Lecture 1: Bacteriology and Mycology (Alkafeel University) PDF

Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one General microbiology Microbiology: is the study of microscopic microbes Medical microbiology: The study of disease causing microorganisms with respect to man. Disease caused by a microorganism is called “infectious...

Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one General microbiology Microbiology: is the study of microscopic microbes Medical microbiology: The study of disease causing microorganisms with respect to man. Disease caused by a microorganism is called “infectious disease” or simply, “infection”. Microbiology includes 1. Bacteriology (positive and negative gram stain) 2. Virology (DNA and RNA) 3. Mycology (multicellular molds and unicellular yeast) 4. Parasitology (protozoa, nematodes, trematodes and cestode) 5. Immunology Nomenclature of the microorganism according to the 1. Domain Example 2. Kingdom 1. Domain Eukaryotes 3. Phylum 2. Kingdom Animal 4. Class ‫ الشعبة‬3. Phylum Chordates 5. Order 4. Class Mammals 6. Family 5. Order Primates 7. Genus 6. Family Hominids 8. Species 7. Genus Homo 8. Species Sapiens All microorganisms can be writing according to the Binomial nomenclature which is the biological system of naming the organisms in which the name is composed of two terms, where, the first term indicates the genus and the second term indicates the species of the organism. Comparison of Eukaryotes, Prokaryotes Criteria Prokaryotes Eukaryotes Domains Archaea and bacteria protest, fungi, plants and animals Nucleus Absent Present Endoplasmic reticulum Absent Present Mitochondria Absent Present Cytoskeleton Absent Present 1  Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one Ribosomes Smaller Larger Cell wall Usually present Only in plant cell and fungi Breath Microorganism Overview Pressure Property Bacteria Rickettsia Chlamydia Fungi Virus Rate Skin Diameter 2X1-5 µm 500 nm 300 nm 1-5 µm 25-250 nm Speech Type of nucleic acid DNA & DNA & DNA & DNA & DNA or RNA RNA RNA RNA RNA Binary fission + + + + - ‫تبرعم‬ Budding - + + Spore formation + + - Synthesis of proteins + + + + - Ribosomes + + + + - Machinery of energy + + - + - production Growth on artificial + - - + - media Sensitive to antibiotics + + + + - Sensitive to interferon - - - - + Intracellular infection Some + + - + Infectious Disease Principles and Epidemiology Definitions  Host : organism which provides nutrients to another organism  Parasite: organism which lives at the expense of its host  Pathogen: microorganism that is capable of causing disease.  Opportunistic: microorganisms that may or may not cause disease generally colonize, but do not infect  Disease: an upset in the homeostasis of the host, resulting in generation of observable changes like fever, rash, vomiting, headache, anorexia  Infectivity: is the ability of agent to cause infection  Virulence : a measure of pathogenicity, which is the ability to cause disease Transmission of Infectious Diseases  Direct transmission via 1. Not intimate contact (shaking hands) 2. Intimate contact (sexual contact)  Indirect transmission via 1. Vectors ‫وﺳﻂ ﻧﺎﻗﻞ‬ 2. Fomites ‫أدوات ﻣﻼﺑﺲ‬ 2  Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one Pathogenesis Steps  Contact the host  Colonize the host  Infect the host  Evade the host defense system  Damage host tissues Epidemiology Principles ‫علم األوبئة‬  Epidemiology: study of the occurrence of disease in a human population, ‫ﻣﺴﺒﺒﺎت‬ especially the etiology and transmission of disease  Epidemic: (upon the people), commonly refers to an unusually high incidence of a disease in a community at one time.  Pandemic : (all the people) indicates an epidemic involving more than one continent  Endemic (in the people) a disease is constantly present, usually at low incidence, in a population  Outbreak: appearance of several cases of a disease, usually in a short period of time, in an area previously experiencing no cases or only sporadic cases certain disease. ‫نسبة‬  Prevalence: the proportion of diseased individuals in a population at one time  Incidence: the number of diseased individuals in a population at one time  Morbidity : sickness  Mortality: death  Reservoir: a site in which infectious agents remain viable (alive)  Carrier : an infected individual which is not showing obvious signs or symptoms of clinical disease, but which is shedding the etiologic agent for a long period of time  Zoonosis: diseases which occur primarily in animals but are occasionally transmitted to people (plague, Lyme disease, rocky mountain spotted fever)  Vector: living agent (ticks, fleas, flies mosquitoes) which transmits infectious agent to human or animals  Fomite: non-living object (food, water) that transmits infectious agents (pencil, doorknob, handkerchief) Public Health Measures for Control of Epidemics  Immunization programs of people  Blocking vehicle-mediated transmission 1. Water purification 2. Effective cooking 3. Prevention of food contamination with infectious agents  Quarantine  Elimination of animal reservoirs 3 Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one 1. Immunization of animals that act as reservoirs of diseases such as bovine tuberculosis, brucellosis 2. Eradication of animals that act as reservoirs of diseases such as tularemia, plague, Lyme disease Vaccines: Is a material preparation containing microbial antigens that are used to stimulate immune responses without causing disease Types of vaccines  Toxoid vaccines: a chemically inactivated toxin  Killed vaccines : chemically inactivated microbe 1. Whole microbe vaccines 2. split microbe vaccines  Live attenuated vaccines but less virulent  Recombinant vaccines 1. Vector vaccines via bacteria or viruses 2. Food vaccines via bananas or tomatoes  DNA vaccines  Childhood immunizations (vaccinations) 1. Hepatitis B 2. DTaP (diphtheria, pertussis, tetanus) 3. hepatitis A 4. Hib (Haemophilus influenza b) 5. poliomyelitis 6. MMR (measles, mumps, rubella) 7. Varicella (Chickenpox) 8. Menomune ( Neisseria meningitides) 9. Prevnar (Streptococcus pneumoniae) 10.Rotashield (Rotavirus) 11.Smallpox vaccine Food Microbiology  Food spoilage 1. Perishability  Highly perishable foods ( fish poultry, eggs, milk, most fruits and vegetables )  Semi-perishable foods ( potatoes, some apples, nuts)  Non-perishable foods (sugar, flour, rice, dry beans) 2. Factors induce perishability ‫رطوبة‬  Moisture content (high)  pH (above 5, below 8)  Salinity (low) ?  Food preservation 4 Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one 1. Control of perishability factors  Moisture content (lower)  pH (below 5, above 8)  Salinity (high) 2. Storage temperature (below 4C, above 60C) 3. Chemical preservatives retard microbial growth like sodium benzoate Bacteria Bacteria are microscopic single-celled prokaryotic organisms that play a crucial role in the ecosystem and have a significant impact on human health. Bacteria can be found all over the world, including the top of the mountains or the deeper trenches in the oceans. They are also present in our bodies like in the mouth, skin, digestive system, reproductive system and urinary tract. Bacteria can be both harmful and useful for humans. Bacterial structure:  Capsule: This thick protective gelatinous layer around some bacterial cells is related to the virulence of bacteria. Example: Capsule formation in Diplococcus pneumoniae.  Cell Wall: This rigid outer layer provides shape and protection to the cells.  The Gram-positive bacteria have a thick layer of Peptidoglycan, while Gram- negative bacteria have a thinner layer along with an outer membrane.  Cytoplasmic Membrane: This inner layer surrounds the cytoplasm and controls the flow of molecules in and out of the cell. It also houses various cellular processes.  Cytoplasm: This semi-fluid substance contains various cellular structures.  Nucleoid: Instead of a nucleus, bacteria have a nucleoid.It is an area where the genetic material (DNA) remains.  Ribosomes: These are the tiny granules present in the cytoplasm and are the centers of protein synthesis. 5 Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one  Vacuoles: These are fluid-containing cavities present within the cytoplasm.  Glycogen and Volutin Granules: These are stored food granules present within the cytoplasm.  Flagella and Pili: These are external appendages that aid in movement and adhesion, respectively.Flagella are long, whip-like structures, while pili are shorter, hair-like projections. ‫اﻻﺑﻮاغ‬  Endospores: Some Gram-positive bacteria like Anaerobacter, Bacillus, Clostridium, Heliobacterium, etc. can form dormant (without detectable metabolism) structures within the cytoplasm, known as endospores.  They can survive extreme chemical and physical stress.  They can cause diseases like anthrax by Bacillus anthracis and tetanus by Clostridium tetani. Bacterial Classification Bacteria can be classified into various categories based on their features and characteristics. The classification of bacteria is mainly based on the following: Items Types 1. Infection 1. causing diseases 2. non causing diseases 2. Shape 1. Cocci (coccus, diplococci, tetrads, sarcina, ‫ﻣﻜﻮرة‬ streptococci, staphylococci ) 2. Bacillus (diplobacilli , streptobacilli, Corynibacterium, coccobacilli) 3. Spiral (Spirilla,Spirochete) 4. Vibrio (Comma-shaped) 5. Mycoplasma 6. Actinomycetes 3. Gram staining 1. Gram Positive 2. Gram Negative 3. Acid fast staining 4. Composition of the cell wall 1. Peptidoglycan cell wall (Gram-positive bacteria) 2. Lipopolysaccharide cell wall (Gram-negative bacteria) 5. Mode of respiration 1. Aerobic 2. Obligate aerobes 3. Anaerobic 6 Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one 4. Facultative anaerobes 5. Microaerophilic 6. Capnophiles 6. Mode of nutrition 1. Phototrophs 2. Chemotrophs 3. Autotrophs 4. Heterotrophs 7. Mode of locomotion 1. Monotrichous ‫ﺳﻮط واﺣﺪ‬ 2. Amphitrichous ‫ﺳﻮط ﻓﻲ ﻛﻞ طﺮف‬ 3. Lophotrichous ‫ﻣﺠﻤﻮﻋﺔ ﻣﻦ إﻻﺳﻮاط ﺑﻄﺮﯾﻘﺔ ﻋﺸﻮاﺋﯿﺔ‬ 4. Peritrichous ‫ﻣﺠﻤﻮﻋﺔ ﻣﻦ اﻷﺳﻮاط ﺑﻄﺮﯾﻘﺔ ﻣﺘﺴﺎوﯾﺔ‬ 8. Temperature requirement 1. Phsychropliles 15‫درﺟﺔ‬ 2. Mesophiles 20-45 3. Thermopliles 45-80 4. Hyper thermophiles 80 9. pH 1. Acidophiles 2. Alkaliphiles 3. Neutriphiles 10. Salt 1. Halophiles 2. Halotolerant 11. Spores 1. Spore forming (endospore and exospore) 2. Non spore forming Metabolism and growth - Biofilm In nature, microorganisms grow mainly in biofilms, complex and dynamic ecosystems that form on a variety of environmental surfaces, from industrial conduits and water treatment pipelines to rocks in river beds. A biofilm is a community of microorganisms, such as bacteria, that are capable of living and reproducing as a collective entity known as a colony. The human body harbors many types of biofilms, some beneficial and some harmful. For example, the layers of normal microbiota lining the intestinal and respiratory mucosa play a role in warding off infections by pathogens. However, other biofilms in the body can have a detrimental effect on health. For example, the plaque that forms on teeth is a biofilm that can contribute to dental, periodontal disease, wound infection, cystic fibrosis and medical devices used in or on the 7 Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one body, causing infections in patients with in-dwelling catheters, artificial joints, or contact lenses. Pathogens embedded within biofilms exhibit a higher resistance to antibiotics than their free-floating counterparts. - Binary fission The bacterial cell cycle involves the formation of new cells through the replication of DNA and partitioning of cellular components into two daughter cells. The most common mechanism of cell replication in bacteria is a process called binary fission Before dividing, the cell grows and increases its number of cellular components. Next, the replication of DNA starts at a location on the circular chromosome called the origin of replication, where the chromosome is attached to the inner cell membrane. Replication continues in opposite directions along the chromosome until the terminus is reached. The center of the enlarged cell constricts until two daughter cells are formed, each offspring receiving a complete copy of the parental genome and a division of the cytoplasm (cytokinesis). This process of cytokinesis and cell division is directed by a protein called FtsZ. - Generation time The generation time is the time between the same points of the life cycle in two successive generations. Escherichia coli can double in as little as 20 minutes under optimal growth conditions in the laboratory. Mycobacterium tuberculosis, the causative agent of tuberculosis, has a generation time of between 15 and 20 hours. - Growth curve Microorganisms grown in closed culture (batch culture), in which no nutrients are added and most waste is not removed, follow a reproducible growth pattern referred to as the growth curve. Infections of the body do not always follow the growth curve. When an organism is inoculated into a nutrient solution four distinct growth phases are noted: 1. Lag Phase - where the organisms are "getting used to the medium and physical conditions" - that is they are inducing the necessary enzymes for growth. 8 Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one 2. Logarithmic (Log) Growth Phase - This is the phase where the generation time is measured. The more ideal the conditions, the faster the growth - up to the maximum growth rate for the species. 3. Stationary Phase - during this phase the number of new cells equals the number of dead cells so that there is no net increase in viable cells. Nutrients are becoming depleted, the pH is changing, toxic wastes are building up, and oxygen levels are becoming depleted. 4. Death Phase - Rate of cell death is faster than regeneration. Death may accelerate and become exponential. Bacterial Genetics RNA, DNA, extrachromosomal DNA 1. Plasmids: Extra chromosomal DNA substances varying from less than 5 to more than several 100 kbp 2. Transposons: A type of mobile DNA of 2000–20,000 bp Transfer of DNA among bacterial cells Methods of transfer Mechanism Objectives + + F Conjugation (F × It involves the transfer of an F+ Beta lactamase transfer for F– Mating) plasmid but not chromosomal penicillin resistance DNA from a donor cell to a recipient cell Hfr Conjugation F+ plasmid integrates with the (Hfr+ × F– Mating) chromosome to become an Hfr+ cell. It then behaves like a donor cell that transfers its Hfr chromosome to the recipient F– cell. Transformation Recipient cell uptake of free H.influenza DNA released into the S.pneumonia environment N. meningitides Transduction Transfer of a portion of DNA Group A erythrogenic toxin from one bacterium to another by Botulinum toxin bacteriophage Cholera toxin Diphtheria toxin Shiga toxin Transposition Transposition in bacteria refers to Enterococcus (VRE) a genetic phenomenon where Transform st.aureus into (VRSA) specific segments of DNA, 9 Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one known as transposons or "jumping genes," are able to move from one location within the bacterial genome to another Mycology The fungi are a group of eukaryotic microorganisms, some of which are capable of causing superficial, cutaneous, subcutaneous, or systemic disease. Fungi can be yeast or mold 1. Yeast: Blastomyces, Candida, Histoplasma, Coccidioides, Cryptococcus 2. Molds: Aspergillus, Dermatophytes, Mucor Comparison between yeast and mold Criteria Yeast Mold Structure Yeast are mostly unicellular and Mold are multicellular with exist in either individually or with tubular and filamentous hyphae buds growing on them Structural Appearance Round or oval shaped Thread like filamentous Color appearance Dull color and mostly Wide variety of coloration monochromatic Habitat or Occurance Most occur naturally in soil or Occur in any organic ocean environment having moist and humid atmosphere Types More than 1500 types More than 400000 types Tolerance to environmental More tolerate to drying Less tolerate to harse whether condition condition Method of reproduction Mainly by budding or binary Mainly by spore formation fission (sexual and asexual spore both) Application or uses Use in industries for ethanol Used in biodegradation, production, baking, food additive bioremediation as well as in or flavor etc antibiotic production Oxygen requirement Aerobic and facultative Strictly aerobic (obligate anaerobes aerobes) Examples Saccharomyces cerevisiae, Candida Rhizopus, Mold, Penicillium, albicans, Cryptococcus neoformans Aspergillus 10 Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one Classification of the fungi Items Types Site of infection M: Mold Y: Yeast D: Dimorphic 1. Systemic infection  Coccidioidomycosis (D).  Paracoccidioidomycosis (D).  Histoplasmosis (D).  Blastomycosis (D). 2. Subcutaneous infection  Sporotrichosis (D).  Chromoblastomycosis (Y).  Mycetoma (M).  Phaeohyphomycosis (M). 3. Opportunistic infection  Systemic candidiasis (Y-LIKE).  Cryptococcosis (Y).  Aspergillosis (M).  Hyalohyphomycosis (M).  Phaeohyphomycosis (M).  Mucormycosis (M).  Penicilliosis (D). 4. Cutaneous infection  Dermatophytosis (M).  Candidiasis (Y-LIKE). 5. Superficial infection  Pityriasis Versicolor (Y).  Tinea Nigra (M).  White Piedra (M).  Black Piedra (M). Sexual reproduction  Zygomycota  Ascomycetes  Deuteromycetes (Fungi imperfecti )  Basidiomycetes Morphology  Dimorphic  Molds  Yeast  Yeast-like Nutrition  Saprophytic(Decomposer)  Symbiotic(Mycorrhizal)  Parasitic 11 Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one Antibacterial and antifungal drugs Antimicrobial Chemotherapeutic Agents (CTAs) Origins 1. Antibiotics: naturally occurring substances made by certain bacteria and fungi 2. Synthetic antibiotics: chemicals substances made from antibiotics in industrial settings Antimicrobial Agents Developed Recently 1. Antibacterials are continually being modified to enhance their usefulness 2. Antifungals are being developed and improved 3. Antiprotozoals and antihelminthics are still difficult to develop, but we are making some progress here, too 4. Antivirals are being developed rapidly Mechanisms of Action: 1. Metabolites: sulfa drugs, INH (isoniazid) 2. Membranes: nystatin , amphotericin, azoles, polymyxin B 1. Cell wall damage : penicillin, cephalosporin, bacitracin, vancomycin 2. Protein synthesis : streptomycin, tetracycline, erythromycin 3. Nucleic acid synthesis: rifampin, acyclovir Considerations for use of CTAs  Spectrum: indicates the range of microbes that killed by antimicrobial (broad and narrow spectrum)  Selective toxicity: a selectively toxic agent is harmful to the microbes but not to the tissues  Route and Dosage: CTAs must be administered by an appropriate route so they can reach infected sites in an appropriate concentration to act against the organism(s) within their spectrum (im, iv, subcutaneous, orally)  Susceptibility and Resistance (Antimicrobial susceptibility testing) 1. Susceptible microbes ( killed or growth is inhibited) 2. Resistant microbes (not killed and growth is not inhibited )  Allergenic potential 12 Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one Antibacterial drugs Mode of Action Target Drug Class Inhibit cell wall biosynthesis Penicillin-binding β-lactams: penicillins, proteins cephalosporins, monobactams, carbapenems Peptidoglycan subunits Glycopeptides Peptidoglycan subunit Bacitracin transport Inhibit biosynthesis of proteins 30S ribosomal subunit Aminoglycosides, tetracyclines 50S ribosomal subunit Macrolides, lincosamides, chloramphenicol, oxazolidinones Disrupt membranes Lipopolysaccharide, Polymyxin B, colistin, inner and outer daptomycin membranes Inhibit nucleic acid synthesis RNA Rifamycin DNA Fluoroquinolones Antimetabolites Folic acid synthesis Sulfonamides, trimethoprim enzyme Mycolic acid synthesis Isonicotinic acid hydrazide enzyme Mycobacterial adenosine Mycobacterial ATP Diarylquinoline triphosphate (ATP) synthase synthase inhibitor Antifungal drugs Type Action Example Polyenes Altering the wall of the fungal Nystatin cells to be more porous, thus Amphotericin B making them more likely to burst. Azoles Inhibiting the C14α Clotrimazole Imidazole demethylation of lanosterol in Ketoconazole 13 Alkafeel University- Bacteriology and mycology-Dr Ahmed Alshammari –lecture one fungi, which interferes with Miconazole the synthesis of ergosterol in Azoles the fungal cell membrane Fluconazole Triazoles Isavuconazole Itraconazole Posaconazole Voriconazole Allylamines Inhibiting an enzyme that the Terbinafine membrane of the cell requires to operate correctly Echinocandins Interfere with an enzyme Anidulafungin involved in creating the fungal Caspofungin cell wall Micafungin 14