Lecture 2.1 - Introduction to Microbiology PDF

Lecture 1 Introduction to Microbiology Dr Carlos Pestana [email protected] Lecture 1 1  What will we look at? We will learn and understand the role of microorganisms in infectious...

Lecture 1 Introduction to Microbiology Dr Carlos Pestana [email protected] Lecture 1 1  What will we look at? We will learn and understand the role of microorganisms in infectious disease This includes:  How the organism spreads within a population Lecture 1 2  What will we look at? We will learn and understand the role of microorganisms in infectious disease This includes:  How the organism spreads within a population  How the organism gains access to the host Lecture 1 3  What will we look at? We will learn and understand the role of microorganisms in infectious disease This includes:  How the organism spreads within a population  How the organism gains access to the host  How the organism causes the disease Lecture 1 4  What will we look at? We will learn and understand the role of microorganisms in infectious disease This includes:  How the organism spreads within a population  How the organism gains access to the host  How the organism causes the disease  How to identify the organism causing the disease Lecture 1 5  What will we look at? We will learn and understand the role of microorganisms in infectious disease This includes:  How the organism spreads within a population  How the organism gains access to the host  How the organism causes the disease  How to identify the organism causing the disease  How to eliminate the organism after infection Lecture 1 6  What will we look at? We will learn and understand the role of microorganisms in infectious disease This includes:  How the organism spreads within a population  How the organism gains access to the host  How the organism causes the disease  How to identify the organism causing the disease  How to eliminate the organism after infection  How to prevent infection taking place Lecture 1 7 History of Medical Microbiology  History of medical microbiology In the 19th century Koch worked on anthrax What he did not know then: Caused by rod-shaped gram-positive bacteria Robert Heinrich Hermann Koch Now called Bacillus anthracis 1843 - 1910 Naturally occur in soil and commonly affect domestic and wild animals Lecture 1 9  History of medical microbiology He collected blood from infected cattle Using a microscope, he was able to identify bacterial cells He injected infected blood into healthy animals – Robert Heinrich Hermann Koch killing them 1843 - 1910 He then cultivated bacteria from infected blood When pure cultures of these organisms were injected into animals this also caused their death – proving they were responsible for anthrax Lecture 1 10  History of medical microbiology The organism responsible for this infection was later named Bacillus anthracis This work was published in 1876 Robert Heinrich Hermann Koch http://edoc.rki.de/documents/rk/508-5-26/PDF/5-26.pdf 1843 - 1910 - this paper is written in German, so might pose problems to read it, but it serves as a useful reminder that it is still possible to access the original publication of work from decades ago. Lecture 1 11  History of medical microbiology Confirmed the idea that infectious diseases are caused by microorganisms Koch proposed different criteria which must be met in order that a condition falls under the remit of an infectious disease These conditions (4 in total) are referred to as Koch’s Postulates Have been altered slightly since, but are still relevant today Lecture 1 12  Germ theory of disease – Koch’s Postulates 1. The organism responsible MUST be present in EVERY case 2. It MUST be possible to isolate the organism from a diseased individual and grow it in pure culture – not always the easiest thing to achieve! 3. It MUST be able to cause the disease when a healthy animal is infected with the pure culture 4. The organism MUST be recoverable from an animal which has been experimentally infected Lecture 1 13  Koch’s Postulates Note that although this example shows blood, other modes of infection are possible instead. Lecture 1 14  Types of microbes Bacteria Fungi Protozoa Viruses Algae Lecture 1 15  Some general properties of these Bacteria organisms Algae Prokaryotes Multi- and unicellular Lack organelles Eukaryotes No nucleus Photosynthetic Capable of causing potent toxins Protozoa, fungi Eukaryotes Contain a nucleus – may even contain multiple nuclei Contain organelles – e.g., mitochondria, hydrogenosomes Viruses Incapable of independent life – require a host for replication Lecture 1 16  Examples of bacteria which can cause human diseases Escherichia coli – found in digestive tract Neisseria gonorrhoeae – causes gonorrhoea Clostridium tetani – causes tetanus Mycobacterium tuberculosis – causes tuberculosis Borrelia burgdorferi – causes Lyme Disease Lecture 1 17  Examples of fungi relevant to humans Trichophyton rubrum – involved in athlete’s foot Penicillium chrysogenum - source of penicillin Aspergillus nidulans – involved in farmer’s lung Saccharomyces cerevisiae – brewing and baking industries Lecture 1 18  Examples of protozoa associated with diseases Giardia lamblia – giardiasis (digestive tract infection) Trypanosoma brucei – sleeping sickness Entamoeba histolytica - amoebiasis (digestive tract infection) Trichomonas vaginalis – trichomoniasis (STI) Lecture 1 19  Examples of viruses associated with diseases Human Immunodeficiency Virus Ebolavirus Hepatitis Viruses West Nile Virus Corona Virus Lecture 1 20  Examples of algae associated with diseases Gambierdiscus toxicus – ciguatera fish poisoning Various – amnesic, paralytic, diarrheal, neurotoxic shellfish poisoning Raphidiopsis raciborskii – Palm Island Mystery disease Alexandrium catenella – Saxitoxin (nerve agent – classed as WMD) Lecture 1 21 Microbes in the Body  Microbial Flora of Human Body Internal organs are generally free of microorganisms In this context digestive / urinary etc. tracts counts as outside the body Surface tissue has lots of microorganisms Lecture 1 23  Microbial Flora of Human Body Collectively the microbiota (microbial community ) associated with an organism is called its microbiome Lecture 1 24  Distribution of human microbiome This slide shows the idea of the microbiome being found in different places Some outside body, others inside It also introduces the idea of different levels of diversity Lecture 1 25  Types of microbes Most species of microbe in the human microbiome are bacteria These colonise from birth onwards The population changes over time Lecture 1 26  Types of microbes Early colonisers are commensal bacteria Normally mutualistic / symbiotic relationship with the host Access to nutrients Defence Multiple factors influence early colonisers Diet Environmental factors Geographic location Use of antibiotics Lecture 1 27  Microbial adhesion and attack Healthy (intact) skin acts as a reliable barrier to most bacterial attacks However, many microbes will adhere to the surface of the skin Lecture 1 28  Microbial adhesion and attack Some bacteria can attach to surfaces and grow (biofilms) Often involves attachment of bacterial adhesins to the glycoproteins of the skin surface Lecture 1 29  External Microbial Flora - Skin However, although bacteria can colonise much of the skin, the distribution is not even Certain areas have more microbes than others. Also, different species in different places Lecture 1 30  External Microbial Flora - Skin Factors influencing distribution Nutrients Moisture Temperature pH Skin shedding Fluid osmolarity Potential inhibitors Lecture 1 31  External Microbial Flora - Skin Largest numbers of bacteria tend to be found in regions with most apocrine sweat glands Lecture 1 32  Microbiology of Skin Two groups of skin-associated microbes Resident microbes Transient microbes Skin is in constant contact with environment allowing contact with microbes Transient microbes tend to come in contact with the skin and may attach However, conditions are often not favourable for them, and they cannot replicate and multiply, so die off Lecture 1 33  Microbiology of Skin Note that the resident population tend to have evolved to preserve their access to nutrients in this niche They often produce bacteriocins which can kill the transient species, or help the resident species to outcompete transients Lecture 1 34  Transient skin microbes Exposed areas of the body have higher numbers of transients Typically face, neck, hands, etc. Influenced by environmental, domestic and occupational factors Lecture 1 35  Internal Microbial Flora The digestive tract, respiratory tract and urogenital tract have direct contact with the outside of the body They also have their own microbial community Lecture 1 36  Oral Cavity The oral cavity provides an excellent environment for microbial growth Constant temperature Moist environment Ready supply of nutrients Range of surfaces for attachment Due to food and drink being ingested, there is a risk that the microbes will be washed away Therefore, microbes attach to surfaces and also form biofilms Lecture 1 37  Oral Cavity There are several different attachment sites available: Tongue Epithelial cells Oral Thrush Teeth Corners of the mouth / lips Gums Gingivitis can be caused by infections of Streptococcus, Fusobacterium, Actinomyces, Veilonella, Treponema Herpes Simplex infection Lecture 1 38  Nasal Cavity/Respiratory Tract The nasal cavity also provides favourable conditions for microbial growth Moist conditions, relatively constant temperature, nutritional sources from secretions Lecture 1 39  Nasal Cavity/Respiratory Tract Microbes enter the nasal cavity during inhalation In more distal areas of the respiratory tract this can also be true, but the mouth provides a point of contact via pharynx Lecture 1 40  Stomach The stomach contains VERY acidic conditions (pH 1.5 to 2.0) However, there are still organisms in this region Passed person-person or from food Lecture 1 41  Stomach Note that many of the probiotic microbes available act best in the lower gut – but have to survive the acidic conditions of the stomach to get there Lecture 1 42  Stomach However, some species preferably live in this environment One such organism is Helicobacter pylori This is a major source of gastric Helicobacter pylori ulcers Lecture 1 43  Stomach Once into the stomach Helicobacter can colonise the Nobel prize in Physiology or Medicine 2005 mucosal surfaces Barry James Marshall Once attached it can cause inflammation and then ulceration Lecture 1 44  Small intestine The microbial community of the small intestine changes due to several variables: Age Diet Geographical distribution Antibiotic exposure Health pH Lecture 1 45  Small intestine The numbers of microbes in the figure are expressed in terms of numbers per gram of digesta Examples of organisms present here are species from the genera Enterococcus, Bacteroides and Lactobacillus Lecture 1 46  Large intestine The hindgut population contains numerous species – very diverse Many of them are obligate anaerobes – oxygen is toxic to them pH in this area is relatively neutral (4 to 7) Lecture 1 47  Large intestine The relationship is generally symbiotic Human supplies nutrients Bacteria help to break down food and synthesize molecules such as some vitamins Microbial numbers and composition change with age Potential links to increased predisposition to diarrhoea in the elderly Lecture 1 48  Large intestine Diet can impact on the composition and distribution of the microbial community Vegetarian diet versus those that eat meat Differences in those eating red meat versus those eating white meat A range of different probiotics exist They are sold to “enhance” digestive efficiency Lactobacillus casei Bifidobacterium animalis lactis (Bifidus) Lecture 1 49  Rectum The rectal bacterial population is very dense – due to water being reabsorbed Bacterial population produce several metabolites Hydrogen sulphide Methane Hydrogen Volatile fatty acids (VFAs) Lecture 1 50  Rectum Around a third of faecal matter is made up of bacteria Defecated pathogens can then cause infection via faecal-oral transfer C. difficile infections are a major problem – particularly antibiotic resistant strains Lecture 1 51  Microbiology Lecture 2 Bacteria Lecture 1 52