Serotyping: Process of determining and distinguishing species of bacteria or viruses based on antigens they share.Agglutination Tests: Tests that are dependent on the clumping of cells, microorganisms, or particles when mixed with specific antiserum. (From Stedman, 26th ed)Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.O Antigens: The lipopolysaccharide-protein somatic antigens, usually from gram-negative bacteria, important in the serological classification of enteric bacilli. The O-specific chains determine the specificity of the O antigens of a given serotype. O antigens are the immunodominant part of the lipopolysaccharide molecule in the intact bacterial cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Streptococcus pneumoniae: A gram-positive organism found in the upper respiratory tract, inflammatory exudates, and various body fluids of normal and/or diseased humans and, rarely, domestic animals.Campylobacter fetus: A species of bacteria present in man and many kinds of animals and birds, often causing infertility and/or abortion.Campylobacter Infections: Infections with bacteria of the genus CAMPYLOBACTER.Pneumococcal Infections: Infections with bacteria of the species STREPTOCOCCUS PNEUMONIAE.Electrophoresis, Gel, Pulsed-Field: Gel electrophoresis in which the direction of the electric field is changed periodically. This technique is similar to other electrophoretic methods normally used to separate double-stranded DNA molecules ranging in size up to tens of thousands of base-pairs. However, by alternating the electric field direction one is able to separate DNA molecules up to several million base-pairs in length.Antigens, Bacterial: Substances elaborated by bacteria that have antigenic activity.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Campylobacter: A genus of bacteria found in the reproductive organs, intestinal tract, and oral cavity of animals and man. Some species are pathogenic.Multiplex Polymerase Chain Reaction: Methods for using more than one primer set in a polymerase chain reaction to amplify more than one segment of the target DNA sequence in a single reaction.Campylobacter jejuni: A species of bacteria that resemble small tightly coiled spirals. Its organisms are known to cause abortion in sheep and fever and enteritis in man and may be associated with enteric diseases of calves, lambs, and other animals.Bacterial Capsules: An envelope of loose gel surrounding a bacterial cell which is associated with the virulence of pathogenic bacteria. Some capsules have a well-defined border, whereas others form a slime layer that trails off into the medium. Most capsules consist of relatively simple polysaccharides but there are some bacteria whose capsules are made of polypeptides.Salmonella enterica: A subgenus of Salmonella containing several medically important serotypes. The habitat for the majority of strains is warm-blooded animals.Streptococcus agalactiae: A bacterium which causes mastitis in cattle and occasionally in man.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Molecular Typing: Using MOLECULAR BIOLOGY techniques, such as DNA SEQUENCE ANALYSIS; PULSED-FIELD GEL ELECTROPHORESIS; and DNA FINGERPRINTING, to identify, classify, and compare organisms and their subtypes.Bacteriophage Typing: A technique of bacterial typing which differentiates between bacteria or strains of bacteria by their susceptibility to one or more bacteriophages.Pasteurella multocida: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria normally found in the flora of the mouth and respiratory tract of animals and birds. It causes shipping fever (see PASTEURELLOSIS, PNEUMONIC); HEMORRHAGIC BACTEREMIA; and intestinal disease in animals. In humans, disease usually arises from a wound infection following a bite or scratch from domesticated animals.Streptococcal Infections: Infections with bacteria of the genus STREPTOCOCCUS.Disease Outbreaks: Sudden increase in the incidence of a disease. The concept includes EPIDEMICS and PANDEMICS.Salmonella: A genus of gram-negative, facultatively anaerobic, rod-shaped bacteria that utilizes citrate as a sole carbon source. It is pathogenic for humans, causing enteric fevers, gastroenteritis, and bacteremia. Food poisoning is the most common clinical manifestation. Organisms within this genus are separated on the basis of antigenic characteristics, sugar fermentation patterns, and bacteriophage susceptibility.Campylobacter coli: A species of gram-negative, rod-shaped bacteria isolated from the intestinal tract of swine, poultry, and man. It may be pathogenic.Neisseria meningitidis: A species of gram-negative, aerobic BACTERIA. It is a commensal and pathogen only of humans, and can be carried asymptomatically in the NASOPHARYNX. When found in cerebrospinal fluid it is the causative agent of cerebrospinal meningitis (MENINGITIS, MENINGOCOCCAL). It is also found in venereal discharges and blood. There are at least 13 serogroups based on antigenic differences in the capsular polysaccharides; the ones causing most meningitis infections being A, B, C, Y, and W-135. Each serogroup can be further classified by serotype, serosubtype, and immunotype.Nasopharynx: The top portion of the pharynx situated posterior to the nose and superior to the SOFT PALATE. The nasopharynx is the posterior extension of the nasal cavities and has a respiratory function.DNA Fingerprinting: A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.Agglutination: The clumping together of suspended material resulting from the action of AGGLUTININS.Immune Sera: Serum that contains antibodies. It is obtained from an animal that has been immunized either by ANTIGEN injection or infection with microorganisms containing the antigen.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Haemophilus: A genus of PASTEURELLACEAE that consists of several species occurring in animals and humans. Its organisms are described as gram-negative, facultatively anaerobic, coccobacillus or rod-shaped, and nonmotile.Pleuropneumonia: Inflammation of the lung parenchyma that is associated with PLEURISY, inflammation of the PLEURA.Ureaplasma: A genus of gram-negative, nonmotile bacteria which are common parasitic inhabitants of the urogenital tracts of humans, cattle, dogs, and monkeys.Carrier State: The condition of harboring an infective organism without manifesting symptoms of infection. The organism must be readily transmissible to another susceptible host.Hemagglutination Tests: Sensitive tests to measure certain antigens, antibodies, or viruses, using their ability to agglutinate certain erythrocytes. (From Stedman, 26th ed)Pasteurella Infections: Infections with bacteria of the genus PASTEURELLA.Klebsiella: A genus of gram-negative, facultatively anaerobic, rod-shaped bacteria whose organisms arrange singly, in pairs, or short chains. This genus is commonly found in the intestinal tract and is an opportunistic pathogen that can give rise to bacteremia, pneumonia, urinary tract and several other types of human infection.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)Cross Reactions: Serological reactions in which an antiserum against one antigen reacts with a non-identical but closely related antigen.Molecular Epidemiology: The application of molecular biology to the answering of epidemiological questions. The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples.Antibodies, Bacterial: Immunoglobulins produced in a response to BACTERIAL ANTIGENS.Brachyspira hyodysenteriae: A species of anaerobic, spiral bacteria that was formerly classified as Serpulina hyodysenteriae and Treponema hyodysenteriae (and for a short while, Serpula hyodysenteriae). This organism is the agent of swine dysentery.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Food Microbiology: The presence of bacteria, viruses, and fungi in food and food products. This term is not restricted to pathogenic organisms: the presence of various non-pathogenic bacteria and fungi in cheeses and wines, for example, is included in this concept.Multilocus Sequence Typing: Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.Feces: Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.Ribotyping: RESTRICTION FRAGMENT LENGTH POLYMORPHISM analysis of rRNA genes that is used for differentiating between species or strains.Salmonella Infections: Infections with bacteria of the genus SALMONELLA.Ureaplasma urealyticum: A species of gram-negative bacteria found in the human genitourinary tract (UROGENITAL SYSTEM), oropharynx, and anal canal. Serovars 1, 3, 6, and 14 have been reclassed into a separate species UREAPLASMA parvum.Latex Fixation Tests: Passive agglutination tests in which antigen is adsorbed onto latex particles which then clump in the presence of antibody specific for the adsorbed antigen. (From Stedman, 26th ed)Evaluation Studies as Topic: Studies determining the effectiveness or value of processes, personnel, and equipment, or the material on conducting such studies. For drugs and devices, CLINICAL TRIALS AS TOPIC; DRUG EVALUATION; and DRUG EVALUATION, PRECLINICAL are available.Antibodies, Monoclonal: Antibodies produced by a single clone of cells.Hantavirus Infections: Infections with viruses of the genus HANTAVIRUS. This is associated with at least four clinical syndromes: HEMORRHAGIC FEVER WITH RENAL SYNDROME caused by viruses of the Hantaan group; a milder form of HFRS caused by SEOUL VIRUS; nephropathia epidemica caused by PUUMALA VIRUS; and HANTAVIRUS PULMONARY SYNDROME caused by SIN NOMBRE VIRUS.Flagellin: A protein with a molecular weight of 40,000 isolated from bacterial flagella. At appropriate pH and salt concentration, three flagellin monomers can spontaneously reaggregate to form structures which appear identical to intact flagella.Rotavirus: A genus of REOVIRIDAE, causing acute gastroenteritis in BIRDS and MAMMALS, including humans. Transmission is horizontal and by environmental contamination. Seven species (Rotaviruses A thru G) are recognized.Microbial Sensitivity Tests: Any tests that demonstrate the relative efficacy of different chemotherapeutic agents against specific microorganisms (i.e., bacteria, fungi, viruses).Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Neisseria gonorrhoeae: A species of gram-negative, aerobic bacteria primarily found in purulent venereal discharges. It is the causative agent of GONORRHEA.Diarrhea: An increased liquidity or decreased consistency of FECES, such as running stool. Fecal consistency is related to the ratio of water-holding capacity of insoluble solids to total water, rather than the amount of water present. Diarrhea is not hyperdefecation or increased fecal weight.Ureaplasma Infections: Infections with bacteria of the genus UREAPLASMA.Counterimmunoelectrophoresis: Immunoelectrophoresis in which immunoprecipitation occurs when antigen at the cathode is caused to migrate in an electric field through a suitable medium of diffusion against a stream of antibody migrating from the anode as a result of endosmotic flow.Polysaccharides, Bacterial: Polysaccharides found in bacteria and in capsules thereof.Random Amplified Polymorphic DNA Technique: Technique that utilizes low-stringency polymerase chain reaction (PCR) amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments. RAPD technique may be used to determine taxonomic identity, assess kinship relationships, analyze mixed genome samples, and create specific probes.Psittaciformes: An order of BIRDS comprised of several families and more than 300 species. It includes COCKATOOS; PARROTS; PARAKEETS; macaws; and BUDGERIGARS.Swine Diseases: Diseases of domestic swine and of the wild boar of the genus Sus.Swine Erysipelas: An acute and chronic contagious disease of young pigs caused by Erysipelothrix insidiosa.Enteritis: Inflammation of any segment of the SMALL INTESTINE.Haemophilus Infections: Infections with bacteria of the genus HAEMOPHILUS.Gastroenteritis: INFLAMMATION of any segment of the GASTROINTESTINAL TRACT from ESOPHAGUS to RECTUM. Causes of gastroenteritis are many including genetic, infection, HYPERSENSITIVITY, drug effects, and CANCER.Pneumococcal Vaccines: Vaccines or candidate vaccines used to prevent infections with STREPTOCOCCUS PNEUMONIAE.Actinobacillus pleuropneumoniae: A species of gram-negative, facultatively anaerobic coccobacillus-shaped bacteria that has been isolated from pneumonic lesions and blood. It produces pneumonia with accompanying fibrinous pleuritis in swine.Providencia: Gram-negative rods isolated from human urine and feces.Shigella: A genus of gram-negative, facultatively anaerobic, rod-shaped bacteria that ferments sugar without gas production. Its organisms are intestinal pathogens of man and other primates and cause bacillary dysentery (DYSENTERY, BACILLARY).Enzyme-Linked Immunosorbent Assay: An immunoassay utilizing an antibody labeled with an enzyme marker such as horseradish peroxidase. While either the enzyme or the antibody is bound to an immunosorbent substrate, they both retain their biologic activity; the change in enzyme activity as a result of the enzyme-antibody-antigen reaction is proportional to the concentration of the antigen and can be measured spectrophotometrically or with the naked eye. Many variations of the method have been developed.Erysipelothrix: A genus of gram-positive, facultatively anaerobic, rod-shaped bacteria that has a tendency to form long filaments. Its organisms are widely distributed in nature and are found in MAMMALS; BIRDS; and FISHES. Erysipelothrix may appear gram-negative because they decolorize easily.Escherichia coli Infections: Infections with bacteria of the species ESCHERICHIA COLI.Poultry Diseases: Diseases of birds which are raised as a source of meat or eggs for human consumption and are usually found in barnyards, hatcheries, etc. The concept is differentiated from BIRD DISEASES which is for diseases of birds not considered poultry and usually found in zoos, parks, and the wild.Bacterial Outer Membrane Proteins: Proteins isolated from the outer membrane of Gram-negative bacteria.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Anti-Bacterial Agents: Substances that reduce the growth or reproduction of BACTERIA.Drug Resistance, Bacterial: The ability of bacteria to resist or to become tolerant to chemotherapeutic agents, antimicrobial agents, or antibiotics. This resistance may be acquired through gene mutation or foreign DNA in transmissible plasmids (R FACTORS).Bacterial Proteins: Proteins found in any species of bacterium.Haemophilus parasuis: A species of gram-negative bacteria in the genus HAEMOPHILUS found, in the normal upper respiratory tract of SWINE.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Dysentery, Bacillary: DYSENTERY caused by gram-negative rod-shaped enteric bacteria (ENTEROBACTERIACEAE), most often by the genus SHIGELLA. Shigella dysentery, Shigellosis, is classified into subgroups according to syndrome severity and the infectious species. Group A: SHIGELLA DYSENTERIAE (severest); Group B: SHIGELLA FLEXNERI; Group C: SHIGELLA BOYDII; and Group D: SHIGELLA SONNEI (mildest).Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Listeria monocytogenes: A species of gram-positive, rod-shaped bacteria widely distributed in nature. It has been isolated from sewage, soil, silage, and from feces of healthy animals and man. Infection with this bacterium leads to encephalitis, meningitis, endocarditis, and abortion.Gonorrhea: Acute infectious disease characterized by primary invasion of the urogenital tract. The etiologic agent, NEISSERIA GONORRHOEAE, was isolated by Neisser in 1879.Haemophilus influenzae: A species of HAEMOPHILUS found on the mucous membranes of humans and a variety of animals. The species is further divided into biotypes I through VIII.Serratia marcescens: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria found in soil, water, food, and clinical specimens. It is a prominent opportunistic pathogen for hospitalized patients.Environmental Microbiology: The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.Streptococcus pyogenes: A species of gram-positive, coccoid bacteria isolated from skin lesions, blood, inflammatory exudates, and the upper respiratory tract of humans. It is a group A hemolytic Streptococcus that can cause SCARLET FEVER and RHEUMATIC FEVER.Genetic Variation: Genotypic differences observed among individuals in a population.Proteus vulgaris: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria that occurs in soil, fecal matter, and sewage. It is an opportunistic pathogen and causes cystitis and pyelonephritis.Enterovirus: A genus of the family PICORNAVIRIDAE whose members preferentially inhabit the intestinal tract of a variety of hosts. The genus contains many species. Newly described members of human enteroviruses are assigned continuous numbers with the species designated "human enterovirus".Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Listeriosis: Infections with bacteria of the genus LISTERIA.Immunodiffusion: Technique involving the diffusion of antigen or antibody through a semisolid medium, usually agar or agarose gel, with the result being a precipitin reaction.Meningococcal Infections: Infections with bacteria of the species NEISSERIA MENINGITIDIS.Hantavirus: A genus of the family BUNYAVIRIDAE causing HANTAVIRUS INFECTIONS, first identified during the Korean war. Infection is found primarily in rodents and humans. Transmission does not appear to involve arthropods. HANTAAN VIRUS is the type species.Preservation, Biological: The process of protecting various samples of biological material.Hantaan virus: The type species of the genus HANTAVIRUS infecting the rodent Apodemus agrarius and humans who come in contact with it. It causes syndromes of hemorrhagic fever associated with vascular and especially renal pathology.Infant, Newborn: An infant during the first month after birth.Proteus Infections: Infections with bacteria of the genus PROTEUS.Proteus: A genus of gram-negative, facultatively anaerobic, rod-shaped bacteria that occurs in the intestines of humans and a wide variety of animals, as well as in manure, soil, and polluted waters. Its species are pathogenic, causing urinary tract infections and are also considered secondary invaders, causing septic lesions at other sites of the body.Swine: Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).Salmonella Infections, Animal: Infections in animals with bacteria of the genus SALMONELLA.Genes, Bacterial: The functional hereditary units of BACTERIA.Pasteurella: The oldest recognized genus of the family PASTEURELLACEAE. It consists of several species. Its organisms occur most frequently as coccobacillus or rod-shaped and are gram-negative, nonmotile, facultative anaerobes. Species of this genus are found in both animals and humans.Tetrathionic Acid: A sulfuric acid dimer, formed by disulfide linkage. This compound has been used to prolong coagulation time and as an antidote in cyanide poisoning.Penicillin Resistance: Nonsusceptibility of an organism to the action of penicillins.Brachyspira: A genus of spiral bacteria of the family Brachyspiraceae.Actinobacillus Infections: Infections with bacteria of the genus ACTINOBACILLUS.Chlamydophila psittaci: A genus of CHLAMYDOPHILA infecting primarily birds. It contains eight known serovars, some of which infect more than one type of host, including humans.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Cross Infection: Any infection which a patient contracts in a health-care institution.Drug Resistance, Microbial: The ability of microorganisms, especially bacteria, to resist or to become tolerant to chemotherapeutic agents, antimicrobial agents, or antibiotics. This resistance may be acquired through gene mutation or foreign DNA in transmissible plasmids (R FACTORS).DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Foodborne Diseases: Acute illnesses, usually affecting the GASTROINTESTINAL TRACT, brought on by consuming contaminated food or beverages. Most of these diseases are infectious, caused by a variety of bacteria, viruses, or parasites that can be foodborne. Sometimes the diseases are caused by harmful toxins from the microbes or other chemicals present in the food. Especially in the latter case, the condition is often called food poisoning.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Bacteriological Techniques: Techniques used in studying bacteria.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Antibody Specificity: The property of antibodies which enables them to react with some ANTIGENIC DETERMINANTS and not with others. Specificity is dependent on chemical composition, physical forces, and molecular structure at the binding site.Streptococcus suis: A species of STREPTOCOCCUS isolated from pigs. It is a pathogen of swine but rarely occurs in humans.Shigella boydii: One of the SHIGELLA species that produces bacillary dysentery (DYSENTERY, BACILLARY).Rotavirus Infections: Infection with any of the rotaviruses. Specific infections include human infantile diarrhea, neonatal calf diarrhea, and epidemic diarrhea of infant mice.Vaccines, Conjugate: Semisynthetic vaccines consisting of polysaccharide antigens from microorganisms attached to protein carrier molecules. The carrier protein is recognized by macrophages and T-cells thus enhancing immunity. Conjugate vaccines induce antibody formation in people not responsive to polysaccharide alone, induce higher levels of antibody, and show a booster response on repeated injection.