Microbiology NURS 1111 Classification PDF

Unit 2 -- MAIN GROUPS OF\ MICRO-ORGANISMS **MICROBIOLOGY** **NURS 1111** **OBJECTIVES:** - **A) List the characteristics of each group of micro-organisms** - **B) Identify the structures that are unique to each group of micro-organisms** - **C) Note the main groups of micro-organisms...

Unit 2 -- MAIN GROUPS OF\ MICRO-ORGANISMS **MICROBIOLOGY** **NURS 1111** **OBJECTIVES:** - **A) List the characteristics of each group of micro-organisms** - **B) Identify the structures that are unique to each group of micro-organisms** - **C) Note the main groups of micro-organisms of medical importance** - **D) Investigate emerging micro-organisms** **Recap:** - **Major classes of Microorganisms** - Bacteria - Viruses - Fungi - Algae - Protozoa Taxonomy - Is defined as the science of biological classification consist of 3 separate but interrelated parts: - Classification - Nomenclature - Identification - Once a classification scheme is selected, it is used to group organisms into groups called taxa base om mutual similarity Taxonomy NOMENCLATURE - It is the branch of taxonomy concerned with the assignment of names to taxonomic groups in agreement with published rules IDENTIFICATION - The practical side of taxonomy which determine if te isolate belongs to the recognised taxon Systematics Bacterial Taxonomy Based on *Bergey's Manual* - *Bergey's Manual of Determinative Bacteriology* -- five volume resource covering all known procaryotes - - - CAROLUS LINNAEUS - CAROLUS LINNAEUS developed the first natural classification based largely on anatomical characteristics in the mid 18 th century - In practice the genus and specie of a new prokaryote was determines - phenetic classification - Phylogenetic - Genotypic Comparison of the three domains Classification Systems in the Procaryotae - Microscopic morphology - Macroscopic morphology -- colony appearance - Physiological / biochemical characteristics - Chemical analysis - Serological analysis - Genetic and molecular analysis - - - **Characteristics -- provides data for identification and classification** - **BACTERIA** - Smallest living cells (0.1 to 10µm) - About 5,000 species known - Occur in almost any natural habitat - Some species may have many different strains - More than 90% either harmless or beneficial to humans  - Can be grown in artificial culture **Morphology of Bacteria** - Prokaryotic - no membrane-bound organelles - Cytoplasmic membrane surrounded by rigid cell wall (peptidoglycan), capsule or slime with flagella, pili/fimbriae - Cytoplasm contains ribosomes, mesosomes, double-stranded DNA chromosome, inclusion bodies - Free-living, tiny metabolic factories which synthesize proteins - Lack of a cell nuclues - Nucleoid - - Plasmids - - Typical bacterial cell **Shapes** - Different species of bacteria possess different shapes, and they are classified according to these shapes. - Cocci (Spherical) - Bacilli (Rods) - Spirochetes (Spiral) - Vibrio (curved) **Motility** - Bacteria that are able to 'swim' are said to be **motile**; while those unable to 'swim' are **nonmotile**. - This movement is due to the presence of a **flagella** or **axial filament.** **Nutrition and Growth** - Most BACTERIA are **[PARASITES]**; they get their energy by consuming live Organic Matter as a source of Nutrition. - **[HETEROTROPHS]** break down materials that they obtain from other organisms, such as dead or decaying material. These bacteria are called **[SAPROPHYTES]**. - **[AUTOTROPHS]** obtain their energy by making their own food from SUNLIGHT OR MINERALS. Nutrition & Growth cont'd - Bacteria that use oxygen during cellular respiration are called **[AEROBES].** - Those that do not use oxygen are called **[ANAEROBES.]** (energy is typically obtained through fermentation. - **[OBLIGATE AEROBES]**  are bacteria that cannot live without oxygen. -  **[OBLIGATE ANAEROBES]** - bacteria that CANNOT live in the presence of oxygen. -  **[FACULTATIVE ANAEROBES]** -- can use oxygen when it is available, but they do not depend upon it. Nutrition & Growth cont'd - Most bacteria grow BEST at a pH of 6.5 to 7.5 pH affects the rate of enzyme action. - Bacteria have varying temperature requirements for growth. - - - - **Reproduction** - Predominantly asexual by binary fission - **Reproduction** - Endospore formation - - - - Formation of Endospore - DNA is aligned into long filament - Duplicate and divide into two, cytoplasmic membrane begins to invaginate - DNA completely surrounded by membrane - Cortex form and initial spore coat form - Mature spore forms - The cell wall lyses releasing the endospore Other reproductive methods -  BACTERIA CAN EXCHANGE GENES BY ONE OF **THREE SPECIAL MEANS**: **[CONJUGATION, TRANSFORMATION, OR TRANSDUCTION]** - **Conjugation** Part of a chromosome is transferred from donor cell to recipient through pilus Requires contact between the donor and recipient Transfer only in one direction **Conjugation\ ** - Cell to cell contact - **Transformation** Living cell picks up fragments of DNA released by dead cells (Streptococci pneumoniae) DNA is transferred as "naked" DNA - **Transduction** Fragments of DNA carried from one cell to another by viruses **VIRUSES** - **Viruses --are simple nucleo-protein complexes which infect and replicate in living cells (parasitic at genetic level)** - **Smallest biological entity** - **Exist throughout nature and can affect plants, humans, animals, birds, insects, rodents, bacteria** - **Ultra-microscopic (10-300 nanometre (nm)** -  equal to one billionth of a [metre] (0.000000001 m) - **Ultra-filterable agents (viruses can pass through a 0.22 micron filter which can retain most bacteria)** - **Have no cell wall, NOT a cell (hence non-living)** - **Some have RNA only, some have DNA only** - **Some are enveloped, some are not** **Morphology of Viruses** - Basic Structure of a virus - - - **Morphology of Viruses cont'd** - The morphological virus types include: -**Helical** - These viruses are composed of a single type of capsomer stacked around a central axis to form a helical structure, which may have a central cavity, or hollow tube. **Morphology of Viruses cont'd** -**Icosahedral** - Most animal viruses are icosahedral or near-spherical with icosahedral symmetry. \- All faces are identical. \- Larger viruses contain more capsomers -**Complex** - These viruses possess a capsid that is neither purely helical nor purely icosahedral, and that may possess extra structures such as protein tails or a complex outer wall. - Nucleic acid -- - this contains the genetic material essential for replication. - may be single-stranded or double-stranded - may be linear or circular - may be segmented or non-segmented Capsid - protects the genetic material - provides the structural symmetry of the virus - site of receptors (attachment) - induces antibody production, serves as antigenic determinant Structural Features cont'd Envelope a lipoprotein - derived from the host cell membrane & virus specific protein. - composed of glycoproteins (spikes) -acquired through budding from the host's cell membrane in the course of maturation. - -confers instability to the virus due to loss of infectivity from the disruption or loss of lipid (this makes viruses become more sensitive to heat, ultra-violet radiation, detergents and lipid solvents) **Motility** - Viruses are not motile - they have no structural features that assist them in moving on their own. - Viruses use the skeletal network of the host's cells to move about. **Nutrition and Growth** - Since viruses are classified as non-living, they cannot: - - - - **Reproduction?? More Replication** - Viruses cannot reproduce or express their genes without the help of a living cell.  - Once a virus has \"infected\" a cell, it will \"marshal\" the cell\'s ribosomes, enzymes and much of the cellular machinery to reproduce. - Viral reproduction produces many, many progeny, that when complete, leave the host cell to infect other cells in the organism. **Viral Replication** - Absorption or Attachment - Penetration - Uncoating - Transcription - Translation - Assembly - Release Lytic and Lysogenic Cycles - Lytic: - -virus injects nucleic acid into healthy cell - multiple copies are made of the virus's protein coat and nucleic acid - these are then assembled into new viruses - Lysogenic: - Some viruses, such as herpes and HIV, remain latent in the host cells for years. - the function of the cell is unaffected by inclusion of viral nucleic acid, until at some time, the acid becomes active and breaks away from the host cell's genetic material. -the host cell is destroyed and new viruses are released. - **FUNGI -- true fungi are called Mycota or Eumycota** - **All are eukaryotic** - possess membrane-bound nuclei (containing chromosomes) and a range of membrane-bound cytoplasmic organelles (e.g. mitochondria, vacuoles, endoplasmic reticulum). - **Most are filamentous** - \- composed of individual microscopic filaments called **hyphae,** which exhibit apical growth and which branch to form a network of hyphae called a **mycelium.** - Some are **unicellular** - e.g. yeasts. - **Protoplasm of a hypha or cell is surrounded by a rigid wall** - composed primarily of chitin and glucans, although the walls of some species contain cellulose. - All fungi require water and oxygen **FUNGI** - **Many reproduce both sexually and asexually** -- both sexual and asexual reproduction often result in the production of spores. - **All are achlorophyllous --** they lack chlorophyll pigments and are incapable of photosynthesis. - **All are chemoheterotrophic (chemo-organotrophic)** -- they utilise pre-existing organic sources of carbon in their environment and the energy from chemical reactions to sythesise the organic compounds they require for growth and energy. - **Possess characteristic range of storage compounds** -- - e.g.  glycogen, sugar alcohols and lipids. - **May be free-living or may form intimate relationships with other organisms** - \- i.e. parasitic or mutualistic (symbiotic). **Morphology of Fungi** - Many fungi produce only single cells (unicells). If they lack flagella, such cells are called yeasts. Hyphae - Tubular - Hard wall of chitin - Crosswalls may form compartments (± cells) - Multinucleate - Grow at tips **MOTILITY** - Fungi are non-motile (they don't move) - Simple fungi produce motile spores - zoospores **Nutrition and Growth** - Fungi are heterotrophs that get food and energy from other organisms - They secrete digestive enzymes into the environment, then absorb the nutrients released by those enzymes. - Most fungi are decomposers: they live on decaying organisms. - Some fungi are parasites: they extract food from living organisms. - Fungi grow better at a pH of 5, which is too acidic for most bacteria **Reproduction** - Fungi reproduce by means of spores - which can be sexual (the products of meiosis) or asexual (the products of mitosis). - Each group of fungi has a unique set of spores. - Asexual reproduction is more common than sexual. - Formed: - - - **ALGAE** - **Simple eukaryotic photosynthetic autotrophs.** - **Kingdom Protista.** -  Most are photosynthetic and \"simple\" because they lack the many distinct cell and organ types found in land plants. -  Some algae are microscopically small and consist of only one cell (= **unicellular** algae), while others are large and **are multi-cellular**; \ - the largest algae are brown algae (or kelp) which can reach lengths of up to 70 - 100 feet! - **Most are found in the ocean or other bodies of water. Need water for support, reproduction, and nutrition.** - **Absorb nutrients from the water over entire surface.** - **Reproduction: All reproduce asexually. Some can also reproduce sexually.** - **Most are not pathogens. A few produce toxins that are harmful to humans.** Brown Algae (Kelp) **Vegetative Structures of multicellular algae** - - - - - **Comparison of Algae and Plant Structure** **Protozoa** - - - - - - - - - Many have developed means of locomotion. - They can be aquatic or terrestrial, and free-living, symbiotic or parasitic. - Over 64,000 species are named; half are fossils. - Although they are unicellular organisms, protozoan cell organelles are highly specialized. - They are ecologically diverse, widely dispersed, but many are limited to narrow environmental ranges. - They can be fantastically numerous, forming gigantic ocean soil deposits - They move by pseudopodia, flagella, cilia and they can direct cell movements. - Pseudopodia in - ***AMOEBA***. Cilia in - ***PARAMECIUM*** Flagella in -***EUGLENA*** **MEDICALLY IMPORTANT SPECIES** - **BACTERIA** There are many different bacteria that exist and can cause infection in humans. However, we shall concentrate on only some of the commonly met forms. Staphylococcus - **Staphylococcus aureus** - - - - - - **Non-bullous impetigo -- pus/fluid forming, itchy, not painful, honey coloured crusts** Streptococci - Like staphylococci, there are many species of streptococci found normally in the human body. - Gram positive - Certain strains of streptococci cause some of the most serious diseases in humans. - **Streptococcus pyogenes** (strep group A) is the main cause of bacterial pharyngitis (strep throat) in people. Untreated strep throat can lead to serious sequelae like rheumatic fever (heart valves) and glomerulonephritis (kidneys). - Other infections include impetigo and the devastating \"flesh eating bacteria\" otherwise known as necrotizing fasciitis. In necrotizing fasciitis, there is rapid destruction of the soft tissues and muscle. This is a frequently fatal disease and rapid treatment is necessary. - Pharyngitis **THE GRAM-NEGATIVE BACILLI\ ** - There are dozens of different species of gram-negative bacilli, with many species normally found in the intestinal tract. - In the intestinal tract they have a beneficial effect on the body by preventing overgrowth of potential pathogens. However, if by surgery or trauma these bacteria get out of the intestine, they can cause serious, life-threatening disease. - One of the more common gram-negative bacilli that cause disease in humans is **Escherichia coli.** - E. coli is by far the most common cause of uncomplicated community acquired urinary tract infections and is frequently seen in wound infections. - Main cause of gastroenteritis.\ \ Salmonella and Shigella are two gram-negative bacilli well known for being causes of food poisoning and dysentery, respectively.\ \ The gram-negative bacilli have been implicated in infections as diverse as pneumonia to ear infections. Escherichia Coli  Signs and symptoms include: - Diarrhea, which may range from mild and watery to severe and bloody - Abdominal cramping, pain or tenderness - Nausea and vomiting, in some people - Children present with symptoms more than adults - The bacteria can also spread from one person to another, usually when an infected person does not wash his or her hands well after a bowel movement. *E. coli* can spread from an infected person\'s hands to other people or to objects. Treatment - Most people get better in about a week. They often don\'t see a doctor and don\'t know that *E. coli* caused their problems. **Neisseria -- gram negative bacteria\ ** - The majority of Neisseria species are found normally in the mouth and female genital tract. However, there are two species that can cause very serious disease in humans.\ \ **Neisseria gonorrhoeae** is the cause of the sexually transmitted infection gonorrhea. This is a major public health issue in the United States and worldwide. Untreated infections of gonorrhea can lead to more serious disease like gonococcal arthritis and pelvic inflammatory disease (PID). \ \ **Neisseria meningitis** is the causative agent of meningococcal meningitis, a serious, potentially life-threatening disease of the spinal fluid and meninges. **Neisseria -- diplococci bacteris** - Herpesvirus - Adenovirus - Poxvirus - Papovavirus \- Parvovirus \- Hepadnavirus **Examples of RNA Viruses** - Orthomyxovirus - Paramyxovirus - Rhabdovirus - Togavirus - Flavivirus - Bunyavirus - Reovirus - Picornavirus - Coronavirus - Calicivurus - Retrovirus - Arenavirus Influenza virus -- a RNA virus **HIV- RNA VIRUS** FUNGI -- The Pathogens CUTANEOUS MYCOSES\ -DERMATOPHYTOSES EPIDEMIOLOGY - Three genera-Trichophyton, Epidermophyton, Microsporum - ***Anthropophilic***-reside on the human skin - ***Zoophilic***-reside on the skin of domestic and farm animals - ***Geophilic***-reside in the soil - Transmission from humans or animals is by infected skin scales CLINICAL SIGNIFICANCE - DERMATOPHYTOSES - Characterized by itching,scaling skin patches that can become inflamed and weeping - Infection in different sites may be due to different organisms but is given one name Tinea pedis(Athlete\`s foot) - Common organisms are Trichophyton rubrum , Trichophyton mentagrophytes and Epidermophyton floccosum. - Initially between the toes spreads to nails, yellow and brittle - Secondary bacterial infection - Id Reaction (rash spreads to other parts of the body, often the hands and chest.) Tinea corporis( Ringworm) - Epidermophyton floccosum, Trichophyton, Microsporum - Advancing annular rings with scaly center - Periphery of ring area of active fungal growth, usually inflammed and vesiculated - Non-Hairy areas of trunks mostly Tinea capitis( scalp ringworm) - Trichophyton and Microsporum species - Depends on area - Small scaling patches to involvement of entire hair with hairloss - Microsporum infects hair shafts , Wood\`s lamp - More common in children due to medium chain fatty acids Treatment - Samples to be sent for fungal staining and culture - Infected skin may be treated with topical application of antifungal agents miconazole,nystatin and clotrimazole - Refractory lesions oral griseofulvin and itraconazole, terbinafine - Infections of hair and nails usually require systemic ( oral) therapy SUBCUTANEOUS MYCOSES(dermis, subcutaneous tissues and Bone) - Causative organisms reside in the soil and in decaying or live vegetation - Almost always acquired through traumatic lacerations or puncture wounds - Common among those who work with soil and vegetation and have little protective clothing - Not usually transmitted humans to humans - Usually confined to tropics and subtropics with exception of Sporotrichosis in USA **Systemic infections** -   These occur when fungi get into the bloodstream and generally cause more serious diseases. Systemic fungal infections may be caused either by an opportunistic organism that attacks a person with a weakened immune system, or by an invasive organism that is common in a specific geographic area, such as cocci and histoplasma. Unlike superficial infections, systemic fungal infections can be life-threatening. CANDIDIASIS(candidiosis) - *Candida albicans* and other candida species which are normal flora in the mouth, skin , vagina and intestines - *C.albicans* is dimorphic - May occur as a result of overgrowth as suppression of bacteria by antibiotics - Manifestations depend on the site e.g. oral candidiasis and vaginal candidiasis and disseminated candidiasis in cancer patients, post GI surgery and AB\`s, systemic corticosteroids PROTOZOA - *Entamoeba histolytica*  which causes **amoebic dysentery**. The organism produces protective cysts which pass out of the intestines of the infected host and are ingested by the next host (fecal-oral route). - *Acanthamoeba* can infect the **eye, blood, spinal cord, and brain **and is transmitted by waterborne cysts picked up while swimming in contaminated water, crossing the mucous membranes. - *Giardia lamblia* can cause a gastrointestinal infection called **giardiasis**. Cysts pass out of the intestines of the infected host and are ingested by the next host (fecal-oral route). - *Trichomonas vaginalis* infects the **vagina and the male urinary tract**. It does not produce a cysts stage and is usually transmitted by sexual contact. **Emerging micro-organisms** - New microorganisms capable of causing disease in humans continue to be detected. Whether an emerging microorganism develops into a public health threat depends on factors related to the **microorganism** **and its environment**, or the **infected human and his/her environment.** - Such factors include ease of transmission between animals and people and among people, potential for spread beyond the immediate outbreak site, severity of illness, availability of effective tools to prevent and control the outbreak, and ability to treat the disease. SARS - Severe acute respiratory syndrome (SARS) is a viral respiratory illness caused by a coronavirus **(SARS CoV).** - SARS was first reported in Asia in February 2003. The illness spread to more than two dozen countries in North America, South America, Europe, and Asia before the SARS global outbreak of 2003 was contained. - **SARS is a contagious disease that typically leads to a potentially fatal form of pneumonia.** - Experts say that a coronavirus strain which used to only affect small mammals mutated, and then started to infect humans and became human-transmissible (passed from person-to-person). - The pandemic was brought under control in July 2003, thanks to close cooperation between affected countries, according to WHO. During that year, all airline passengers travelling from the affected countries were screened at airports. - In 2004, a small SARS outbreak was reported in China. However, it was not caused by person-to-person transmission, but as a result of contact with a laboratory virus sample. - Unlike smallpox, SARS cannot be eradicated, because it could still be present in animal populations where it could mutate and infect humans. Signs & Symptoms - SARS symptoms usually start off like those of the common cold, and gradually become more flu-like. - Extreme  fatigue (tiredness), malaise (general feeling of being unwell) - Headaches - Fever - above 38 °C (100.4 °F). According to WHO, this is the only symptom that is common to all patients with SARS - Lethargy - Confusion - Rash - Loss of appetite - Myalgia - pain in the muscles. Many describe it as an overall feeling of discomfort, and body aches - Chills - Diarrhea  may affect 10% to 20% of patients - **From 3 to 7 days after exposure, respiratory symptoms develop as infection spreads to the airways and lungs, and may include:** - Dry cough - Runny nose (less common) - Sore throat (less common) - Shortness of breath (breathing problems) - Gradual fall in blood-oxygen level (fatal) - Nearly all patients develop pneumonia after about day 7 **How does SARS spread?** - **An airborne virus** - like influenza (flu) and the common cold, SARS is an airborne virus. It spreads in small droplets of water that infected people sneeze or cough into the air. Others breathe the droplets in and become infected themselves. Those most at risk need to be within three feet of somebody who coughs and sneezes. - **Touching contaminated surfaces** - you can also become infected if you touch a surface that an infected person had previously touched, such as a door handle, elevator button or telephone. Infected people who do not wash their hands after going to the toilet (passing stools) can also spread the disease by touch. Good hand hygiene is extremely important in stemming the spread of SARS. - **Close proximity** - people who care for or live with somebody who is infected with SARS are at very high risk of developing the infection.\ \ Experts believe that SARS also spreads by other ways that are not yet known.  **How is SARS diagnosed?\ ** - There are no rapid screening tests for SARS. - In areas where a SARS outbreak is known, the doctor will order lab tests to be done. - In areas where there is no known SARS outbreak, the doctor may consider the possibility of SARS if the patient has pneumonia which is confirmed by an X-ray, as well as some other details: \- Has the patient recently travelled to an area where there is a SARS outbreak, or known cases of SARS have been reported? \- Does the patient work in a place where there might be a risk of exposure to viruses that cause SARS, such as a laboratory -Does the patient have atypical pneumonia without another diagnosis and is part of a cluster of cases? **Diagnostic laboratory tests for SARS** - There are currently three possible diagnostic tests for SARS, however, each has its limitations: **-ELISA (enzyme-linked immunosorbent assay)** - this test detects SARS antibodies. It is a reliable test, but can only be used 21 days after symptoms started. **-Immunofluorescence assay** - this test can identify antibodies 10 days after symptoms first appear. However, it is time- and labor-intensive and requires an immunofluorescence microscope and people who know how to use the equipment. **-PCR (polymerase chain reaction) test** - this test can detect SARS virus genetic material in samples of stools, tissue, sputum and blood. It is a specific but not very sensitive test. Positive test results nearly certainly mean the person has SARS, while a negative test does not completely rule it out. **\ \ What are the treatment options for SARS?** - **There are no medications which target the SARS coronavirus directly**. - Supportive - helping the patient breathe and keeping the fever under control with supplemental oxygen and ventilation support as well as antipyretics (medications for fever). - Isolation of patient H7N9 - A bird flu strain of the Influenza virus A. - can infect and replicate in a variety of mammals, including humans. - first reported to have infected humans in 2013 in China. - most of the reported cases of human infection have resulted in severe respiratory illness. - does not kill poultry, but can kill humans - information is still limited about the full spectrum of illness that infection with avian influenza A(H7N9) virus might cause. Signs & Symptoms - Fever - cough - shortness of breath, which may progress to severe pneumonia - Blood poisoning - Organ failure **How does H7N9 spread?** - At this point it is not known how persons are becoming infected. Some of the confirmed cases had contact with animals or with environments where animals are housed. - The virus has now been found in chickens, ducks, and captive-bred pigeons at live bird markets near locations where cases have been reported. The possibility of an animal source of the infection is being investigated, as is the possibility of person-to-person transmission. - The eating of well-cooked poultry and eggs does not transmit the virus **\ \ \ How is H7N9 diagnosed?\ ** - real-time reverse-transcriptase--polymerase chain reaction assay - viral isolation - H7N9 serologic testing using modified hemagglutination-inhibition assays. - THANK YOU