MAH Intro Slides.pdf

latrobe.edu.au Introductory Microbiology 1.1 Gene Drendel [email protected] La Trobe University CRICOS Provider Code Number 00115M ...

latrobe.edu.au Introductory Microbiology 1.1 Gene Drendel [email protected] La Trobe University CRICOS Provider Code Number 00115M  latrobe.edu.au The Discipline of Microbiology The study of organisms too small to see with the naked eye Encompasses aspects of their: Growth Habitat Morphology Macroscopic and microscopic Epidemiology Impact on environment Food production Medicinal properties  latrobe.edu.au Comparative sizes of Microorganisms 1 millimetre = 1000 micrometres (μm) 1 micrometre = 1000 nanometres (nm) https://upload.wikimedia.org/wikipedia/commons/0/06/Figure_04_02_02.jpg 3  latrobe.edu.au Prokaryotic versus Eukaryotic cells Prokaryotic Eukaryotic 1-5 µm x 1 µm Larger in size (start 10x Simple internal structure bigger) No membrane-bound Complex internal structure organelles Membrane bound organelles Cell wall (different) E.g. Nucleus, mitochondria, chloroplasts (plants) Cell wall in plant cells (different) 4  latrobe.edu.au Prokaryotes were integral to the development of Eukaryotes Endosymbiosis Internalisation of a prokaryotic cell by an ancient Archaea to form organelles Mitochondria within eukaryotic cells Chloroplasts in photosynthetic eukaryotes; plants and algae Definition source: David P. Clark, Nanette J. Pazdernik, Molecular Evolution in Molecular Biology (Second Edition), 2013 Image source: https://opentextbc.ca/biology2eopenstax/chapter/eukaryotic-origins/  latrobe.edu.au Universal Tree of life Evolutionary history of cells Three domains under which cells can be classified Based on ribosomal RNA genes Ubiquitous across all lineages 6  latrobe.edu.au Species names and Binomial Classification We refer to species using binomial classification Including their Genus, and Species names e.g Genus name (Pseudomonas) followed by species name (aeruginosa) Within a species we can distinguish further using strains Each species is typically defined by one “type strain” Strains are distinct isolates of a species with their own traits Type strain of P. aeruginosa (DSM50071) One of the most commonly grown lab strains, PAO1 PA14 is a well known virulent strain https://en.wikipedia.org/wiki/Kingdom_(biology)  latrobe.edu.au Classification within the Tree of Life https://en.wikipedia.org/wiki/Kingdom_(biology) https://www.bbc.com/future/article/20220225-the-people-eavesdropping-on-life-underground https://www.sciencefocus.com/the-human-body/what-is-the-human-body-made-of/ Microbes are ubiquitous in the environment Throughout soil and waters Extreme environments and conditions On and within living organisms Slide 9 https://envirobites.org/2021/05/06/new-discovery-of-microbes-gobbling-up-greenhouse-gases-in-extreme-environments/  latrobe.edu.au Microorganisms – on/in our body ‘Normal flora’ or microbiota - collectively ‘microbiome’ Ears, nose, throat, vagina, urethra, stomach, intestine, mucous membranes of the git, urinary and respiratory tract, eye surface Essential to our health (microbiome) Understanding interactions of microbes is essential for anyone working in human/animal health There are more microbial cells in our body than human cells May be ‘opportunistic’ pathogens When growth is increased or in ‘wrong spot’ Where there is damage to host In immune suppressed individuals Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, et al. Molecular cartography of the human skin surface in 3D. Proc Natl Acad Sci USA;112. Epub ahead of print 28 April 2015. DOI: 10.1073/pnas.1424409112. 10 https://78.media.tumblr.com/20615c72aceebc88904d94d6db5f5885/tumblr_ovw664rRZv1qzt7d8o3_500.gif https://gfycat.com/darkgargantuanaustrianpinscher Growth of Microorganisms Slide 11 https://archinect.com/news/article/150019407/bacterial-cities-and-their-building-codes Morphology Macroscopic: what we can see the with the naked eye Gene Drendel https://www.researchgate.net/figure/Macroscopic-view-of-Aspergillus-flavus-on-Czapek-yeast-extract- agar-25-C-7-days_fig2_352129470 https://microscopesandmonsters.wordpress.com/tag/spirogyra/ Microscopic: details under the Gene Drendel Gene Drendel microscope Slide 12 http://textbookofbacteriology.net/diphtheria.html https://www.aspergillus.org.uk/zcombined_images/aspergillus-flavus-13/ https://www.ephotozine.com/photo/spirogyra-60470066  latrobe.edu.au Epidemiology Causes of disease Distribution patterns Incidence Prevalence Transmission Risk factors Health-related conditions Doesn’t have to just include epidemics Spreading of the 2019-nCoV Epidemic 13 https://www.cell.com/trends/molecular-medicine/fulltext/S1471-4914(20)30065-4  latrobe.edu.au Microbes impact on the environment Decomposition of organic matter Nutrient cycles Form the basis of the food chain Used in waste management https://aosts.com/role-microbes-microorganisms-used-wastewater- https://www.onlinebiologynotes.com/nitrogen-cycle-steps-of-nitrogen-cycle/ sewage-treatment/ 14  latrobe.edu.au Bacteria Lecture 1.2 15  latrobe.edu.au Features of bacteria Micron (µm) in size range – microscopic Light microscope Unicellular Lack membrane bound organelles No membrane around genetic material Most harmless Few are pathogens Defined morphology Most are free living, but some are in symbiotic relationship Bacterial Cell Anatomy and Internal Structure. Jack0m/Getty Images 16  latrobe.edu.au Bacterial reproduction via binary fission Bacteria reproduce asexually using a process called binary fission Binary fission Following replication of DNA bacterial cells elongate Continued elongation pulls apart the original and replicated DNA The cells being to split and form a new cell wall dividing them Once completed each of the two daughter cells is identical https://bio.libretexts.org/Courses/University_of_California_Davis/BIS_2A%3A_Introductory_Biology_- Unless errors occurred during DNA replication _Molecules_to_Cell/Fall_2021_Bis2A_Singer_Modules/Bis2A_Singer_Cell_Division 17  latrobe.edu.au Bacterial cell shapes Coccus or spherical Staphylococcus aureus Etiologic agent of boils, pimples, styes, food poisoning Rod Shaped Salmonella enterica Etiologic agent of gastroenteritis Spiral Treponema pallidum Etiologic agent of Syphilis Some have a variable shape due to a lack of cell wall Chlamydia trachomatis Etiologic agent of STD, Chlamydia 18  latrobe.edu.au Surface structures of bacterial cells Flagella Locomotion Can be sensory organelle Dennis kunkel microscopy / science photo library Michael Abbey/Science Source Pili/Fimbriae Cell surface attachment Pili – bacterial conjugation Capsules (tightly bound to cells wall) Virulence factor Protects cells and prevents phagocytosis Slime layer (loosely bound to cell wall) Mainly aids in adherence (biofilms) http://textbookofbacteriology.net/structure_2.html 19  latrobe.edu.au Cytoplasmic structures Nucleoid – chromosomal DNA Inclusions Ribosomes Plasmids Extrachromosomal DNA Small circular DNA (most common) Virulence/conjugative/resistance/degradati ve/Col Genetic information not essential to cell Important in pathogenicity https://courses.lumenlearning.com/microbiology/chapter/unique-characteristics-of- prokaryotic-cells/ 20 https://commons.wikimedia.org/wiki/File:Plasmid_(english).svg  latrobe.edu.au Endospores Form under unfavourable conditions “Resting cells” Have tough spore coat Ensures survival of bacterium Resistant to Temperature, starvation, chemical disinfectants, ultraviolet/gamma radiation http://www.devbio.biology.gatech.edu/wp-content/uploads/2011/01/nrmicro750-f1.gif http://textbookofbacteriology.net/Bacillus_3.html 21  latrobe.edu.au The Bacterial Cell Wall and the Gram Stain Lecture 1.3 22  latrobe.edu.au Cell envelope Cell/cytoplasmic membrane Encloses cells interior Permeable allowing transport of molecules in and out of cell Cell wall Structural integrity of cell Different in Gram +ve and -ve bacteria Outer membrane Lipopolysaccharide layer in Gram -ve cells https://abx4dummies.weebly.com/bacterial-cell-wall.html Glycocalyx (external layer) Capsule Slime layer 23  latrobe.edu.au Cytoplasmic membrane Cells need to acquire nutrients and eliminate wastes Maintain internal conditions despite external pressures Passive transport – diffusion down concentration gradient across phospholipid bilayer Active transport - facilitated diffusion using a protein channel in membrane https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(OpenStax)/03%3A_The_Cell/3.3%3A_ Unique_Characteristics_of_Prokaryotic_Cells 24  latrobe.edu.au Cell wall Maintains structure and shape of cell Prevents lysis from osmotic pressure Aids in classification of microbes based on composition Distinguishes between two types of bacteria Gram positive Gram negative Not all bacteria have a cell wall Mycoplasma 25 https://www.nature.com/articles/nrmicro3480/figures/1  latrobe.edu.au Peptidoglycan Polysaccharide made up of sugars alternating in long chains NAG NAM Cross-linked by peptides Creates a lattice-like effect Target of some antibiotics (bacteria) Virulence factor https://open.oregonstate.education/generalmicrobiology/chapter/bacteria-cell-walls/ 26  latrobe.edu.au Gram positive Peptidoglycan (20-80nm thick) Can be 90% of cell wall Has no outer membrane Teichoic acid/Lipoteichoic acid Glycopolymer Helps maintains strength of cell wall Negatively charged E.g. Staphylococcus sp., Bacillus sp. 27  latrobe.edu.au Gram negative Peptidoglycan (7-8nm thick) 5-10% of cell wall Not has highly crosslinked Outer membrane Lipopolysaccharide projects into the environment O-antigen/polysaccharide (immune response) Core polysaccharide Lipid A Lipid A is an endotoxin Fever/diarrhea Endotoxic shock e.g. E. coli, Salmonella 28 https://open.oregonstate.education/generalmicrobiology/chapter/bacteria-cell-walls/  latrobe.edu.au Mycobacteria Different to Gram +ve and -ve cell walls Peptidoglycan Arabinogalactan Mycolic acids Acids make the cell impermeable to the Gram stain Use acid fast stain instead 29  latrobe.edu.au Staining bacteria: role of the cell wall Cell wall composition can affect treatment Coloured stains can be used to examine structure Contributes to diagnosis/identifica tion of pathogen 30  latrobe.edu.au Staining cells for microscopic observation Staining creates contrast & readily allows microscopic observation Simple stain – allows visualization of outline of cell eg. methylene blue Differential stain - does not stain all cells the same eg Gram Stain Selective stain – allows visualisation of certain structures e.g. endospore stain 31  latrobe.edu.au Identifying bacteria – the Gram stain The most commonly used staining method by microbiologists Identifies key differences in the composition of bacterial cell walls Gram positive :Purple Gram negative : Pink 32  latrobe.edu.au Hans Christian Joachim Gram (1853 - 1938). Gram stain method Danish bacteriologist perfected this method of staining bacteria in 1884 MORDANT: a chemical that fixes a dye in or on a substance by combining with the dye to form an insoluble compound In the gram stain Iodine acts as a mordant as it binds with crystal violet to form crystasl violet iodine complex (CVI) 33  latrobe.edu.au GRAM STAINING REACTIONS 34  latrobe.edu.au Bacterial Growth & Environmental Effects on Growth Lecture 1.4 35  latrobe.edu.au Bacterial growth Prokaryotes grow and replicate more quickly than eukaryotes Binary fission much simpler than meiosis and mitosis Some simple eukaryotes use binary fission Don’t have multiple chromosomes Doubling times (D) of bacteria vary E. coli D = 20 mins Causes infection in humans (e.g. food poisoning) Mycobacterium D = 24 hours Causes chronic disease (e.g. Tuberculosis) 36  latrobe.edu.au Factors that impact on the growth of bacteria Temperature pH https://twitter.com/lockstin/status/1252294616625233920 Oxygen requirements Nutrients Water activity https://unsplash.com/s/photos/grand-prismatic-spring All of these will determine the diverse habitats the bacteria live in 37 https://antarcticsun.usap.gov/science/1765/  latrobe.edu.au Nutrients Necessary for bacterial growth and all living things C, N, S, K, P, Mg, O, Ca Need energy and carbon Heterotrophs – Use organic carbon Autotrophs – Use CO2 Some bacterial are easy to culture in the lab (non fastidious) Do not need extra nutrients supplemented into basic media Others require more complex nutrients in order to grow (fastidious) Require extra growth factors supplemented into media e.g. Blood 38 https://sciencing.com/nutritional-types-bacteria-2515.html  latrobe.edu.au Temperature Bacteria can grow in a wide range of temperatures Classified on optimal temperature for growth Cardinal temperatures are the minimum and maximum temperature range for growth Human pathogens are mesophiles Other bacteria can live in extreme conditions Hydrothermal vents Ice sheets Hot springs 39  latrobe.edu.au Oxygen Some bacteria require oxygen for growth Obligate aerobes Obligate anaerobes Bacteria that require oxygen to grow Oxygen is toxic, need anaerobic For others oxygen is toxic E.g. Pseudomonas environment for growth E.g. Clostridium Some require reduced oxygen environments While others can grow in the presence or absence of oxygen Aerotolerant anaerobes tolerate oxygen but do not use it for growth Facultative anaerobe Microaerophile Use respiration in presence of O2 Grow best with reduced oxygen Use fermentation in absence of O2 concentration E.g. E. coli E.g. Streptococcus pneumoniae 40  latrobe.edu.au pH Most bacteria grow at a neutral pH (Neutrophillic) Some have adapted to live in acidic environments (Acidophile) Some grow in more alkaline environments (Alkaliphiles) pH in the human body Skin: 5.4-5.9 Saliva: 6.2-7.6 The gut: 5.7 in the caecum, 7.4 in the terminal ileum 41  latrobe.edu.au Water availability (αw) Values of αw Vary: 0 – no free water 1 – pure water Depends on: Concentration of solutes in the water Moist/dry environment Most organisms prefer a αw of 0.9 and above 42  latrobe.edu.au Bacterium Genus: Escherichia Species: coli (Strains: O157: pathogens) Summary Mesophile Neutraphile example Facultative anaerobe Escherichia coli Gram negative rod: LPS Motile: flagella/pili No endospore Divides every 20 mins https://education.nationalgeographic.org/resource/escherichia-coli-e-coli 43  latrobe.edu.au Modes of Transmission Lecture 1.5 44  latrobe.edu.au MODES OF TRANSMISSION AIRBORNE TRANSMISSION e.g. transmission of Bordetella pertussis Microorganisms can survive in air, most cannot grow in air Survival time varies depending on the natural ‘robustness’ of the organism, physical parameters (temp, UV-level, humidity), encasement in mucous etc Survival enables transmissions from & between sources: - from human &/or animals - from food, soil, water (by evaporation or disturbance) 45  latrobe.edu.au MODES OF TRANSMISSION Aerosol transmission Pathogen occurs within small ‘droplet nuclei’ (1-4 µm) Small droplets are transmitted over a long distance (> 1 meter) Sources of small droplets: coughing, sneezing, speaking a surgical mask will not entrap all small droplets Droplet transmission The pathogen occurs within larger droplets (> 5 µm) Gravity has a greater effect on large droplets than small ones Large droplets are transmitted over a shorter distance (< 1 meter) surgical masks are more effective in trapping large droplets 46  latrobe.edu.au https://www.sciencedirect.com/science/article/pii/S0196655316305314?utm_content=buffer05aa4&utm_medium=social& utm_source=twitter.com&utm_campaign=buffer 47  latrobe.edu.au MODES OF TRANSMISSION 3 CONTACT TRANSMISSION Contact with the source/reservoir of the pathogen Contact with infected host - symptomatic or asymptomatic Direct contact - physical contact with the infectious source Person-to-person transmission: touching; kissing; sexual contact Mother-to-infant during childbirth Mother-to-foetus Contact with body secretions or infectious lesions https://life4me.plus/zh/articles/2-2-transmission-routes/ Indirect contact - transmission via contaminated intermediary Inanimate objects (= fomites): surfaces, objects (thermometers, cups, eating utensils, shared syringes, tattooing equipment), clothing, bedding, towels & water, food, blood 48  latrobe.edu.au Vector Borne Transmission Involves living transmitters of a pathogen Vector(s) essential component in the transmission process elimination of the vector(s) would prevent transmission Most vectors are arthropods (usually insects) fleas, mites, ticks, mosquitos Human-to-human transmission of malaria protozoa via the mosquito Rat-to-human transmission of the plague bacterium via the rat flea Various arthropod vectors for transmission of arboviruses eg Dengue Virus Vertebrates can also be vectors (or they may be an intermediate host) Transmission of Hendra virus (HV) from bats (the reservoir and vector) → horses (intermediate host) → humans https://www.nature.com/scitable/topicp HV causes Hendra disease in horses and humans; bats are age/dengue-transmission-22399758/ unaffected 49  latrobe.edu.au Vector-borne diseases Mosquitoes: Aedes à Yellow fever, Zika virus, Dengue fever, Chikungunya. Anopheles à Malaria Fruit bats: Hendra disease Rat flea: Bubonic plague Ticks: Lyme disease 50  latrobe.edu.au Zika Virus Urban and Sylvatic transmission cycle Multiple species of mosquito Human to human transmission Rhesus monkey reservoir https://www.frontiersin.org/files/Articles/270086/fmicb-08-01417-HTML/image_m/fmicb-08-01417-g001.jpg 51  latrobe.edu.au Understanding transmission is essential in understanding disease prevention Case Study Patient presents with large single lesion that appears rough on surface and dry in middle No other symptoms reported at that time Other smaller red spots appear under armpit Seeks medical advice Diagnosed as having fungal infection at the major large lesion and smaller rash thought to be scabies (burrowing mite - Sarcoptes scabiei Scabies treatment commences and all bedding, towels, clothes etc are washed with every use. 52  latrobe.edu.au Yersinia pestis Black plague Flea vector In the modern day Y. pestis has many modes of transmission through Urban areas Urban mammals to humans Human to human Sylvatic (forest/rural) areas Non-urban mammals and birds Credit “diagram”: modification of work by Stenseth NC, Atshabar BB, Begon M, Belmain SR, Bertherat E, Carniel E, Gage KL, Leirs H, and Rahalison L; credit “cat”: modification of work by “KaCey97078”/Flickr) https://en.wikipedia.org/wiki/Yersinia_pestis 53  latrobe.edu.au https://blog.csiro.au/vaccine-arrives-to-boost-the-frontline-fight-against-hendra-virus/ 54  latrobe.edu.au Learning Objectives Explain the 3 domains of life and binomial classification Know the key components of the prokaryotic cells compared to eukaryotic cells Know the key components of a bacterial cell Understand the structure of the bacterial cell wall as it relates to the gram stain Identify how the environment affects microbial growth Understand the parameters that effect growth of microbes Learn the range of habitats where microbes reside Learnt the types and examples of different modes of transmission