Diagnostic microbiology

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Diagnostic microbiology is the study of microbial identification. Since the discovery of the germ theory of disease, scientists have been finding ways to harvest specific organisms. Using methods such as differential media or genome sequencing, physicians and scientists can observe novel functions in organisms for more effective and accurate diagnosis of organisms. Methods used in diagnostic microbiology are often used to take advantage of a particular difference in organisms and attain information about what species it can be identified as, which is often through a reference of previous studies. New studies provide information that others can reference so that scientists can attain a basic understanding of the organism they are examining.

Contents

Aerobic vs anaerobic

Anaerobic organisms require an oxygen-free environment. When culturing anaerobic microbes, broths are often flushed with nitrogen gas to extinguish oxygen present, and growth can also occur on media in a chamber without oxygen present. [1] Sodium resazurin can be added to indicate redox potential. [2] Cultures are to be incubated in an oxygen-free environment for 48 hours at 35 °C before growth is examined. [3]

Gas-Pak jar Gas-Pak jar.jpg
Gas-Pak jar

Anaerobic bacteria collection can come from a variety of sources in patient samples, including blood, bile, bone marrow, cerebrospinal fluid, direct lung aspirate, tissue biopsies from a normally sterile site, fluid from a normally sterile site (like a joint), dental, abscess, abdominal or pelvic abscess, knife, gunshot, or surgical wound, or severe burn. [4]

Incubation length

Incubation times vary based upon the microbe that requires culturing. Traditional culturing techniques, for example, require less than 24 hours culture time for Escherichia coli but 6–8 weeks for successful culturing of Mycobacterium tuberculosis before definitive results are expressed. [5] A benefit of non-culture tests is that physicians and microbiologists are not handicapped by waiting periods.

Incubation follows a growth curve variable for every microorganism. Cultures follow a lag, log, stationary, and finally death phase. [6] The lag phase is not well known in microbiology, but it is speculated that this phase consists of the microorganism adjusting to its environment by synthesizing proteins specific for the surrounding habitat. [6] The log phase is the period where a culture experiences logarithmic growth until nutrients become scarce. The stationary phase is when culture concentration is the highest and cells stop reproducing. When nutrients in the environment are depleting, organisms enter the death phase where toxic metabolites become abundant and nutrients are depleted to the point where cell death exceeds reproduction. [5]

Rapid identification after culture

Automated culturing systems

Automatic cell culturing systems are becoming popular because of their ability to maintain a sterile growth environment and remove strain on the laboratory staff involving repetitive experimentation. [7] Laboratories can also set incubation times to adjust for the lag period involved in bacterial growth.

Blood cultures

Blood cultures can allow for diagnostic results after culture. Recent development of DNA based PCR diagnostics have provided faster diagnostic results as opposed to overnight biochemical tests. DNA diagnostic test can diagnose with near the same specificity as biochemical test, resulting in the same diagnostic result in 90% of cases. [8]

Breath tests

Breath test for microbial diagnosis on patients has been used in a clinical setting for bacteria, including Helicobacter pylori . [9] Diagnostic test using the breath of patients look for metabolites excreted that were manufactured by the infectious microorganism. H. pylori is tested by testing patients for CO2 concentration, increased because of the organism’s ability to convert urea into other derivatives. [10]

Conventional tests

Antibody detection

A benefit of antibody detection (ELISA) is that protein identification on a microorganism becomes faster than a western blot. Antibody detection works by attaching an indicator to an antibody with a known specificity and observing whether the antibody attaches. [11] ELISA can also indicate viral presence and is highly specific, having a detection specificity of 10−9-10−12 moles per litre detection. By knowing the epitope sequence of the antibody, ELISA can also be used for antigen detection in a sample. [12]

Histological detection and culture

Histological methods used for microbiology are useful because of their ability to quickly identify a disease present in a tissue biopsy.

Rapid antigen tests

Immunofluorescence

Immunofluorescence ANCA ETHANOL AND FORMALIN.JPEG
Immunofluorescence

Immunofluorescence is performed by the production of anti-antibodies with a fluorescent molecule attached, making it a chemiluminescent molecule, which provides a glow when subject to ultraviolet light. [13] Antibodies are added to a bacterial solution, providing an antigen for the binding of fluorescent anti-antibody adherence.

Immunofluorescence Immunofluorescence.jpg
Immunofluorescence

Mass spectrometry

MALDI-TOF (Matrix-assisted laser desorption/ionization - time of flight) is a specific type of mass spectrometry that is able to identify microorganisms. A pure culture is isolated and spread directly on a stainless steel or disposable target. The cells are lysed and overlaid with a matrix, which forms protein complexes with the bacterial proteins. The MALDI fires a laser and ionizes the protein complexes, which break off and travel up the vacuum where they are detected based on mass and charge. The resulting protein spectra is compared to a known database of previously catalogued organisms, resulting in rapid diagnosis of microorganisms. [14] Recent studies have suggested that these tests can become specific enough to diagnose down to the sub-species level by observing novel biomarkers. [14]

The MALDI-TOF identification method requires pure cultures that are less than 72 hours old. This places the organism in log phase with an abundance of ribosomal proteins, which are the most common proteins detected in the spectra. Identifications with this technology can also be impacted if the culture is exposed to cold temperatures, as this would change the typical protein distribution.

Biochemical Profile-based Microbial Identification Systems

Phenotypic tests are used to identify microbes based on metabolic and biochemical pathways present in those microbes. [15] There are many automated and semi-automated commercial systems available. These methods can be very informative but are not as accurate as MALDI-TOF or genotypic methods.

6.5% salt broth

The 6.5% salt broth test is used to analyze the tolerance level of various bacteria under halophilic conditions. This test is used because most organisms cannot survive in high salt concentrations while Staphylococci, Enterococci, and Aerococci are all expected to tolerate 6.5% NaCl concentrations. [16]

Acetate utilization

The acetate utilization test is used primarily to differentiate between Escherichia coli from members of the genus Shigella . Many of the Escherichia coli strains have the capability of the utilization of acetate for a sole carbon and energy source, while Shigella does not. Since acetate utilization results in an increase in pH, an indicator is added that changes color under conditions of acetate utilization.

ALA

An ALA (delta-aminolevulinic acid) test is used to test for the presence of porphyrin and cytochrome compounds. Finding hemin synthesis indicates that the organism is likely Haemophilus . [17]

Aminopeptidase

The aminopeptidase test analyzes bacteria for the production of the enzyme L-alanine-aminopeptidase, an enzyme found in many gram-negative bacteria. Adding L-Alanine-4-nitroanilide hydrochloride to a bacterial culture works as an indicator, changing to a yellow color in the presence of L-alanine-aminopeptidase. [18]

Analytical profile index

API 20NE rapid test system, one day after sample application Api20ne.jpg
API 20NE rapid test system, one day after sample application

An analytical profile index is a fast identification system based on biochemical incubation tests. Usually, this test is used to quickly diagnose clinically relevant bacteria by allowing physicians to run about 20 tests at one time. [19]

Antibiotic disks

Antibiotic susceptible bacteria Antibiotic suceptible bacteria.jpg
Antibiotic susceptible bacteria

Antibiotic disks are used to test the ability for an antibiotic to inhibit growth of a microorganism. This method, which is commonly used with Mueller–Hinton agar, is used by evenly seeding bacteria over a petri dish and applying an antibiotic treated disk to the top of the agar. By observing the ring formed around the disk formed due to the lack of bacterial growth, the zone of inhibition can be found, which is used to find the susceptibility of an organism to an antibiotic. [19]

Bile esculin agar

The bile esculin test is used to differentiate members of the genus Enterococcus from Streptococcus.[ citation needed ]

Bile solubility

Bile solubility is used to test for Streptococcus Pneumoniae due to their unique ability to be lysed by sodium deoxycholate. Lysis indicates S. Pneumoniae while no lysis does not. [20]

CAMP

A positive CAMP test with the characteristic arrowhead shaped zone of hemolysis CAMP test.JPG
A positive CAMP test with the characteristic arrowhead shaped zone of hemolysis

A CAMP test is used to differentiate between Streptococcus agalactiae and other species of beta-hemolytic Streptococcus. This biochemical test uses the fact that Streptococcus agalactiae excretes a CAMP substance, making it slightly more hemolytic, which can be observed on blood agar media. [21]

Catalase

The catalase test tests whether a microbe produces the enzyme catalase, which catalyzes the breakdown of hydrogen peroxide. Smearing a colony sample onto a glass slide and adding a solution of hydrogen peroxide (3% H2O2) will indicate whether the enzyme is present or not. Bubbling is a positive test while nothing happening is a negative result. [22]

Cetrimide agar

Cetrimide agar slants is a selective agar used to isolate Pseudomonas aeruginosa .

CLO tests

The CLO test is used to diagnose H. Pylori in patient biopsies. A sample of the biopsy is places in a medium containing urea, which H. Pylori can use in some of its biochemical pathways. Consumption of urea indicates a positive test result. [23]

Coagulase

The coagulase test determines whether an organism can produce the enzyme coagulase, which causes the fibrin to clot. Inoculating a plasma test tube with the microbe indicates whether coagulase is produced. A clot indicates the presence of coagulase, while no clot indicates the lack of coagulase. [24]

DNA hydrolysis

DNase agar is used to test whether a microbe can produce the exoenzyme deoxyribonuclease (DNase), which hydrolyzes DNA. Methyl green is used as an indicator in the growth medium because it is a cation that provides an opaqueness to a medium with the presence of negatively charged DNA strands. When DNA is cleaved, the media becomes clear, showing the presence of DNase activity. DNA hydrolysis is tested by growing an organism on a DNase Test Agar plate (providing nutrients and DNA) and then checking the plate for hydrolysis. The agar plate has DNA-methyl green complex, and if the organism on the agar does hydrolyze DNA then the green color fades and the colony is surrounded by a colorless zone. [25]

Gelatin

The gelatin test is used to analyze whether a microbe can hydrolyze gelatin with the enzyme gelatinase. The gelatin makes the agar solid, so if an organism can produce gelatinase and consume gelatin as an energy and carbon source, the agar will become liquid during growth. [26]

Gonocheck II

The Gonochek II test, a commercial biochemical test, is used to differentiate between Neisseria lactamica , Neisseria meningitidis , N. gonorrhoeae and Moraxella catarrhalis. The principle behind this test is to use enzymes native to the organism to create a colored product in the presence of foreign molecules. The chemical 5-bromo-4-chloro-3-indolyl-beta-D-galactoside is used in the test because N. lactamica can hydrolyze it with the production of β-galactosidase, turning the solution into a blue color. Gamma-glutamyl-p-nitroanilide is added to the solution to indicate whether the bacteria is N. meningitides, which hydrolyzes the molecule with the enzyme gamma-glutamylaminopeptidase, producing a yellow end-product. Prolyl-4-methoxynaphthylamide is in the solution to identify N. gonorrhoeae because of its ability to hydrolyze the molecule with the enzyme hydroxyprolylaminopeptidase, creating a red-pink derivative. M. catarrhalis contains none of these enzymes, rendering the solution colorless. This process of identification takes approximately 30 minutes in total. [27]

Hippurate

The Hippurate diagnostic test is used to differentiate between Gardnerella vaginalis , Campylobacter jejuni, Listeria monocytogenes and group B streptococci using the chemical Hippurate. The Hippurate hydrolysis pathway, capable by organisms with the necessary enzymes, produces glycine as a byproduct. Using the indicator ninhydrin, which changes color in the presence of glycine, will display either a colorless product, a negative result, of a dark blue color, a positive result. [28]

Indole butyrate disk

An indole butyrate disc is used to differentiate between Neisseria gonorrhoeae (negative result) and Moraxella catarrhalis (positive result). This test involves a butyrate disk, which when smeared with a culture, will change color for a positive result after 5 minutes of incubation. A blue color is the result of a positive test. [29]

Lysine iron agar slant

The lysine iron agar slant test is used to tell whether an organism can decarboxylate lysine and/or produce hydrogen sulfide.

Lysostaphin

The lysostaphin test is used to differentiate between Staphylococcus and Micrococcus bacteria. Lysostaphin can lyse Staphylococcus, but Micrococcus bacteria are resistant to the chemical. [30]

Methyl red test

Color transition of Methyl red solution under different acid-base conditions Color transition of Methyl red solution under different acid-base conditions.jpg
Color transition of Methyl red solution under different acid-base conditions

The methyl red test is used to analyze whether a bacterium produces acids through sugar fermentation.[ citation needed ]

Microdase

Microdase is a modified oxidase test used to differentiate Micrococcus from Staphylococcus by testing for the presence of cytochrome c. A positive result produces a dark color around the inoculant while negative result produces no color change. [31]

Nitrite test

The nitrite test is commonly used to diagnose urinary tract infections by measuring the concentrations of nitrite in solution, indicating the presence of a gram-negative organism. A simple nitrite test can be performed by adding 4 M sulfuric acid to the sample until acidic, and then adding 0.1 M iron (II) sulfate to the solution. A positive test for nitrite is indicated by a dark brown solution, arising from the iron-nitric oxide complex ion. [ citation needed ]

Oxidase

The oxidase test indicates whether a microbe is aerobic. By using the chemical N,N,N,N-tetramethyl-1,4-phenylendiamin, an electron acceptor that changes color when oxidized by cytochrome c oxidase, one can deduce whether a microbe can perform aerobic respiration. A color change to purple indicates oxidative respiration while no color change provides evidence that the organism does not have cytochrome c oxidase. [22]

Phenylalanine deaminase

The phenylalanine deaminase test is used to tell whether an organism can produce the enzyme deaminase. Deaminase is the enzyme that can deaminate the amino acid phenylalanine into the products ammonia and phenylpyruvic acid. The test is performed by adding phenylalanine to the growth medium and allowing growth to occur. After incubation, 10% ferric chloride is added to the solution, which will react with phenylpyruvic acid in solution to make a dark green color, resulting in a positive test result. [32]

PYR

The PYR test is used to check if an organism has enzymes to hydrolyze L-pyrrolidonyl- β-napthylamide. A positive result indicates that the organism is either group A streptococcus and/or group D enterococcus . [33]

Reverse CAMP

The reverse CAMP test utilizes the synergetic hemolytic abilities of the CAMP factor produced by Streptococcus agalactiae with the α-toxin produced by Clostridium perfringens . Streaking these two organisms perpendicular to each other on a blood agar plate will yield a “bow-tie” clearing of the blood agar by the hemolytic capabilities of the two organisms’ toxins. Incubation requires 24 hours at 37 °C. [34]

Simmons' citrate agar

Simmons' citrate agar is used to test whether an organism can utilize citrate for its sole carbon source.[ citation needed ]

Spot indole

TSI Agar Agar tsi.JPG
TSI Agar

The spot indole test is used to determine if a microbe can deaminate tryptophan to produce indole. This test is performed by saturating a piece of filter paper with Indole Kovacs Reagent and scraping a portion of microbe onto the paper. A color to a pink-red color indicates a positive result while no color change indicates the lack of tryptophanase. [35]

Sulphide indole motility medium

The sulfide indole motility medium is a three-part test for an organism’s ability to reduce sulfates, produce indoles, and motile ability.[ citation needed ]

TSI slant

The triple sugar iron (TSI) test is a differential media used to tell whether an organism can ferment glucose, sucrose, and/or lactose and whether an organism can produce hydrogen sulfide gas. [36]

Urea agar slant

Raoultella planticola on urea agar Raoultella planticola on urea agar.jpg
Raoultella planticola on urea agar

The urease agar slant is used to measure an organism’s ability to produce urease, an enzyme capable to digesting urea in carbon dioxide and ammonia through hydrolysis. Because ammonia is alkaline, the media contains phenol red, an indicator that changes from orange to pink when a pH increases above 8.1. When ammonia is increased to high enough concentrations, the media will change to a pink color, indicating the presence of urease production. [37]

Voges–Proskauer test

The Voges-Proskauer test detects whether a bacterium is producing the product acetoin from the digestion of glucose. [38]

Cellular fatty acid based identification

Mycolic acid analysis

Mycolic acid analysis has been an evolving field of study for gas-liquid chromatography, as it offers a solution to slow growth rates in Mycobacterium. Mycolic acid is a fatty acid found in the disease tuberculosis, offering a chemical target for diagnosticians to look for. [39]

Nucleic acid extraction techniques

Cesium chloride / Ethidium bromide density gradient centrifugation

Tabletop centrifuge Tabletop centrifuge.jpg
Tabletop centrifuge

With high speed buoyant density ultracentrifugation, a density gradient is created with caesium chloride in water. DNA will go to the density that reflects its own, and ethidium bromide is then added to enhance the visuals the nucleic acid band provides. [40]

Magnetic bead method

New extraction techniques have been developed using magnetic beads for the purification of nucleic acids by taking advantage of the charged and polymeric nature of long strand of DNA. Beads are both uncoated to increase surface are and yield, while others are more selective by being coated with functional groups that interact with the polymers present in microbes. [41] One common method is to use polyethylene glycol to drive DNA binding to the magnetic beads. The molecular weight and concentration of the PEG will control what molecular weight DNA binds.

Phenol–chloroform extraction

Phenol-Chloroform extraction is a liquid-liquid method used by biochemists to separate nucleic acids from proteins and lipids after cells have been lysed. [42] [ citation needed ] This method has fallen out of favor with scientists and microbiologists as there are easier methods available which require less hazardous chemicals.

Solid phase extraction

Solid phase extraction which separates long polymers like DNA from other substances found in the cells. This is similar to magnetic beads, where the solid phase is fixed and selectively binds a cellular component, allowing for its isolation.

Methods with electrophoretic outputs

Gel electrophoresis is a technique to separate macromolecules by taking advantage of the charge on many of the molecules found in nucleic acids and protein. This is also the key method for Sanger sequencing. Fluorescent-labeled DNA fragments move through a polymer and are separated with one base precision. A laser excites the fluorescent tag and is captured by a camera. The result is an electropherogram which reads the DNA sequence.

Restriction enzyme based

Optical mapping

Optical mapping is a technique using multiple restriction enzymes to create a genomic “barcode” which can be referenced back to diagnose an unknown microbe.

Pulsed-field gel electrophoresis

Pulsed-field gel electrophoresis is a technique used to separate large DNA in an electric field that periodically changes direction. By cutting segments of the DNA with restriction enzymes, pulse-field can be used to separate out the segments of DNA.

Restriction enzymes then gel electrophoresis

Restriction enzymes are first used to recognize and then cut specific nucleic acid sequences. These cut pieces of DNA can be run through a gel electrophoresis to allow diagnostics of the organism by referencing back to previous gel electrophoresis results.

Ribotyping

Ribotyping is a rapid automated method for microbial diagnostics, testing for rRNA in bacteria using restriction enzyme digestion and Southern blot technology. [43]

PCR-based

Multiple loci VNTR analysis

Multiple-locus VNTR analysis is a test used to detect variable number tandem repeats, which act as a DNA fingerprint in microbial diagnostics. [44]

DNA sequence-based methods

Multi-locus sequence typing

Multilocus sequence typing (MLST) is the sequencing of numerous loci to diagnose an organism by comparing DNA sequences to a database of known organisms. [45] [46] This method is often used to compare isolates or strains of the same species to see if they are indistinguishable or different from each other. This is common for tracking food-borne illnesses and public health outbreaks. Most MLST assays are published in scientific journals so consistent methods are used worldwide. There are also public databases available for tracking and comparisons.

Single-locus sequence typing

Single-locus sequence typing (SLST) is the sequencing of a single locus of an organism to produce data that can be used for strain-level comparisons between isolates of the same species. [47]

Genotypic identifications

For bacterial identifications, microbiologists sequence the 16S rRNA gene and for fungal identifications, sequence the ITS regions. Both regions are part of the ribosomal operon so they are well-conserved but provide enough variation to allow for speciation. Accurate identifications require high quality sequence data, a robust data analysis, and a broad microbial database of known organisms. It is also useful to use a Neighbor Joining tree or some other phylogenetic approach to make the identification.

Whole genome sequencing (WGS)

Whole genome sequencing and genomics applications can be used for large-scale alignment and comparative analysis with both bacteria and fungi. WGS can be used to diagnose, identify, or characterize an organism down to the individual base pairs by sequencing the entire genome. [48] WGS can also be used to compare the genomes or average nucleotide identity (ANI) of the shared genes between two strains and can be a robust way to compare genetic relatedness and if often used for investigating organisms involved in foodborne illness and other outbreaks.

Related Research Articles

<span class="mw-page-title-main">Bacteriology</span> Subdiscipline of microbiology that studies bacteria

Bacteriology is the branch and specialty of biology that studies the morphology, ecology, genetics and biochemistry of bacteria as well as many other aspects related to them. This subdivision of microbiology involves the identification, classification, and characterization of bacterial species. Because of the similarity of thinking and working with microorganisms other than bacteria, such as protozoa, fungi, and viruses, there has been a tendency for the field of bacteriology to extend as microbiology. The terms were formerly often used interchangeably. However, bacteriology can be classified as a distinct science.

<span class="mw-page-title-main">Agar plate</span> Petri dish with agar used to culture microbes

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.

<span class="mw-page-title-main">Microbiological culture</span> Method of allowing microorganisms to multiply in a controlled medium

A microbiological culture, or microbial culture, is a method of multiplying microbial organisms by letting them reproduce in predetermined culture medium under controlled laboratory conditions. Microbial cultures are foundational and basic diagnostic methods used as research tools in molecular biology.

<span class="mw-page-title-main">Bacteriological water analysis</span>

Bacteriological water analysis is a method of analysing water to estimate the numbers of bacteria present and, if needed, to find out what sort of bacteria they are. It represents one aspect of water quality. It is a microbiological analytical procedure which uses samples of water and from these samples determines the concentration of bacteria. It is then possible to draw inferences about the suitability of the water for use from these concentrations. This process is used, for example, to routinely confirm that water is safe for human consumption or that bathing and recreational waters are safe to use.

<span class="mw-page-title-main">Coagulase</span> Class of bacterial proteins

Coagulase is a protein enzyme produced by several microorganisms that enables the conversion of fibrinogen to fibrin. In the laboratory, it is used to distinguish between different types of Staphylococcus isolates. Importantly, S. aureus is generally coagulase-positive, meaning that a positive coagulase test would indicate the presence of S. aureus or any of the other 11 coagulase-positive Staphylococci. A negative coagulase test would instead show the presence of coagulase-negative organisms such as S. epidermidis or S. saprophyticus. However, it is now known that not all S. aureus are coagulase-positive. Whereas coagulase-positive Staphylococci are usually pathogenic, coagulase-negative Staphylococci are more often associated with opportunistic infection.

<span class="mw-page-title-main">Blood culture</span> Test to detect bloodstream infections

A blood culture is a medical laboratory test used to detect bacteria or fungi in a person's blood. Under normal conditions, the blood does not contain microorganisms: their presence can indicate a bloodstream infection such as bacteremia or fungemia, which in severe cases may result in sepsis. By culturing the blood, microbes can be identified and tested for resistance to antimicrobial drugs, which allows clinicians to provide an effective treatment.

<span class="mw-page-title-main">Coliform bacteria</span> Group of bacterial species

Coliform bacteria are defined as either motile or non-motile Gram-negative non-spore forming bacilli that possess β-galactosidase to produce acids and gases under their optimal growth temperature of 35–37 °C. They can be aerobes or facultative aerobes, and are a commonly used indicator of low sanitary quality of foods, milk, and water. Coliforms can be found in the aquatic environment, in soil and on vegetation; they are universally present in large numbers in the feces of warm-blooded animals as they are known to inhabit the gastrointestinal system. While coliform bacteria are not normally causes of serious illness, they are easy to culture, and their presence is used to infer that other pathogenic organisms of fecal origin may be present in a sample, or that said sample is not safe to consume. Such pathogens include disease-causing bacteria, viruses, or protozoa and many multicellular parasites. Every drinking water source must be tested for the presence of these total coliform bacteria.

<span class="mw-page-title-main">Growth medium</span> Solid, liquid or gel used to grow microorganisms or cells

A growth medium or culture medium is a solid, liquid, or semi-solid designed to support the growth of a population of microorganisms or cells via the process of cell proliferation or small plants like the moss Physcomitrella patens. Different types of media are used for growing different types of cells.

<i>Staphylococcus epidermidis</i> Species of bacterium

Staphylococcus epidermidis is a Gram-positive bacterium, and one of over 40 species belonging to the genus Staphylococcus. It is part of the normal human microbiota, typically the skin microbiota, and less commonly the mucosal microbiota and also found in marine sponges. It is a facultative anaerobic bacteria. Although S. epidermidis is not usually pathogenic, patients with compromised immune systems are at risk of developing infection. These infections are generally hospital-acquired. S. epidermidis is a particular concern for people with catheters or other surgical implants because it is known to form biofilms that grow on these devices. Being part of the normal skin microbiota, S. epidermidis is a frequent contaminant of specimens sent to the diagnostic laboratory.

The oxidase test is used to determine whether an organism possesses the cytochrome c oxidase enzyme. The test is used as an aid for the differentiation of Neisseria, Moraxella, Campylobacter and Pasteurella species. It is also used to differentiate pseudomonads from related species.

<span class="mw-page-title-main">Antibiotic sensitivity testing</span> Microbiology test used in medicine

Antibiotic sensitivity testing or antibiotic susceptibility testing is the measurement of the susceptibility of bacteria to antibiotics. It is used because bacteria may have resistance to some antibiotics. Sensitivity testing results can allow a clinician to change the choice of antibiotics from empiric therapy, which is when an antibiotic is selected based on clinical suspicion about the site of an infection and common causative bacteria, to directed therapy, in which the choice of antibiotic is based on knowledge of the organism and its sensitivities.

<span class="mw-page-title-main">Simmons' citrate agar</span> Differential culture medium

Simmons' citrate agar is used for differentiating gram-negative bacteria on the basis of citrate utilization, especially for distinguishing Gammaproteobacteria of the family Enterobacteriaceae or even between species of the same genus. For example, Salmonella enteritidis would yield a positive (blue) result on Simmons’ agar and thus be distinguished from other Salmonella species like Salmonella typhi, Salmonella pullorum, and Salmonella gallinarum, which would yield a negative (green) result.

<span class="mw-page-title-main">Medical microbiology</span> Branch of medical science

Medical microbiology, the large subset of microbiology that is applied to medicine, is a branch of medical science concerned with the prevention, diagnosis and treatment of infectious diseases. In addition, this field of science studies various clinical applications of microbes for the improvement of health. There are four kinds of microorganisms that cause infectious disease: bacteria, fungi, parasites and viruses, and one type of infectious protein called prion.

<span class="mw-page-title-main">Mannitol salt agar</span> Culture medium used in microbiology

Mannitol salt agar or MSA is a commonly used selective and differential growth medium in microbiology. It encourages the growth of a group of certain bacteria while inhibiting the growth of others. It contains a high concentration of salt (NaCl) which is inhibitory to most bacteria - making MSA selective against most Gram-negative and selective for some Gram-positive bacteria that tolerate high salt concentrations. It is also a differential medium for mannitol-fermenting staphylococci, containing the sugar alcohol mannitol and the indicator phenol red, a pH indicator for detecting acid produced by mannitol-fermenting staphylococci. Staphylococcus aureus produces yellow colonies with yellow zones, whereas other coagulase-negative staphylococci produce small pink or red colonies with no colour change to the medium. If an organism can ferment mannitol, an acidic byproduct is formed that causes the phenol red in the agar to turn yellow. It is used for the selective isolation of presumptive pathogenic (pp) Staphylococcus species.

In microbiology, the phenotypic testing of mycobacteria uses a number of methods. The most-commonly used phenotypic tests to identify and distinguish Mycobacterium strains and species from each other are described below.

<span class="mw-page-title-main">IMViC</span> Microbiological and biochemical method for identification

The IMViC tests are a group of individual tests used in microbiology lab testing to identify an organism in the coliform group. A coliform is a gram negative, aerobic, or facultative anaerobic rod, which produces gas from lactose within 48 hours. The presence of some coliforms indicate fecal contamination.

The analytical profile index, or API, is a classification of bacteria based on biochemical tests, allowing fast identification. The system was developed for the quick identification of clinically relevant bacteria. It can only be used to identify known species from an index.

In microbiology, the term isolation refers to the separation of a strain from a natural, mixed population of living microbes, as present in the environment, for example in water or soil, or from living beings with skin flora, oral flora or gut flora, in order to identify the microbe(s) of interest. Historically, the laboratory techniques of isolation first developed in the field of bacteriology and parasitology, before those in virology during the 20th century.

<span class="mw-page-title-main">Colonial morphology</span> Examination of microbial colonies

In microbiology, colonial morphology refers to the visual appearance of bacterial or fungal colonies on an agar plate. Examining colonial morphology is the first step in the identification of an unknown microbe. The systematic assessment of the colonies' appearance, focusing on aspects like size, shape, colour, opacity, and consistency, provides clues to the identity of the organism, allowing microbiologists to select appropriate tests to provide a definitive identification.

Peptidiphaga gingivicola is a Gram-positive, non-spore forming, coccus shaped bacterium. Coccus are spherical and generally round in shape. Coccus are differentiated by their groupings that can range from chains, groups, or grape-like clusters. Peptidiphaga gingivicola was observed to grow in groups of 2-5 cocci between 0.2-0.9 mm in diameter. Growth was observed when cultured under anaerobic conditions between 33 and 40 degrees celsius on Blood Brucella agar for 4 days. Peptidiphaga gingivicola has been cultured from patients with periodontal disease, primarily caused by bacterial plaque formation on the gum and teeth of the oral cavity. The microbe is known to break down peptides of the gum causing tissue damage and tooth decay, leading to serious implications for oral health.

References

  1. ↑ Stieglmeier, Michaela; Wirth, Reinhard; Kminek, Gerhard; Moissl-Eichinger, Christine (2009-06-01). "Cultivation of Anaerobic and Facultatively Anaerobic Bacteria from Spacecraft-Associated Clean Rooms". Applied and Environmental Microbiology. 75 (11): 3484–3491. Bibcode:2009ApEnM..75.3484S. doi:10.1128/AEM.02565-08. ISSN   0099-2240. PMC   2687301 . PMID   19363082.
  2. ↑ Pubchem. "Resazurin sodium salt | C12H6NNaO4 - PubChem". pubchem.ncbi.nlm.nih.gov. Retrieved 2017-04-03.
  3. ↑ "Anaerobic Bacteria Culture - procedure, blood, complications, time, infection, types, children, Definition". www.surgeryencyclopedia.com. Retrieved 2017-04-03.
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  41. ↑ Martinez, Lluis. "Magnetic DNA Purification: History and recent developments" . Retrieved 2017-04-03.
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  48. ↑ Wu, Xueling; Wu, Xiaoyan; Shen, Li; Li, Jiaokun; Yu, Runlan; Liu, Yuandong; Qiu, Guanzhou; Zeng, Weimin (2019). "Whole Genome Sequencing and Comparative Genomics Analyses of Pandoraea sp. XY-2, a New Species Capable of Biodegrade Tetracycline". Frontiers in Microbiology. 10: 33. doi: 10.3389/fmicb.2019.00033 . ISSN   1664-302X. PMC   6361800 . PMID   30761094.
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