Microbiology and Parasitology PDF

MICROBIOLOGY AND PARASITOLOGY OCCURRENCE AND - not an apt descriptor of an acute condition NON-OCCURRENCE OF INFECTION - persons included in the denominator must have the Infection Process – Ep...

MICROBIOLOGY AND PARASITOLOGY OCCURRENCE AND - not an apt descriptor of an acute condition NON-OCCURRENCE OF INFECTION - persons included in the denominator must have the Infection Process – Epidemiologic Triad potential for being in the numerator (at risk for the disease 1. Agent or condition) - infectious microorganism or pathogen; organism’s - often expressed after multiplication by 100(%), 1000, or pathogenicity; a disease factor; 100,000 - must be present for disease to occur. 2. Environment Two (2) Common Measures of Prevalence - extrinsic factors that affect the agent and the opportunity 1. Period Prevalence for exposure - prevalence of outcome of interest during a specified - physical factors such geology and climate period of time 3. Host - less frequently used - person who will receive the agent - number of cases that occurred in a specified period of - involves the extrinsic and intrinsic factors that enable the time/number in the defined population during this period. agent to travel - generally ranges from 0 to 100%; theoretically can exceed - involves intrinsic risk factors, influence 100% (if you allow individuals who had the disease more susceptibility/response to a causative agent than once to be counted for each case of the disease within the reporting period.) - behavioral influence = sexual practices, hygiene, and 2. Point Prevalence other personal choices as well as age and sex - prevalence of condition of interest at a specific time Steps When Investigating Disease Outbreaks - number of existing cases on a specific date/number in the 1. Verify the diagnosis related to the outbreak defined population on this state 2. Identify the existence of the outbreak - ranges from 0 to 100(%) 3. Create a case definition to define who/what is included as - can be estimated from a cross-sectional survey or disease a case registry data by calculating the percentage with a 4. Map the spread of the outbreak particular disease or condition on a particular date’ 5. Develop a hypothesis (if there appears to be a cause of the outbreak Stages of Infection 6. Study hypothesis (collect data and perform analysis) 1. Incubation Stage 7. Refine hypothesis and carry out further study - period from exposure to a pathogen until symptoms start. 8. Develop and implement control and prevention systems - infected person is unaware of impending illness as the 9. Release findings to greater communities pathogens grow and multiply within the body - duration ay vary depending on the type of infection Outbreak Patterns - measles (incubation period) averages 10-12 days 1. common source – all victims acquire the infection from the same source (e.g., contaminated water supply) 2. Prodromal Stage 2. continuous source – common source outbreak where - pathogen continues replicating, which activates the body’s the exposure occurs in less than one incubation period. immune response, allowing mild, nonspecific symptoms to 3. propagated – transmission occurs from person-to-person appear. - this stage lasts from several hours to several days. Measuring Disease Occurrence - people can transmit infections during this stage. 1. Incidence - symptoms can include: low-grade fever and fatigue. - count of new cases - expressed as a portion of those at risk 3. Illness Stage - denominator (includes all persons at risk for the disease - Infected person shows noticeable symptoms of infectious or condition; would not include persons who already have disease the disease or condition) - symptoms may be localized or systemic - can also be expressed in terms of person-time at risk - localized symptoms affect only one body area - systemic symptoms affect the entire body and are Two (2) Common Measures of Incidence commonly observed with infections, systemic symptoms a. Incidence Density Rate affect the entire body - aka incidence rate or person-time rate - number of persons who newly experience the outcome Illness Duration during a specified period of time divided by the sum of the - last up to a week for many viral respiratory infections (flu) time that each member of the population is at risk - HepB last several weeks or even years b. Cumulative Incidence - HSV and VZV can hide in a dormant state within nerve - consists of the number of persons who newly experience cells the disease or studied outcome during a specified period - chickenpox symptoms usually last between 4 and 7 of time divided by the total population at risk days - this calculation assumes all persons in the denominator contribute an equal amount of time to the measure 4. Decline Stage - number of infectious microbes begins to decrease, and 2. Prevalence symptoms gradually improve; the body’s immune system - counts both new and existing cases effectively fights off the infection - directly related to the duration of the disease CARTAGENAS, V. J. A.BSN 2B  MICROBIOLOGY AND PARASITOLOGY - a person can develop secondary infections during this - facultative intracellular pathogens: meaning they can stage if the primary infection has weakened their immune reproduce either inside or outside of host cellsl system. - enter to a cell by endocytosis - during this stage, the virus can still transmit to other a. relies on effector proteins (trigger entry into the host cell) people. o membrane ruffling (secreted effector molecules can cause protrusions of membrane 5. Convalescence ruffles that bring the bacterial cell in) - can last days, weeks, or even months b. relies on surface proteins (bind to receptors on the host - the body fully recovers from the infection, and symptoms cell, resulting in entry) disappear; the immune system remains vigilant to prevent reinfection. 4. Infection - viruses make us sick by killing cells or disrupting cell function o our bodies often respond with fever (heat inactivates many viruses), the secretion of a chemical called interferon o interferon: blocks viruses from reproducing - bacteria make us sick the same way o it multiply so rapidly they crowd out host tissues and disrupt normal function a. local infection – confined to a small area of the body, typically near the portal of entry b. systemic infection – when an infection becomes disseminated throughout the body. Transmission of Disease Secretions and Excretions can transport pathogens out of Stages of Pathogenesis other portals of exit. 1. Exposure - encounter with a potential pathogen Types of Infection - not all contacts result in infection and disease 1. Viral Infection - infection: successful access to a portal of entry - millions of different viruses may exist, but researchers - these include the skin, mucous membranes, and have only identified about 5,000 types to date parenteral routes - viruses: contain a small piece of genetic code, and a coat - mucosal surfaces: the most important portals of entry for of protein and lipid (fat) molecules protects them microbes; these include the mucous membranes of the - include: common cold, encephalitis and meningitis, respiratory tract, the gastrointestinal tract, and the warts and skin infections, gastroenteritis genitourinary tract. 2. Bacterial Infection 2. Adhesion - Single-cell microorganisms, also known as prokaryotes - capability of pathogenic microbes to attach to the cells of - bacteria environment, extreme heat to intense cold, and the body using adhesion factors some can even survive in radioactive waste - adhesins: molecules (either proteins or carbohydrates) found on the surface of certain pathogens and bind to 3. Fungal Infection specific receptors (glycoproteins) on host cells. - higher risk of developing a fungal infection include people - adhesins: present on the fimbriae and flagella… who: (1) use antibiotics for a long time, (2) have a - protozoans: use hooks and barbs for adhesion weakened immune system, (3) have undergone a - spike proteins: also enhance viral adhesion transplant - biofilm growth: can also act as an adhesion factor 4. Prion Disease - biofilm: community of bacteria that produce a - prion: protein that contains no genetic material and is glycocalyx, which contributes to the extrapolymeric usually harmless. substances (EPS) that allows the biofilm to attach to a - If a prion folds into an abnormal shape, it can become a surface rogue agent and cause infection - EPS: allows the microbe to adhere to the host cells… prions 3. Invasion - can affect the structure of the brain or other parts of the - dissemination of a pathogen throughout local tissues or nervous system; they do not replicate or feed on the host; the body instead, they trigger abnormal behavior in the body’s cell - pathogens may produce exoenzymes or toxins, which and proteins. serve as virulence factors that allow them to colonize - cause degenerative brain diseases, all of which are rare and damage host tissues as they spread deeper into the but progress rapidly and are currently fatal (Bovine body Spongiform Encephalopathy – referred as mad cow - pathogens enter the host’s cells and reproducing. disease and Creutzfeldt-Jakob Disease (CJD). - obligate intracellular pathogens: meaning they can only reproduce inside of host cells 5. Other Types of Infection CARTAGENAS, V. J. A.BSN 2B  MICROBIOLOGY AND PARASITOLOGY Protozoan – single celled organism with a nucleus; commonly 3. Contact Transmission show features similar to those of animals, such as mobility, and a. Direct Contact Transmission – pathogens are they can survive outside the human body. transferred from one infected person to another person Helminths – larger, multicellular organisms that tend to be without a contaminated intermediate object or person. visible to the naked eye when fully grown (flatworms and b. Indirect Contact Transmission – happens when roundworms) pathogens are transferred via a contaminated Ectoparasites – including mites, ticks, lice, and fleas – can intermediated object or person. cause infection by attaching or burrowing into the skin; can also Major Factors Contributing to include blood-sucking arthropods (mosquitoes) Healthcare-Associated Infections 1. An ever-increasing number of drug-resistant pathogens Healthcare Associated Infection (HAI) 2. The failure of healthcare personnel to follow infection control Infectious Diseases (Infectio) – can be divided into two guidelines categories depending on where the person became infected. 3. An increased number of immunocompromised patients a. Healthcare-Associated Infections (HAIs) - infections that are acquired within hospitals or other Additionally contributing factors are: healthcare facilities indiscriminate use of antimicrobial agents – which has - erupt within 14 days of hospital discharge resulted in an increase in the number of drug resistant and b. Community-Acquired Infections multidrug-resistant pathogens - infections that are acquired outside of healthcare facilities false sense of security about antimicrobial agents – leading - (CDC) those that are present or incubating at the time of to a neglect of aseptic techniques and other infection control hospital admission procedures. lengthy, more complicated types of surgery Pathogens Most Often Involved in overcrowding of hospitals and other healthcare facilities, as Healthcare-Associated Infections well as shortages of staff 1. Gram-positive cocci increased use of less-highly trained healthcare workers, who a. Staphylococcus aureus (including methicillin-resistant are often unaware of infection control strains of MRSA) b. Coagulase-negative staphylococci (1) Patients Most Likely To Develop c. Enterococcus spp. (including vancomycin-resistant Healthcare-Associated Infections enterococci) 1. Patients having an organ transplant. 2. Patients receiving treatment with steroids, anticancer drugs, 2. Gram-negative cocci antilymphocyte serum, or radiation a. Escherichia coli 3. Immunosuppressed patients (i.e., patients whose immune b. Pseudomonas aeruginosa systems are not functioning properly) c. Enterobacter spp. 4. Patients who are paralyzed or are undergoing renal dialysis or d. Klebsiella spp. urinary catheterization 5. Patients with indwelling devices such as endotracheal tubes, Most Common Types of central venous and arterial catheters, and synthetic implants. Healthcare-Associated Infections 1. UTIs – which represent about 32% of all HAIs and cause about (2) Patients Most Likely To Develop 13% of the deaths associated with HAIs Healthcare-Associated Infections 2. Surgical Site Infections – which represent about 22% of all 1. Women in labor and delivery HAIs and case about 8% of the deaths associated with HAIs 2. Premature infants and newborns 3. Lower Respiratory Tract Infections (primarily pneumonia) 3. Surgical and burn patients – which represent about 15% of HAIs and cause about 36% of 4. Patients with diabetes or cancer the deaths associated with HAIs 5. Patients with cystic fibrosis 4. Bloodstream Infections (septicemia) – which represent about 14% of HAIs and cause about 31% of the deaths associated with HAIs Mode of Transmission of Healthcare-Associated Infections 1. Airborne Transmission - occurs with dissemination of either airborne droplet nuclei or small particles containing pathogens - airborne droplets are defined as being less than or equal to 5 mm in size 2. Droplet Transmission - respiratory droplets carrying pathogens transmit infection when they travel from the respiratory tract of an infectious individual (e.g., by sneezing or coughing) to susceptible mucosal surfaces of a recipient - droplets traditionally have been defined as being larger than 5 mm in size CARTAGENAS, V. J. A.BSN 2B MICROBIOLOGY AND PARASITOLOGY CARTAGENAS, V. J. A.BSN 2B  MICROBIOLOGY AND PARASITOLOGY well organized and tightly packed, which explains its BACTERIA resistance to staining under the microscope The Importance of Studying Bacteria protection from a variety of different threats to the cell: (1) Cultured buttermilk is prepared from milk inoculated with a desiccation, (2) hydrophobic toxic materials (i.e., starter culture of Lactococcus (usually L. lactis or L. lactis detergents), and (3) bacterial viruses cremoris) can enhance the ability of bacterial pathogens to cause disease Yogurt and fermented milk products and can provide protection from phagocytosis (engulfment Cheeses – acid-producing bacterium such as L. lactis causes by white blood cells known as phagocytes) the casein to precipitate as curd. help in attachment to surfaces Lactobacillus casei, Streptococcus thermophilus, and Propionibacterium shermanii – responsible for the ripening 2. Bacterial Cell: Slime Layer of Swiss cheese. Typically composed of polysaccharides and it completely Anaerobic sugar fermentation reactions by various bacteria surrounds the cell produce different end products like ethanol. protection from various threats: (1) desiccation and (2) Specific bacteria carry out the oxidation of alcohol to acetic antibiotic; it can also allow for adherence to surfaces acid in the production of vinegar. made of loose, unorganized layer that is easily stripped from Organic compounds, such as acetone, isopropanol, and the cell that made it, as opposed to a capsule which integrates butyric acid – are produced in fermentation by various firmly around the bacterial cell wall. Clostridium species and can be prepared on an industrial made of secreted proteins or glycoproteins that self-assemble scale. into a matrix on the outer part of the cell wall Product Bacterium Application or Substrate anchored into the cell wall, although it is not considered to be Amylases Thermophilic used in brewing to break down amyloses to maltoses Bacillus species officially part of the cell wall in bacteria Cellulases Clostridium release of sugars from cellulose in waste from help maintain overall rigidity of the cell wall and surface thermocellus agriculture and papermaking Proteases Thermus aquaticus, used in brewing, baking, cheese processing, removal layers, as well as cell shape, which are important for (Thermolysim, Bacillus species of hair from hides in the leather industry, and reproduction. Subtilisin, laundering protect the cell from ion/pH changes, osmotic stress, Aqualysin) Glucose Bacillus coagulans conversion of glucose to fructose as a sweetener in detrimental enzymes, bacterial viruses, and predator bacteria Isomerase the food industry provide cell adhesion to other cells or surfaces. Beta- Thermus aquaticus hydrolysis of lactose in milk whey to glucose galactosidase Vinegar Acetobacter species from alcohol 3. Bacterial Cell: Biofilm Monosodium Micrococcus species from sugar already discussed… Glutamate Dextran Leuconostoc from sucrose mesenteroides 4. Bacterial Cell: Fimbriae thin filamentous appendages that extend from the cell, often General Concepts of Bacteria in the tens or hundreds single-celled composed of pilin proteins and are used by the cell to attach no nucleus or membrane-bound organelles to surfaces. control center contain single loop of DNA 5. Bacterial Cell: Pili some bacteria have a plasmid often contains genes that give thin filamentous appendages that extend from the cell and the bacterium some advantage over other bacteria like are made of pilin proteins resistant to a certain antibiotic use for attachment as well, to both surfaces and host cells, found in every habitat on Earth such as Neisseria gonorrhea cells that use their pili to grab approximately 10 times as many bacterial cells as human cells onto sperm cells, for passage to the next human host. in the human body mostly at lining of digestive system typically, longer than fimbriae, with only 1-2 present on each some of them live in the soil or on dead plant matter where cell they play an important role in the cycling of nutrients or in decomposition. process of entering: capsule/slime layer/biofilm – cell membrane – some types cause food spoilage and crop damage cell wall others are incredibly useful in the production of fermented foods such as yoghurt and soy sauce Parts of the Bacterial Cell: Flagella relatively few bacteria are parasites or pathogens that cause flexible whip-like tail utilizing microtubules that are powered by disease in animals and plants ATP. when cultured on agar, bacteria grow as colonies that contain rigid in nature, operates more like the propeller on a boat, and many individual cells is powered by energy from the proton motive force General Concepts of Bacteria Bacteria are placed under the Kingdom Protista and are 1. filament prokaryotic cells. - long thin appendage that extends from the cell surface Largest known bacteria in the world is – Thiomargarita - composed of the protein flagellin and is hollow namibiensis - flagellin proteins: are transcribed in the cell cytoplasm Smallest known bacteria in the world is – Mycoplasma and then transported across the cell membrane and cell genitalium wall Longest known bacteria in the world is – Epulopiscium - flagellin units are guided into place by a protein cap fishelsoni (fish) 1. Bacterial Cell: Capsule 2. hook polysaccharide layer that completely envelopes the cell CARTAGENAS, V. J. A. AND AMBID, E. B. S. BSN 2B  MICROBIOLOGY AND PARASITOLOGY - curved coupler that attaches the filament to the flagellar - about 80% of the cytoplasm of bacteria is composed of water. motor - cytosol: liquid component of the cytoplasm - within this can be found nucleic acids, enzymes and amino 3. motor acids, carbohydrates, lipids, inorganic ions, and many low - rotary motor that spans both the cell membrane and the molecular weight compounds cell wall, with additional components for the gram negative - site of most bacterial metabolism outer membrane - bacterial cytoplasm: contains helical actin-like proteins that - has 2 components: along with the cell wall, contribute to cell shape. a. basal body – provides the rotation; consists of a central shaft surrounded by protein rings, two in the gram positive bacteria and four in the gram negative bacteria b. stator – provides the torque necessary for rotation to occur; consist of Mot proteins that surround the ring(s) embedded within the cell membrane 6. Cytoplasmic Membrane lies internal to cell wall and encloses the cytoplasm of the bacterium selective permeable membrane and act as an osmotic or permeability barrier. most dynamic structure of a prokaryotic cell Bacterial Nucleus structure of bacterial plasm membrane is that of unit membrane - do not have a true nucleus enclosed by a nuclear membrane; (phospholipid bilayer – composed of 40% phospholipids, and instead, their genetic material (DNA) is organized in a region 60% peripheral and integral proteins molecules called nucleoid phospholipids of bacterial cell membranes do not contain - nucleoid: dense region within the bacterial cell that contains sterols as in eukaryotes, but instead consist of saturated or the circular chromosome monounsaturated fatty acids (rarely, polyunsaturated fatty - lack of nuclear envelope: the bacterial nucleoid is not acids) surrounded by a membrane. hopanoids (sterol-like molecules) – most likely stabilize the - circular chromosome: bacterial DNA is typically a single, bacterial cytoplasmic membrane. circular chromosome, whereas eukaryotic DNA is organized phospholipids – amphoteric molecules with a polar into multiple linear chromosomes hydrophilic glycerol “head” attached via an ester bond to 2 - smaller size: the bacterial nucleoid is generally smaller and non-polar hydrophobic fatty acid “tails”. less complex than a eukaryotic nucleus phospholipid bilayer – arranged such that the polar ends of the molecules form the outermost and innermost surface of the membrane while the non-polar ends form the center of the membrane. plasma membrane – contains proteins, sugars, and other lipids in addition to the phospholipids. Fluid Mosaic Model – model that d escribes the arrangement of these substances in lipid bilayer. Enzymatic Proteins – carry out most membrane functions. Peripheral Proteins – some membrane proteins are located and function on one side or another of the membrane. Integral Proteins – other proteins are partly inserted into the membrane, or possibly even traverse the membrane as channels from the outside to the inside. - bacterial chromosome: responsible for formation of proteins; site of insertion for flagella, chemotaxis (both motility per se and transcription and translation are continuous process in sensing functions), waste removal, formation of endospores bacteria - DNA gyrase: required for the unwinding, replication, and rewinding of the circular, super coiled bacterial DNA - Sulphonamides: block enzyme required for the synthesis of tetrahydrofolic acid (cofactor needed for bacteria to make the nucleotide bases). Without tetra-hydrofolic acid, the bacteria cannot synthesize DNA or RNA. Plasmid - small extra chromosomal, covalently closed, circular, GRAM POSITIVE VS. NEGATIVE CELL WALL double stranded DNA molecules - endosymbionts of bacteria, i.e, utilize the replication system of host chromosome for their replication. Cytoplasm CARTAGENAS, V. J. A. AND AMBID, E. B. S. BSN 2B  MICROBIOLOGY AND PARASITOLOGY - carry additional genetic information and replicate independently of the chromosome. - Usually contain between 5 and 100 genes - not essential for normal bacterial growth and bacteria may lose or gain them without harm - along with the nucleoid, they make the total bacterial genome. ⮚ Property of Plasmid 1. Physical Properties: circular in shape, consists of one molecule of super coiled DNA, autonomous in existence. 2. Size: 1 Kb to more than 400 Kb. 3. Replication: carries genes for autonomous replication 4. Curing: can be removed spontaneously or inducibly by curing agents 5. Incompatibility: Two members of same group cannot co-exist Transposons in the same cell - transposable or mobile genetic elements 6. Transferability: some small plasmids are seld-transferable - small pieces of DNA aka “jumping genes” 7. Recombination: some plasmids can integrate with the host - may be found in nucleoid (conjugative transposons) or in chromosome (episome) plasmids and usually have 1-12 genes 8. Relationship with Host: not necessary for survival of host cell - encode enzymes transposase that move the transposon from one DNA location to another and integrate there ⮚ Functions of Plasmid - transposase: catalyzes the cutting and resealing of the DNA - formation of bacteriocins, enzymes, toxins, such as the during transposition. tetanus exotoxin and Escherichia coli enterotoxin - Plasmid - transfer genetic material between genomes - surface antigens, capsule, pili, and other virulence factors - Transposon - transfer genetic material between chromosomes - resistance to heavy metals and antibiotics within the same genome - ability to degrade unusual carbon compounds - Integrons - vector for transfer of genetic materials from one organism to - transposons that can carry multiple gene clusters called another gene cassettes that move as a unit from one piece of DNA to another. - Plasmids can acquire a number of different antibiotic resistance genes by means of integrons. - In this way, a number of different antibiotic resistance genes can be transferred as a unit from one bacterium to another. - An enzyme called integrase enables these gene cassettes to integrate and accumulate within the integron. - R-plasmids: found in some gram-negative bacteria, often have genes coding for both production of a conjugation Ribosomes pilus and resistance to antibiotics A typical bacterium may have as many as 15,000 - Responsible for transferring antimicrobial resistance to ribosomes. bacteria of same or other species/genus/family by process of Chemically, the ribosomes are composed of ribosomal conjugation RNA (rRNA) and protein. The ribosomes of prokaryotes are smaller than of eukaryotes. Bacterial ribosomes are composed of two subunits with densities of 30S and 50S. The two subunits combine during protein synthesis to form a complete 70S ribosome about 25nm in diameter. As a workbench for protein synthesis. Translation of mRNA into proteins. During protein synthesis, mRNA (codon) attach to 30s subunit and CARTAGENAS, V. J. A. AND AMBID, E. B. S. BSN 2B  MICROBIOLOGY AND PARASITOLOGY tRNAs carrying anti-codon and aminoacid attach to 50s Cell Wall subunit. Some teichoic acid is covalently linked to NAM residue of the murein or a glycolipid in the underlying cell to form a Lipoteichoic acid. Inclusion Granules Techoic acids are found only in Gram positive cells Contained in the cytoplasm of some bacteria as an and constitute the major antigenic determinants of the cell energy or nutrient reserve. surface. The number increase under favorable conditions and Gram Positive Cell Envelope decrease in adverse conditions. Techoic acid – Polymer – phosphorus – ribitol or glycerol ○ metachromatic granules or volutin granules backbone ○ polysaccharide granules (usually glycogen or Teichuronic acid – Polymer – no phosphorus – glucoronic starch) acid backbone ○ lipid includions (e.g., PHB granules) Outer Membrane ○ sulfur granules Major permeability barrier consisting of: ○ carboxysomes (ribulose 1,5-diphosphate ○ Lipopolysaccharide carboxylase) ○ Phospholipids ○ magnetosomes (Fe3O4) ○ Proteins –Porins ○ cyanophycin granules (nitrogen) and gas Outermembrane is made of an endotoxin (LPS). vacuoles LPS consists of: Some inclusion bodies are actually membranous ○ lipid A - the toxic component of the endotoxin vesicles into the cytoplasm, which contain photosynthetic ○ A core polysaccharide - containing unusual pigments or enzymes. carbohydrate residues Constant in structure among related species of bacteria Gram Negative cell wall outer membrane Cell Wall LPS serve as the barrier that blocks the passage of Protect from mechanical disruption due to osmotic virtually all organic molecules into the cell. pressure (cell interior is hypertonic relative to the It has porins or matrix of proteins forming pores in the environment. outer membrane allowing hydrophilic molecules to The wall provides barrier against toxic chemical and diffuse into periplasm biologic agent. Acid-Fast Bacteria Cell Wall The rigid wall (except mycoplasma) form the shape of the Consists of: bacteria. ○ Peptidoglyacn layer linked to arabinogalactan Providing attachment sites for bacteriophage - teichoic ○ Arabinogalactan (D-arabinose and D- acid. galactose) and mycolic acid layers Providing a rigid platform for surface appendages - ○ Mycolic acid layer is overlaid with a layer of flagella, fimbriae, and pili. polypeptides and free mycolic acids Cell Wall: Gram Positive ○ Other glycolopids include lipoarabinomannan Peptidoglycan - may be up to 40 layers of this polymer. and phosphatidyinositol mannosides (PIM) Teichoic and Teichuronic acids - surface antigens ○ The body activates innate immunity by Murein - a linear glycan chain of two alternating sugars recognizing molecules unique to (N-acetylglucosamine (NAG) and N-aceytlmuramic acid microorganisms that are not associated with (NAM)). is the component of the cell wall. It is thicker human cells called pathogen-associated than the gram negative cell wall. molecular patterns of PAMPS Cell Wall: Gram Negative ○ Acid fastness is a physical property that gives Complex a bacterium the ability to resist decolorization Consists of: by acids during the staining procedures. This ○ a periplasmic space - enzymes means that once the bacterium is stained, it ○ an inner membrane - one or two laters or cannot be decolorized using acids. peptidoglycan beyond the periplasm ○ Outer membrane (LPS - Lipopolysaccharide) - external to Classifications of Bacteria peptidoglycan Based on DNA Relatedness ○ Braun's lipoproteins - anchoring outer 1. Genome size membrane to inner. Used to distinguish Legionella pneumophilia ○ Porins - through ehich some molecules may (the legionnaire's disease bacterium) from pass easily. Bartonella (Rickettsia) quintana, the agent of The protein solution in Gram negative periplasm trench fever consists of: L. pneumophilia has a genome size of about 3 ○ Enzymes with hydrolytic function (such as × 109; that of B. quintana is about 1 × 109 alkaline phosphate) 2. Guanine-plus-cytosone (G+C) content ○ Antibiotic-inactivating enzymes Two strains with a similar G+C content may or ○ Binding proteins with roles in chemotaxis and may not belong to the same species. If the G+C the active transport of solute into the cell contents are very different, however, the strains ○ Oligosaccharides secreted into the periplasm cannot be members of the same species to create an osmotic pressure buffer. 3. DNA relatedness under conditions optimal for DNA reassociation CARTAGENAS, V. J. A. AND AMBID, E. B. S. BSN 2B  MICROBIOLOGY AND PARASITOLOGY Allowing single-stranded DNA from one strain to Serotyping can help to identify the reassociate with single-stranded DNA from a specific strain of a bacterium causing second strain, to form a double stranded DNA a disease. This information can be molecule crucial for selecting appropriate Many studies indicate that a bacterial species treatments and public health is composed of strains that are 70 to 100 interventions. percent related ▪ Outbreak investigation 4. Thermal stability of related DNA sequences Serotyping can be used to track the Allows assessment of divergence between spread of a disease and identify the related nucleotide sequences source of an outbreak. 5. DNA relatedness under conditions supraoptimal for ▪ Vaccine development DNA reassociation By understanding the antigenic When the incubation temperature used for DNA diversity of a bacterium, scientists can reassociation is raised from 25-30° C below the develop vaccines that target multiple denaturation temperature to only 10-15° C serotypes, providing broader below the denaturation temperature, only very protection against the disease. closely related (and therefore highly thermally Phage typing (determining the susceptibility pattern of an stable) DNA sequences can reassociate isolate to a set of specific bacteriophages) Strains from the same species are 60 percent or Identified and classified largely on the basis of their more related at these supraoptimal incubation reactions in a series of biochemical tests. temperatures Some tests are used routinely for many groups of bacteria Based on Phenotype (oxidase, nitrate reduction, amino acid degrading 1. Morphologic Characteristics enzymes, fermentation or utilization of carbohydrates); o Indicate the Gram reaction of the organism; others are restricted to a single family, genus, or species whether it is acid-fast; its motility; the (coagulase test for staphylococci, pyrrolidonyl arrangement of its flagella; the presence of arylamidase test for Gram-positive cocci). spores, capsules, and inclusion bodies; shape 2. Growth Characteristics Based on Morphology o Whether an organism grows aerobically, 1. Cocci – spherical or oval cells. On the basis of anaerobically, facultatively (i.e., in either the arrangement of individual organisms, they can be presence or absence of oxygen), or described as: microaerobically (i.e., in the presence of a less o Monococci (Cocci in singles) – Monococcus than atmospheric partial pressure of oxygen). o Diplococci (Cocci in pairs) – Streptococcus 3. Antigens and Phage Susceptibility pneumonia o Cell wall (O), flagellar (H), and capsular (K) o Staphylococci (Cocci in grape-like clusters) antigens are used to aid in classifying certain Staphylococcus aureus organism at the species level, to serotype o Streptococci (Cocci in chains) Streptococcus strains of medically important species for pyogenes epidemiologic purposes, or to identify serotypes o Tetrad (Cocci in group of four) – Micrococcus of public health importance. o Octard (Cocci in group of eight) – Sarcinae o Cell wall (O): a rigid layer outside the cell 2. Bacilli – rod-shaped bacteria. On the basis of membrane that provides structural support and arrangement of organisms, they can be described as: protection for the bacteria cell. It is often o Diplobacilli composed of peptidoglycan. o Streptobacilli o Flagellar (H): whip-like structures that extend o Palisades from the bacterial cell and allow it to move. They o Chinese-letter form are powered by rotary motor. o Coccobacilli o Capsular (K)L layer of polysaccharide or protein o Comma-shaped that surrounds the cell wall. It can provide 3. Actinomycetes – (actin- ray, mykes-fungus) protection from the environment help the o These are rigid organisms like true bacteria but bacterium adhere to surfaces, and evade the they resemble fungi in that they exhibit immune system. branching and tend to form filaments. o Serotyping is used to distinguish strains of o They are termed such because of their exceptional virulence of public health resemblance to sun rays when seen in tissue importance, for example with V. cholerae (01 is sections. the pandemic strain) and E. coli 4. Spirochetes – These are relatively long, slender, non- (enteropathogenic serotypes). branched microorganisms of the spiral shape having o Serotyping is a method used to classify several coils. bacteria based on their antigenic properties. 5. Mycoplasma – These bacteria lack in the rigid cell wall ntigens are molecules, often proteins or (cell wall lacking) and are highly pleomorphic and of carbohydrates, that can stimulate an immune indefinite shape. They occur in round or oval bodies and response. By identifying the specific antigens in interlacing filaments. present on the surface of a bacterium, scientists 6. Rickettsiae and Chlamydiae - These are very small, can classify it into a particular serotype. obligate parasites, and at one time were considered o Why is serotyping important? closely related to the viruses. Now, these are regarded as ▪ Disease identification bacteria. CARTAGENAS, V. J. A. AND AMBID, E. B. S. BSN 2B  MICROBIOLOGY AND PARASITOLOGY Based on Anatomical o Obligate aerobes – Those organisms that 1. Capsule: Capsulate– Streptococcus pneumonial; Non- strictly require O2 for their growth are called capsulate – Viridans streptococci Obligate aerobes or Obligate aerobic organisms 2. Flagella: Flagellate –Monotrichous, Lophotrichous, e.g. Pseudomonas aeruginosa. Amphitrichous, Peritrichous o Microaerophilic – Those organisms that grow 3. Aflagellate: Shigella spp. under reduced O2, 5-10% and increased CO2, 4. Spore: Spore-forming – Bacillus spp.; Non-sporing – 8-10% are called Microaerophilic organisms or Escherichia coli microaerophiles e.g. – Campylobacter jejuni, Helicobacter pylori. Based on Staining Reaction o Facultative anaerobe – Those organisms that 1. Gram’s stain are capable of growing either in presence or o Gram-positive cocci – Staphylococcus aureus absence of O2 are called facultative anaerobes o Gram-negative cocci – Nesseria gonorrhoeae or facultatively anaerobic organisms. – coli. o Gram-positive rods – Clostridium o Obligate anaerobe – Those organisms that o Gram-negative rods – coli strict absence of oxygen for the growth is called 2. Acid-fast stain obligate anaerobe or obligate anaerobic o Acid-fast bacilli – Mycobacterium tuberculosis organisms. e.g. – Clostridium o Non-acid-fast bacilli – Salmonella typhi o Capnophilic – Those organisms that require increased concentration of CO2, i.e., 5-10% for Based on Cultural Characteristics the growth is called Capnophilic organism or 1. Extra growth factors requirements capnophile e.g. influenzae, N. gonorrhoeae. o Fastidious – Hemophilus influenza o Aerotolerant – Those organisms which cannot o Non-fastidious – Escherichia coli use oxygen for growth, but tolerate its presence 2. Hemolysis on Sheep Blood Agar are called Aerotolerant organisms. e.g. – o Alpha-hemolysis – Streptococcus pneumonia Streptococcus, Clostridium o Beta-hemolysis – Streptococcus pyogenes 3. pH Dependence 3. Utilization of Carbohydrates o Acidophiles – pH less than 3 – e.g. – o Oxidative – Micrococcus Lactobacillus acidophilus o Fermentative – Escherichia coli o Alkaliphiles – pH roughly 8.5–11 – e.g. – Vibrio 4. Growth Rate o Neutralophiles (pH 6.5-8) – e.g. – o Rapid growers– Vibrio cholera Streptococcus pneumoniae, Pseudomonas o Slow growers – Mycobacterium tuberculosis aeruginosa 5. Pigment Production o Majority of the medically important bacteria o Pigment producer – Staphylococcus aureus grow best at neutral or slightly alkaline reaction o Pigment non-producer – Escherichia col (pH 7.2-7.6). 4. Salt Concentration Based on Nutrition o Non – Halophiles – Unable to grow in high salt 1. Phototrophs - Those organisms which get energy from concentration. e.g. – E.coli. photochemical reactions are called as Phototrophs or o Halotolerant – Tolerate low level of salt phototrophic organisms. concentrations i.e. up to 8% salt concentration 2. Chemotrophs - – Those which get energy from chemical e.g. – reactions are called as Chemotrophs or chemotropic o Halophiles – those organisms that grow in high organisms. salt concentration are called Halophiles or 3. Autotrophs - Those organisms which can synthesize halophilic (salt-loving) organisms. These are essential metabolites from inorganic sources are called as further classified as – Autotrophs or Autotrophic organisms. a. Slightly halophilic – require 0.5-3% salt 4. Heterotrophs - Those organisms which cannot concentration for growth e.g. – Vibrio, synthesize their essential metabolites and depend upon Pseudomonas external sources are Heterotrophs or heterotrophic b. Moderately halophilic – requires 3-15% salt organisms. Most of the pathogens are heterotrophic. concentration for growth e.g. – Bacillus, Micrococcus Based on Environmental Factors c. Extremely halophilic – requires 15-30% salt 1. Temperature Dependence concentration for growth e.g. – Halobacterium, o Psychrophiles (15-200C) – Pseudomonas Halococcus, Natranococcus spp. fluorescens o Mesophiles (20-400C) – Escherichia coli, Salmonella enterica, Staphylococcus aureus o Thermophiles (50-600C) – Bacillus stearothermophillus o Extremely Thermophiles (as high as 2500C) – 2. Oxygen Dependence o Aerobe – Those organisms that use oxygen for the growth and metabolism are called aerobes or aerobic organisms. They obtain energy from oxidative processes. E.g. – Staphylococcus spp., Streptococcus spp. CARTAGENAS, V. J. A. AND AMBID, E. B. S. BSN 2B  MICROBIOLOGY AND PARASITOLOGY o The cell wall ruptured and the librated tiny gonidia grow into new bacterium cell under suitable conditions B. Sporulation 1. Conidia o Many filamentous bacteria (e.g.,Streptomyces) form chains of small, spherical sporelike conidia at the tips of the filaments. o A conidium develops by the formation of a transverse wall at the tip of the filament. o The filament bearing conidia are known as conidiophores. After liberation each conidium gives rise to a new filamentous bacterium, provided conditions for germination are favourable. 2. Odiospores o In another member Actinomyces he hypha insead of obstructing spore in succession at the free end, undergodes additional separation through its lnght to form numerous small reproductive units known as oidiospores. o Each oidiospores on germination produces, a filamentous bacterium. 3. Sporangiospores o In some branching bacteria sporangia like structure may developed at the end of certain hyphae. o The protoplast of the sporangia may divided to form tiny sporangiospores. o On libration of these spores germinate under suitable condition, each producing a filamentous bacterium. C. Endospore o During the unfavorable condition, eubacteria have the ability to become endospores. o In this state, the bacteria can tolerate Asexual Reproduction exceedingly high and low temperatures, acidic A. Vegetative reproduction and basic conditions, and large amounts of 1. Binary Fission: The most common way by radiation. which the bacteria reproduce itself is the Binary. o Endospores are extremely hard to kill. Process. It is a process by which a single Surprisingly, they can be boiled for hours and bacterial cell simply divides into two in half an still survive. hour time. o Endospores can only be made by Grampositive 2. Budding: bacteria. o Bud develops at one end of the cell. o Within the endospore remains the bacterial o Genome replication follows, and one copy of the DNA, but the cytoplasm has a decreased water genome gets into the bud. concentration. o Then the bud enlarges, eventually become a o The bacteria will take on a tough coating daughter cell and finally gets separated from the composed of calcium and dipicolinic acid, parent cell. creating a dense and impregnable barrier to 3. Cysts stabilize the DNA within the cell. o The entire protoplast of the cell recedes from the o DNA repair enzymes are also still active, aiding cell wall and becomes rounded. in the resistance of the endospore. o A thick wall is then secreted around it to form resistant structure somewhat similar to the Sexual Reproduction endospore. 1. Conjugation o It is called the cyst. These are formed in certain o Bacteria showing conjugation are dimorphic, species of Azobacter. i.e., they have two types of cells, male (F+) or o Under suitable environment conditions the cyst donor and female (F-) or recipient. germinate to produce the new bacterium. o The male or donor cell possesses 1-4 sex pili on 4. Segmentation the surface and fertility factor (transfer factor, o In some other species of bacteria reproduce sex factor) in its plasmid. Fertility factor contains vegetative called segmentation genes for producing sex pili and other o In this case the protoplast of the bacterium cell characters needed for gene transfer at some stage, divides to form very tiny body a. Sterile Male Method: (F+ x F– → F called gonidia. – becomes F+): The plasmid having CARTAGENAS, V. J. A. AND AMBID, E. B. S. BSN 2B  MICROBIOLOGY AND PARASITOLOGY fertility factor replicates. A copy of it a. Physical Barrier – many bacteria produce a capsule, a gets transferred to the recipient cell thick, slimy layer surrounding their cell wall. This capsule through the conjugation tube. The acts as a physical barrier, preventing phagocytes from recipient cell also becomes donor. adhering to the bacterial surface. The phenomenon of reversibility of b. Recognition Interference – the capsule can also sex is called sexduction interfere with the recognition of pathogen-associated b. Fertile Male Method: (Hfr x F – →F molecular patterns (PAMPs) by phagocytes), making it – remains F –): The F+ plasmid or more difficult for the immune cells to identify the bacteria fertility factor of the donor cell gets as a threat. integrated to bacterial chromosome or 2. Protein M Modification – some bacteria can modify surface DNA. The attachable plasmid is proteins, such as M proteins, to prevent recognition by known as episome. phagocytes. These modifications can interfere with the binding 2. Transformation oof opsonins (proteins that coat bacteria to make them more o It is the absorption of DNA segment from the susceptible to phagocytosis) or directly inhibit phagocytic surrounding medium by a living bacterium. The activity. phenomenon was discovered by Griffith in 3. Toxin Production 1928. Its mechanism was worked out by Avery a. Impairment of Phagocytosis – certain bacteria produce (1944). toxins that can impair the function of phagocytes. For o In transformation, a bacterium takes in DNA example, some toxins can disrupt the phagocytic process from its environment, often DNA that's been or kill the phagocyte itself. shed by other bacteria. If the DNA is in the form 4. Immune System Suppression – some pathogens can of a circular DNA called a plasmid, it can be produce factors that suppress the immune response, making it copied in the receiving cell and passed on to its more difficult for phagocytes and other immune cells to function descendants. effectively. o Receptivity for transformation is present for a 5. Rapid Replication brief period when the cells have reached the a. Overwhelming Phagocytosis – by replicating rapidly, end period of active growth. At this time they pathogens can overwhelm the phagocytic response and develop specific receptor sites in the wall. establish an infection. Normally E.coli does not pick up foreign DNA 6. Genetic and Molecular Basis for Virulence but it can do so in the presence of calcium a. Bacterial virulence factors – may be encoded on chloride chromosomal, plasmid, transposon, or temperate 3. Transduction bacteriophage DNA o It is the transfer of foreign genes by means of b. Virulence factor genes on transposons or temperate viruses. Transduction was first discovered by bacteriophage DNA – may integrate into the bacterial Zinder and his teacher Lederberg (1952) in chromosome. Salmonella typhimurium. 7. Host-mediated Pathogenesis – in certain infections (e.g., o Such a virus is never virulent. It passes over the tuberculosis), tissue damage results from the toxic mediators gene of the previous host to the new host. released by lymphoid cells rather than from bacterial toxins. Transducing viruses may carry the same genes 8. Intracellular Growth (restricted transduction) or different genes a. Some bacteria (e.g., Rickettsia species) can grow only (generalized transduction) at different times. within eukaryotic cells, whereas others (e.g., Salmonella o The genetic recombination in which genetic species) invade cells but do not require them for growth. material is transferred by phage virus between b. Most pathogenic bacteria multiply in tissue fluids and not two bacteria is called transduction. in host cells. Bacterial Pathogenesis Virulence Factors 1. Host Susceptibility – resistance to bacterial infections is - help bacteria to: enhanced by phagocytic cells and an intact immune system a. Invade the host - Initial resistance is due to nonspecific mechanisms b. Cause disease - Specific immunity develops over time. Susceptibility to c. Evade host defenses some infections is higher in the very young and the very old and in immunosuppressed patients. Types of Virulence Factors 2. Bacterial Infectivity – results from a disturbance in the 1. Adherence Factors – many pathogenic bacteria colonize balance between bacterial virulence and host resistance. mucosal sites by using pili (fimbriae) to adhere to cells. - Objective (Bacteria): multiply rather than to cause 2. Invasion Factors – surface components that allow the disease; it is in the best interest of he bacteria not to kill bacterium to invade host cells can be encoded on plasmids, but the host more often are on the chromosome. 3. Host Resistance – bacteria invading tissues encounter 3. Capsules – many bacteria are surrounded by capsules that phagocytic cells that recognize them as foreign, and through protect them from opsonization and phagocytosis. a complex signaling mechanism involving interleukins, 4. Endotoxins – the lipopolysaccharide endotoxins on Gram- eicosanoids, and complement, mediate an inflammatory negative bacteria cause fever, changes in blood pressure, response in which many lymphoid cells participate. inflammation, lethal shock, and many other toxic events. 5. Exotoxins – include several types of protein toxins and Mechanisms to Prevent Phagocytosis enzymes produced and/or secreted from pathogenic bacteria. 1. Capsule Formation CARTAGENAS, V. J. A. AND AMBID, E. B. S. BSN 2B  MICROBIOLOGY AND PARASITOLOGY Major categories include cytotoxins, neurotoxins, and Hemolysin Destroy red blood cell enterotoxins. Collagenase Dissolve collagen 6. Siderophores – iron-binding factors that allow some bacteria Leukodin Kills white blood cell to compete with the host for iron, which is bound to hemoglobin, Exotoxin and Endotoxin Interfere with normal metabolic transferrin, and lactoferrin. process Bacteria that Release Cytotoxins Digestive Tract – has a series of effective barriers, including 1. Staphylococcus aureus – produces alpha-toxin, beta-toxin, stomach acid, pancreatic enzymes, bile, and intestinal and Panton-Valentine leucocidin (PVL) secretions. These substances can kill bacteria or prevent them 2. Clostridium difficile – produces toxins A and B, which can from multiplying. damage the lining of the intestines Male urethra is long, while the female urethra is shorter. 3. Pseudomonas aeruginosa – produces pyocyanin & elastase. Eyes – the mucous membranes of the eyes are bathed in tears. 4. Escherichia coli – some strains of E. coli produce cytotoxins These membranes are coated with secretions that fight that can cause severe illness, such as hemorrhagic colitis and microorganisms and protect the eyes from infection. hemolytic uremic syndrome. Nose and Airways – are coated with mucus. Mucus removal 5. Clostridium botulinum – produces botulinum toxin, which is a is aided by the coordinated beating of tiny hairlike projections potent neurotoxin that can cause paralysis. (cilia) that line the airways. The cilia sweep the mucus up the airways, away from the lungs. Bacteria that Release Neurotoxins Vagina – normally acidic, the acidity of this prevents harmful 1. Clostridium botulinum – produces botulinum toxin, which is a bacteria from growing and helps maintain the number of potent neurotoxin that can cause paralysis. protective bacteria. 2. Clostridium tetani – produces tetanus toxin, which can cause The number of neutrophils increases first, but if an infection muscle spasms and seizures. persists, the number of monocytes increases. 3. Vibrio cholerae – produces cholera toxin, which can cause Eosinophils – increases in allergic reactions and many severe diarrhea and dehydration. parasitic infection, while neutrophil increases in bacterial 4. Bacillus cereus – produce cereulide, a neurotoxin that can infections. cause vomiting and diarrhea. 5. Listeria monocytogenes – produce listeriolysin O, toxin that Different Types of White Blood Cells damage nerve cells; Listeriosis in pregnant women & newborns. Bacteria that Release Enterotoxins 1. Staphylococcus aureus – produces enterotoxins that can cause nausea, vomiting, and diarrhea within a few hours of consumption. 2. Clostridium perfringens – produces enterotoxins that can cause abdominal cramps, diarrhea, and vomiting. 3. Baciillus cereus – can cause 2 types of food poisoning: emetic type 9associated with rice) and a diarrheal type (associated with meat and vegetables). 4. Escherichia coli – produce enterotoxins, including Shinga toxin, which can cause severe diarrhea and hemolytic uremic syndrome (HUS) 5. Vibrio cholerae – produces cholera toxin, which can cause severe diarrhea and dehydration. 6. Salmonella – produces enterotoxins that can cause abdominal cramps, diarrhea, and fever. Responses of the Body to Bacterial Infection Antibacterial Drugs Natural barriers and the immune system – defend the body Action of Antibiotics on Ribosomes: against organisms that can cause infection. - Interfere with translation and thereby causing faulty Natural Barriers: protein synthesis. A. Skin (dry, keratinized) a. Tetracyclines for ribosomes (tetracycline, doxycycline, B. Mucous (lysozyme, lactoferrin, and immunoglobulins that minocycyline, etc) bind reversibly to the 30S subunit, can directly kill or inhibit the growth of bacteria) distorting it in such a way that the anticodons of charged C. Tears (has lysozyme break down bacterial cell walls) tRNAs cannot align properly with the codons of the mRNA. D. Earwax (fatty acids and enzymes inhibit the growth) b. Macrolides for amino acids (erythromycin, azithromycin, E. Stomach Acid clarithromycin, etc) bind reversibly to the 50S subunit. F. Flow of Urine can wash out microorganisms They inhibit elongation of the protein by preventing the enzyme peptidyl-transferase from forming peptide bonds Substance Causing Actions/Effects in the Human between the amino acids. They also prevent the transfer Virulence Body of the peptidyl-tRNA from the A-site to the P-site. Hyaluronidase Increase permeability of tissue spaces to bacterial cells Other Action of Antibiotics Coagulase Increase resistance of bacteria to 1. Penicillin – inhibits cell wall synthesis in Gram Positive phagocytosis 2. Ampicillin – inhibits cell wall synthesis in Broad Spectrum CARTAGENAS, V. J. A. AND AMBID, E. B. S. BSN 2B  MICROBIOLOGY AND PARASITOLOGY 3. Bacitracin – inhibits cell wall synthesis in Gram Positive 4. Cephalosporin – inhibits cell wall synthesis in Gram Positive 5. Tetracycline – inhibits protein synthesis in Broad Spectrum 6. Streptomycin – inhibits protein synthesis in Gram Negative (PTB) 7. Sulfa drug – inhibits cell metabolism in Bacterial meningitis (UTI) 8. Rifampin – inhibits RNA synthesis in Gram Positive, some Neg 9. Quinolones – inhibits DNA synthesis (UTI Tx) Common: Rifampin, penicillin, erythromycin, clindamycin, tetracyclin, streptomycin Resident Bacteria CARTAGENAS, V. J. A. AND AMBID, E. B. S. BSN 2B