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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. [1]
The analytical profile index (API) was invented in the 1970s in the United States by Pierre Janin of Analytab Products Inc. [2] The API test system is currently manufactured by bioMérieux. [3] The API range introduced a standardized and miniaturized version of existing techniques, which up until then were complicated to perform and difficult to read.
Identification is only possible with a microbiological culture. API test strips consist of wells containing dehydrated substrates such as the redox substrates, electrogenic substrates and luminogenic substrates to detect enzymatic activity, usually related to the fermentation of carbohydrate or catabolism of proteins or amino acids by the inoculated organisms. A bacterial suspension is used to rehydrate each of the wells and the strips are incubated. During incubation, metabolism produces color changes that are either spontaneous or revealed by the addition of reagents. For example, when carbohydrates are fermented, the pH within the well decreases and that is indicated by a change in the color of the pH indicator. All test results are compiled to obtain a profile number, which is then compared with profile numbers in a commercial codebook (or online) to determine the identification of the bacterial species. [4]
Before starting a test, one must confirm the cultured bacteria are Enterobacteriaceae, this is done by a quick oxidase test for cytochrome coxidase. Enterobacteriaceae are typically oxidase negative, meaning they either do not use oxygen as an electron acceptor in the electron transport chain, or they use a different cytochrome enzyme for transferring electrons to oxygen. [5] If the culture is determined to be oxidase-positive, alternative tests must be carried out to correctly identify the bacterial species. API-20E is specific for differentiating between members of the Gram-negative bacteria family Enterobacteriaceae. [6] [7] Another API system, API-Staph, is specific for Gram-positive bacteria, including Staphylococcus species, Micrococcus species, and related organisms. [7]
The API 20E/NE fast identification system allows the identification of a limited number of Gram-negative Enterobacteriaceae or non-Enterobacteriaceae. The test systems are stored in 20 small reaction tubes, which include the substrates.
Enterobacteriaceae is a large family of Gram-negative bacteria. It includes over 30 genera and more than 100 species. Its classification above the level of family is still a subject of debate, but one classification places it in the order Enterobacterales of the class Gammaproteobacteria in the phylum Pseudomonadota. In 2016, the description and members of this family were emended based on comparative genomic analyses by Adeolu et al.
Proteus vulgaris is a rod-shaped, nitrate-reducing, indole-positive and catalase-positive, hydrogen sulfide-producing, Gram-negative bacterium that inhabits the intestinal tracts of humans and animals. It can be found in soil, water, and fecal matter. It is grouped with the Morganellaceae and is an opportunistic pathogen of humans. It is known to cause wound infections and other species of its genera are known to cause urinary tract infections.
Plesiomonas shigelloides is a species of bacteria and the only member of its genus. It is a Gram-negative, rod-shaped bacterium which has been isolated from freshwater, freshwater fish, shellfish, cattle, goats, swine, cats, dogs, monkeys, vultures, snakes, toads and humans. It is considered a fecal coliform. P. shigelloides is a global distributed species, found globally outside of the polar ice caps.
Proteus mirabilis is a Gram-negative, facultatively anaerobic, rod-shaped bacterium. It shows swarming motility and urease activity. P. mirabilis causes 90% of all Proteus infections in humans. It is widely distributed in soil and water. Proteus mirabilis can migrate across the surface of solid media or devices using a type of cooperative group motility called swarming. Proteus mirabilis is most frequently associated with infections of the urinary tract, especially in complicated or catheter-associated urinary tract infections.
The Pseudomonadaceae are a family of bacteria which includes the genera Azomonas, Azorhizophilus, Azotobacter, Mesophilobacter, Pseudomonas, and Rugamonas. The family Azotobacteraceae was recently reclassified into this family.
Enterobacter is a genus of common Gram-negative, facultatively anaerobic, rod-shaped, non-spore-forming bacteria of the family Enterobacteriaceae. Cultures are found in soil, water, sewage, feces and gut environments. It is the type genus of the order Enterobacterales. Several strains of these bacteria are pathogenic and cause opportunistic infections in immunocompromised hosts and in those who are on mechanical ventilation. The urinary and respiratory tracts are the most common sites of infection. The genus Enterobacter is a member of the coliform group of bacteria. It does not belong to the fecal coliforms group of bacteria, unlike Escherichia coli, because it is incapable of growth at 44.5 °C in the presence of bile salts. Some of them show quorum sensing properties.
NADPH oxidase is a membrane-bound enzyme complex that faces the extracellular space. It can be found in the plasma membrane as well as in the membranes of phagosomes used by neutrophil white blood cells to engulf microorganisms. Human isoforms of the catalytic component of the complex include NOX1, NOX2, NOX3, NOX4, NOX5, DUOX1, and DUOX2.
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.
A bacterium, despite its simplicity, contains a well-developed cell structure which is responsible for some of its unique biological structures and pathogenicity. Many structural features are unique to bacteria and are not found among archaea or eukaryotes. Because of the simplicity of bacteria relative to larger organisms and the ease with which they can be manipulated experimentally, the cell structure of bacteria has been well studied, revealing many biochemical principles that have been subsequently applied to other organisms.
Bacteroides fragilis is an anaerobic, Gram-negative, pleomorphic to rod-shaped bacterium. It is part of the normal microbiota of the human colon and is generally commensal, but can cause infection if displaced into the bloodstream or surrounding tissue following surgery, disease, or trauma.
Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.
Photobacterium damselaesubsp.piscicida is a gram-negative rod-shaped bacterium that causes disease in fish.
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.
Klebsiella aerogenes, previously known as Enterobacter aerogenes, is a Gram-negative, oxidase-negative, catalase-positive, citrate-positive, indole-negative, rod-shaped bacterium. Capable of motility via peritrichous flagella, the bacterium is approximately 1–3 microns in length.
Etest is a way of determining antimicrobial sensitivity by placing a strip impregnated with antimicrobials onto an agar plate. A strain of bacterium or fungus will not grow near a concentration of antibiotic or antifungal if it is sensitive. For some microbial and antimicrobial combinations, the results can be used to determine a minimum inhibitory concentration (MIC). Etest is a proprietary system manufactured by bioMérieux. It is a laboratory test used in healthcare settings to help guide physicians by indicating what concentration of antimicrobial could successfully be used to treat patients' infections.
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 species of the genus Aquabacterium are motile, rod-shaped, Gram-negative, oxidase-positive, catalase-negative bacteria which were isolated from drinking water biofilms in Berlin. Identified species include Aquabacterium citratiphilum, Aquabacterium parvum, and Aquabacterium commune. Three bacterial strains isolated from biofilms of the Berlin drinking water system were characterized with respect to their morphological and physiological properties and their taxonomic position. Phenotypically, the bacteria investigated were motile, Gram-negative rods, oxidase-positive and catalase-negative, and contained polyalkanoates and polyphosphate as storage polymers. They displayed a microaerophilic growth behaviour and used oxygen and nitrate as electron acceptors, but not nitrite, chlorate, sulfate, or ferric iron. The substrates metabolized included a broad range of organic acids, but no carbohydrates at all. The three species can be distinguished from each other by their substrate use, ability to hydrolyse urea and casein, cellular protein patterns, and growth on nutrient-rich media, as well as their temperature, pH, and NaCl tolerances. Phylogenetic analysis, based on 16S rRNA gene sequence comparison, revealed that the isolates are affiliated to the beta 1-subclass of Proteobacteria. The isolates constitute three new species with internal levels of DNA relatedness ranging from 44.9 to 51.3%. It is proposed that a new genus, Aquabacterium gen. nov., should be created, including Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov., and Aquabacterium commune sp. nov. The type species of the new genus is Aquabacterium commune.
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.
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.
Corynebacterium striatum is a bacterium that is a member of the Corynebacterium genus. It is classified as non-diphtheritic. The bacterium is a gram-positive prokaryote that assumes a 'club-like' morphology, more formally known as a corynebacteria structure. It is non-lipophilic and undergoes aerobic respiration and is also a facultative anaerobe it is catalase negative and oxidase positive glucose and sucrose fermenter.
