Bacteriology Notes Summary PDF

Microbiology encompasses the study of microorganisms, including bacteria, fungi, algae, protozoa, and viruses, focusing on their roles in health and disease. Bacteria are classified by shape (cocci, bacilli, spirilla) and can be gram-positive or gram-negative, each with distinct structural characte...

Microbiology encompasses the study of microorganisms, including bacteria, fungi, algae, protozoa, and viruses, focusing on their roles in health and disease. Bacteria are classified by shape (cocci, bacilli, spirilla) and can be gram-positive or gram-negative, each with distinct structural characteristics. Fungi are categorized into yeasts, molds, and dimorphic fungi, with various reproductive strategies and significant roles in both pathogenic and beneficial contexts. Medical microbiology examines pathogenic organisms and their relationship to diseases, emphasizing diagnosis through sampling, culturing, and serological methods. Industrial and agricultural microbiology utilize microorganisms for food processing, fermentation, and soil fertility, highlighting their economic importance. Food Microbiology is used in food processing and food ripening and are not pathogenic. It also can cause food poisisng such at s. aureus and e. coli. They can cause food poising as well. Pharmaceutical miicobiology It's the use of M.O. in the production of pharmaceutical products such as antibiotics, alcohols, enzymes and vitamins. **Agricultural Microbiology:** Studies the N (nitrogen), C (carbon) and S (sulfur) cycle in nature **Environmental microbiology (microbial ecology):** concern about pollution of soil, air, water, sewage, food and dairy products cycling of elements by microbial, environmental and geochemical processes. What is the significance of microbial classification? **Classification allows researchers to categorize microorganisms, facilitating the study of their characteristics, behaviours, and roles in various ecosystems and health.** How do antibiotics work against bacterial infections? **Antibiotics target specific bacterial functions or structures, such as cell wall synthesis or protein production, inhibiting their growth and reproduction** What are the primary differences between gram-positive and gram-negative bacteria? **Gram-positive bacteria have a thicker cell wall without an outer membrane, while gram-negative bacteria possess a thinner cell wall and an outer membrane containing lipopolysaccharides.** Why are fungi important in both pathogenic and beneficial roles? **Fungi can cause diseases in humans and plants but also play crucial roles in decomposition, nutrient cycling, and food production through fermentation processes.** **Food microbiology** Can cause food infections and poisoning by S. aureus and E. coli, they can cause food spoilage. Preservation of food eg. Jamming, salting and freezing **Fungi** - Eukaryotic (have membrane-bound nucleus) - Obtain food from other organisms - Possess cell walls 🞄 Molds -- multicellular; have hyphae; reproduce by sexual and asexual spores 🞄 Yeasts -- unicellular; reproduce asexually by budding; some produce sexual spores **Protozoa** - Single-celled eukaryotes  **Algae** Unicellular or multicellular Categorized on the basis of pigmentation, storage products, and composition of cell wall e.g. purple sulphur algae **\ ** **Bacteria size is 0.3 to 5 uv micrometers** - three basic forms: **cocci, straight rods, and curved or spiral rods** - Nucleoid consists of a very **thin, long, circular DNA molecular double strand that is not surrounded by a membrane** - The **cytoplasmic membrane harbors numerous proteins**, such as permeases.( substance that catalyzes the transport of another substance across a cell membrane.) - The **membrane is surrounded by the cell wall**  **Cytoplasm** - The cytoplasm contains a large number of solute low- and high-molecular- weight substances, RNA and approximately 20 000 ribosome per cell - Bacteria have **70S ribosome comprising 30S and 50S subunits** - **Bacterial ribosome** function as the organelles for protein synthesis - The cytoplasm is also frequently used to store reserve substances (glycogen depots, polymerized met phosphates, lipids) Mycology Fungi eukaryotic microorganisms The **basic morphological element of filamentous fungi is the Hypha** and a web of **intertwined hyphae is called a mycelium.** - The **basic form of a unicellular fungus is the yeast cell** **Dimorphic fungi usually assume the form of yeasts in the parasitic stage and the form of mycelia in the saprophytic stage (obtain nutrients by decomposing dead organic material).** - **Dermatophytes: causes skin disease in animals and humans** - **yeast: solitary cells that reproduce by budding** - **Mold: hyphae with dust-like spores** - **Dimorphic :can either have a mold or yeast-like state** The **saprophytic fungi** take carbon compounds from dead organic material whereas **biotrophic fungi** (parasites or symbionts) require living host organisms - **Dermatophytes**: - **Species Example**: *Trichophyton rubrum* - **Description**: Dermatophytes responsible for infections like athlete\'s foot, jock itch, and ringworm. Dermatophytes primarily infect keratinized tissues such as skin, hair, and nails. - **Mold**: - **Species Example**: *Aspergillus fumigatus* - **Description**: This is a common mold that can be found in the environment and is capable of causing aspergillosis (infection of the lungs), particularly in individuals with weakened immune systems or pre-existing lung conditions. - **Dimorphic Fungi**: - **Species Example**: *Histoplasma capsulatum* - **Description**: *Histoplasma capsulatum* exhibits dimorphism, meaning it can exist as a mold in the environment and as a yeast-like form in host tissues. It is the causative agent of histoplasmosis, a respiratory infection that can become systemic in severe cases. **Two morphological forms of fungi are observed: Hypha (mold), Yeast** - **Hypha:** this is the basic element of filamentous fungi with a branched, tubular structure - **Mycelium:** this is the web or mat like structure of hyphae. **Substrate mycelia** (specialized for nutrition) penetrate the nutrient substrate, whereas **aerial mycelia** (for asexual propagation) develop above the nutrient medium - **Fungal thallus:** this is the entirety of the mycelia and is also called the fungal body or colony. SPORES **ASEXUAL** - Arthrospore-common in some dermatophytes like *Coccidioides immitis*. Generates from hypae fragments - Blastospore-Asexual and is produced by budding eg such as *Candida albicans*, - Chamydospore- thick-walled spores that form within the hyphae and are seen in species like *Candida albicans* and *Histoplasma capsulatum*. - Conidia: are asexual, non-motile spores that are produced by many different types of fungi - Microconidia Microconidia are small, single-celled conidia, found in species like *Trichophyton* and *Fusarium*. - Macroconidia Macroconidia are larger, multicellular conidia, often with a more complex shape, such as spindle or club-shaped. They are also produced by fungi like *Trichophyton* and *Fusarium* Topographic grouping of fungi Superficial- Grows on the outer most layer of the skin and hair. No inflammatory response due to it being remote from living tissues. Contaneous- In keratin of skin, hair, and, nails. Causes diseases such as dermatophytosis or dermatomycosis, They are responsible for eczema interruptions. Subcutaenous- Involve in the deep layer of the skin and muscle tissue. **Systemic -** Attack the deep tissues and organ systems; often creating symptoms that resemble other diseases eg *Histoplasma capsulatum, Blastomyces dermatitidis, Coccidioides immitis, Paracoccidioides braziliensis* Lecture 2- General Sampling Techniques Samples are collected on clinical signs - Samples should be obtained from the edge of lesions and some macroscopically normal tissue included - Microbial replication will be most active at the lesion's edge - It is important to collect specimens as **aseptically** as possible, otherwise the relevant pathogen may be overgrown by numerous contaminating bacteria In certain circumstances a guarded swab should be used to bypass an area with a large population of normal flora. **LECTURE 3** **Staphylococci is gram positive.** **S. aureus lives in the respiratory tract and skin** **S. Epidermidis lives on skin and in mucous membrane.** **S. Hominis lives in the sweat glands** **S. Capitis lives on scalp and face and external ears** **S. Saprophyticus lives on the skin, intestine and vagina** **General characteristics** **Lack spores and flagella** **May have capsules spherical cells arranged in irregular shapes.** **Commonly found in the skin and mucous membrane** ***S. aureus* (left) and *S. epidermidis* (right) on mannitol salt agar. Most pathogenic bacteria, other than the staphylococci, are inhibited by the 7.5% NaCl. Coagulase-positive strains usually ferment the mannitol producing a pH change from pink to yellow. (Phenol red indicator).** **Cultural characteristics** Grow in large, round colonies at 37 ^0^C , facultative anaerobe, best seen in blood agar and is surrounded by the hemolysis. Withstands high salts and extremes in pH. **Biochemical Properties** Produces many virulence factors eg, enzymes and toxins **Virulence factors of S. aureus** **Enzymes** **Toxins** ---------------------------------------------------------- --------------------------------------------------------------------------------------------------- **Cogulase cause plasma and blood to clot** **Hemolysins Lyse red blood cells** **Hyaluronidase digest connective tissue** **Leukocidin Lyses neutrophils and macrophages** **Staphylokinase disgets blood clots** **Enterotoxin Induce gastrointestinal distress** **DNase digest DNA** **Extfoliative toxin seperates epidermis and dermis** **Lipases digest oils and enhance colonization on skin** **TSST Toxic shoc syndrome Toxin Induces fever and vomitti ng and shock, systemic organ damage.** **Penicillinase activates penicillin** **Pathogenesis - the origination and development of a disease** Carriage rate for healthy adults is 20 -60 %, Present in mostly humans environment. Mosltly on the skin and nasopharynx and intestine. Staphylococcal Disease Localized cutaneous infections- invade skin through wounds, follicles and glands. Systematic infection- Osteomyelitis- done infection Bacteremia- transfer of bacteria from one infected site to the next eg. Endocarditis Toxegenic Diseases Food intoxication- Ingestion of heat stable enterotoxins and gastrointestinal distress Staphylococcal scaled skin syndrome- Indues bright red flush and blisters Toxic shock syndrome- toxemia leading to shock and organ failure. Laboratory Diagnostics Found in urine, pus, blood and tissue exudates Types of diagnosis Gram staining- Gram positive bacteria is found in clumps. Culture- Uses blood agar. 10ml of venous blood is inoculated in 50ml glucose broth. Haemolysis and yellow pigmentation suggest S. aureus. Coagulase test 1 rnight broth suspension mixed with human plasma 1ml an incubated at 37 oc and left for 3 to 6 hours.   **Treatment** **Penincillin and ampicillin. Cephalosporins are drug of choic in case of penincillin resistabce.** **Prevention of Staphylococcal Infections** **Universal precautions by heathcare providers to prevent nosocomial infections** **Hygiene and cleasing.**  A close-up of a text Description automatically generated   A close-up of a list of drugs Description automatically generated  A close-up of a list of medical information Description automatically generated  **Lecture 4** Streptococcus spp. Mastistis / Strangles Streptococci and enterococci are both gram positive. They are facultative anaerobes and catalase negative, oxidase neg. and non motile. Streptococci use blood or serum media to grow. Can form capsules, Sensitive to drying, heat and disinfectants. Enterococci tolerates Mac Conkey agar and appears as small pin-point colonies on this agar. **Pathogenisis** **1. Adehesion and colonization**- Streptococci adhere to epithelial surfaces using adhesins, enabling them to colonize tissues, such as the respiratory tract in horses (Streptococcus equi) or the respiratory and CNS in pigs (Streptococcus suis). **2. Immune Evasion.** Streptococci evade immune defenses with: ○ Capsules that prevent phagocytosis. ○M-proteins that block complement activation. ○ Streptolysins that lyse host cells. **3. Tissue Damage**- Enzymes (e.g., hyaluronidase, streptokinase) help break down host tissues, allowing deeper infection, while exotoxins cause inflammation and damage, as seen in strangles caused by S. equi. **4. Systemic spread**- Bacteremia can lead to systemic infections like septicemia, meningitis, and endocarditis (S. suis in pigs, S. agalactiae in cows with mastitis). 5**. Virulence Factors**- Capsule, streptolysins, exotoxins, and enzymes help streptococci evade host defenses, invade tissues, and cause disease. Streptococcal infections in animals include strangles in horses, mastitis in cows, and meningitis in pigs, highlighting the bacteria's wide-ranging impact in veterinary medicine. **S.Pyogenes** Most serious streptococcal pathogen. It a parasite and inhabits throat, nasopharynx, occasionally skin. **Morphology-** Gram-positive Spherical/ ovoid cocci arranged in long chains. Non motile. Can form capsules. **Cultural Characteristics** Facultative anaerobes, Best growth achieved at pH 7.4-7.6 at a temp.37^0^C. ** ** Required enriched media for growth. Colonies are around 1mm in diameter, surrounded by a zone of clear hemolysis, semi transparent and vary in appearance. **Virulence factors of S. Pyogenes** ►Enzymes: Streptokinase - digests fibrin clots Hyaluronidase - breaks down connective tissue DNase - hydrolyzes DNA ►Toxins: Streptolysins (hemolysins) :- streptolysin O (SLO) and streptolysin S (SLS) - both cause cell and tissue In Jury. Erythrogenic toxin (pyrogenic):- Induces fever and typical red rash. Superantigens:- Strong monocyte and lymphocyte stimulants; cause the release of tissue necrotic factor. **Pathogenesis.** Humans are the only reservoir. In apparent carriers.(visible carriers of toxins and enzyme) Transmission is through contact, droplets, food, fomites Portal of entry is generally through skin or pharynx. Children are predominant group affected for cutaneous and throat infections Systemic infections and progressive diseases may occur if untreated. **S. Pyogenes diseases.** Impetigo (pyoderma)- It is a skin infection \\t\\Tith superficial lesions that break and form highly contagious crust. Throat infections Rheumatic fever - It has subclinical pharyngitis in children; carditis \\t\\Tith extensive heart valve damage possible, arthritis, chorea, fever. Acute glomerulonephritis - It is the inflammation of the nephrons. **Laboratory Diagnosis** Isolated from skin, throat, sputum, urine and blood. Gram staining- gram positive Culture- The organism is cultured on blood agar with an added bacitracin antibiotic disk to show beta-hemolytic colonies and sensitivity (zone of inhibition around the disk) for the antibiotic. Catalase test- A positive result is the rapid evolution of oxygen (within 5-10 sec.) as evidenced by bubbling. A negative result is no bubbles or only a few scattered bubbles. S. Pyogenes are catalase ne ative. **Treatment** treated with penicillin Erythromycin is recommended for patients who are allergic to penicillin. **STREPTOCOCCUS PNEUMONIAE** **Morphology** They are gram positive cocci., Measures 0.5 - 1.25 µm, Non motile and non sporing Capsulated, Small, oval-shaped cells arranged in pairs and short chains. Cultural characteristics Blood or chocolate agar, Growth improved by 5-l0o/o CO2, Facultative anaerobes. Best growth achieved temperature 25 - 40° C. Colonies are surrounded by greenish hemolysis under aerobic conditions and clear under anaerobic conditions. **Biochemical properties** No significant toxin is produced in pneumococc1. Presence of some of the extra cellular products -Haemolysin, Immunoglobilin Al protease, N euraminidase, Hyaluronidase Lack catalase and peroxidases. Ferment glucose, lactose and sucrose with production of acid. **Pathogenesis** 5-50% of all people carry it as normal flora in the nasopharynx. Young children, elderly, immune compromised, those with other lung diseases or viral infections, are at risk. Gains access to middle ear by way of eustachian tube. **Pneumococci diseases** Pneumonia : infection of lung parenchyma. Otitis media : infection of middle ear **Laboratory diagnosis** Isolated from blood wound, CSF, sputum, Gram staining ! Quellung test Culture -The organism is cultured on blood agar or chocolate agar with incubation in an environment of carbon dioxide. The organism is cultured on blood agar with an added optochin disk to show alpha-hemolytic colonies Catalase test-S. pneumococci is catalase negative **TREATMENT AND PREVENTION** Traditionally treated with penicillin G or V. Broad spectrum antibiotics are recommended for patients who are allergic to penicillin. Two vaccines available for high risk individuals: -Capsular antigen vaccine for older adults and other high risk individuals - effective 5 years. -Conjugate vaccine for children 2 to 23 months **S. VIRIDANS** It is alpha haemolytic streptococci. It is oval in shape and found in short chains. It has six species groups (viridans group);S.mutans, S. oralis, S. salivarus, S. sanguis, S. milleri, S. mitis Found in gums and teeth, oral cavity, and also in nasopharynx, genital tract, skin. Not very invasive; dental or surgical procedures facilitate entrance. It causes dental caries, sepsis and endocarditis. Persons with preexisting heart conditions should receive prophylactic antibiotics before surgery or dental procedures. **S.Fecalis** It is also known as enterococci. It is a Gram-positive Oval cocci in pairs or short chains. Identified in MaConkey agar. Colonies are magenta in color and pin point. It can grow in the range of 10 to 45°C and survive at temperatures of 60° ( for 30 min. It is non-motile, facultative anaerobic microbe. It ferments glucose and does not produce a catalase. It is associated with urinary tract infections, biliary tract infections, septicemia, endocarditis and intra abdominal abscess. Aminogycosides are drug of choice. **Lecture 5** Staining method 1 Acidic -- Nidrosin, Malachite green and Acid Fuchsin. 2 Basic Crystal violet, Methylene blue, Safranin and Basic fuchsin 3 Neutral -- Giemsa, Lesihman and Wright Simple staining includes flooding slid with methylene blue for 5 to 10 mins. Wash off stain and sowly running tap water. Allow to dry Then add immersion. Differentional staining. -2 dye are used for this organism. Types of staining Gram staining method Acid fast stain ( zeihl neelsen method) Spore stain Culture medium Culture media is used for recognition and identification of microorganism. Types of culture **Physical State**- Liquid mediua eg. Nurtient broth ,peptone water. Primarliy used for cultivation. **Solid media.** Eg Mac conkey, blood, and nutrient agar. Used for bacteria cultivation **Semisolid media**- used to cultivate spirochetes and study motility. Ans have 0.4-0.8 agar agar % According to the media usage **Simple or basal media** eg. Nutrient agar and nutrient broth. **Special purpose media-** eg enriched, differential, transport, sensitivity. **Enriched media**- Simple media enriched with appropriate subs. 3g blood, glucose, serum and ascetic fluid. Chocolate **Selective Medi**a- contains inhibitory substance. Eg bile salt, antibiotics. They either grow or inhibit growth of certain organisms, eg mac cokey agar, potassium tellurite agar. **Differential media**- They allow certain characteristic grow and is recognized easily. Eg hemolytic and non hemolytic. **Mac Conkey differs between lactose and non lactose fermenter gram positive bacilli** Antibotic suseceptibility testing on Mueller hinton agar is used to know the appropriate antimicrobial agent to use treat causative bacteria. **Disk diffusion test-** The culture media is inoculated by the pathogenic bacteria and a paper discs impregnated by a different type of antibiotic. Incubated at 37 0c for 24 to 48 hurs. Results- A zone of inhibition no growth, sensitive to the agent. If the growth is at the edge then it is resistant to the antimicrobial drug.  Types of culture Streak plate method -- Uses isolation of pure culture of bacteria and mixed population. Eg. Urine Techniques include. Sterilize loop in benzene and streak specimen a Re sterilize and cool, and streak B from where A stops Continue until C and D are completed Incubate at 37 0c for 24 hurs. Pour plate method -- Serial dilution of specimen and mixed with melted media. Then pour th content within sterile plates Cultural characteristics Growth requirement Colonial morphology -- Size measured in mm, shape,( circular, irregular), Elevation( concave or convex), Margin ( filamentous or lobulated), Consistency ( dry or mucoid), surface texture( rough, smooth), Color of pigmentation, Optical density( translucent or opaque), Changes in the inoculated medium, odor **Stock culture** Means they can reserve microorganism in a culture for future study and can last up to 1 month at 4 0c. Technique of stock culture. Uses universal bottle containing medium in slanted position. Using sterile loop to inculate the surface of the medium of a few culture Incubate at 37 0c for 24 hrs and store at 4oc.