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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. 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."

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) and more, and it also may have the facilities for environmental microbiology. A variety of specimen types will be tested, including urine, blood, stool, tissues, and precious fluids, as well as skin, mucosal, and genital swabs.

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." 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. 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.

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.) Growth can be demonstrated in multiple ways:

• 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" 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. However, detecting this growth is rarely straightforward and has its own set of complications. This may necessitate other methods such as Gram staining or fluorescence in situ hybridization (FISH) for quicker and more accurate detection of growth.

• 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.

• 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. There are multiple approaches to antibiograms for a wide variety of susceptibility testing, common to microbiology labs. 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.

• 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. PCR assays designed to detect single pathogens to high-throughput parallel sequencing of DNA designed to detect multiple species simultaneously

• 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) automated microscope designed to collect high‑resolution image data from microscopic slides. Re: Colony counts - Such high‑resolution image analysis systems can detect small and mixed colonies, which a human eye cannot.