''Publication date''': April 2024


{{As of|May 2019}}, market researchers such as Research and Markets have estimated the global market for laboratory informatics applications will reach $3.8 billion (U.S.) by 2024, up from roughly $2.6 billion in 2019. "The increasing need for laboratory automation; development of integrated lab informatics solutions; need to comply with regulatory requirements; and the growing demand in biobanks/biorepositories, academic research institutes, and CROs are the major factors driving the growth of the laboratory informatics market," says Research and Markets.<ref name="PRN3.8Bn19">{{cite web |url=https://www.prnewswire.com/news-releases/3-8-bn-laboratory-informatics-market---global-forecasts-to-2024-growing-demand-in-biobanksbiorepositories-academic-research-institutes-and-cros-300848731.html |title=$3.8 Bn Laboratory Informatics Market - Global Forecasts to 2024: Growing Demand in Biobanks/Biorepositories, Academic Research Institutes, and CROs |author=Research and Markets |work=PR Newswire |date=14 March 2019 |accessdate=19 March 2020}}</ref>
==Introduction==
The medical [[microbiology]] [[laboratory]] has a variety of testing and workflow requirements that manage to separate it from other biomedical labs.  


==Sub-elements in laboratory informatics==
This brief topical article will examine the typical types of testing that occur in medical microbiology labs.


Laboratory informatics is often modeled as a central component or hub for other branching elements of the field. However, looking at the architecture in this fashion oversimplifies the field of laboratory informatics and risks giving the false appearance that branched elements of the field have greater importance than others. Instead, a multi-layered, non-hierarchical model of these elements that places an emphasis on an individual laboratory's identified business needs may be more appropriate.<ref name="CLIPaper" /> A cottage industry of businesses and consultants has developed from this philosophy, helping laboratories map their informatics needs to their corporate strategy.<ref name=">{{cite web |url=http://www.labvantage.com/services/laboratory-strategy.aspx |archiveurl=https://web.archive.org/web/20130213132659/http://www.labvantage.com/services/laboratory-strategy.aspx |title=Laboratory Informatics Strategy |publisher=Labvantage Solutions, Inc |archivedate=13 February 2013 |accessdate=06 January 2022}}</ref>


Yet it's difficult to deny the existence of branching elements of laboratory informatics. Many scientific pursuits require a laboratory, from medicine to astrophysics. This has led to special "sub-applications" of [[informatics]] to more specialized laboratories. [[Genome informatics]] developed as genetics laboratories sought more efficient ways to manage the large amounts of data being acquired from experiments and research. As scientists continue their pursuit of unlocking the secrets of the brain, [[neuroinformatics]] and its associated technology has developed to aid those researchers in their endeavors. And as hydrologists tackle the issues of equitable and efficient use of water for many different purposes, [[hydroinformatics]] and computational hydraulics have emerged.  
==The medical microbiology lab in general==
A medical [[microbiology]] [[laboratory]] helps detect, identify, and characterize [[microorganism]]s for both individual patient treatment and broader population disease prevention and control. In the course of its work towards aiding in the diagnosis of individual patients' ailments, the lab may identify infectious agents of concern and trends in those infections as part of a greater [[public health]] effort. By extension, medical microbiology laboratories are also responsible for reporting those identification and trends to various public health agencies (city, county, state, and federal). These reports are then used by [[Public health laboratory|public health laboratories]], in tandem with medical microbiology labs, to track incidences and attempt to identify outbreaks.<ref name="RhoadsClin14" /> In particular, the medical microbiology lab is uniquely suited to confirming infectious disease cases as part of outbreak investigations, with its analytical and interpretive "methods that are not commonly available in a routine laboratory setting."<ref name="ECDCCore10">{{cite web |url=https://www.ecdc.europa.eu/sites/default/files/media/en/publications/Publications/1006_TER_Core_functions_of_reference_labs.pdf |format=PDF |title=Core functions of microbiology reference laboratories for communicable diseases |author=European Centre for Disease Prevention and Control |date=June 2010 |publisher=European Centre for Disease Prevention and Control |isbn=9789291932115 |doi=10.2900/29017 |accessdate=24 April 2024}}</ref>


These sub-applications of laboratory informatics are also discussed in [[ASTM International]]'s [[ASTM E1578|ASTM E1578-18]] Standard Guide for Laboratory Informatics. Updated in mid-2018, the standard not only covers applications of informatics to general laboratories but also to environmental, life science, medical, industrial, and public sector labs. The update brought with it new insights into laboratory informatics tools and how to integrate them into laboratory [[workflow]], and with other hardware and software. And though relatively in their infancy in laboratory application, the revision added content about the application of the [[internet of things]] (IoT), [[artificial intelligence]] (AI), and smart objects to the laboratory.<ref name="ASTME1578">{{cite web |url=https://www.astm.org/e1578-18.html |title=ASTM E1578-18 Standard Guide for Laboratory Informatics |publisher=ASTM International |accessdate=06 January 2022}}</ref><ref name="JonesASTME1578_18">{{cite web |url=https://cdn2.mindmeister.com/943721819/astm-e1578-scope-elements-of-laboratory-informatics?fullscreen=1 |title=ASTM 1578 (Scope & Elements of Laboratory Informatics) |author=Jones, J. |work=MindMeister |date=2018 |accessdate=19 March 2020}}</ref>
A standard consolidated medical microbiology laboratory will have the facilities for rapid microbiology, [[Microscope|microscopy]], [[Cell culture|cell culturing]], serology, molecular biology, parasitology, virology, communicable disease management (i.e., public health or reference activities<ref name="ECDCCore10" />) and more, and it also may have the facilities for environmental microbiology.<ref name="VandenbergConsol20">{{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> A variety of specimen types will be tested, including urine, blood, stool, tissues, and precious fluids, as well as skin, mucosal, and genital swabs.<ref name="VandenbergConsol20" />


===Additional considerations in laboratory informatics===
Culture-based and other microbiology test methods have largely been performed manually up until recently. As Antonios ''et al.'' noted at the end of 2021, "the introduction of automation in microbiology was considered difficult to apply for several reasons such as the complexity and variability of sample types, the variations of specimens processing, the doubtful cost-effectiveness especially for small and average-sized laboratories, and the perception that machines could not exercise the critical decision-making skills required to process microbiological samples."<ref name="AntoniosCurrent21">{{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> However, economic, employment, and other societal drivers have necessarily brought [[laboratory automation]] and [[large language model]]s (LLMs) more fully to the medical microbiology lab in recent years.<ref name="VandenbergConsol20" /><ref name="AntoniosCurrent21" /><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> This has allowed these labs to move from a traditional partial-day work schedule to a more 24-hour work schedule by, for example, the use of automated front-end plating systems.<ref name="AntoniosCurrent21" />
The actual processes that involve information management in the laboratory should not be overlooked. Laboratories are usually required to meet regulatory requirements that dictate what data should be managed; when it should be collected and stored; how it should be collected, used, and stored; where it should be housed; and who has access to it.<ref name="MatsushitaCompl09">{{cite journal |title=Compliance with laboratory requirements regarding the secondary use of clinical specimens and laboratory data |journal=Rinsho Byori |author=Matsushita, H.; Miyachi, H. |volume=57 |issue=7 |pages=678–82 |year=2009 |pmid=19708538}}</ref><ref name="PoosaAnExpl15">{{cite web |url=http://www.bcsolutionsrfn.com/wp-content/uploads/2015/11/explanation-of-laboratory-governing-bodies-regulations-and-applicable-laws.pdf |archiveurl=https://web.archive.org/web/20200319213139/http://www.bcsolutionsrfn.com/wp-content/uploads/2015/11/explanation-of-laboratory-governing-bodies-regulations-and-applicable-laws.pdf |format=PDF |title=An Explanation of Laboratory Governing Bodies, Regulations, and Applicable Laws |author=Poosa, S. |publisher=BC Solutions, LLC |date=November 2015 |archivedate=19 March 2020 |accessdate=06 January 2022}}</ref> This type of regulation has, of course, had an impact on the development of software in general<ref name="Hamou-LhadjRegulatory10">{{cite journal |title=Regulatory Compliance and its Impact on Software Development |journal=Proceedings from the First Workshop on Law Compliancy Issues in Organisational Systems and Strategies (iComply10) |author=Hamou-Lhadj, A. |pages=1–5 |year=2010 |url=https://www.semanticscholar.org/paper/Regulatory-Compliance-and-its-Impact-on-Software-Hamou-Lhadj/033e3f4cb88026804d1de861b6e1944d652cbd74?p2df |format=PDF}}</ref><ref name="MiriComply18">{{cite journal |title=Complying With GDPR: An Agile Case Study |journal=ISACA Journal |author=Miri, M.; Foomany, F.H.; Mohammed, N. |volume=2 |pages=1–7 |year=2018 |url=https://www.isaca.org/resources/isaca-journal/issues/2018/volume-2/complying-with-gdpr-an-agile-case-study}}</ref>, including laboratory informatics applications. Developers of these applications must take into account<ref name="ASTME1578" />:


* [[Audit trail|audit trail implementation]]
Whether manual or automated, successful medical microbiology workflows rely on specific quality controls, reporting, instruments, and test methods to achieve overall laboratory and healthcare objectives. The next section will specifically examine the types of testing that occur within a medical microbiology laboratory.
* [[wikipedia:Authentication protocol|authentication protocol]]s
* [[wikipedia:Configuration management|configuration management]]
* [[Backup|data backup]]
* [[data integrity]]
* [[Electronic signature|electronic signature implementation]]
* [[encryption]]
* [[information privacy]]
* [[network security]]


These and other considerations are discussed in standards such as ASTM E1578-18<ref name="ASTME1578" /> and [[ISO/IEC 17025]].<ref name="ISO17025Peak">{{cite web |url=https://www.iso.org/obp/ui/#iso:std:iso-iec:17025:ed-3:v1:en |title=ISO/IEC 17025:2017(en) - General requirements for the competence of testing and calibration laboratories |work=ISO Online Browsing Platform (OBP) |publisher=International Organization for Standardization |date=2017 |accessdate=19 March 2020}}</ref>
==Medical microbiology testing==
Within the scope of detecting, identifying, and characterizing microorganisms, medical microbiology labs depend on a variety of scientific subspecialties (e.g., bacteriology, mycology, virology) and test methods to achieve their goals. What follows are examples of the more common detection, identification, and characterization activities and testing conducted in these labs.


==Technology of laboratory informatics==
*'''Detection of microbial growth''': By detecting the telltale signs of living microorganisms, such as growth (i.e., an increase in the number of cells), microbiologists can then make an initial diagnosis of microbiological infection and take a deeper dive into identifying the microorganism(s). (Note that measuring microbial growth is not a direct proxy for measuring microbial metabolism, however.<ref>{{Cite journal |last=Braissant |first=Olivier |last2=Astasov-Frauenhoffer |first2=Monika |last3=Waltimo |first3=Tuomas |last4=Bonkat |first4=Gernot |date=2020-11-17 |title=A Review of Methods to Determine Viability, Vitality, and Metabolic Rates in Microbiology |url=https://www.frontiersin.org/articles/10.3389/fmicb.2020.547458/full |journal=Frontiers in Microbiology |volume=11 |pages=547458 |doi=10.3389/fmicb.2020.547458 |issn=1664-302X |pmc=PMC7705206 |pmid=33281753}}</ref>) Growth can be demonstrated in multiple ways<ref name=":0">{{Cite book |last=Washington, J.A. |date=1996 |editor-last=Baron |editor-first=Samuel |title=Medical microbiology |chapter=Chapter 10: Principles of Diagnosis |edition=4th ed |publisher=University of Texas Medical Branch at Galveston |place=Galveston, Tex |isbn=978-0-9631172-1-2 |pmid=21413287}}</ref>:


Important hardware and software systems that play a role in laboratory informatics include but are not limited to:
*confirming turbidity, gas, or discrete colonies in broth;
*confirming discrete colonies in on agar plates;
*confirming cytopathic effects or inclusions that distort the structures of cells in culture;
*confirming "genus- or species-specific antigens or nucleotide sequences"<ref name=":0" /> in the specimen, culture medium, or culture system.
 
Cell culturing plays an important role, as hinted at above. Those cultures can occur in liquid broth, agar plates, or some other enhanced culture medium, as found with blood cultures in specific bottles or tubes. Cultures are incubated to allow time for any microorganisms to multiply. Then signs of growth are sought out.<ref name=":0" /> However, detecting this growth is rarely straightforward and has its own set of complications.<ref>{{Cite journal |last=Zengler |first=Karsten |date=2009-12 |title=Central Role of the Cell in Microbial Ecology |url=https://journals.asm.org/doi/10.1128/MMBR.00027-09 |journal=Microbiology and Molecular Biology Reviews |language=en |volume=73 |issue=4 |pages=712–729 |doi=10.1128/MMBR.00027-09 |issn=1092-2172 |pmc=PMC2786577 |pmid=19946138}}</ref><ref name="ŹródłowskiClass20">{{Cite journal |last=Źródłowski |first=Tomasz |last2=Sobońska |first2=Joanna |last3=Salamon |first3=Dominika |last4=McFarlane |first4=Isabel M. |last5=Ziętkiewicz |first5=Mirosław |last6=Gosiewski |first6=Tomasz |date=2020-02-29 |title=Classical Microbiological Diagnostics of Bacteremia: Are the Negative Results Really Negative? What is the Laboratory Result Telling Us About the “Gold Standard”? |url=https://www.mdpi.com/2076-2607/8/3/346 |journal=Microorganisms |language=en |volume=8 |issue=3 |pages=346 |doi=10.3390/microorganisms8030346 |issn=2076-2607 |pmc=PMC7143506 |pmid=32121353}}</ref> This may necessitate other methods such as Gram staining or [[wikipedia:Fluorescence in situ hybridization|fluorescence ''in situ'' hybridization]] (FISH) for quicker and more accurate detection of growth.<ref name="ŹródłowskiClass20" />
 
*'''Taxonomic identification''': (Phenotypic or biochemical identification) Databases are commonly used for the identification of microorganisms. Common databases include biochemical reaction databases, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrum databases, and nucleic acid sequence databases, and less frequently, high-performance liquid chromatography databases are used for the identification of mycobacteria.<ref name="RhoadsClin14" />
 
*'''Antibiograms and antimicrobial susceptibility testing (AST)''': 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> The nuances of susceptibility testing and antibiograms drive reporting requirements, particularly to the standard CLSI M39 ''Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data''.<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>{{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>
 
*'''Nucleic acid testing or antigen testing''': While the majority of microbial methods performed in microbiology laboratories are phenotypic (biochemical or proteomic based), genotypic methods can prove useful for assessing sterility test and media fill failures, and for tracking the route of contamination as part of a contamination control strategy.<ref name="SandleEnhanc21" /> PCR assays designed to detect single pathogens to high-throughput parallel sequencing of DNA designed to detect multiple species simultaneously<ref name="RhoadsClin14" />
 
*'''Digital image analysis''': screening slides for acid-fast bacilli (74), interpretation of colony Gram stains (75), or simple bacterial culture interpretations (e.g., colony counts)<ref name="RhoadsClin14" /> automated microscope designed to collect high‑resolution image data from microscopic slides.<ref name="SandleEnhanc21" /> Re: Colony counts - Such high‑resolution image analysis systems can detect small and mixed colonies, which a human eye cannot.<ref name="SandleEnhanc21" />
 
==Conclusion==


* [[Chromatography data system]]s (CDS)
* [[Electronic laboratory notebook]]s (ELN)
* Enterprise content management applications (ECM)
* Enterprise resource planning applications (ERP)
* [[Laboratory execution system]]s (LES)
* [[Laboratory information management system]]s (LIMS)
* [[Laboratory information system]]s (LIS)
* Manufacturing enterprise systems (MES)
* Process analytical technology (PAT)
* [[Scientific data management system]]s (SDMS)


==References==
==References==
{{Reflist|colwidth=30em}}
{{Reflist|colwidth=30em}}


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US Navy 070905-N-0194K-029 Lt. Paul Graf, a microbiology officer aboard Military Sealift Command hospital ship USNS Comfort (T-AH 20), examines wound cultures in the ship's microbiology laboratory.jpg

Title: What types of testing occur within a medical microbiology laboratory?

Author for citation: Shawn E. Douglas

License for content: Creative Commons Attribution-ShareAlike 4.0 International

Publication date: April 2024

Introduction

The medical microbiology laboratory has a variety of testing and workflow requirements that manage to separate it from other biomedical labs.

This brief topical article will examine the typical types of testing that occur in medical microbiology labs.


The medical microbiology lab in general

A medical microbiology laboratory helps detect, identify, and characterize microorganisms for both individual patient treatment and broader population disease prevention and control. In the course of its work towards aiding in the diagnosis of individual patients' ailments, the lab may identify infectious agents of concern and trends in those infections as part of a greater public health effort. By extension, medical microbiology laboratories are also responsible for reporting those identification and trends to various public health agencies (city, county, state, and federal). These reports are then used by public health laboratories, in tandem with medical microbiology labs, to track incidences and attempt to identify outbreaks.[1] In particular, the medical microbiology lab is uniquely suited to confirming infectious disease cases as part of outbreak investigations, with its analytical and interpretive "methods that are not commonly available in a routine laboratory setting."[2]

A standard consolidated medical microbiology laboratory will have the facilities for rapid microbiology, microscopy, cell culturing, serology, molecular biology, parasitology, virology, communicable disease management (i.e., public health or reference activities[2]) and more, and it also may have the facilities for environmental microbiology.[3] A variety of specimen types will be tested, including urine, blood, stool, tissues, and precious fluids, as well as skin, mucosal, and genital swabs.[3]

Culture-based and other microbiology test methods have largely been performed manually up until recently. As Antonios et al. noted at the end of 2021, "the introduction of automation in microbiology was considered difficult to apply for several reasons such as the complexity and variability of sample types, the variations of specimens processing, the doubtful cost-effectiveness especially for small and average-sized laboratories, and the perception that machines could not exercise the critical decision-making skills required to process microbiological samples."[4] However, economic, employment, and other societal drivers have necessarily brought laboratory automation and large language models (LLMs) more fully to the medical microbiology lab in recent years.[3][4][5] This has allowed these labs to move from a traditional partial-day work schedule to a more 24-hour work schedule by, for example, the use of automated front-end plating systems.[4]

Whether manual or automated, successful medical microbiology workflows rely on specific quality controls, reporting, instruments, and test methods to achieve overall laboratory and healthcare objectives. The next section will specifically examine the types of testing that occur within a medical microbiology laboratory.

Medical microbiology testing

Within the scope of detecting, identifying, and characterizing microorganisms, medical microbiology labs depend on a variety of scientific subspecialties (e.g., bacteriology, mycology, virology) and test methods to achieve their goals. What follows are examples of the more common detection, identification, and characterization activities and testing conducted in these labs.

  • Detection of microbial growth: By detecting the telltale signs of living microorganisms, such as growth (i.e., an increase in the number of cells), microbiologists can then make an initial diagnosis of microbiological infection and take a deeper dive into identifying the microorganism(s). (Note that measuring microbial growth is not a direct proxy for measuring microbial metabolism, however.[6]) Growth can be demonstrated in multiple ways[7]:
  • confirming turbidity, gas, or discrete colonies in broth;
  • confirming discrete colonies in on agar plates;
  • confirming cytopathic effects or inclusions that distort the structures of cells in culture;
  • confirming "genus- or species-specific antigens or nucleotide sequences"[7] in the specimen, culture medium, or culture system.

Cell culturing plays an important role, as hinted at above. Those cultures can occur in liquid broth, agar plates, or some other enhanced culture medium, as found with blood cultures in specific bottles or tubes. Cultures are incubated to allow time for any microorganisms to multiply. Then signs of growth are sought out.[7] However, detecting this growth is rarely straightforward and has its own set of complications.[8][9] This may necessitate other methods such as Gram staining or fluorescence in situ hybridization (FISH) for quicker and more accurate detection of growth.[9]

  • Taxonomic identification: (Phenotypic or biochemical identification) Databases are commonly used for the identification of microorganisms. Common databases include biochemical reaction databases, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrum databases, and nucleic acid sequence databases, and less frequently, high-performance liquid chromatography databases are used for the identification of mycobacteria.[1]
  • Antibiograms and antimicrobial susceptibility testing (AST): 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.[10] There are multiple approaches to antibiograms for a wide variety of susceptibility testing, common to microbiology labs.[11] The nuances of susceptibility testing and antibiograms drive reporting requirements, particularly to the standard CLSI M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data.[1][12]
  • Nucleic acid testing or antigen testing: While the majority of microbial methods performed in microbiology laboratories are phenotypic (biochemical or proteomic based), genotypic methods can prove useful for assessing sterility test and media fill failures, and for tracking the route of contamination as part of a contamination control strategy.[5] PCR assays designed to detect single pathogens to high-throughput parallel sequencing of DNA designed to detect multiple species simultaneously[1]
  • Digital image analysis: screening slides for acid-fast bacilli (74), interpretation of colony Gram stains (75), or simple bacterial culture interpretations (e.g., colony counts)[1] automated microscope designed to collect high‑resolution image data from microscopic slides.[5] Re: Colony counts - Such high‑resolution image analysis systems can detect small and mixed colonies, which a human eye cannot.[5]

Conclusion

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 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. 
  2. ↑ 2.0 2.1 European Centre for Disease Prevention and Control (June 2010). "Core functions of microbiology reference laboratories for communicable diseases" (PDF). European Centre for Disease Prevention and Control. doi:10.2900/29017. ISBN 9789291932115. https://www.ecdc.europa.eu/sites/default/files/media/en/publications/Publications/1006_TER_Core_functions_of_reference_labs.pdf. Retrieved 24 April 2024. 
  3. ↑ 3.0 3.1 3.2 Vandenberg, Olivier; Durand, Géraldine; Hallin, Marie; Diefenbach, Andreas; Gant, Vanya; Murray, Patrick; Kozlakidis, Zisis; van Belkum, Alex (18 March 2020). "Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies" (in en). Clinical Microbiology Reviews 33 (2): e00057–19. doi:10.1128/CMR.00057-19. ISSN 0893-8512. PMC PMC7048017. PMID 32102900. https://journals.asm.org/doi/10.1128/CMR.00057-19. 
  4. ↑ 4.0 4.1 4.2 Antonios, Kritikos; Croxatto, Antony; Culbreath, Karissa (30 December 2021). "Current State of Laboratory Automation in Clinical Microbiology Laboratory" (in en). Clinical Chemistry 68 (1): 99–114. doi:10.1093/clinchem/hvab242. ISSN 0009-9147. https://academic.oup.com/clinchem/article/68/1/99/6490228. 
  5. ↑ 5.0 5.1 5.2 5.3 Sandle, T. (22 December 2021). "Enhancing rapid microbiology methods: how AI is shaping microbiology". European Pharmaceutical Review. https://www.europeanpharmaceuticalreview.com/article/166302/enhancing-rapid-microbiology-methods-how-ai-is-shaping-microbiology/. Retrieved 17 April 2024. 
  6. ↑ Braissant, Olivier; Astasov-Frauenhoffer, Monika; Waltimo, Tuomas; Bonkat, Gernot (17 November 2020). "A Review of Methods to Determine Viability, Vitality, and Metabolic Rates in Microbiology". Frontiers in Microbiology 11: 547458. doi:10.3389/fmicb.2020.547458. ISSN 1664-302X. PMC PMC7705206. PMID 33281753. https://www.frontiersin.org/articles/10.3389/fmicb.2020.547458/full. 
  7. ↑ 7.0 7.1 7.2 Washington, J.A. (1996). "Chapter 10: Principles of Diagnosis". In Baron, Samuel. Medical microbiology (4th ed ed.). Galveston, Tex: University of Texas Medical Branch at Galveston. ISBN 978-0-9631172-1-2. PMID 21413287. 
  8. ↑ Zengler, Karsten (1 December 2009). "Central Role of the Cell in Microbial Ecology" (in en). Microbiology and Molecular Biology Reviews 73 (4): 712–729. doi:10.1128/MMBR.00027-09. ISSN 1092-2172. PMC PMC2786577. PMID 19946138. https://journals.asm.org/doi/10.1128/MMBR.00027-09. 
  9. ↑ 9.0 9.1 Źródłowski, Tomasz; Sobońska, Joanna; Salamon, Dominika; McFarlane, Isabel M.; Ziętkiewicz, Mirosław; Gosiewski, Tomasz (29 February 2020). "Classical Microbiological Diagnostics of Bacteremia: Are the Negative Results Really Negative? What is the Laboratory Result Telling Us About the “Gold Standard”?" (in en). Microorganisms 8 (3): 346. doi:10.3390/microorganisms8030346. ISSN 2076-2607. PMC PMC7143506. PMID 32121353. https://www.mdpi.com/2076-2607/8/3/346. 
  10. ↑ Antimicrobial Resistance and Stewardship Initiative, University of Minnesota (February 2020). "How to Use a Clinical Antibiogram" (PDF). https://arsi.umn.edu/sites/arsi.umn.edu/files/2020-02/How_to_Use_a_Clinical_Antibiogram_26Feb2020_Final.pdf. Retrieved 17 April 2024. 
  11. ↑ Gajic, Ina; Kabic, Jovana; Kekic, Dusan; Jovicevic, Milos; Milenkovic, Marina; Mitic Culafic, Dragana; Trudic, Anika; Ranin, Lazar et al. (23 March 2022). "Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods" (in en). Antibiotics 11 (4): 427. doi:10.3390/antibiotics11040427. ISSN 2079-6382. PMC PMC9024665. PMID 35453179. https://www.mdpi.com/2079-6382/11/4/427. 
  12. ↑ Simner, Patricia J.; Hindler, Janet A.; Bhowmick, Tanaya; Das, Sanchita; Johnson, J. Kristie; Lubers, Brian V.; Redell, Mark A.; Stelling, John et al. (19 October 2022). Humphries, Romney M.. ed. "What’s New in Antibiograms? Updating CLSI M39 Guidance with Current Trends" (in en). Journal of Clinical Microbiology 60 (10): e02210–21. doi:10.1128/jcm.02210-21. ISSN 0095-1137. PMC PMC9580356. PMID 35916520. https://journals.asm.org/doi/10.1128/jcm.02210-21. 


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