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| <div class="nonumtoc">__TOC__</div> | | <div class="nonumtoc">__TOC__</div> |
| [[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]]
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| '''Title''': ''What types of testing occur within a medical microbiology laboratory?''
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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]] has a variety of testing and workflow requirements that manage to separate it from other biomedical labs.
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| This brief topical article will examine the typical types of testing that occur in medical microbiology labs.
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| ==The medical microbiology lab in general==
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| 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>
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| 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" />
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| 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" />
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| 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.
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| ==Medical microbiology testing==
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| 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.
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| *'''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>:
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| *confirming turbidity, gas, or discrete colonies in broth;
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| *confirming discrete colonies in on agar plates;
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| *confirming cytopathic effects or inclusions that distort the structures of cells in culture;
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| *confirming "genus- or species-specific antigens or nucleotide sequences"<ref name=":0" /> in the specimen, culture medium, or culture system.
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| 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" />
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| *'''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" />
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| *'''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>
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| *'''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" />
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| *'''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" />
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| ==Conclusion==
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| ==References==
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| {{Reflist|colwidth=30em}}
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