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Colony-forming unit

From Wikipedia, in a visual modern way
For the human hematopoietic cell, see Hematopoietic stem cell.

In microbiology, colony-forming unit (CFU, cfu or Cfu) is a unit which estimates the number of microbial cells (bacteria, fungi, viruses etc.) in a sample that are viable, able to multiply via binary fission under the controlled conditions. Counting with colony-forming units requires culturing the microbes and counts only viable cells, in contrast with microscopic examination which counts all cells, living or dead. The visual appearance of a colony in a cell culture requires significant growth, and when counting colonies, it is uncertain if the colony arose from one cell or a group of cells. Expressing results as colony-forming units reflects this uncertainty.

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Microbiology

Microbiology

Microbiology is the scientific study of microorganisms, those being unicellular, multicellular, or acellular. Microbiology encompasses numerous sub-disciplines including virology, bacteriology, protistology, mycology, immunology, and parasitology.

Bacteria

Bacteria

Bacteria are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.

Virus

Virus

A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, more than 9,000 of the millions of virus species have been described in detail. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. The study of viruses is known as virology, a subspeciality of microbiology.

Viable count

Viable count

Viable count is a method used in cell culture to determine the number of living cells in a culture. This is different from other cell counting techniques because it makes a distinction between live and dead cells.

Cell culture

Cell culture

Cell culture or tissue culture is the process by which cells are grown under controlled conditions, generally outside of their natural environment. The term "tissue culture" was coined by American pathologist Montrose Thomas Burrows. This technique is also called micropropagation. After the cells of interest have been isolated from living tissue, they can subsequently be maintained under carefully controlled conditions the need to be kept at body temperature (37 °C) in an incubator. These conditions vary for each cell type, but generally consist of a suitable vessel with a substrate or rich medium that supplies the essential nutrients (amino acids, carbohydrates, vitamins, minerals), growth factors, hormones, and gases (CO2, O2), and regulates the physio-chemical environment (pH buffer, osmotic pressure, temperature). Most cells require a surface or an artificial substrate to form an adherent culture as a monolayer (one single-cell thick), whereas others can be grown free floating in a medium as a suspension culture. This is typically facilitated via use of a liquid, semi-solid, or solid growth medium, such as broth or agar. Tissue culture commonly refers to the culture of animal cells and tissues, with the more specific term plant tissue culture being used for plants. The lifespan of most cells is genetically determined, but some cell culturing cells have been “transformed” into immortal cells which will reproduce indefinitely if the optimal conditions are provided.

Colony (biology)

Colony (biology)

In biology, a colony is composed of two or more conspecific individuals living in close association with, or connected to, one another. This association is usually for mutual benefit such as stronger defense or the ability to attack bigger prey.

Theory

A dilution made with bacteria and peptoned water is placed in an Agar plate (Agar plate count for food samples or Trypticase soy agar for clinic samples) and spread over the plate by tipping in the pattern shown.
A dilution made with bacteria and peptoned water is placed in an Agar plate (Agar plate count for food samples or Trypticase soy agar for clinic samples) and spread over the plate by tipping in the pattern shown.

The purpose of plate counting is to estimate the number of cells present based on their ability to give rise to colonies under specific conditions of nutrient medium, temperature and time. Theoretically, one viable cell can give rise to a colony through replication. However, solitary cells are the exception in nature, and most likely the progenitor of the colony was a mass of cells deposited together. In addition, many bacteria grow in chains (e.g. Streptococcus) or clumps (e.g., Staphylococcus). Estimation of microbial numbers by CFU will, in most cases, undercount the number of living cells present in a sample for these reasons. This is because the counting of CFU assumes that every colony is separate and founded by a single viable microbial cell.[1]

The plate count is linear for E. coli over the range of 30 to 300 CFU on a standard sized Petri dish.[2] Therefore, to ensure that a sample will yield CFU in this range requires dilution of the sample and plating of several dilutions. Typically, ten-fold dilutions are used, and the dilution series is plated in replicates of 2 or 3 over the chosen range of dilutions. Often 100µl are plated but also larger amounts up to 1ml are used. Higher plating volumes increase drying times but often don't result in higher accuracy, since additional dilution steps may be needed.[3] The CFU/plate is read from a plate in the linear range, and then the CFU/g (or CFU/mL) of the original is deduced mathematically, factoring in the amount plated and its dilution factor (e.g. CLSI VET01S).

A solution of bacteria at an unknown concentration is often serially diluted in order to obtain at least one plate with a countable number of bacteria. In this figure, the "x10" plate is suitable for counting.
A solution of bacteria at an unknown concentration is often serially diluted in order to obtain at least one plate with a countable number of bacteria. In this figure, the "x10" plate is suitable for counting.

An advantage to this method is that different microbial species may give rise to colonies that are clearly different from each other, both microscopically and macroscopically. The colony morphology can be of great use in the identification of the microorganism present.

A prior understanding of the microscopic anatomy of the organism can give a better understanding of how the observed CFU/mL relates to the number of viable cells per milliliter. Alternatively it is possible to decrease the average number of cells per CFU in some cases by vortexing the sample before conducting the dilution. However many microorganisms are delicate and would suffer a decrease in the proportion of cells that are viable when placed in a vortex.

Log notation

Concentrations of colony-forming units can be expressed using logarithmic notation, where the value shown is the base 10 logarithm of the concentration.[4][5][6] This allows the log reduction of a decontamination process to be computed as a simple subtraction.

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Agar plate

Agar plate

An agar plate is a Petri dish that contains a growth medium solidified with agar, used to culture microorganisms. Sometimes selective compounds are added to influence growth, such as antibiotics.

Trypticase soy agar

Trypticase soy agar

Trypticase soy agar or tryptone soya agar (TSA) and Trypticase soy broth or tryptone soya broth (TSB) with agar are growth media for the culturing of bacteria. They are general-purpose, nonselective media providing enough nutrients to allow for a wide variety of microorganisms to grow. They are used for a wide range of applications, including culture storage, enumeration of cells (counting), isolation of pure cultures, or simply general culture.

Colony (biology)

Colony (biology)

In biology, a colony is composed of two or more conspecific individuals living in close association with, or connected to, one another. This association is usually for mutual benefit such as stronger defense or the ability to attack bigger prey.

Streptococcus

Streptococcus

Streptococcus is a genus of gram-positive coccus or spherical bacteria that belongs to the family Streptococcaceae, within the order Lactobacillales, in the phylum Bacillota. Cell division in streptococci occurs along a single axis, so as they grow, they tend to form pairs or chains that may appear bent or twisted. This differs from staphylococci, which divide along multiple axes, thereby generating irregular, grape-like clusters of cells. Most streptococci are oxidase-negative and catalase-negative, and many are facultative anaerobes.

Staphylococcus

Staphylococcus

Staphylococcus is a genus of Gram-positive bacteria in the family Staphylococcaceae from the order Bacillales. Under the microscope, they appear spherical (cocci), and form in grape-like clusters. Staphylococcus species are facultative anaerobic organisms.

Petri dish

Petri dish

A Petri dish is a shallow transparent lidded dish that biologists use to hold growth medium in which cells can be cultured, originally, cells of bacteria, fungi and small mosses. The container is named after its inventor, German bacteriologist Julius Richard Petri. It is the most common type of culture plate. The Petri dish is one of the most common items in biology laboratories and has entered popular culture. The term is sometimes written in lower case, especially in non-technical literature.

Serial dilution

Serial dilution

A serial dilution is the stepwise dilution of a substance in solution. Usually the dilution factor at each step is constant, resulting in a geometric progression of the concentration in a logarithmic fashion. A ten-fold serial dilution could be 1 M, 0.1 M, 0.01 M, 0.001 M ... Serial dilutions are used to accurately create highly diluted solutions as well as solutions for experiments resulting in concentration curves with a logarithmic scale. A tenfold dilution for each step is called a logarithmic dilution or log-dilution, a 3.16-fold (100.5-fold) dilution is called a half-logarithmic dilution or half-log dilution, and a 1.78-fold (100.25-fold) dilution is called a quarter-logarithmic dilution or quarter-log dilution. Serial dilutions are widely used in experimental sciences, including biochemistry, pharmacology, microbiology, and physics.

Vortex mixer

Vortex mixer

A vortex mixer, or vortexer, is a simple device used commonly in laboratories to mix small vials of liquid. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup the motion is transmitted to the liquid inside and a vortex is created. Most vortex mixers are designed with 2 or 4-plate formats, have variable speed settings ranging from 100 to 3,200 rpm, and can be set to run continuously, or to run only when downward pressure is applied to the rubber piece.

Common logarithm

Common logarithm

In mathematics, the common logarithm is the logarithm with base 10. It is also known as the decadic logarithm and as the decimal logarithm, named after its base, or Briggsian logarithm, after Henry Briggs, an English mathematician who pioneered its use, as well as standard logarithm. Historically, it was known as logarithmus decimalis or logarithmus decadis. It is indicated by log(x), log10 (x), or sometimes Log(x) with a capital L. On calculators, it is printed as "log", but mathematicians usually mean natural logarithm rather than common logarithm when they write "log". To mitigate this ambiguity, the ISO 80000 specification recommends that log10 (x) should be written lg(x), and loge (x) should be ln(x).

Log reduction

Log reduction

Log reduction is a measure of how thoroughly a decontamination process reduces the concentration of a contaminant. It is defined as the common logarithm of the ratio of the levels of contamination before and after the process, so an increment of 1 corresponds to a reduction in concentration by a factor of 10. In general, an n-log reduction means that the concentration of remaining contaminants is only 10−n times that of the original. So for example, a 0-log reduction is no reduction at all, while a 1-log reduction corresponds to a reduction of 90 percent from the original concentration, and a 2-log reduction corresponds to a reduction of 99 percent from the original concentration.

Uses

Colony-forming units are used to quantify results in many microbiological plating and counting methods, including:

  • The Pour Plate method wherein the sample is suspended in a Petri dish using molten agar cooled to approximately 40–45 °C (just above the point of solidification to minimize heat-induced cell death). After the nutrient agar solidifies the plate is incubated.[7]
  • The Spread Plate method wherein the sample (in a small volume) is spread across the surface of a nutrient agar plate and allowed to dry before incubation for counting.[7]
  • The Membrane Filter method wherein the sample is filtered through a membrane filter, then the filter placed on the surface of a nutrient agar plate (bacteria side up). During incubation nutrients leach up through the filter to support the growing cells. As the surface area of most filters is less than that of a standard Petri dish, the linear range of the plate count will be less.[7]
  • The Miles and Misra Methods or drop-plate method wherein a very small aliquot (usually about 10 microliters) of sample from each dilution in series is dropped onto a Petri dish. The drop dish must be read while the colonies are very small to prevent the loss of CFU as they grow together.

However, with the techniques that require the use of an agar plate, no fluid solution can be used because the purity of the specimen cannot be unidentified and it is not possible to count the cells one by one in the liquid.[8]

Tools for counting colonies

The traditional way of enumerating CFUs with a "click-counter" and a pen. When the colonies are too numerous, it is common practice to count CFUs only on a fraction of the dish.
The traditional way of enumerating CFUs with a "click-counter" and a pen. When the colonies are too numerous, it is common practice to count CFUs only on a fraction of the dish.

Counting colonies is traditionally performed manually using a pen and a click-counter. This is generally a straightforward task, but can become very laborious and time-consuming when many plates have to be enumerated. Alternatively semi-automatic (software) and automatic (hardware + software) solutions can be used.

Software for counting CFUs

Colonies can be enumerated from pictures of plates using software tools. The experimenters would generally take a picture of each plate they need to count and then analyse all the pictures (this can be done with a simple digital camera or even a webcam). Since it takes less than 10 seconds to take a single picture, as opposed to several minutes to count CFU manually, this approach generally saves a lot of time. In addition, it is more objective and allows extraction of other variables such as the size and colour of the colonies.

  • OpenCFU[1] is a free and open-source program designed to optimise user friendliness, speed and robustness. It offers a wide range of filters and control as well as a modern user interface. OpenCFU is written in C++ and uses OpenCV for image analysis.[9]
  • NICE is a program written in MATLAB that provides an easy way to count colonies from images.[10][11]
  • ImageJ and CellProfiler: Some ImageJ macros[12] and plugins and some CellProfiler pipelines[13] can be used to count colonies. This often requires the user to change the code in order to achieve an efficient work-flow, but can prove useful and flexible. One main issue is the absence of specific GUI which can make the interaction with the processing algorithms tedious.

In addition to software based on traditional desktop computers, apps for both Android and iOS devices are available for semi-automated and automated colony counting. The integrated camera is used to take pictures of the agar plate and either an internal or an external algorithm is used to process the picture data and to estimate the number of colonies. [14][15][16][17]

Automated systems

Many of the automated systems are used to counteract human error as many of the research techniques done by humans counting individual cells have a high chance of error involved. Due to the fact that researchers regularly manually count the cells with the assistance of a transmitted light, this error prone technique can have a significant effect on the calculated concentration in the main liquid medium when the cells are in low numbers.

An automated colony counter using image processing.
An automated colony counter using image processing.

Completely automated systems are also available from some biotechnology manufacturers.[18][19] They are generally expensive and not as flexible as standalone software since the hardware and software are designed to work together for a specific set-up. Alternatively, some automatic systems use the spiral plating paradigm.

Some of the automated systems such as the systems from MATLAB allow the cells to be counted without having to stain them. This lets the colonies to be reused for other experiments without the risk of killing the microorganisms with stains. However, a disadvantage to these automated systems is that it is extremely difficult to differentiate between the microorganisms with dust or scratches on blood agar plates because both the dust and scratches can create a highly diverse combination of shapes and appearances.[20]

Alternative units

Instead of colony-forming units, the parameters Most Probable Number (MPN) and Modified Fishman Units (MFU) can be used. The Most Probable Number method counts viable cells and is useful when enumerating low concentrations of cells or enumerating microbes in products where particulates make plate counting impractical.[21] Modified Fishman Units take into account bacteria which are viable, but non-culturable.

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Free and open-source software

Free and open-source software

Free and open-source software (FOSS) is a term used to refer to groups of software consisting of both free software and open-source software where anyone is freely licensed to use, copy, study, and change the software in any way, and the source code is openly shared so that people are encouraged to voluntarily improve the design of the software. This is in contrast to proprietary software, where the software is under restrictive copyright licensing and the source code is usually hidden from the users.

C++

C++

C++ is a high-level, general-purpose programming language created by Danish computer scientist Bjarne Stroustrup. First released in 1985 as an extension of the C programming language, it has since expanded significantly over time; modern C++ currently has object-oriented, generic, and functional features, in addition to facilities for low-level memory manipulation. It is almost always implemented as a compiled language, and many vendors provide C++ compilers, including the Free Software Foundation, LLVM, Microsoft, Intel, Embarcadero, Oracle, and IBM.

OpenCV

OpenCV

OpenCV is a library of programming functions mainly for real-time computer vision. Originally developed by Intel, it was later supported by Willow Garage, then Itseez. The library is cross-platform and licensed as free and open-source software under Apache License 2. Starting in 2011, OpenCV features GPU acceleration for real-time operations.

MATLAB

MATLAB

MATLAB is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages.

ImageJ

ImageJ

ImageJ is a Java-based image processing program developed at the National Institutes of Health and the Laboratory for Optical and Computational Instrumentation. Its first version, ImageJ 1.x, is developed in the public domain, while ImageJ2 and the related projects SciJava, ImgLib2, and SCIFIO are licensed with a permissive BSD-2 license. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using ImageJ's built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging to radiological image processing, multiple imaging system data comparisons to automated hematology systems. ImageJ's plugin architecture and built-in development environment has made it a popular platform for teaching image processing.

CellProfiler

CellProfiler

CellProfiler is free, open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. Advanced algorithms for image analysis are available as individual modules that can be placed in sequential order together to form a pipeline; the pipeline is then used to identify and measure biological objects and features in images, particularly those obtained through fluorescence microscopy.

Human error

Human error

Human error is an action that has been done but that was "not intended by the actor; not desired by a set of rules or an external observer; or that led the task or system outside its acceptable limits". Human error has been cited as a primary cause contributing factor in disasters and accidents in industries as diverse as nuclear power, aviation, space exploration, and medicine. Prevention of human error is generally seen as a major contributor to reliability and safety of (complex) systems. Human error is one of the many contributing causes of risk events.

Spiral plater

Spiral plater

A spiral plater is an instrument used to dispense a liquid sample onto a Petri dish in a spiral pattern. Commonly used as part of a CFU count procedure for the purpose of determining the number of microbes in the sample. In this setting, after spiral plating, the Petri dish is incubated for several hours after which the number of colony forming microbes (CFU) is determined. Spiral platers are also used for research, clinical diagnostics and as a method for covering a Petri dish with bacteria before placing antibiotic discs for AST.

Most probable number

Most probable number

The most probable number method, otherwise known as the method of Poisson zeroes, is a method of getting quantitative data on concentrations of discrete items from positive/negative (incidence) data.

Source: "Colony-forming unit", Wikipedia, Wikimedia Foundation, (2023, January 10th), https://en.wikipedia.org/wiki/Colony-forming_unit.

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Further Reading

Agar plate

Replica plating

Microbiological culture

Bacteriological water analysis

Growth medium

Streaking (microbiology)

Petrifilm

Spiral plater

Colonial morphology
See also
References
  1. ^ Goldman, Emanuel; Green, Lorrence H (24 August 2008). Practical Handbook of Microbiology, Second Edition (Google eBook) (Second ed.). USA: CRC Press, Taylor and Francis Group. p. 864. ISBN 978-0-8493-9365-5. Retrieved 2014-10-16.
  2. ^ Breed RS, Dotterrer WD (May 1916). "The Number of Colonies Allowable on Satisfactory Agar Plates". Journal of Bacteriology. 1 (3): 321–31. doi:10.1128/JB.1.3.321-331.1916. PMC 378655. PMID 16558698.
  3. ^ Schug, Angela R.; Bartel, Alexander; Meurer, Marita; Scholtzek, Anissa D.; Brombach, Julian; Hensel, Vivian; Fanning, Séamus; Schwarz, Stefan; Feßler, Andrea T. (2020-12-01). "Comparison of two methods for cell count determination in the course of biocide susceptibility testing". Veterinary Microbiology. 251: 108831. doi:10.1016/j.vetmic.2020.108831. PMID 33202368. S2CID 225308316.
  4. ^ "Log10 Colony Forming Units per Gram". Titi Tudorancea Encyclopedia. Retrieved September 25, 2016.
  5. ^ Daniel Y. C. Fung (2009). "Viable Cell Counts". Bioscience International. Retrieved September 25, 2016.
  6. ^ Martin Cole (November 1, 2005). "Principles of microbiological testing: Statistical basis of sampling" (PDF). International Commission on Microbiological Specifications for Foods (ICMSF). Archived from the original (PDF) on October 31, 2017. Retrieved September 25, 2016.
  7. ^ a b c "USP 61: Microbial Enumeration Tests" (PDF). United States Pharmacopeia. Retrieved 24 March 2015.
  8. ^ Reynolds, Jackie. "Serial Dilution Protocols". www.microbelibrary.org. Archived from the original on 2015-11-17. Retrieved 2015-11-15.
  9. ^ Geissmann Q (2013). "OpenCFU, a new free and open-source software to count cell colonies and other circular objects". PLOS ONE. 8 (2): e54072. arXiv:1210.5502. Bibcode:2013PLoSO...854072G. doi:10.1371/journal.pone.0054072. PMC 3574151. PMID 23457446.
  10. ^ "NIST's Integrated colony enumerator (NICE)". Archived from the original on 2014-06-27. Retrieved 2017-07-13.
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  12. ^ Cai Z, Chattopadhyay N, Liu WJ, Chan C, Pignol JP, Reilly RM (November 2011). "Optimized digital counting colonies of clonogenic assays using ImageJ software and customized macros: comparison with manual counting". International Journal of Radiation Biology. 87 (11): 1135–46. doi:10.3109/09553002.2011.622033. PMID 21913819. S2CID 25417288.
  13. ^ Vokes MS, Carpenter AE (April 2008). Using CellProfiler for automatic identification and measurement of biological objects in images. Current Protocols in Molecular Biology. Vol. Chapter 14. pp. Unit 14.17. doi:10.1002/0471142727.mb1417s82. ISBN 978-0471142720. PMC 4302752. PMID 18425761.
  14. ^ "Promega Colony Counter". App Store. Retrieved 2018-09-28.
  15. ^ "APD Colony Counter App PRO - Apps on Google Play". play.google.com. Retrieved 2018-09-28.
  16. ^ Austerjost, Jonas; Marquard, Daniel; Raddatz, Lukas; Geier, Dominik; Becker, Thomas; Scheper, Thomas; Lindner, Patrick; Beutel, Sascha (August 2017). "A smart device application for the automated determination of E. coli colonies on agar plates". Engineering in Life Sciences. 17 (8): 959–966. doi:10.1002/elsc.201700056. ISSN 1618-0240. PMC 6999497. PMID 32624845.
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  18. ^ "Colony Counters: Robotic Colony Counter - Plate Handler". www.neutecgroup.com. Retrieved 2018-09-28.
  19. ^ "Fully Automatic Colony Counter by AAA Lab Equipment Video | LabTube". www.labtube.tv. Retrieved 2018-09-28.
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