The document discusses the classification of bacteria in the family Enterobacteriaceae. It covers the historical methods of classification based on phenotypes as well as modern genetic methods using DNA-DNA hybridization and 16S rRNA gene sequencing. The key events in the classification of the family Enterobacteriaceae from the 1800s to present are outlined, noting changing taxonomy and increasing recognition of new species through molecular techniques.
The genus Shigella exclusively infects human intestine.
Shigella dysenteriae is the causative agent of bacillary dysentery or shigellosis in humans.
It is a diarrheal illness which is characterized by frequent passage of blood stained mucopurulent stools.
The four important species of the genus Shigella are:
Shigella dysenteriae
Shigella flexneri
Shigella sonnei
Shigella boydii.
- Escherichia coli (E. coli) is a common bacteria that normally lives in the intestines of humans and animals. However, some strains of E. coli can cause illness, including diarrhea.
- E. coli that causes diarrhea is divided into six groups that produce diarrhea through different pathogenic mechanisms, such as the production of heat-stable or heat-labile toxins. One group, enterotoxigenic E. coli (ETEC), commonly causes travelers' diarrhea.
- In addition to diarrhea, E. coli can cause other illnesses like urinary tract infections, wound or blood infections, and even sepsis. The type of specimen collected for testing depends on the suspected infection.
The document discusses the taxonomy, characteristics, and clinical significance of the family Enterobacteriaceae. It describes key genera including Citrobacter, Enterobacter, Klebsiella, and their roles as normal gut flora but also opportunistic pathogens. Klebsiella pneumoniae is highlighted as an important cause of nosocomial infections like pneumonia, meningitis, and sepsis. Laboratory identification involves culture-based methods and biochemical tests to distinguish lactose fermenters from non-fermenters. Treatment requires combination antibiotics and is guided by susceptibility testing due to rising multidrug resistance.
Actinomycetes and Nocardia, Bacteria but similar to fungi usually because of its morphological feature of forming a branching filament network, causing Actinomycosis, Actinomycetoma, Farmer's Lung, etc. Demonstrated under microscope by Gram's stain and ZN staining. Cultured on BHI and Thioglycolate broth. Characteristically produce Supher granules. Penicillin is the drug of choice in allergic to penicillin can be replaced by Erythromycin or Tetracycline. In worst cases surgical removal of affected tissue required.
Shigella are Gram-negative bacilli that cause shigellosis (bacillary dysentery) in humans. There are four species (S. dysenteriae, S. flexneri, S. boydii, S. sonnei) which are differentiated based on antigen types. Shigellosis ranges from asymptomatic to severe diarrhea with blood/mucus and is typically transmitted through the fecal-oral route. The bacteria invade the colonic epithelium through attachment and enterotoxins can cause electrolyte/nutrient absorption issues leading to symptoms. Treatment focuses on rehydration while prevention emphasizes water/sewage sanitation and antibiotic treatment of carriers.
pseudomonas aeruginosa is one of the leading cause of hospital-associated infection. mainly Pseudomonas is a multi drug resistant bacteria.
they are oxidase positive, non fermenters, strictly aerobic bacteria.
they are pigment producing, pigment can be appreciated on nutrient agar.
Haemophilus influenzae is a Gram-negative coccobacillus first isolated in 1892 during an influenza outbreak. It is classified within the phylum Proteobacteria and can cause several diseases in humans like meningitis, pneumonia, epiglottitis and cellulitis. H. influenzae possesses several virulence factors like a capsule, lipopolysaccharides and IgA1 protease that help it evade the immune system and cause disease. Diagnosis involves culture and identification of the bacteria from clinical specimens as well as antigen and molecular detection techniques. Vaccination against H. influenzae type b is available to prevent disease.
The genus Shigella exclusively infects human intestine.
Shigella dysenteriae is the causative agent of bacillary dysentery or shigellosis in humans.
It is a diarrheal illness which is characterized by frequent passage of blood stained mucopurulent stools.
The four important species of the genus Shigella are:
Shigella dysenteriae
Shigella flexneri
Shigella sonnei
Shigella boydii.
- Escherichia coli (E. coli) is a common bacteria that normally lives in the intestines of humans and animals. However, some strains of E. coli can cause illness, including diarrhea.
- E. coli that causes diarrhea is divided into six groups that produce diarrhea through different pathogenic mechanisms, such as the production of heat-stable or heat-labile toxins. One group, enterotoxigenic E. coli (ETEC), commonly causes travelers' diarrhea.
- In addition to diarrhea, E. coli can cause other illnesses like urinary tract infections, wound or blood infections, and even sepsis. The type of specimen collected for testing depends on the suspected infection.
The document discusses the taxonomy, characteristics, and clinical significance of the family Enterobacteriaceae. It describes key genera including Citrobacter, Enterobacter, Klebsiella, and their roles as normal gut flora but also opportunistic pathogens. Klebsiella pneumoniae is highlighted as an important cause of nosocomial infections like pneumonia, meningitis, and sepsis. Laboratory identification involves culture-based methods and biochemical tests to distinguish lactose fermenters from non-fermenters. Treatment requires combination antibiotics and is guided by susceptibility testing due to rising multidrug resistance.
Actinomycetes and Nocardia, Bacteria but similar to fungi usually because of its morphological feature of forming a branching filament network, causing Actinomycosis, Actinomycetoma, Farmer's Lung, etc. Demonstrated under microscope by Gram's stain and ZN staining. Cultured on BHI and Thioglycolate broth. Characteristically produce Supher granules. Penicillin is the drug of choice in allergic to penicillin can be replaced by Erythromycin or Tetracycline. In worst cases surgical removal of affected tissue required.
Shigella are Gram-negative bacilli that cause shigellosis (bacillary dysentery) in humans. There are four species (S. dysenteriae, S. flexneri, S. boydii, S. sonnei) which are differentiated based on antigen types. Shigellosis ranges from asymptomatic to severe diarrhea with blood/mucus and is typically transmitted through the fecal-oral route. The bacteria invade the colonic epithelium through attachment and enterotoxins can cause electrolyte/nutrient absorption issues leading to symptoms. Treatment focuses on rehydration while prevention emphasizes water/sewage sanitation and antibiotic treatment of carriers.
pseudomonas aeruginosa is one of the leading cause of hospital-associated infection. mainly Pseudomonas is a multi drug resistant bacteria.
they are oxidase positive, non fermenters, strictly aerobic bacteria.
they are pigment producing, pigment can be appreciated on nutrient agar.
Haemophilus influenzae is a Gram-negative coccobacillus first isolated in 1892 during an influenza outbreak. It is classified within the phylum Proteobacteria and can cause several diseases in humans like meningitis, pneumonia, epiglottitis and cellulitis. H. influenzae possesses several virulence factors like a capsule, lipopolysaccharides and IgA1 protease that help it evade the immune system and cause disease. Diagnosis involves culture and identification of the bacteria from clinical specimens as well as antigen and molecular detection techniques. Vaccination against H. influenzae type b is available to prevent disease.
Haemophilus is a genus of bacteria that includes species normally found in the human respiratory tract as well as pathogenic species. H. influenzae is the most clinically important species and is a cause of pneumonia, septic arthritis, epiglottitis, and meningitis. H. influenzae is a small, non-motile, gram-negative coccobacillus that requires both Factor X and V for growth. Serotype b of H. influenzae causes the majority of invasive disease and was an important cause of childhood meningitis prior to the introduction of the Hib vaccine.
This document discusses the laboratory diagnosis of Staphylococcus, including sample collection, direct smear microscopy, culture techniques, biochemical reactions, antibiotic sensitivity testing, and typing of Staphylococcus aureus. Appropriate samples are collected based on the site of infection and transported to the laboratory for analysis. Direct smear microscopy can identify Gram-positive cocci clusters. Culture techniques help isolate and identify Staphylococcus colonies based on morphology and biochemical reactions provide further characterization. Antibiotic sensitivity testing determines effective treatment options and typing methods like bacteriophage typing are used for epidemiological purposes.
Most medically important family of non–spore-forming gram-negative rods.
Most species are normal flora of the GI tract. Salmonella, Shigella, and Yersinia are not normal GI flora.
Major cause of nosocomial infections
Diseases include UTIs, gastroenteritis, septicemia, food poisoning, wound infections, peritonitis, pneumonia, and meningitis
The family exhibits four serological characteristics:
O (somatic) antigen-A cell wall antigen-LPS (heat stable), Used for serological grouping of Salmonella & Shigella.
K (envelope) antigen-Capsular antigen (heat labile)
H (flagellar) antigen-Flagellar antigen-protein (heat labile), Used to serotype Salmonella.
Vi antigen-Capsular antigen of Salmonella Typhi-polysaccharide (heat labile), Role in preventing phagocytosis, may mask O Ag, removed by heating.
Enterobacteriaceae are facultative anaerobes, ferment glucose. Positive nitrate and catalase, non-hemolytic. Except for Plesiomonas, they are oxidase negative.
Corynebacterium diphtheriae is a gram-positive, club-shaped bacterium that causes diphtheria. It produces a powerful exotoxin that inhibits protein synthesis and causes the formation of pseudomembranes at infection sites. Diagnosis involves isolating the bacterium from throat swabs and performing biochemical and virulence tests. Treatment consists of antitoxin and antibiotics like penicillin or erythromycin. Active immunization with diphtheria, pertussis, and tetanus vaccine helps prevent diphtheria.
This document provides information on Bordetella, the bacteria that causes whooping cough. It discusses the three main Bordetella species (B. pertussis, B. parapertussis, B. bronchiseptica), their morphology, culture characteristics, antigenic structure, pathogenesis of whooping cough, laboratory diagnosis, and prophylaxis with DPT vaccine. The key points are that B. pertussis causes the most common form of whooping cough in children, has a distinctive paroxysmal cough stage, and is diagnosed through culture or PCR of respiratory samples and confirmed with specific staining or agglutination.
Clostridium perfringens is a gram-positive, anaerobic bacterium that can cause gas gangrene. It forms spores that allow it to survive in soil and intestines. C. perfringens produces several toxins that damage tissues and cause diseases like gas gangrene. The bacterium thrives under low-oxygen conditions in dead or damaged tissue where it releases toxins and enzymes that destroy muscle and skin. Its toxins and enzymes damage cells and spread the infection, resulting in tissue necrosis if not treated with antibiotics.
Neisseria meningitidis is an aerobic, gram-negative coccus that appears in pairs and can cause meningitis or meningococcemia. There are 8 major serogroups, with A, B, and C being most common. It normally lives harmlessly in the nasopharynx of 5-15% of the population but can spread via respiratory droplets. It uses pili to adhere to epithelium and enter the bloodstream, where it can proliferate rapidly and release endotoxins, activating the complement and coagulation cascades and potentially causing septic shock. Symptoms of meningitis include fever, neck stiffness, and headache, while meningococcemia presents with fever,
Nocardia are aerobic, gram-positive bacteria that are ubiquitous environmental saprophytes found in soil. They cause opportunistic infections in both immunocompromised and immunocompetent individuals. Nocardia infections can manifest as cutaneous disease, pulmonary disease, disseminated disease, or central nervous system infections such as brain abscesses. Diagnosis involves microscopic examination of samples showing branching filaments, culture growth on selective media, and molecular techniques such as PCR and 16S rRNA sequencing. Treatment involves prolonged courses of antibiotics such as trimethoprim-sulfamethoxazole or amikacin depending on the species.
This document provides an overview of bacteriology concepts including definitions of aerobic and anaerobic bacteria. It discusses specimen collection and transport for aerobic bacteriology as well as the Gram stain procedure. Common aerobic agar media and identification of Gram positive cocci such as Staphylococcus, Streptococcus, and Enterococcus are summarized. Key details are provided about pathogenic species and their associated diseases.
This document provides information on Neisseria meningitidis, the bacteria that causes meningococcal meningitis. It describes the morphology and virulence factors of N. meningitidis, including its capsular polysaccharide and outer membrane proteins. The epidemiology, transmission, pathogenesis, clinical features, diagnosis and treatment of meningococcal meningitis are discussed in detail. Serious complications like meningococcemia and Waterhouse-Friderichsen syndrome are also summarized.
Staphylococcus is a genus of gram-positive bacteria that can cause a variety of infections and diseases in humans and other animals. Staphylococcus aureus is one of the most important species due to its ability to cause serious infections such as pneumonia, meningitis, endocarditis, toxic shock syndrome, and food poisoning. It produces several virulence factors like coagulase, hemolysins, enterotoxins and exotoxins that enable it to evade host defenses and cause tissue damage. Common diseases include skin and soft tissue infections like impetigo, folliculitis, boils; respiratory infections; food poisoning caused by enterotoxins; and toxic shock syndrome caused by toxic
Eschericia coli is a gram-negative, facultative anaerobic bacterium that is commonly found in the lower intestine of warm-blooded organisms. It can cause several types of infections including urinary tract infections, enteric infections like traveler's diarrhea, and other rare infections. Laboratory diagnosis involves microscopic examination of samples showing gram-negative bacilli, as well as culture-based identification using selective media and biochemical tests to confirm lactose fermentation and other properties. Treatment depends on the severity and type of infection, ranging from supportive care to antibiotics for serious complications.
This document provides an overview of Streptococcus bacteria, including characteristics, diseases caused, taxonomy, and methods for identification. Key points include:
- Streptococcus is a genus of spherical, Gram-positive bacteria that grow in chains. It includes over 50 species that are part of normal oral flora but can also cause diseases.
- Major diseases caused by different Streptococcus species include pharyngitis, pneumonia, toxic shock syndrome, and neonatal infections.
- Identification involves examining colony morphology on blood agar plates, microscopic appearance, and biochemical tests like catalase, optochin, and bile esculin tests.
- Classification is based on carbohydrate antigens identified through Lancefield grouping
This document provides information on the bacteria Proteus, including its characteristics, virulence factors, infections it causes, identification and treatment. It notes that Proteus is a gram-negative, motile bacillus that is commonly found in the intestines and can cause urinary tract and nosocomial infections. Its main virulence factors include urease production, which allows it to colonize the urinary tract, and fimbriae, which aid in attachment and colonization. Identification involves culturing on media like blood agar where it displays swarming motility and testing for properties such as being urease positive and oxidase negative. Treatment involves antibiotics like beta-lactams, aminoglycosides
Neisseria meningitidis, commonly known as meningococcus, is a Gram-negative bacterium that can cause meningitis and sepsis. It is a leading cause of bacterial meningitis, with highest incidence in children aged 1-5 years. The bacterium is usually carried harmlessly in the throat but can invade the bloodstream and brain. Symptoms of meningococcal disease include fever, headache, stiff neck and a rash. Timely treatment with antibiotics is crucial to recovery.
This document discusses Escherichia coli (E. coli), a common bacterium found in the intestines of humans and animals. It describes E. coli's morphology, identification, and ability to cause diseases like urinary tract infections, neonatal meningitis, and intestinal diseases. Prevention methods are outlined, including good hygiene practices like handwashing and thoroughly cooking meats to avoid transmission. Treatment focuses on fluid replacement rather than antibiotics in most cases unless the disease has progressed to a systemic stage.
This document provides information on the bacteria Neisseria gonorrhoeae and Neisseria meningitidis. It discusses their classification, characteristics, pathogenicity, epidemiology, laboratory diagnosis, treatment and prevention. Key differences between the two pathogens are that N. gonorrhoeae causes the sexually transmitted infection gonorrhea, while N. meningitidis can cause meningitis. Laboratory diagnosis involves culturing samples on selective media and identifying colonies based on morphology and biochemical tests. Treatment of gonorrhea now involves ceftriaxone or ciprofloxacin plus other antibiotics due to emerging resistance.
Adenoviridae is a group of medium sized, non-enveloped, double stranded DNA viruses that replicate and produce disease in the eye and in the respiratory, gastrointestinal and urinary tracts;
Klebsiella is a genus of Gram-negative, facultatively anaerobic, rod-shaped bacteria that is commonly found in soil and water. The most important species in medicine are K. pneumoniae, K. aerogenes, K. oxytoca, and K. rhinoscleromatis. K. pneumoniae is an opportunistic pathogen that can cause infections of the urinary tract, wounds, pneumonia, and sepsis. It is identified through Gram staining, growth on selective media, and biochemical testing. Treatment involves cephalosporins and aminoglycosides as Klebsiella often produces beta-lactamases making it resistant to ampicillin.
The complement fixation test (CFT) involves mixing antigen, antibody, and complement. If the antibody is specific to the antigen, it will bind and "fix" the complement, preventing it from lysing red blood cells. In a positive test, lysis does not occur, while a negative test results in lysis. CFT is used to detect antibodies against pathogens like syphilis, and can detect antibody levels below 1 microgram/ml. It has limitations like being time-consuming and labor-intensive. Variations involve using different complement sources or detection methods depending on the pathogen.
DNA Bar-code to Distinguish the SpeciesRoya Shariati
This document discusses DNA barcoding, which is a method for identifying species using short gene sequences from standardized portions of the genome. It provides background on Carl Linnaeus who established the system of classifying organisms, and discusses how DNA barcoding can be used to establish reference libraries to identify unknown specimens by comparing DNA sequences. While not intended to replace traditional taxonomy, DNA barcoding is presented as a useful tool that can help create a 21st century research environment for taxonomy.
bacterial systematics in the diversity of bacteriatanvirastogi16
This document provides an overview of bacterial systematics and taxonomy. It discusses the key concepts of classification, identification, nomenclature, and evolutionary relationships. The three main types of systematics are described as evolutionary, numerical, and phylogenetic. The importance of taxonomy is explained for effective communication, cataloging species, and aiding research. Key methods for bacterial classification discussed include phenotypic characterization, analysis of rRNA sequences, multilocus sequence analysis, restriction fragment length polymorphism, and fatty acid methyl ester profiling.
Haemophilus is a genus of bacteria that includes species normally found in the human respiratory tract as well as pathogenic species. H. influenzae is the most clinically important species and is a cause of pneumonia, septic arthritis, epiglottitis, and meningitis. H. influenzae is a small, non-motile, gram-negative coccobacillus that requires both Factor X and V for growth. Serotype b of H. influenzae causes the majority of invasive disease and was an important cause of childhood meningitis prior to the introduction of the Hib vaccine.
This document discusses the laboratory diagnosis of Staphylococcus, including sample collection, direct smear microscopy, culture techniques, biochemical reactions, antibiotic sensitivity testing, and typing of Staphylococcus aureus. Appropriate samples are collected based on the site of infection and transported to the laboratory for analysis. Direct smear microscopy can identify Gram-positive cocci clusters. Culture techniques help isolate and identify Staphylococcus colonies based on morphology and biochemical reactions provide further characterization. Antibiotic sensitivity testing determines effective treatment options and typing methods like bacteriophage typing are used for epidemiological purposes.
Most medically important family of non–spore-forming gram-negative rods.
Most species are normal flora of the GI tract. Salmonella, Shigella, and Yersinia are not normal GI flora.
Major cause of nosocomial infections
Diseases include UTIs, gastroenteritis, septicemia, food poisoning, wound infections, peritonitis, pneumonia, and meningitis
The family exhibits four serological characteristics:
O (somatic) antigen-A cell wall antigen-LPS (heat stable), Used for serological grouping of Salmonella & Shigella.
K (envelope) antigen-Capsular antigen (heat labile)
H (flagellar) antigen-Flagellar antigen-protein (heat labile), Used to serotype Salmonella.
Vi antigen-Capsular antigen of Salmonella Typhi-polysaccharide (heat labile), Role in preventing phagocytosis, may mask O Ag, removed by heating.
Enterobacteriaceae are facultative anaerobes, ferment glucose. Positive nitrate and catalase, non-hemolytic. Except for Plesiomonas, they are oxidase negative.
Corynebacterium diphtheriae is a gram-positive, club-shaped bacterium that causes diphtheria. It produces a powerful exotoxin that inhibits protein synthesis and causes the formation of pseudomembranes at infection sites. Diagnosis involves isolating the bacterium from throat swabs and performing biochemical and virulence tests. Treatment consists of antitoxin and antibiotics like penicillin or erythromycin. Active immunization with diphtheria, pertussis, and tetanus vaccine helps prevent diphtheria.
This document provides information on Bordetella, the bacteria that causes whooping cough. It discusses the three main Bordetella species (B. pertussis, B. parapertussis, B. bronchiseptica), their morphology, culture characteristics, antigenic structure, pathogenesis of whooping cough, laboratory diagnosis, and prophylaxis with DPT vaccine. The key points are that B. pertussis causes the most common form of whooping cough in children, has a distinctive paroxysmal cough stage, and is diagnosed through culture or PCR of respiratory samples and confirmed with specific staining or agglutination.
Clostridium perfringens is a gram-positive, anaerobic bacterium that can cause gas gangrene. It forms spores that allow it to survive in soil and intestines. C. perfringens produces several toxins that damage tissues and cause diseases like gas gangrene. The bacterium thrives under low-oxygen conditions in dead or damaged tissue where it releases toxins and enzymes that destroy muscle and skin. Its toxins and enzymes damage cells and spread the infection, resulting in tissue necrosis if not treated with antibiotics.
Neisseria meningitidis is an aerobic, gram-negative coccus that appears in pairs and can cause meningitis or meningococcemia. There are 8 major serogroups, with A, B, and C being most common. It normally lives harmlessly in the nasopharynx of 5-15% of the population but can spread via respiratory droplets. It uses pili to adhere to epithelium and enter the bloodstream, where it can proliferate rapidly and release endotoxins, activating the complement and coagulation cascades and potentially causing septic shock. Symptoms of meningitis include fever, neck stiffness, and headache, while meningococcemia presents with fever,
Nocardia are aerobic, gram-positive bacteria that are ubiquitous environmental saprophytes found in soil. They cause opportunistic infections in both immunocompromised and immunocompetent individuals. Nocardia infections can manifest as cutaneous disease, pulmonary disease, disseminated disease, or central nervous system infections such as brain abscesses. Diagnosis involves microscopic examination of samples showing branching filaments, culture growth on selective media, and molecular techniques such as PCR and 16S rRNA sequencing. Treatment involves prolonged courses of antibiotics such as trimethoprim-sulfamethoxazole or amikacin depending on the species.
This document provides an overview of bacteriology concepts including definitions of aerobic and anaerobic bacteria. It discusses specimen collection and transport for aerobic bacteriology as well as the Gram stain procedure. Common aerobic agar media and identification of Gram positive cocci such as Staphylococcus, Streptococcus, and Enterococcus are summarized. Key details are provided about pathogenic species and their associated diseases.
This document provides information on Neisseria meningitidis, the bacteria that causes meningococcal meningitis. It describes the morphology and virulence factors of N. meningitidis, including its capsular polysaccharide and outer membrane proteins. The epidemiology, transmission, pathogenesis, clinical features, diagnosis and treatment of meningococcal meningitis are discussed in detail. Serious complications like meningococcemia and Waterhouse-Friderichsen syndrome are also summarized.
Staphylococcus is a genus of gram-positive bacteria that can cause a variety of infections and diseases in humans and other animals. Staphylococcus aureus is one of the most important species due to its ability to cause serious infections such as pneumonia, meningitis, endocarditis, toxic shock syndrome, and food poisoning. It produces several virulence factors like coagulase, hemolysins, enterotoxins and exotoxins that enable it to evade host defenses and cause tissue damage. Common diseases include skin and soft tissue infections like impetigo, folliculitis, boils; respiratory infections; food poisoning caused by enterotoxins; and toxic shock syndrome caused by toxic
Eschericia coli is a gram-negative, facultative anaerobic bacterium that is commonly found in the lower intestine of warm-blooded organisms. It can cause several types of infections including urinary tract infections, enteric infections like traveler's diarrhea, and other rare infections. Laboratory diagnosis involves microscopic examination of samples showing gram-negative bacilli, as well as culture-based identification using selective media and biochemical tests to confirm lactose fermentation and other properties. Treatment depends on the severity and type of infection, ranging from supportive care to antibiotics for serious complications.
This document provides an overview of Streptococcus bacteria, including characteristics, diseases caused, taxonomy, and methods for identification. Key points include:
- Streptococcus is a genus of spherical, Gram-positive bacteria that grow in chains. It includes over 50 species that are part of normal oral flora but can also cause diseases.
- Major diseases caused by different Streptococcus species include pharyngitis, pneumonia, toxic shock syndrome, and neonatal infections.
- Identification involves examining colony morphology on blood agar plates, microscopic appearance, and biochemical tests like catalase, optochin, and bile esculin tests.
- Classification is based on carbohydrate antigens identified through Lancefield grouping
This document provides information on the bacteria Proteus, including its characteristics, virulence factors, infections it causes, identification and treatment. It notes that Proteus is a gram-negative, motile bacillus that is commonly found in the intestines and can cause urinary tract and nosocomial infections. Its main virulence factors include urease production, which allows it to colonize the urinary tract, and fimbriae, which aid in attachment and colonization. Identification involves culturing on media like blood agar where it displays swarming motility and testing for properties such as being urease positive and oxidase negative. Treatment involves antibiotics like beta-lactams, aminoglycosides
Neisseria meningitidis, commonly known as meningococcus, is a Gram-negative bacterium that can cause meningitis and sepsis. It is a leading cause of bacterial meningitis, with highest incidence in children aged 1-5 years. The bacterium is usually carried harmlessly in the throat but can invade the bloodstream and brain. Symptoms of meningococcal disease include fever, headache, stiff neck and a rash. Timely treatment with antibiotics is crucial to recovery.
This document discusses Escherichia coli (E. coli), a common bacterium found in the intestines of humans and animals. It describes E. coli's morphology, identification, and ability to cause diseases like urinary tract infections, neonatal meningitis, and intestinal diseases. Prevention methods are outlined, including good hygiene practices like handwashing and thoroughly cooking meats to avoid transmission. Treatment focuses on fluid replacement rather than antibiotics in most cases unless the disease has progressed to a systemic stage.
This document provides information on the bacteria Neisseria gonorrhoeae and Neisseria meningitidis. It discusses their classification, characteristics, pathogenicity, epidemiology, laboratory diagnosis, treatment and prevention. Key differences between the two pathogens are that N. gonorrhoeae causes the sexually transmitted infection gonorrhea, while N. meningitidis can cause meningitis. Laboratory diagnosis involves culturing samples on selective media and identifying colonies based on morphology and biochemical tests. Treatment of gonorrhea now involves ceftriaxone or ciprofloxacin plus other antibiotics due to emerging resistance.
Adenoviridae is a group of medium sized, non-enveloped, double stranded DNA viruses that replicate and produce disease in the eye and in the respiratory, gastrointestinal and urinary tracts;
Klebsiella is a genus of Gram-negative, facultatively anaerobic, rod-shaped bacteria that is commonly found in soil and water. The most important species in medicine are K. pneumoniae, K. aerogenes, K. oxytoca, and K. rhinoscleromatis. K. pneumoniae is an opportunistic pathogen that can cause infections of the urinary tract, wounds, pneumonia, and sepsis. It is identified through Gram staining, growth on selective media, and biochemical testing. Treatment involves cephalosporins and aminoglycosides as Klebsiella often produces beta-lactamases making it resistant to ampicillin.
The complement fixation test (CFT) involves mixing antigen, antibody, and complement. If the antibody is specific to the antigen, it will bind and "fix" the complement, preventing it from lysing red blood cells. In a positive test, lysis does not occur, while a negative test results in lysis. CFT is used to detect antibodies against pathogens like syphilis, and can detect antibody levels below 1 microgram/ml. It has limitations like being time-consuming and labor-intensive. Variations involve using different complement sources or detection methods depending on the pathogen.
DNA Bar-code to Distinguish the SpeciesRoya Shariati
This document discusses DNA barcoding, which is a method for identifying species using short gene sequences from standardized portions of the genome. It provides background on Carl Linnaeus who established the system of classifying organisms, and discusses how DNA barcoding can be used to establish reference libraries to identify unknown specimens by comparing DNA sequences. While not intended to replace traditional taxonomy, DNA barcoding is presented as a useful tool that can help create a 21st century research environment for taxonomy.
bacterial systematics in the diversity of bacteriatanvirastogi16
This document provides an overview of bacterial systematics and taxonomy. It discusses the key concepts of classification, identification, nomenclature, and evolutionary relationships. The three main types of systematics are described as evolutionary, numerical, and phylogenetic. The importance of taxonomy is explained for effective communication, cataloging species, and aiding research. Key methods for bacterial classification discussed include phenotypic characterization, analysis of rRNA sequences, multilocus sequence analysis, restriction fragment length polymorphism, and fatty acid methyl ester profiling.
This document discusses microbial diversity from morphological, structural, metabolic, and genetic perspectives. It describes the various shapes, sizes, structures, and metabolisms of microbes. Molecular and genomic methods for assessing diversity are also covered, including analysis of 16S rRNA, lipids, proteins, and whole genomes. The importance of microbial diversity for biogeochemistry, environmental issues, and potential applications are summarized.
The document discusses the topic of phylogenetics. It begins with definitions of key terms like phylogeny, phylogenetic tree, clade, and orthologous genes. It then provides examples of how phylogenetic methods are used in fields like epidemiology, conservation biology, and pharmaceutical research. The document also discusses choosing appropriate genetic sequences to use in phylogenetic analysis and introduces molecular clock models.
Microbial Taxonomy - Dr. R Subashkumar, Associate Professor in Biotechnology, Sri Ramakrishna College of Arts and Science (Autonomous), Coimbatore-641006
This document provides information on taxonomy of bacteria and archaea. It discusses their nomenclature, classification, and identification. It describes rules for naming bacteria and archaea and includes examples. It also discusses classification systems including artificial and phylogenetic approaches. Methods for taxonomy like numerical taxonomy, use of homologous genes for phylogenetic trees, and 16S rRNA are covered. Classification of major bacterial and archaeal groups is presented.
This document discusses taxonomy and classification of organisms. It describes how taxonomy involves classifying organisms into groups based on similarities and evolutionary relationships. There are three domains of life - Archaea, Bacteria, and Eukarya. Bacteria are prokaryotic cells that are classified based on characteristics like cell structure, staining properties, shape, and biochemical reactions. Proper classification and naming of bacteria according to taxonomic rules is important for effective communication among microbiologists and organizing biological knowledge.
Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, a...Jonathan Eisen
This document describes research into using metagenomic data to search for novel lineages in the tree of life. The researchers developed methods to search for deeply branching small subunit rRNA genes in Global Ocean Sampling data, but were unable to robustly identify any novel lineages due to difficulties aligning short, distantly related sequences. They had more success identifying novel branches in the RecA and RpoB gene families. Some novel sequences likely come from unknown viruses or ancient paralogs, while others may represent truly novel cellular lineages not previously characterized. Metagenomic analysis offers potential for discovering major undiscovered branches in the tree of life.
This document discusses microbial taxonomy and classification. It describes how taxonomy involves the classification, naming, and identification of organisms. Microbes are classified using both natural and polyphasic taxonomy, which incorporates phenotypic and phylogenetic analysis. Key methods for determining microbial relationships include analyzing nucleic acid sequences, genomic fingerprints, and protein sequences. Phylogenetic trees are used to represent evolutionary relationships between microbes.
Microbial taxonomy involves classifying microorganisms into taxonomic groups based on their similarities and differences. There are three domains of life - Archaea, Bacteria, and Eukarya. Within bacterial taxonomy, bacteria are classified based on various phenotypic and biochemical characteristics as well as genetic relationships. The ultimate goal is to delineate bacterial taxa and generalize knowledge about their characteristics.
Virus_Classification of plant virus in virusReddykumarAv
Virus classification is the process of naming viruses and placing them into a taxonomic system similar to the classification systems used for cellular organisms. Viruses are classified by phenotypic characteristics, such as morphology, nucleic acid type, mode of replication, host organisms, and the type of disease
8 chapter 10 a survey of the microbial worldUiTM Jasin
This document provides a summary of methods used to classify and identify microorganisms. It discusses the three domains of life (eukaryotes, bacteria, archaea) and how evolution, phylogeny, and ribosomal RNA comparisons help determine relationships between organisms. It then describes various morphological, biochemical, serological, and nucleic acid-based techniques used to classify and identify unknown microbes, including Bergey's manual, staining, biochemical tests, phage typing, fatty acid profiles, and DNA/RNA sequencing.
Classification and Nomenclature of Microorganisms.pptxasmafirdous5
1. Taxonomy is the classification, naming, and identification of microorganisms according to a standardized international system.
2. Classification involves organizing microbes into taxonomic groups based on their properties, nomenclature refers to naming taxa according to rules, and identification is using the classification to identify unknown microbes.
3. A Swedish botanist, Carolus Linnaeus, is considered the founder of modern taxonomy for developing the binomial nomenclature system of classifying organisms into genera and species that is still used today.
Taxonomy is the science of classifying organisms based on evolutionary relationships. It includes identification, nomenclature, and classification. Bacteria were originally classified as part of the plant and animal kingdoms but are now placed in their own domains. Carl Woese proposed classifying all life into three domains based on rRNA sequences: Archaea, Bacteria, and Eukarya. Each domain has distinct cellular features. Bergey's Manual is the standard reference for bacterial taxonomy and classification, which has evolved from phenotypic to phylogenetic approaches based on genetic analysis.
1.2-Classification of bacthhhf fteria(0).pptseraphimkassa
This document provides information on bacterial classification and nomenclature. It defines taxonomy as the science of classifying organisms in a hierarchical system up to the species level based on their similarities and differences. Bacteria are classified through phenotypic, analytical, and genotypic methods. Phenotypic classification is based on microscopic and macroscopic characteristics. Analytical classification examines cell composition. Genotypic classification analyzes genetic material. Bacteria are named using binomial nomenclature, with a capitalized genus name and lowercase species name (e.g. Staphylococcus aureus). The document also distinguishes between prokaryotic and eukaryotic cells, and covers bacterial morphology and staining techniques.
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Similar to Classification of Enterobacteriaceae family (20)
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2. Basis of Bacterial Classification
Taxonomy –the principles and practice of classifying
bacteria (OR)
The orderly classification of organisms based on
their presumed natural relationships
Classification –arrangement of strains into natural
groups (taxa)-phenetic(phenotypic and genetic) and
phylogenetic (OR)
The theory and process of ordering the
organisms, on the basis of shared properties, into
groups.
3. Nomenclature –allocation of names to
these groups
Identification-processes by which
unknowns are referred to known
taxa.
Species – a collection of bacterial cells which
share an overall similar pattern of traits in
contrast to other bacteria whose pattern
differs significantly .
4. Genus: represent natural evolutionary groups as
defined by techniques that actually measure
evolutionary distance and these natural groups share
phenotypic similarities that differentiate them from
other genera. OR
"a group of species which are grouped together for
convenience rather than because of a close
evolutionary relationship“.
A biogroup (synonym,biovar) is defined to be a
group of strains that have a common biochemical
reaction pattern, which is often unusual for the
particular species.
5. • Classification
• Organization into
groups
• Car
• Truck
• SUV
• Van
• Identification
• Distinguishing features
• Engine size
• Mileage
• Number of passengers
• Type of transmission
Nomenclature
Providing a formal name
Genus & species
Honda City
Maruti 800
Ambassador Nova
Fiat 1800D
Trinity of Classification,
Nomenclature, and
Identification =
TAXONOMY ( S.T.
Cowan)
6. PHENETICS
A method of natural classification. It
is based on empirical classification of
general characters.
It may or may not include genetic
information.
When it excludes genetic information
it is called PHENOTYPIC
CLASSIFICATION.
7. Methods of Classification
Historically, prokaryotes were classified on the basis
of their phenotype (morphology, staining reactions,
biochemistry, substrates/products, antigens etc). In
other words a phenotypic characterization was based
on the information carried in the products of the
genes. These classification systems were artificial.
Modern characterization is based on the information
carried in the genes i.e. the genome. This is genetic
information and can also tell us something about the
evolution of the organism. In other words
phylogenetics.
8. Phenotypic Classification:
Numerical Taxonomy
Adanson(1763), PHA Sneath (1957)
Mathematical and statistical methodology
A large number of tests (~100) are carried out
and the results are scored as positive or
negative. Several control species are included
in the analysis.
1 = trait is present, 0=absent
All characteristics are given equal weight and a
computer based analysis is carried out to group
the bacteria according to shared properties.
9. Numerical Taxonomy
It gives results that broadly coincide
with non-numerical classification.
Has been found useful for the study
of certain groups thought to be
difficult to classify like Rhodococcus
group.
11. DNA Base Composition
It denotes the relative amounts of G=C and
A=T amounts. Conventionally GC base
composition is used.
12. Melting curve for a double-stranded DNA molecule. As the
temperature is raised during the experiment, the double-
stranded DNA is converted to the single-stranded form and
the UV absorbance of the solution increases. The midpoint
temperature, Tm, can be calculated from the curve.
13. Graph showing the direct relationship between mol % G + C
and midpoint temperature (Tm) of purified DNA in thermal
denaturation experiments.
14. DNA Homology
DNA-DNA pairing ( Schildkraut 1961)
provide a great deal of information
about the relationship between
organisms at species level.
Not found useful in revealing broader
groups among bacteria.
Strains with values of 70% or
greater are considered to be the
same species.
15. 16s rRNA Gene Sequence
ADVANTAGES
Universal presence
16S rRNA gene is present in all bacteria
Large Subunit (LSU) gene is present in all
fungi
Gene structure
Conserved regions
identical in all microorganisms
used for PCR primer location
Divergent regions
different in many microorganisms
used for identification (sequencing)
16. Advantages
High content of information
500 bp sequence with 4 different bases
→ 4500
= 1 x 10301
variants
15 biochemical tests with “yes/no”
result
→ 215
= 3 x 104
variants
16S rDNA has become the Standard for
Taxonomic Classification.
## Gold Standard for species identification:
DNA-DNA homology.
17. 16s r RNA Methodology
First step:
Determination of the ribosomal RNA
gene sequence of an unknown
microorganism
Second step:
Comparison of the generated sequence
with the sequences of known
microorganisms present in a
database
19. Methodology
NCBI Genebank webpage
Nucleotide-Nucleotide BLAST (Basic Local
Alignment Search Tool) : Paste in the linear
sequence data and submit. Search is
performed and list of matches provided
~ 99%-100%: Species confirmed
~97% -99% : Genus confirmed, new
species
< 97% : New Genus, New species
20. Bacterial Species
1. If there is >70% homology based
on hybridization
2. Usually have 99%-100% rRNA
sequence identity
3. Less than 50
C difference in thermal
stability
Organisms with less than 98% 16S
rRNA sequence and < 70% DNA:DNA
are likely to be different species.
23. Detailed phylogenetic tree of the major lineages (phyla)
of Bacteria based on 16S ribosomal RNA sequence
comparisons
24. 16s rRNA Sequencing- Conclusion
Can better discriminate bacterial
isolates than many phenotypic
methods.
Can identify novel, poorly described,
rarely isolated, or phenotypically
aberrant strains
Can define relatedness of organisms
+ evolutionary distance.
Can be used for organisms that have
not been cultured (Uncultivable
bacteria).
25. International groups
International Committee for Systematic
Bacteriology (ICSB) supervises the
Bacteriological Code. It regularly provides list of
recent validly published species names and
proposed changes in nomenclature
First in Int J of Systematic Bacteriology
Then in Int J Of Systematic and Evolutionary
Microbiology
The status of the scheme is reviewed every 10
years in Bergey’s Manual of Systematic
Bacteriology (Latest edition 2001, Edition 2; 5
volumes. Vol 2 (2005) The Proteobacteria.
27. Enterobacteriaceae: the 1800s
The first member Serratia marcescens
was discovered by Bizio in 1823 on a
dish of Italian barley (Polenta).
After more than 50 years, Klebsiella
and Proteus were discovered in 1880s.
Theobald Smith in 1893: Lactose
Fermenter ( Benign
Organisms/Coliforms) and Non lactose
fermenters (Dangerous pathogens)
In 1897, third group- Paracolon bacilli
(Delayed lactose fermentation)
28. Enterobacteriaceae: 1900-1950
Gram negative facultative bacilli were being
discovered and named arbitrarily based on
place/person/some unique character.
( Bathesda –Ballerup, Providence groups/
Morgan’s bacilli/ Proteus etc) and
designated LF/NLF/ or Paracolon bacilli.
During the same time, two nondescript
genera were being used to house the
bacteria: Bacterium ( B.coli) and Bacillus
( B.cloacae).
29. 1900-1950
Otto Rahn in 1937 first proposed the name
Enterobacteriaceae family for a group of
biochemically and morphologically similar
organisms with a single genus
Enterobacter. It was used to put together
112 species.
The first publication of the Kauffmann-
White scheme (Salmonella Subcommittee,
1934,)listed 44 serovars of the Salmonella.
30. 1900-1950
Borman, Stuart, Wheeler (1944)
defined the family as :Gram-negative,
non-sporogenic rods widely
distributed in nature. Grow well on
artificial media. All species attack
glucose, forming acid or acid and
visible gas (H2 present).
Characteristically, nitrites are
produced from nitrates. When
motile,the flagella are peritrichous.
31. 1900-1950
They proposed 8 genera in this family:
Genus I Serratia Genus V Shigella
Genus II ColobactrumGenus VI Paracolobactrum
Genus III Proteus Genus VII Erwinia
Genus IV SalmonellaGenus VIII Proshigella
33. 1950 1970
During this period various other
methods were used for identification
and classification:
1. Chemotaxonomy (Gas liquid
chromatography for Fatty acids)
2. Carbon utilization assay
3. Phage typing
4. Antigenic types etc.
34. 1970- Till Date
Don Brenner at CDC in early 1970s
pioneered the use of DNA-DNA
hybridization as the gold standard for
defining relatedness. This, together with
Numerical taxonomy had two important
effects:
1. A number of organisms regarded as
separate species were found to be single
genomic species. EX: E. coli and Shigella,
All salmonella
2. Recognition of numerous new species
previously thought to be aberrant biotypes
of particular species.
35. 1970- Till date
The advent of 16s rRNA sequencing helped in
identifying many clinical and environmental isolates to
species level, unidentifiable by conventional methods.
In 1972, there were 11 genera and 26 species.
In 1985, 22 genera, 69 species
In 2004, 40 genera, and 200 species.
At present, 47 genera (http://www.bacterio.cict.fr)
Type Genus: Escherichia
Type Species: E.coli
36. 1970- Till date
Farmer JJ et al in 1985 reviewed all
the existing genera and species of the
family and described their phenotypic
characters.
It has a series of differential charts
to assist in identification and a large
chart with the reactions of 98
different organisms for 47 tests often
used in identification.
37. Proposed Changes
Inclusion of the Genus Plesiomonas : Based on 16s
rRNA sequence, it is closer to Enterobacteriaceae than
Vibrionaceae family. It also contains the common
enterobacterial antigens.
Klebsiella to Raoultella : Three species K.terrigena,
K.ornithinolytica, K.planticola .
Calymmatobacterium granulomatis to genus
Klebsiella: This is an un-cultivable bacteria . Shares
nucleotide sequences with Klebsiella, and the disease
Granuloma inguinale resembles rhinoscleroma.
38. Proposed Changes
SALMONELLA
Good agreement on some issues, but still with
several problem areas.
All serotypes of Salmonella probably belong to on
DNA hybridization group.
The genospecies was named S. cholerasuis, and later
changed to S. enterica. (1982)
Seven subgroups (subspecies): enterica, salamae,
arizonae, diarizonae, houtenae, bongori, and indica.
Subgroup Bongori should be elevated to species level
based on DNA hybridization and MLEE studies.
(1989).
39. Proposed Changes
Citrobacter diversus and C. koseri
Both the names have been used, but C.
diversus have been used more frequently.
In 1980, C. diversus became the correct
name for this organism, but in 1993 ICSB
issued an opinion that C. koseri should be
used.
Both have similar properties, but different
type strains exist.
40. Proposed Changes
Enterobacter sakazakii
Enterobacter sakazakii was defined as
a new species in 1980
In the original study fifteen biogroups
of E. sakazakii were described
Full length 16S rRNA gene sequences,
comprising greater than 1300bp has
been done along with DNA
hybridization.
41. Proposed changes
These organisms are a microbiological
hazard
Occurring in the infant food chain with
historic high morbidity and mortality in
neonates.
Therefore Cronobacter gen. nov. has been
proposed after the Greek mythological god,
Cronos, who was described as swallowing
his children at birth.
(Iversen et al. BMC evolutionary Biology, 2007)
42. What the future holds?
Taxonomy is a dynamic and ongoing
process.
New species and genera will continue to be
added.
A number of named organisms are known
to contain multiple species although the
phenotypic methods cannot unambiguously
separate them. Ex. E.cloacae,
H.alvei,Rahnella aquatilis, Serratia
liquefaciens.
43. Future
The increasing knowledge concerning
Enterobacteriaceae will continue to
challenge the microbiologists to
redefine and re evaluate the concepts
regarding the biochemical
characteristics, ecologic relationships,
biosphere distribution, and disease
producing potential of this family.
44. The Silver Lining
Many of the new organisms may never be seen in a
given clinical microbiology laboratory, but will be
encountered more frequently by reference
laboratories.
80 to 95% of all isolates seen in a general hospital
setting will be Escherichia coli, Klebsiella pneumoniae,
or Proteus mirabilis.
Over 99% of all clinical isolates will belong to only 23
species.
Keep this distribution in mind and not be
overwhelmed with the large number of new species.
Adage: "When you hear hoofbeats, think horses, not
zebras.”
45. References
1. Topley and Wilson’s Microbiology: 8th
and 10 th
edition.
2. The Enterobacteria By J. Michael Janda, Sharon L.
Abbott. 2006. ASM.
3. Borman EK , Stuart CA AND Wheeler KM. Taxonomy
of the family Enterobacteriaceae. J Bacteriol
1944;48:351-367.
4. Farmer JJ III, Davis BR, Hickman-Brenner FW.
Biochemical Identification of New Species and
Biogroups of Enterobacteriaceae Isolated from
Clinical Specimens. J Clin Microbiol 1985;21:46-76.