Difference between revisions of "User:Shawndouglas/sandbox/sublevel12"
From LIMSWiki
< User:Shawndouglas | sandbox
Jump to navigationJump to searchShawndouglas (talk | contribs) |
Shawndouglas (talk | contribs) |
||
| Line 23: | Line 23: | ||
== | ==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 cases as part of outbreak investigations, with its "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> | 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> | ||
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 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> | ||
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" /> | |||
==Testing== | ==Testing== | ||
| Line 40: | Line 38: | ||
* '''Detection of microbial growth''': | * '''Detection of microbial growth''': | ||
* '''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" | * '''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" /> | * '''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" /> | ||
Revision as of 18:03, 24 April 2024
 |
This is sublevel12 of my sandbox, where I play with features and test MediaWiki code. If you wish to leave a comment for me, please see my discussion page instead. |
Sandbox begins below
,_examines_wound_cultures_in_the_ship%27s_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]
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]Cite error: Closing </ref> missing for <ref> tag 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]
Testing
- 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.[5] There are multiple approaches to antibiograms for a wide variety of susceptibility testing, common to microbiology labs.[6] 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][7]
- Detection of microbial growth:
- 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.[8] 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.[8] Re: Colony counts - Such high‑resolution image analysis systems can detect small and mixed colonies, which a human eye cannot.[8]
Conclusion
References
- ↑ 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.
- ↑ 2.0 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.
- ↑ 3.0 3.1 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.
- ↑ 4.0 4.1 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 8.0 8.1 8.2 Cite error: Invalid
<ref>tag; no text was provided for refs namedSandleEnhanc21
