This document provides an introduction to microbiology and microorganisms. It discusses the different types of microbes including bacteria, viruses, fungi and protozoa. It describes the structures and characteristics of bacteria, how they reproduce, and how they are classified. It covers the role of microbes in disease, explaining pathogenicity, virulence factors, and the mechanisms by which pathogens cause infection. It also discusses normal flora and their beneficial relationships with the host. Finally, it defines and describes nosocomial infections, the pathogens that commonly cause them, and methods for prevention.
This document provides an introduction to microbiology and microorganisms. It discusses the different types of microbes including bacteria, viruses, fungi and protozoa. It describes the structures and characteristics of bacteria, how they reproduce, and how they are classified. It covers the role of microbes in disease, explaining pathogenicity, virulence factors, and the mechanisms by which pathogens cause infection. It also discusses normal flora and their beneficial relationships with the host. Finally, it defines and describes nosocomial infections, the pathogens that commonly cause them, and methods for prevention.
This document provides an introduction to microbiology and microorganisms. It discusses the different types of microbes including bacteria, viruses, fungi and protozoa. It describes the structures and characteristics of bacteria, how they reproduce, and how they are classified. It covers the role of microbes in disease, explaining pathogenicity, virulence factors, and the mechanisms by which pathogens cause infection. It also discusses normal flora and their beneficial relationships with the host. Finally, it defines and describes nosocomial infections, the pathogens that commonly cause them, and methods for prevention.
This document provides an introduction to microbiology and microorganisms. It discusses the different types of microbes including bacteria, viruses, fungi and protozoa. It describes the structures and characteristics of bacteria, how they reproduce, and how they are classified. It covers the role of microbes in disease, explaining pathogenicity, virulence factors, and the mechanisms by which pathogens cause infection. It also discusses normal flora and their beneficial relationships with the host. Finally, it defines and describes nosocomial infections, the pathogens that commonly cause them, and methods for prevention.
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Ch1: INTRODUCTION
1) Microbiology is the science that deals with the study of microorganisms.
2) Microorganisms are organisms that require microscope to be observed. 3) Microbiology plays a role in: a. Disease control b. Development of pharmaceutical products c. Quality control method d. Biotechnology Microorganisms are used to produce vitamins, amino acids, enzymes & growth 4) There are different types of microbes: bacteria fungi algae protozoa viruses 5) Microorganisms are classified based on cell type into eukaryotes and prokaryotes. Eukaryote is an organism that possesses a clearly defined nucleus; e.g. fungi, protozoa Prokaryote is an organism characterized by the absence of a distinct membrane bound nucleus or membrane bound organelles; e.g: bacteria
6)
7) Bacteria: classified as prokaryotes, which are single‐celled organisms with a
simple internal structure that lacks a nucleus Bacteria can live in soil, water and inside the human body. Bacteria can be classified into: normal flora, pathogen and opportunistic pathogen. Reproduce by budding 8) Viruses Viruses do not have a cellular structure. A virus consists of DNA or RNA molecule surrounded by a protein coat. A complete virus particle or virion is made up of: A. core of genetic material either DNA or RNA B. protective coat called capsid made up of protein C. Sometimes the capsid is surrounded by an additional layer a lipid 1) membrane envelope 9) Fungi eukaryotic group May be unicellular or multicellular Non motile Reproduce by budding 10) Protozoa are single celled, eukaryotic organisms. Many protozoa are free living, but others are among the most clinically important parasites of humans. Ch2: Introduction to Bacteria 1) Different shapes of bacteria Cocci Chain = Streptococcus Cluster = Staphylococcus Bacilli Chain = Streptobacillus Coccobacillus Vibrio = curved Spirillum Spirochete Square Star 2) Bacterial Cell Structures: Flagella/ Pili/Capsule/ Plasma Membrane/ Cytoplasm/ Cell Wall/ Lipopolysaccharides/ Teichoic Acids/Inclusions/ Spores 3) Bacterial reproduction Generation time: The time cell takes to divide (double) Bacterial reproduction: Binary Fission Division exactly in half Most common means of bacterial reproduction Forming two equal size progenies Genetically identical offspring Cells divide in a geometric progression doubling cell number 4) Classification of bacteria Bacteria are classified into gram positive and gram negative according to cell wall structure. Gram positive bacteria 5) Cell walls of gram‐positive bacteria are very thick and consist primarily of peptidoglycan. Most gram‐positive cell walls contain additional substances such as teichoic acid. The periplasmic space of gram‐ positive bacteria lies between plasma membrane and cell wall. 6) Gram negative bacteria Cell walls of gram‐ negative bacteria consist of two layers; a thin peptidoglycan layer and a thick outer membrane containing lipopolysaccharide molecules (LPS). It is much more complex than gram positive wall The periplasmic space of gram‐negative bacteria lies between the outer ‐membrane and the cell wall. Outer membrane The outer membrane is unique to gram‐negative negative bacteria and lies outside the peptidoglycan layer. The membrane consists of a phospholipid bilayer in which a large proportion of these phospholipid molecules are replaced by lipopolysaccharide molecules (LPS). lipopolysaccharide (LPS) of the outer membrane is also called endotoxin. lipopolysaccharide (LPS) consists of three parts: 1. lipid A 2. core polysaccharide 3. O‐somatic antigen Function of lipopolysaccharide (LPS) bacterial attachment to surfaces & biofilm formation. creating a barrier restricting the entry of toxic substances that might kill or injure the bacterium. protecting pathogenic gram‐negative bacteria from host defense. The O side chain elicits an immune response and is responsible of production of antibodies. The lipid A domain is responsible for much of the toxicity of Gram‐negative bacteria. When bacterial cells are lysed by the immune system, fragments of membrane containing lipid A are released into the circulation, causing fever, diarrhea, and possible septic shock. Ch 3: Microbial pathogenicity Pathogen is a microorganism that is able to cause disease in a plant, animal or human. Pathogenicity is the ability to produce disease in a host organism. Virulence is the degree of causing disease of the microbe. Mechanism of bacterial pathogenesis Pathogenicity in bacteria may be associated with unique structural components of the cells or active secretion of substances. In order to cause disease, pathogens must: 1. Gain access to the host (through portal of entry) 2. Adhere to host tissues 3. Penetrate host cell and escape/ evade host defenses 4. Damage host tissue (either directly by accumulation of waste products or by production of toxins). 1‐ Portal of entry Mucous membrane(respiratory tract) /skin & parenteral route 2‐Adherence • Adherence is the ability of pathogen to attach to host tissues at portal of entry. • Bacteria usually employ proteins known as adhesin for the attachment process. • Attachment also occurs through ligands present on pathogen that bind to receptor on host cell (sugar). • Most microbial adhesins are glycoproteins or lipoproteins located on the glycocalyx, capsule, capsid, pili, fimbriae or flagella. 3‐Escaping host defenses Most successful pathogens, possess additional structure or biochemical features which allow them to resist host defense such as: damage to host Capsules that protect against phagocytosis Enzymes: many pathogens secrete enzymes that contribute to their pathogenicity. Antigenic variation: Some microbes can change surface antigen to escape the attack by antibodies ex: influenza Virus 4‐ Damage to host tissues Bacteria have the ability to cause damage by: Using host’s nutrients: Iron is required for growth of most pathogenic bacteria. In humans, iron is bound to iron ‐transport protein. To obtain free iron, pathogen secrete siderophore proteins that bind iron more strongly than transport proteins. Direct damage: Pathogen cause direct damage to cells by using host nutrients and producing waste products or by multiplying inside cells causing cell rupture. Production of toxins: There are two types of toxins produced by bacteria: exotoxin and endotoxin Exotoxin: Exotoxins are soluble proteins secreted by living bacteria during exponential growth The production of this type of toxins is generally specific to a particular bacterial species. Virulent strains of the bacterium produce the toxin (or range of toxins) while nonvirulent strains do not.Both Gram‐positive & Gram‐negative bacteria produce exotoxins Endotoxin are part of the outer cell wall of bacteria These toxins are associated with Gram negative bacteria as constituents of the outer membrane of the cell wall. The biological activity of endotoxin is associated with the lipopolysaccharide (LPS) Chap 4: Normal flora Normal microbial flora is a population of microorganisms that are present in the skin and mucous membranes of healthy normal persons. Microbial flora differs by: individual/ age/ geographic location/ health status/ diet Host‐microbe relationships can be: Positive (mutualistic) Neutral (commensalistic) Negative (parasitic or pathogenic) Mutualistic: a relationship between two species of organisms in which both benefit from the association Commensalistic: A relationship between two organisms of different species in which one derives some benefit while the other is unaffected Parasitic: relationship in which the microbe benefits at the expense of the host. microbe causes damage to the host. Role of NORMAL FLORA: In most cases, Host‐microbe relationship will remain positive : host provides a nutrition for the colonizing microbes microbe occupies a space that a potential parasite orpathogen might colonize. microbial communities may even aid in digestion or synthesize nutrients for the host. Location of normal flora Normal flora can be found in many sites of the human body including: skin (staphylococcus aureus) respiratory tract urinary tract digestive tract Areas of the body such as brain, circulatory system &lungs are intended to remain sterile (microbe free) Chap 5: Nosocomial Infections: Nosocomial infection is defined as an infection acquired in hospital by a patient in whom the infection was not present or incubating at the time of admission. The most common types of Health care associated infections (HAIs) are: urinary tract infections surgical site infections Gastroenteritis Meningitis Pneumonia blood stream infection Symptoms for these infections may include: discharge from a wound fever cough, shortness of breathing burning with urination or difficulty urinating Bacteria, fungus, and viruses can cause nosocomial infections Bacteria alone cause about 90 percent of these cases Nosocomial infections result from the interaction of several factors: The microbial agent Patient susceptibility Environmental factors The microbial agent: The most common pathogens that cause nosocomial infections are: Staphylococcus aureus Pseudomonas aeruginosa Esherichia coli Acinetobacter baumanii The source of infection can be endogenous (normal flora) or exogenous (outer source) Preventing nosocomial infections General preventive measures 1‐Observing hand hygiene Hands are the most common vehicle for transmission of organisms. Hand hygiene is the single most effective mean of preventing the horizontal transmission of infections among hospital patients and health care personnel. According to the World Health Organization (WHO), there are Five Moments for Hand Hygiene: 1. Before Patient Contact. 2. Before and Antiseptic Task. 3. After Body Fluid Exposure Risk. 4. After Patient Contact. 5. After Contact with Patient Surroundings. 2‐ Monitoring the use of antibiotics in the hospital. 3‐ Regular change of surface antibacterial for the bacteria do not become resistant products 4‐ Constitution of a committee for the fight against nosocomial infections 5‐ Reducing the length of stay of the patient is an effective method of reducing the rate of nosocomial infections Chap 6: vaccination: A vaccination is the injection of a killed or weakened organism that produces immunity in the body against that organism. Bacterial vaccine types • Live attenuated bacterial vaccines • Killed bacterial vaccines • Toxoid vaccines • Capsular polysaccharide and polypeptide vaccines • Purified protein vaccines 1) Live attenuated vaccines Virulent pathogenic organisms are treated to become attenuated and avirulent but antigenic. Examples: Vaccination against Tuberculosis disease: Vaccination against Typhoid fever: Contains live, attenuated Salmonella typhi. It is indicated for persons living or traveling in areas where there is a high risk of typhoid fever and for persons in close contact with either infected patients or chronic carriers. 2) Toxoid vaccine They are prepared by detoxifying the exotoxins of some bacteria Examples: Corynebacterium diphtheriae vaccine Clostridium tetani vaccine This vaccine contains tetanus toxoid. It is given to everyone both early in life and later as boosters for protection against tetanus. 3) Killed bacterial vaccine Example: Vibrio cholerae vaccine Chap 7: food‐borne diseases Foodborne illness is caused by consuming contaminated foods or beverages. Most foodborne diseases are infections caused by a variety of bacteria, viruses, and parasites. Foodborne diseases are classified into: 1‐ Food‐borne infections Food borne infection is caused by ingestion of food containing live bacteria which grow and establish themselves in human intestinal tract. 2‐ Food‐born intoxications Food borne intoxications is caused by ingesting food containing toxins formed by bacteria which resulted from the bacterial growth in food item. The symptoms of food poisoning range from mild stomach cramps to nausea, vomiting, diarrhea, and fever, which can be life‐threatening to very young children, pregnant women, and people whose immune systems are already weakened. Bacterial causes of diarrhea 1) Cholera: Cholera is an acute diarrheal disease caused by gram negative vibrio cholera bacterium. Mode of transmission The main mode of transmission is through contaminated water and food, or person ‐to ‐person spread in overcrowded, unhygienic situations. Clinical features: After an incubation period of 24 – 48 hours, patients experience sudden watery diarrhea accompanied by vomiting. Fever and abdominal pain are usually absent. Important complications include dehydration, shock, electrolyte disturbances and acute renal failure. Treatment: Oral rehydration Tetracyclines 2) Brucellosis Brucella species are small Gram‐negative coccobacilli, which are part of the normal flora of the genitourinary tract of cows, goats, sheep, pigs, and dogs. Mode of transmission: 1‐Ingestion of unpasteurized raw dairy products 2‐Direct contact with infected animals. Clinical Features The incubation period for Brucella infections ranges from five days to several months. Symptoms are nonspecific and flulike. Untreated, patients may develop an undulating pattern of fever (temperatures repeatedly rise then fall, hence the name “undulant fever” is the traditional name for brucellosis). Manifestations of brucellosis may involve any of a variety of organ systems, including the GI tract, and the skeletal, neurologic, cardiovascular, and pulmonary systems. Treatment: Combination therapy. Prolonged treatment (for example, six weeks) is generally necessary to prevent relapse and to reduce the incidence of complications 3) Salmonella Members of the genus Salmonella can cause a variety of diseases, including gastroenteritis and enteric (typhoid) fever. Mode of transmission: Salmonella invades epithelial cells of the small intestine. Disease may remain localized or become systemic. Clinical features: o Gastroenteritis: This localized disease is caused primarily by (nontyphoidal salmonella). It is characterized by nausea, vomiting, and diarrhea (usually nonblood), which develop generally within 48 hour sof ingesting contaminated food or water. Fever and abdominal cramping are common. o Enteric (typhoid) fever: This is a severe, life-threatening systemic illness, characterized by fever and, frequently, abdominal symptoms. It is caused primarily by serotype typhi (typhoidal salmonella). Nonspecific symptoms may include chills, sweats, headache, anorexia, weakness, sore throat, cough, myalgia, and either diarrhea or constipation. The incubation period varies from 5 to 21 days. Treatment: For gastroenteritis in uncompromised hosts, antibiotic therapy is often not needed, and may prolong the convalescent carrier state. For enteric fever, appropriate antibiotics include β‐ lactams and fluoroquinolones. Prevention of salmonella infection is accomplished by proper sewage disposal, correct handling of food, and good personal hygiene. 4) Escherichia coli E. coli is part of the normal flora in the colon of humans and other animals. Diseases caused by E. coli can be gastrointestinal and/or extraintestinal. There are different strains of Escherichia coli which give rise to diarrhea by different mechanisms.
Viral food‐borne diseases
1) Hepatitis A Hepatitis A virus (HAV) is a member of the genus hepato ‐virus. Mode of Transmission Transmission is by the fecal‐oral route, and the virus is shed in the feces. Symptoms: Fatigue/Sudden nausea and vomiting/Abdominal pain or discomfort, especially on the upper right side/ Clay‐colored bowel movements/ Low‐grade fever/ Yellowing of the skin and the whites of your eyes (jaundice)/ Intense itching Treatment: Immune globulin is used as postexposure prophylaxis. No antiviral agents are currently available for treating HAV infections. Prevention: Vaccines prepared from whole virus inactivated are now available. Immune globulin has been used for many years, mainly as postexposure prophylaxis. Prevention of HAV infection requires taking measures to avoid fecal contamination of food and water. Parasitic food‐borne diseases 1) Toxoplasmosis: Toxoplasmosis is caused by an intracellular parasite known as Toxoplasma gondii. Mode of Transmission Transmission is by accidental ingestion of cat feces, eating raw or undercooked meat, from an infected mother to fetus, or from a blood transfusion. Symptoms swollen lymph glands, especially around the neck. Muscle aches and pains. Headache. Fever. Generally feeling unwell. Inflammation of the lungs. Inflammation of the heart muscle. Inflammation of the eye Treatment The treatment of choice for this infection is the antifolate drug pyrimethamine, given in combination with sulfadiazine. 2) Taeniasis This form of the disease is caused by the larval form of Taenia saginata (beef tapeworm). The disease is transmitted by larvae in undercooked or raw beef. Symptoms most no symptoms or mild symptoms. Tapeworms can cause digestive problems including abdominal pain, loss of appetite, weight loss, and upset stomach. The most visible symptom of taeniasis is the active passing of proglottids (tapeworm segments) through the anus and in the feces. Treatment Taeniasis is typically treated with praziquantel and albendazole. Chap 8: Blood‐borne infections Bloodborne disease, any of a group of diseases caused by pathogens such as viruses or bacteria that are carried in and spread through contact with blood. Common bloodborne diseases include hepatitis B, hepatitis C, and human immunodeficiency virus (HIV). 1) Hepatitis B and C Hepatitis is an inflammation of the liver. The condition can be self‐limiting or can progress to fibrosis (scarring), cirrhosis or liver cancer. Hepatitis viruses are the most common cause of hepatitis in the world. Symptoms of hepatitis can include: fever, fatigue, loss of appetite, nausea, vomiting, abdominal pain, dark urine, light‐colored stools, joint pain, and jaundice.
2) HIV Human immunodeficiency virus (HIV)
is a non‐oncogenic retrovirus. Transmission occurs mainly by one of three routes: sexually with blood or blood products, perinatally (from mom to fetus) Several weeks after the initial infection, during which there is a very high level of virus replication in CD4+ cells. Lymph nodes become infected, which are the sites of virus persistence during the asymptomatic period. The acute phase viremia resolves into a clinically asymptomatic or "latent" period lasting from months to many years. This period is characterized by persistent generalized lymphadenopathy diarrhea, and weight loss. Chap 9: Diseases transmitted by skin contact 1) Rabies Humans are usually infected by the bite of an animal. Following inoculation, the virus may replicate locally, but then travels via the axoplasm of peripheral neurons to the brain, where it replicates primarily in the gray matter. Symptoms Clinical illness may begin with an abnormal sensation at the site of the bite, then progress to a fatal encephalitis, with neuronal degeneration of the brain and spinal cord. Symptoms include hallucinations, seizures, weakness, mental dysfunction, paralysis, coma, and finally death. Many, but not all, patients show the classic rabid sign of hydrophobia. 2) Herpes The herpes simplex virus is a contagious virus that can be transmitted from person to person through direct contact. They then carry the virus with them for the rest of their lives. Symptoms Flu‐like symptoms such as swollen lymph nodes and headache. redness, swelling, pain, or itching where the infection will erupt painful, fluid‐filled blisters on the lips or under the nose. cold sores of fever blisters on or around the mouth. Treatment Acyclovir 3) Mumps Mumps is a contagious disease caused by mumps virus Mode of transmission It spreads through direct contact with saliva or respiratory droplets from the mouth, nose, or throat. Symptoms Mumps is best known for the puffy cheeks and tender, swollen jaw that it causes. This is a result of swollen salivary glands under the ears on one or both sides, often referred to as parotitis. Treatment is symptomatic. 4) Warts Warts are a type of skin infection caused by the human papillomavirus (HPV). The infection causes rough, skin‐colored bumps to form on the skin. Mode of transmission The virus can spread from person to person or from different parts of the body through: Direct contact with a wart. Touching something contaminated with the virus, such as towels, doorknobs and shower floors. Treatment Stronger peeling medicine (salicylic acid). 2. Freezing (cryotherapy) 3. Minor surgery 4. Laser treatment 5) Scabies Scabies is an itchy skin condition caused by a tiny burrowing mite called Sarcoptes scabiei. Scabies is contagious and can spread quickly through close physical contact in a family, child care group, school class and nursing home. Intense itching occurs in the area where the mite burrows. The urge to scratch may be especially strong at night. Treatment Permethrin cream Ivermectin Crotamiton lotion 6) Tetanus Tetanus is an infection caused by a bacterium called Clostridium tetani. Spores of tetanus bacteria are everywhere in the environment, including soil, dust, and manure. The spores develop into bacteria when they enter the body. Mode of transmission The spores can get into the body through broken skin, usually through injuries from contaminated objects. Tetanus bacteria are more likely to infect certain breaks in the skin. Symptoms Jaw cramping Sudden, involuntary muscle tightening (muscle spasms) Painful muscle stiffness all over the body Trouble swallowing seizures Treatment Tetanus is a medical emergency requiring: Care in the hospital Immediate treatment with medicine called human tetanus immune globulin (TIG) Drugs to control muscle spasms Antibiotics Tetanus vaccination Chap 10: Airborne diseases Airborne diseases are caused by pathogenic microbes small enough to be discharged from an infected person via coughing, sneezing, laughing and close personal contact or aerosolization of the microbe. 1) Chicken pox Chickenpox is an infection caused by the varicella‐zoster virus. Mode of transmission Varicella is highly contagious. The virus can be spread from person to person by direct contact, inhalation of aerosols from vesicular fluid of skin lesions of acute varicella or zoster, and possibly through infected respiratory secretions that also may be aerosolized. Symptoms The classic symptom of chickenpox is a rash that turns into itchy, fluid‐filled blisters. The rash may first show up on the chest, back, and face, and then spread over the entire body, including inside the mouth, eyelids, or genital area. It usually takes about one week for all of the blisters to become scabs. Treatment: acyclovir anti‐histamine 2) Measles Measles is a highly contagious infectious disease caused by measles virus. Symptoms usually develop 10–12 days after exposure to an infected person. Mode of transmission Measles is a highly contagious virus that lives in the nose and throat mucus of an infected person. It can spread to others through coughing and sneezing. Symptoms: high fever rash cough runny nose red watery eyes Tiny white spots (Koplik spots) may appear inside the mouth two to three days after symptoms begin There's no specific treatment for measles. 3) Viral rhinitis Rhinitis is a group of disorders characterized by inflammation and irritation of mucus membrane of the nose. Common causes of viral rhinitis include rhinovirus, coronavirus, adenovirus, influenza virus, parainfluenza virus, respiratory syncytial virus, and enterovirus symptoms runny nose, sneezing, congestion, postnasal drip, cough, and a low‐grade fever. Treatment is supportive Decongestant Bed rest Analgesics 4) Influenza Influenza is an acute viral infection of the upper or lower respiratory tract caused by by Influenza viruses are categorized as types A, B, C, and D. Mode of transmission: infection is transmitted from person to person through the respiratory tract, by such means as inhalation of infected droplets resulting from coughing and sneezing. Symptoms Fever Dry, persistent cough Shortness of breath Tiredness and weakness Runny or stuffy nose Sore throat Eye pain Treatment Rest Anti‐pyretic (for fever) Analgesic (for pain) Antiviral agents: oseltamivir (Tamiflu) 5) Pertussis Pertussis, also known as whooping cough, is a highly contagious respiratory disease. It is caused by the bacterium Bordetella pertussis. Treatment The recommended antimicrobial agents for treatment or chemoprophylaxis of pertussis are Azithromycin Clarithromycin 6) Diphtheria Diphtheria is a serious infection caused by strains of bacteria called Corynebacterium diphtheriae that make toxin (poison). Mode of transmission Diphtheria bacteria spread from person to person, usually through respiratory droplets, like from coughing or sneezing. Symptoms a thick grey‐white coating at the back of your throat. a high temperature (fever) of 38C or above swollen glands in your neck. Treatment Antibiotics