Introduction to particular bacteriology Classification Katalin Kristóf MD PhD Introduction to bacteria and bacterial diseases Bacteria, the oldest form of life on earth, are remarkably diverse and exist in astounding numbers Diseases caused by bacteria include some of the most common infections in the world, as well as some of the most important human scourges, past, present, and probably future At the same time, each of us is colonized by more bacterial cells than we have human cells in our bodies Generally, this is a peaceful and even productive (symbiotic) relationship, but occasionally even these welltolerated residents of the human biosphere cause disease Human Microbiome Project study Annu Rev Genomics Hum Gene 2012 Bacterial Taxonomy Includes three components: 1. Classification : orderly arrangement 2. Identification of an unknown unit 3. Nomenclature : naming the units Classification of bacteria Bacteria have been classified according to phenotype, including size, shape, staining properties, and biochemical properties, since the beginning of microbiology In recent years, classification has been dominated by genotype, especially relaying on conserved molecules, such as 16S ribosomal RNA Although there is a considerable degree of overlap between phenotype and genotype, as would be expected, dichotomies occur In the future, taxonomy, understanding of pathogenesis, and diagnostics will be increasingly based on genotype. As bacteriology advances in its differentiation of genera and species, as subspecies diversity is increasingly appreciated, as variation within individual host is better understood, and as the evaluation of pathogens is better outlined, a grounding in evolutionary biology and ecology also will be more critical Hierarchy Evolutionary relationships Species are groups that interbreed (have productive sex) How this goes Species Genus Family Order Class Division Phylum Kingdom (1969) Domain (80’s) The Three-Domain System Domains are above the kingdom level. proposed by Carl Woese based on rRNA studies of prokaryotes domain model more clearly shows prokaryotic diversity The Three-Domain System Have no cell nucleus or any other membrane organelles within their cells. Hot springs, home of thermophiles 6 Kingdom System ARCHAEBACTERIA EUBACTERIA PROTISTA FUNGI PLANTAE ANIMALIA Classification is always a work in progress. The tree of life shows our most current understanding. New discoveries can lead to changes in classification. Until 1866: only two kingdoms, Plantae Animalia and Plantae Animalia Classification is always a work in progress. The tree of life shows our most current understanding. New discoveries can lead to changes in classification. Until 1866: only two kingdoms, Plantae Animalia and Plantae Animalia – 1866: all single-celled organisms moved to kingdom Protista Protista Classification is always a work in progress. The tree of life shows our most current understanding. New discoveries can lead to changes in classification. Until 1866: only two kingdoms, Plantae Animalia and Plantae Animalia – 1866: all single-celled organisms moved to kingdom Protista Protista – 1938: prokaryotes moved to kingdom Monera Monera Classification is always a work in progress. The tree of life shows our most current understanding. New discoveries can lead to changes in classification. Until 1866: only two kingdoms, Plantae Animalia and Plantae Animalia – 1866: all single-celled organisms moved to kingdom Protista Protista – 1938: prokaryotes moved to kingdom Monera – 1959: fungi moved to own kingdom Monera Fungi Classification is always a work in progress. The tree of life shows our most current understanding. New discoveries can lead to changes in classification. Until 1866: only two kingdoms, Animalia and Plantae Plantae Animalia – 1866: all single-celled organisms moved to kingdom Protista Protista – 1938: prokaryotes moved to kingdom Monera Archea – 1959: fungi moved to own kingdom Fungi Bacteria – 1977: kingdom Monera split into kingdoms Bacteria and Archaea The History and Evolution of Bergey’s Manual 1. Bergey’s Manual of Determinative Bacteriology (1923-1994) 9 Editions (1 volume each )-These are mainly phonetic 2. Bergey’s Manual of Systematic Bacteriology: 1s t edition (4volumes);1984-1989; Mix Phylogenetic/Phenetic5 Kingdoms 2nd Edition (5 volumes) (2001-2012);Phylogenetic-3 Domains Bergey’s Manual of Systematic Bacteriology First edition -Published in 4 volumes: Volume 1 (1984) -Gram-negative Bacteria of general, medical, or industrial importance Volume 2 (1986) -Gram-positive Bacteria other than Actinomycetes Volume 3 (1989) -Archaeobacteria, Cyanobacteria, and remaining Gramnegative Bacteria Volume 4 (1989) -Actinomycetes Second Edition-published in 5 volumes: Volume 1-(2001) The Archaea and the deeply branching and phototrophic Bacteria Volume 2-(2005)-The Proteobacteria Volume 3-(2009)- The Firmicutes Volume 4-(2011)- The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes Volume 5-(2012)- The Actinobacteria Bergey’s Overview Volume 2 18 Linnaeus’s System - Nomenclature Binomial nomenclature is a two-part scientific naming system. – uses Latin words – scientific names always written in italics (or underlined) – two parts are the genus name and species descriptor – The genus always begins with a capital letter and the species is always lower case Escherichia coli Escherichia coli Scientific Names Scientific Binomial Source of Genus Name Source of Specific Epithet Klebsiella pneumoniae Pfiesteria piscicida Salmonella typhimurium Streptococcus pyogenes Penicillium chrysogenum Honors Edwin Klebs The disease Honors Lois Pfiester Disease in fish Honors Daniel Salmon Stupor (typh-) in mice (muri-) Forms pus (pyo-) Trypanosoma cruzi Corkscrew-like (trypano-, Honors Oswaldo borer; soma-, body) Cruz Chains of cells (strepto-) Tuftlike (penicill-) Produces a yellow (chryso-) pigment Casual / common name – for local use, varies from country to country e.g. “typhoid bacillus” – Salmonella typhi (scientific name) Species Definition Eukaryotic species: A group of closely related organisms that breed among themselves Prokaryotic species: A population of cells with similar characteristics Clone: Population of cells derived from a single cell Strain: Genetically different cells within a clone Culture: grown in the lab Viral species: Population of viruses with similar characteristics that occupies a particular ecological niche Family – Genus - Species Taxonomy Kingdom: Bacteria; Phylum: Firmicutes; Class: Bacilli; Order: Bacillales; - Family: Acyclobacillaceae (genus: Acyclobacillus); - Family: Bacillaceae (genus: Bacillus, Geobacillus); - species: Bacillus anthracis - Family: Paenibacillaceae (genus: Paenibacillus, Brevibacillus); - Family: Planococcaceae (genus: Sporosarcina). Irregular, non-spore-forming Gram-positive rods Corynebacterium diphteriae Other corynebacterium spp. Listeria monocytogenes Erysipelothrix rhusiopathiae Lactobacillus spp. Corynebacterium diphteriae - diphteria Diphteria is an acut, (exo)toxin-mediated disease caused by the bacterium Corynebacterium diphteriae Name: greek diphteria (leather hide) C. diphteriae aerobic, gram-positive, non-spore forming bacillus related phylogenetically to mycobacteria and actinomycetes (micolic acid) History Hippocrates provided the first clinical description of diphtheria in the 4th century B.C. In the 17th century, murderous epidemics of diphtheria swept Europe; in Spain the disease became known as "El garatillo" (the strangler"), in Italy and Sicily as "the gullet disease". In the 18th century, the disease reached the American colonies where it reached epidemic proportions about 1735. Often, whole families died of the disease in a few weeks. Observed by Klebs in 1883, culture by Loeffler in 1884 in 1884, Loeffler concluded that C. diphtheriae produced a soluble toxin, and thereby provided the first description of a bacterial exotoxin. in 1888, Roux and Yersin demonstrated the presence of the toxin in the cell-free culture fluid of C. diphtheriae which, when injected into suitable lab animals, caused the systemic manifestation of diphtheria. Two years later, von Behring and Kitasato succeeded in immunizing guinea pigs with a heatattenuated form of the toxin and demonstrated that the sera of immunized animals contained an antitoxin capable of protecting other susceptible animals against the disease. This modified toxin was suitable for immunizing animals to obtain antitoxin, but it was found to cause severe local reactions in humans and could not be used as a vaccine. in 1909, Theobald Smith, in the U.S., demonstrated that diphtheria toxin that had been neutralized by antitoxin (forming a Toxin-Anti-Toxin complex, TAT) remained immunogenic and eliminated local reactions seen in the modified toxin. For some years, beginning about 1910, TAT was used for active immunization against diphtheria. TAT had two undesirable characteristics as a vaccine. First, the toxin used was highly toxic, and the quantity injected could result in a fatal toxemia unless the toxin was fully neutralized by antitoxin. Second, the antitoxin mixture was horse serum, the components of which tended to be allergenic and to sensitize individuals to the serum. in 1913, Schick designed a skin test as a means of determining susceptibility or immunity to diphtheria in humans. Diphtheria toxin will cause an inflammatory reaction when very small amounts are injected intracutaneously. The Schick Test involves injecting a very small dose of the toxin under the skin of the forearm and evaluating the injection site after 48 hours. A positive test (inflammatory reaction) indicates susceptibility (nonimmunity). A negative test (no reaction) indicates immunity (antibody neutralizes toxin). in 1929, Ramon demonstrated the conversion of diphtheria toxin to its nontoxic, but antigenic, equivalent (toxoid) by treating with formaldehyde. He provided humanity with one of the safest and surest vaccines of all time, the diphtheria toxoid. in 1951, Freeman made the remarkable discovery that pathogenic (toxigenic) strains of C. diphtheriae are lysogenic, (i.e., are infected by a temperate Beta phage), while non lysogenized strains are avirulent. Subsequently, it was shown that the gene for toxin production is located on the DNA of the Beta phage. in the early 1960s, Pappenheimer and his group at Harvard conducted experiments on the mechanism of a action of the diphtheria toxin. They studied the effects of the toxin in HeLa cell cultures and in cell-free systems, and concluded that the toxin inhibited protein synthesis by blocking the transfer of amino acids from tRNA to the growing polypeptide chain on the ribosome. They found that this action of the toxin could be neutralized by prior treatment with diphtheria antitoxin. Subsequently, the exact mechanism of action of the toxin was shown, and the toxin has become a classic model of an ADP-ribosylating bacterial exotoxin. Pathogenesis Susceptible person may aquire toxigenic diphteria bacilli in the nasopharynx The organism produces a toxin that inhibits cellular protein synthesis and is responsible for local tissue destruction and membrane formation The toxin produced at the site of the membrane is absorbed into the bloodstream and then distributed to the tissues of the body The toxin is responsible for the major complication of myocarditis and neuritis and can also cause low platelet counts and protein in the urine Pathogenesis Toxin mediated disease! Acquisition of phage leads to toxigenicity (lysogenic conversion ) Exotoxin ( polypeptid ) A fragment: toxic function B fragment: transport and binding function The toxic function A fragment: toxic function after binding to the receptor (particularly on the surface of heart & nerve cells, epithelial cells) this is released in the cytoplasm catalyses adenosine diphosphate-ribosylation of elongation factor 2 (EF-2) / this factor is required for the movement of nascent peptide chains on ribosomes/ inactivation of all of the host cell EF-2 molecules causes death of the cell=complete termination of protein synthesis cell death Clinical features Reservoir – only humans Transmission route from human to human by respiratory droplets breathing aerosolized secretions of infected individuals (rarely) by direct physical contact (rarely) Communicability Up to several weeks without antibiotics Incubation period 2-5 days (range:1-10 days) Clinical features (Disease can involve almost any mucous membrane) Localized damage as the results of exotoxin production exudative pharyngitis ( tonsils, pharynx, larynx ) the exudate evolves into a thick pseudomembrane (blood plasma leaks into the area and a fibrin network forms which is interlaced with rapidly-growing C. diphtheriae cells. ) difficult to dislodge without making the underlying tissue bleed – typical symptom! Distal effect Degenerative changes in these tissues, which include heart, muscle, peripheral nerves, adrenals, kidneys, liver and spleen, result in the systemic pathology of the disease Pharyngeal, tonsillar and laryngeal diphteria Early symptoms: sore throat, anorexia, lowgrade fever Bluish-white membrane (varying in size) => greyish-green, or black if bleeding has occured Pharynx of a 39-year-old woman with bacteriologically confirmed diphtheria. The photograph was taken 4 days after the onset of fever, malaise, and sore throat. Hemorrhage caused by removal of the membrane by swabbing appears as a dark area on the left. Pharyngeal, tonsillar and laryngeal diphteria The patient may recover at this point Extensive membrane formation may result in respiratory obstruction If enough toxin is absorbed, develop severe prostation, striking pallor, rapid pulse, stupor, and coma, and may even die within 6 to 10 days Severe disease: marked edema of the submandibular areas and the anterior neck Other localisation Nose : anterior nasal diphteria Wound Skin : cutaneous diphteria Eye vulva Complications The most frequent: myocarditis Abnormal cardiac rhytms Can occur early in the course of illness (often fatal) or weeks later Can lead to hearth failure Neuritis Affects motor nerves and usually resolves completely Paralysis of the soft palate (3.week) Paralysis of eye muscles, limbs, and diaphragm (5.week) The overall case-fatality rate: 5-10 % (<5 y; >40 y) Diagnosis Specific treatment must never be delayed for laboratory reports if the clinical picture is strongly suggestive of diphteria !!! Smears, cultivation ( from nose, throat or other suspected lesions before antimicrobial drugs are admitted ) Testing the virulence = toxin producing Corynebacterium diphteriae Gram staining: Gram-positive, (rather irregular) Some rods are club-shaped, others are slightly curved Cells arranged in a manner like Chinese characters they have the characteristic of forming irregular, club-shaped or V-shaped arrangements in normal growth. Special staining=> Neisser Neisser staining Aim → to show metachromatic or volutin granula (polyphosphate polymers) at the ends of Corynebacteria Stain fixed smear of cultured Corynebacteria with a freshly prepared 2:1 mixture of Neisser I and Neisser II dyes for 10 minutes Rinse the slide with water Strain the smear with crysoidine dye for 2 minutes Do not discard dye Dry the slide with the help of blotting paper Rods with club ends the body of which strains yellow and end stain, metachromatically purple (volutin granula = poli-phosphate) Cells arranged in a manner like Chinese characters Cultivation Blood agar: 1-3mm, small grey colonies, small zone of haemolysis Clauberg medium (K-tellurit medium) Selective differential medium for the isolation of C. diphteriae Contains: potassium-tellurite and blood glycerinate Organisms which grow on this medium reduce the potassium tellurite to tellurium; resulting in black to greyish colonies three biotypes: gravis, mitis, intermedium, Loeffler’s medium ( Loeffler’s serum + garlic smell medium/slope ) Selective differential medium for the isolation of C. diphteriae Contains: clotted serum -Three strains of Corynebacterium diphtheriae are recognized, gravis, intermedius and mitis. - They are listed here by falling order of the severity of the disease that they produce in humans. - All strains produce the identical toxin and are capable of colonizing the throat. - The differences in virulence between the three strains can be explained by their differing abilities to produce the toxin in rate and quantity, and by their differing growth rates After cultivation => species identification Biochemical reaction Testing the sugar break-down Pathogenic versus apathogenic corynebacterium strains Molecular methods MALDI-TOF MS After identification =>Testing the virulence = toxin producing In vivo – „Römer probe”: a culture from Loeffler medium is emulsified in water and 4 ml is injected into each of two guinea pigs, one of which has received antitoxin previously. Testing the virulence = toxin producing In vitro test – „Elek plate „ A strip of filter paper soaked in antitoxin is submerged in the medium and cultures streaked at right angles. The toxin diffuses from the culture streak and the antitoxin diffuses from the filter paper. A line of precipitation is formed where they meet in optimal concentrations. With PCR: the tox gene Tissue culture test ELEK-PROBE A strip of filter paper soaked in antitoxin is submerged in the medium and cultures streaked at right angles. The toxin diffuses from the culture streak and the antitoxin diffuses from the filter paper. A line of precipitation is formed where they meet in optimal concentrations. Other methods Epidemiological investigation Rybotyping PFGE Schick probe Skin test for check of immunity Immunserology Antitoxin level in patient serum (haemagglutination) Treatment and prevention Treatment Antitoxin – immediately! Antimicrobial drugs – penicillin, erythromycin Prevention Toxoid (DPT, DT, boosters) DPT=diphteria toxoid – 2,4,6,15 to 18 months, and at 4 to 6 years ! Regular boosters are particularly important for adults who travel to developing countries (every 10 years!) Once quite common, diphtheria has largely been eradicated in developed nations through wide-spread use of the DPT vaccine Diphtheria is a serious disease, with fatality rates between 5% and 10%. In children under 5 years and adults over 40 years, the fatality rate may be as much as 20%. Outbreaks, although very rare, still occur worldwide, even in developed nations. Following the breakup of the former Soviet Union in the late 1980s, vaccination rates in the constituent countries fell so low that there was a surge in diphtheria cases. In 1991 there were 2,000 cases of diphtheria in the USSR. By 1998, according to Red Cross estimates, there were as many as 200,000 cases in the Commonwealth of Independent States, with 5,000 deaths. Other corynebacteria C. jeikeium Opportunistic pathogen (especially for patient with haematological disorders, with intravascular catheters) with high antibioticum resistance C. urealyticum Opportunistic pathogen Urinary tract infection: strong urease – producer = formation of struvit or renal stones C. ulcerans Similar to clinical diphteria C. minutissimum Superficial infection of axillary and pubic skin (erythrasma) Listeria monocytogenes Morphology small Gram positive rod , motile ( 22ºC!) Culture : agar, blood-agar: characteristic small zone of beta-haemolysis around and under colonies; ! isolation can be enhanced in 4 ºC (“coldenrichment”) Anton-probe:purulens conjunctivitis in a rabbit Resistant: cold, high-salt concentration Serologic classification (slide/latexagglutination): Ia, Ib, IVb (> 90% of human disease) The bacterium Listeria monocytogenes was named in honor of Joseph Lister (1827-1912), an English surgeon, who introduced modern antiseptic surgery. Listeria monocytogenes EM Flagella are produced at room temperature but not at 37°C A particular property of L monocytogenes is the ability to multiply at low temperatures Bacteria therefore can accumulate in contaminated food stored in the refrigerator. Pathogenesis : facultative intracellular pathogen - The bacteria are then taken up by induced phagocytosis, analogous to the situation in Shigella. - An 80 kDa membrane protein called internalin probably mediates invasion. - Hemolysins listeriolysin O (LLO) - protein that mediates actindirected motility (Act-A); direct cell-to-cell spread of Listeria in an infected tissue may occur without an extracellular stage Pathogenesis, clinical findings soil, water, vegetation, birds, fish, variety of mammals, insects spreading way: consumption of contaminated milk, soft cheese, undercooked meat, unwashed, raw vegetables; transplacentar Dangerous for neonates, elderly, impaired cellmediated immunity ( pregnancy, AIDS, lymphoma…) Infections Intrauterin infection: - abortion or granulomatosis infantiseptica (disseminated abscesses and granulomas in multiple organs) early-onset sepsis Perinatal infection: - late-onset syndrome: meningitis, meningoencephalitis, sepsis Immunocompromised patients : meningitis, encephalitis, and/or sepsis Disease in healthy adults: influenza-like illness +/gastroenteritis Perinatal listeriosis - Listeriosis also may be transmitted congenitally across the placenta. - The immunocompetent mother suffers at worst a brief, flu-like febrile illness, but the fetus, whose defense system is still immature, becomes seriously ill. - Depending on the stage of gestation, the fetus is either stillborn or born with signs of congenital infection. - Typically, multiple pyogenic foci are found in several organs (granulomatosis infantiseptica). - The onset of listeriosis is delayed (i.e., a few days after birth) when infection is acquired during labor by bacteria colonizing the genital tract of the mother. Listeriosis: a resurgent foodborne infection Clinical Microbiology and Infection Volume 16, Issue 1, pages 16-23, 10 DEC 2009 DOI: 10.1111/j.1469-0691.2009.03109.x http://onlinelibrary.wiley.com/doi/10.1111/j.1469-0691.2009.03109.x/full#f1 Case report In 2002, a multistate outbreak of L. monocytogenes infections with 46 culture -confirmed cases, seven deaths, and three stillbirths or miscarriages in eight states was linked to eating sliced turkey deli meat. One intact food product and 25 environmental samples from a poultry processing plant yielded L. monocytogenes. Two environmental isolates from floor drains were indistinguishable from that of outbreak patient isolates, suggesting that the plant might be the source of the outbreak. Treatment ampicillin (+ gentamicin), erythromycin Natural resistance to cephalosporins! Immunity Cell-mediated Prevention Do not eat hot dogs and luncheon meats unless they are reheated until steaming hot. Avoid cross-contaminating other foods, utensils, and food preparation surfaces with fluid from hot dog packages, and wash hands after handling hot dogs. Do not eat soft cheeses such as feta, brie and camembert cheeses, blueveined cheeses, and Mexican-style cheeses such as "queso blanco fresco." Cheeses that may be eaten include hard cheeses; semi-soft cheeses such as mozzarella; pasteurized processed cheeses such as slices and spreads; cream cheese; and cottage cheese. Do not eat refrigerated pâtés or meat spreads. Canned or shelf-stable pâtés and meat spreads may be eaten. Do not eat refrigerated smoked seafood, unless it is contained in a cooked dish, such as a casserole. Canned or shelf-stable smoked seafood may be eaten. Do not drink raw (unpasteurized) milk or eat foods that contain unpasteurized milk. Erysipelothrix rhusiopathiae Morphology: Gram positive rod ( some rods are curved and a few are in chains ) Cultivation on blood-agar: small, transparent glistening colonies Erysipelothrix rhusiopathiae (Gram-positive rod) Erysipelothrix rhusiopathiae on blood agar Epidemiology it is distributed an land and sea animals worldwide it causes erysipelas in swine people obtain infection by direct inoculation from animals or animal products ( fishermen, butchers,…) » erysipeloid after 2-7 days incubation : pain, the lesion is raised, violaceus , pus is usually not present! (rarely septicemic disease) Laboratory diagnosis: full-thickness biopsy specimens or deep aspirates from the margin of the lesion Treatment Self-limited in 3-4 weeks or more rapidly with penicillin Prevention vaccination in swine use of gloves Lactobacillus spp. Morphology: Gram positive rod (20% anaerobic), pleomorphic Cultivation: Rogosa medium ( low pH, yeast extract, peptone, …)- anaerobic conditions 1-2 mm, shiny, whit, raised with the smell of yoghurt Blood, tomato-juice, … Lactobacillus sp. - Gram staining Epidemiology They are members of the normal flora of human oral cavity Gut vagina Clinical pictures role in the pathogenesis of caries rarely endocarditis opportunistic septicaemia in an immunocompromised patient Treatment: antibiotics based on the susceptibility tests (vancomycin resistant) Probiotics products designed to deliver potentially beneficial bacterial cells to the microbiotic ecosystem of humans and other animals. Strains of lactic acid bacteria are the most common microbes employed as probiotics, especially Lactobacillus and Bifidobacterium species, but lactococci, some enterococci and some streptococci are also included as probiotics Lactobacillus acidophilus Bifidobacterium bifidum the indigenous bacteria of humans serve a wide range of functions, which include manufacture of some B vitamins and vitamin K, synthesis of some digestive enzymes (e.g. lactase), competition with pathogens for colonization sites, production of antibacterial and antifungal substances that protect against harmful organisms, production of chemicals that have been shown to be anticarcinogenic, and stimulation of the development and activity of the immune system. The natural balance of the body’s bacteria can be upset by several factors such as certain medicines, antibiotics and steroids, increased acidity in the digestive system caused by stress, lack of sleep and poor diet, constipation or diarrhea, yeast overgrowth, fatigue, IBS and other intestinal conditions. Thank you for your attention
© Copyright 2025 Paperzz