Tung Wah College NUR1016 Microbiology and Pharmacology Lecture (L01) 2024/2025 PDF

Tung Wah College NUR1016 Microbiology and Pharmacology AY2024/2025 Semester 2 Microbiology Lecture (L01) Sony SO Jan 2025 Content o Introduction To Microbiology o Classification and Structures of Microorganisms An individual living thing, such as an animal or a plant , is called an organism Emerging & Re-emerging Infectious Diseases 1894 Plague 1968 Hong Kong 1997 Avian Flu 2003 SARS 2009 Swine Flu 2019 Coronavirus (鼠疫) Flu (香港流感) (禽流感) (非典型肺炎) (H1N1) 猪流感 Disease (冠狀病毒病) 清潔大平街一帶 (photo: Wellcome Library, London) Microbiology Microbiology - study of all living organisms that are too small to be visible with the naked eye. This includes bacteria, archaea, viruses, fungi, prions, protozoa and algae, collectively known as 'microbes’/ ‘micro-organisms’. Pharmaceutical Microbiology Food Microbiology Molecular Microbiology Industrial Microbiology Agricultural Microbiology Marine Microbiology exclusive list, just examples Medical Microbiology - the study of the pathogenic microbes and the role of microbes in human illness. This includes the study of microbial pathogenesis and epidemiology and is related to the study of disease pathology and immunology. Clinical Microbiologists – Clinical microbiologists support and oversee the prevention, diagnosis and treatment of illness caused by pathogenic microbes. They identify the best treatment for particular infectious diseases and monitor patients following treatment. Virologists - Virologists are responsible for diagnosing viral infections and also investigate the pharmacological response of viruses to antiviral drugs and the evolution of drug resistance. Parasitologist - Scientist who studies parasites and their biology and pathology, such as the parasitic diseases caused by them (Microbiology Society, n.d.; The Royal College of Pathologists, n.d.) Scientific Committees Centre for Health Protection (CHP) of the Department of Health CHP has set up Scientific Committees to serve as a platform for deliberation and professional exchange among experts, upon which strategies and actions for communicable disease prevention and control can be formulated. To target major communicable diseases of public health importance, six Scientific Committees - Scientific Committee on AIDS and STIScientific Committee on Emerging & Zoonotic Diseases Scientific Committee on Enteric Infections and Foodborne Diseases Scientific Committee on Infection Control Scientific Committee on Vaccine Preventable Diseases Scientific Committee on Vector-borne Diseases Chairman Chairman of SCEZD Chairman of SC AIDS &STI Chairman of SC EI & FD Chairman of SC VPD Chairman of SC VDD Chairman of SC IC 許樹昌教授 , B.B.S 李卓廣醫生 , M.H. 韓錦倫教授陳基湘教授劉宇隆教授翁維雄醫生 , M.H. (CHP, n.d.) Prof. YUEN Kwok-Yung, JP MB BS (HK), MD (HK), FRCS (Glasg), FRCPath, FRCP(Edin, Lond) Academician, Chinese Academy of Engineering (Medicine and Health) Fellow, American Academy of Microbiology Henry Fok Professor in Infectious Diseases Chair of Infectious Diseases Host-Agent-Environment Model / Epidemiologic Triangle Microbes pathogens Environment Contaminated Hoist Diseases/ environment susceptible hosts Infection Ventilation (US CDC, 2012) Three Domains of Life (三域) Six Kingdoms of Life (六界) 三域六界 Three Domains of Life Prokaryotic (NIL Nucleus) Eukaryotic (True Nucleus) (Archaebacteria) (Eukaryote) Eukarya Archaea 真核生物域 Bacteria 细菌域古菌域 Protist Plant Animal Fungi Common Ancestor A phylogenetic tree (生命進化樹 )is a diagram that depicts the lines of evolutionary descent of different species, organisms, or genes from a common ancestor (Kaiser, 2023; Parker et al., 2016) Prokaryotes, Eukaryotes VS Viruses o Prokaryotes - single-celled organisms that do not carry their genetic material in a distinct nucleus, nor do they have other specialized, membrane-bound structures called “organelles”. Bacteria are prokaryotes. o Eukaryotes - may be single-celled or multicellular organisms, which carry their genetic material in the form of chromosomes inside of a distinct nucleus. They have organelles, which carry out specific cell functions. Fungi are examples of eukaryotes that can be single-celled or multicellular organisms. All multicellular organisms are eukaryotes—including humans. Viruses o Viruses - are not cellular organisms. They are packets of genetic material and proteins without any of the structures that distinguish prokaryotes and eukaryotes. SARS-CoV-2 is an example of a virus. (BioMérieux, n.d.) Three Domains of Life - Archaea (Archaebacteria) https://www.youtube.com/watch?v=73c1RIqi0uw Methanogenic Archaea Archaea can survive in extreme hostile environments Psychrophilic Archaea Halophilic Archaea Thermophilic Archaea 嗜冷古菌嗜鹽古菌嗜熱古菌 Methanogens (甲烷古菌) are the only known organisms capable of producing methane and do so under strictly anaerobic condition Kamchatka, Russia. Photo: Russell Lake Hillier, Australia, in pink Deep-sea hydrothermal vent Neches color due to Halophilic Archaea chimney (Duller & Moissl-Eichinger, 2024; Khanna, 2022 ; Ocean News & Technology, 2019) Three Domains of Life - Eukarya│ Protist (原生物) (1 of 2) o member of the Kingdom Protista- organisms that cannot classified as plant, animal and fungi, types including - Animal-like protists are motile and heterotrophic, meaning they feed by consuming (Eukaryotes) bacteria or other protists- protozoa Plant-like protists are aquatic, eukaryotic, photosynthetic, unicellular organisms, they possess a flagellum that is used for locomotion, and they also possess gametangia and pyrenoids- algae fungi-like protists - slime molds and water molds Animal/plant-like protists - are mixotrophic protists, meaning that they have two modes of food acquisition (hunting prey and photosynthesis), eg Euglena spp. o Eukaryotes (True Nucleus); majority are unicellular, some are multicellular. o Membrane-bound organelles are present in them and cell wall may or may not be present. o Protists can be autotrophic (自養) or heterotrophic (異養) or symbiotic (共生) in nature. o Most protists are harmless to people. But a few cause health problems. For example, parasitic protists - Plasmodium spp. (瘧原蟲) cause malaria (瘧疾); Trichomonas vaginalis (陰道毛滴蟲) causes STD Trichomoniasis (陰道滴蟲病) A heterotroph is an organism that cannot produce its own food, instead taking nutrition from other sources (Biology Online, 2023) Multicellular & Unicellular Six Kingdoms of Life (六界) Eubacteria Archaebacteria Protista Plantae Fungi Animalia Bacteria Archaea Protist Plant Fungi Animal Prokaryotic cells Nucleus (NO) Domain Domain Domain Eukaryotic cells Three Domain of Life (三域) Bacteria Archaea Eukarya Nucleus (YES) common ancestor Cavalier-Smith, 2004) Microbes or not Microbes Living or Non-Living “If we had an authoritative definition of the terms “life” and “alive,” and an authoritative list of criteria for life, we would be able to provide an authoritative answer to the question ‘Are robots alive? Microbes- Living or Non-Living; Borderline or no idea Living Microbes Nucleus (NO) Nucleus (YES) Eukaryotic cells Prokaryotic cells “prion” Virus Protozoa Fungus Helminth Bacteria Archaea (變質蛋白) 病毒原蟲真菌蠕虫細菌古菌 Yeast Mold 酵母霉菌 Viruses Living or Non-Living; Borderline or no idea o Viruses aren’t living organisms. But there’s some debate over this. o Viruses are intracellular parasites, because they need hosts to reproduce its offspring ONLY in living host cells o When outside the host’s cell, they DO NOT show any sign of biological activities and can be defined as organic particles made of nucleic acid and protein. However, when in contact with a suitable host, they become active and start showing a fundamental biological trait – replication and transformation of genetic information to future generations. Living Characteristics Non-living Characteristics Reproduction Lack of Cellular Organization (Are Acellular) Presence of Nucleic Acid Lack Metabolic Machinery Seven Life Processes – Lack Autonomous Reproduction Nutrition, Excretion, Respiration, Sensitivity, Reproduction, Growth Do not Grow and Movement. Lack of Response to Stimuli (Aryal, 2023; Microbiology Society, n.d.) Bovine Spongiform Encephalopathy (BSE) (牛海綿狀腦病) commonly called [Mad Cow Disease (瘋牛症病)] prion protein (PrP) is a type of protein that can trigger normal proteins in the brain to fold abnormally PrP is classified as Non-Living Thing o BSE is a progressive, fatal disease of the nervous system of cattle that is caused by the accumulation of an abnormal protein called “prion” (變質蛋白) in nervous tissues. o BSE is considered zoonotic due to its epidemiological link with the emergence of variant Creutzfeldt-Jakob disease (vCJD) (克雅二氏症) in humans. o Creutzfeldt-Jakob disease (CJD) is a rare disease that causes the brain to degenerate and become spongy, leading to dementia and death. Chong, 2017; Hwang , 2022; Scientific Committee on Emerging and Zoonotic Diseases, 2007) Insect is classified as Animal - NOT Microorganism However, they would cause medical diseases/infection Insect is classified as animal, belong to phylum Arthropoda (節肢類動物), with the following features: o a hard external skeleton (called a exoskeleton) o a segmented body o at least three pairs of jointed legs Head Lice – Scabies疥瘡is a skin infection caused by an infestation of tiny mites Pediculus humanus called Sarcoptes scabiei var. hominis https://www.youtube.com/watch?v=hMPoXjnBgrQ 疥蟎蟲 Adult female of P. Egg ('nit') of P. humanus capitis humanus capitis (US CDC, 2019; US CDC, 2023) Taxonomy & Nomenclature Taxonomy o Taxonomy is the science of naming, describing and classifying microbes Domain 「域」 Bacteria (eubacteria) Kingdom 「界」 Pseudomonadati Phylum 「門」 Pseudomonadota Class 「綱」 Gammaproteobacteria Order 「目」 Enterobacterales Escherichia coli O157:H7 Family 「科」 Enterobacteriaceae (腸桿菌科) Genus 「屬」 Escherichia (埃希氏菌屬 )- a group of closely related organisms Species 「種」 Escherichia coli (E. coli) 大腸桿菌 - individual types within the group Image from CDC Public Health Image Library (PHIL) (Kadhila, 2005; Schoch, et al. 2020) Species - Strain, Variant & Subvariant o Species (種) – is one of the taxonomic ranks that lies at the lowest level of this hierarchical system, generally below the genus rank. o Strain (株) – A strain is a subgroup within the species that has unique characteristics that distinguish it from other strains. These differences are often detectable only at the molecular level; However, they may have different biological characteristics, such as the ability to cause more severe disease. o Variant (變異株) - Any change in the DNA sequence of a cell. Variants may be caused by mistakes during cell division, or they may be caused by exposure to DNA-damaging agents in the environment. A variant is sometimes called a mutation. For example - SARS-CoV-2 variant B.1.1.529 (Omicron) Viruses with mutations become variants. If the variant displays different physical properties to the original virus, it is called a new strain. (Lara Herrero, created using BioRender) o Subvariants (亞型變異株) - When a variant develops slight genetic mutations of its own during replication, it becomes a subvariant. Example - Omicron subvariant is BA.5, which developed a spike protein—a molecule on the virus’s surface—that was different from previous Omicron subvariants (HKBIS, 2015; National Cancer Institute, n.d.; RACGP, 2021; White, 2024) Bacterial Species Nomenclature Bacterial Species Nomenclature - Escherichia coli (E. coli) as example Bacterial nomenclature and naming are regulated by the International Code of Nomenclature of Prokaryotes (ICNP) More than 700 serotypes of species name should have two parts as a binomial system E. coli have been identified. Generic name Specific name Serotype starts with capital letter Escherichia starts with lowercase letter coli + O157:H7 Both words/name should be italicized expresses somatic (O) antigen 157 and flagellar (H) antigen 7 abbreviated - Once the complete name of a microbe has been written out once, the genus name E. coli can be abbreviated to just the capital letter provided there is no confusion with other genera Escherichia sp. “sp.” - The designation “sp.” after a genus refers to a single unnamed species Escherichia spp. “spp.” - The designation “spp.” after a genus refers to more than one unnamed species (Oren, et al., 2022; US CDC, 2022) What is Serotype? Serotype - Describes a way of grouping cells or microorganisms, such as bacteria or viruses, based on the antigens or other molecules found on their surfaces. For example E. coli - o E. coli serotypes are determined by surface antigens (O and H) o More than 700 serotypes of E. coli have been identified, and most types do not cause illness, but 5 pathotypes are associated with bloody diarrhea: 1. enterohemorrhagic E. coli (EHEC) 腸道出血性大腸桿菌 - strains capable of producing Shiga toxin, and are also referred to as Shiga–toxin producing E. coli (STEC) (產志賀毒素大腸桿菌) , and sometimes called verocytotoxic E. coli (VTEC). Among the subtypes, E.coli O157:H7 is the most important STEC serotype, because it may lead to a complication haemolytic uremic syndrome (HUS). 2. enterotoxigenic E. coli (ETEC) 腸產毒性大腸桿菌 3. enteropathogenic E. coli (EPEC) 病原性大腸桿菌 4. enteroaggregative E. coli (EAEC) 腸集聚性大腸桿菌 5. enteroinvasive E. coli (EIEC) 腸侵襲性大腸桿菌 (Collins et al., 2023; CFC, 2010) Nomenclature is complicated - species name o Singular form - Italicize species, variety or subspecies, and genus o Plural form - Do not italicize or capitalize genus name o example - The plural form of salmonella & Shigella are salmonellas or salmonellae and shigellas respectively Nomenclature - variety (abbreviated var.) o variety (abbreviated var.; in Latin: varietas) is a taxonomic rank below that of species and subspecies, but above that of form Sarcoptes scabiei var. hominis Sarcoptes scabiei var. canis Means infect Canis (犬属)- Means infect human a genus of the Caninae which includes multiple extant species, such as wolves, dogs. (Dryden, 2023; Frank, n.d.; US CDC, 2019) Nomenclature In Virus Taxonomy Nomenclature In Virus Taxonomy – Family, Subfamily, Genus, Species, Virus Name (1 of 2) Regulated by International Committee on Taxonomy of Viruses (ICTV) Example - Ebola virus o family name ends in the suffix – viridae, in italics Family - o subfamily name ends in the suffix – virinae, in italics Filoviridae o first letter is capitalized Genus - o genus name ends in the suffix – virus, in italics Orthoebolavirus o first letter is capitalized (Fenner et al., 1987) Nomenclature In Virus Taxonomy Family, Subfamily, Genus, Species (Virus Name) (2 of 2) Virus Names are often those that are commonly used and known. The format of virus names lies outside the Virus Species Name remit of the ICTV; virus names are NOT standardized as are the names of species. o Both names (species & genus) should be italic o genus name - starts with capital letter o DO NOT italicize virus name when used generically Species Virus Name Orthoebolavirus bombaliense Bombali virus Orthoebolavirus bundibugyoense Bundibugyo virus Orthoebolavirus restonense Reston virus Orthoebolavirus sudanense Sudan virus Orthoebolavirus taiense Taï Forest virus Orthoebolavirus zairense Ebola virus (Biedenkopf et al., n.d.; ICTV, n.d.; 2022; US CDC, 2022) Hemagglutinin (HA) And Neuraminidase (NA) o Influenza A viruses are divided into subtypes on the basis of two proteins on the surface of the virus: hemagglutinin (HA) neuraminidase (NA) o There are 18 known HA subtypes and 11 known NA subtypes. H1 through H18 and N1 through N11, respectively o Five subtypes of avian influenza A viruses are known to have caused human infections (H5, H6, H7, H9, and H10 viruses) (Langer, 2023) Influenza Virus Nomenclature Influenza virus nomenclature - The name starts with the Influenza virus type, followed by the place where the virus was collected, the virus strain number (often a sample identifier), the year of sample collection, and finally, the Influenza virus subtype. Influenza Type Sample Number Influenza subtype (A, B, C, or D) (e.g., 7, 15, 875543, etc.) (e.g., influenza A(H1N1) virus influenza A(H5N1) virus). (A/California/7/2009(H1N1)) Place of Isolation the geographical place where the Year of Sample collection sample was collected (e.g., (e.g., 1957, 2009 etc.) Denver, Taiwan, etc.) (PAHO/WHO, 2022) Medical Parasitology Simple / Complex Life Cycle of Parasites Simple Life Cycle - Parasite requires only Complex Life Cycle - Parasite requires at least TWO hoists (definitive & intermediate host) to complete its one hoist to complete its development development Giardia duodenalis (藍氏賈第鞭毛蟲) Clonorchis sinensis (中華肝吸蟲) also known as Giardia lamblia (US CDC, 2019; US CDC, 2021) Ecto/ Endoparasite o Endoparasites – parasites that live inside the body of their host with the following two types Extracellular Parasites - are parasites that are capable of growing and reproducing outside the cells of a host, eg inside body cavity - Trichomonas vaginalis causes Trichomoniasis (滴蟲病) [one types of Sexually Transmitted Infections (STD) that would infect both male and female] Trichomoniasis Intracellular Parasites - are microparasites that are capable of growing and reproducing inside the cells of a host, eg Plasmodium spp. (瘧原蟲) cause malaria (瘧疾); virial infection is classified as “Intracellular Parasites”. P. falciparum found inside RBC o Ectoparasite – parasitic that lives on the outer surface of its host eg skin surface or hair Ticks Mites Fleas Lice 蜱蟎蚤蝨短小扇头蜱恙蟎(恙蟎種) 印鼠客蚤 Head lice (頭蝨 ) Rhipicephalus pumilio adult chigger mite (Trombicula spp.) Xenopsylla cheopis Pediculus humanus capitis (Assafa et al., 2004) Host-parasite Relationship o Obligate Parasite (專性寄生蟲) - This parasite is completely dependent on the host during a segment or all of its life cycle, e.g. Plasmodium spp. (瘧原蟲) cause malaria (瘧疾) o Facultative Parasite (兼性寄生蟲) - organism that exhibits both parasitic and non-parasitic modes of living and hence does not absolutely depend on the parasitic way of life, but is capable of adapting to it if placed on a host. E.g. Naegleria fowleri (福氏耐格里變形蟲), a free-living amoeba lives in soil and warm freshwater lakes, rivers, ponds, on some occasions, water containing may infect humans causing primary amebic meningoencephalitis (PAM). o Accidental Parasite (偶然性寄生蟲) - when parasite enter an unnatural host accidently and survives. e.g. Myiasis (蠅蛆病) is the infestation of tissues of humans or vertebrate animals by fly larvae (蒼蠅幼蟲) (maggots 蠅蛆). (Assafa et al., 2004) Oral myiasis in Hong Kong - a case report Tak-shun Poon 潘德信 HK Pract 2006;28:388-393 Summary Oral myiasis - is the medical term for the invasion of parasitic larvae of flies in the oral cavity. … We present a case of oral myiasis in a 90-year old Chinese woman, who attended our emergency department in November 2004 because of fever and upper lip swelling. We also discuss cases reported in Hong Kong, the life cycle and characteristics of the Chrysomya bezziana, and identify the predisposing factors among local patients and its intervention. 20 Living maggots were removed Maggots were found inside Adult - Chrysomya bezziana Larvae – Chrysomya the mouth 蛆症金蠅 bezziana A female fly can lay as many as 150-500 eggs each time. The eggs hatch within 8-24 hours and newly emerged larvae burrow through the skin to the underlying tissues where they usually congregate together. Larvae tend to penetrate deeply into tissues so that infections near the eyes, nose and mouth or wound (PCAS FEHD, 2022; Poon, 2006) 在 Symbiosis (Symbiotic Relationships) (共生關係) Symbiosis is to describe the types of relationship regarding close and long term biological interaction between host and parasite, types including following - o Mutualism (互利共生) – both the parasite and the host get benefit from their relationship. For example, human microbiota, in particular intestinal normal flora keep host's physiological metabolic system health, and such flora get benefit from obtaining nutrients and habitat they need. o Commensalism (偏利共生) – the host is neither harmed nor benefited from the relationship, but the parasite gets the benefit. mite specie - Demodex folliculorum reside on the skin of humans, feeding on dead skin cells, they are usually harmless but can cause problems for people with weakened immune systems. o Parasitism (寄生關係) – the parasite gets benefit and in return it harms the hoist from the relationship, e.g. worms like Roundworms (Ascaris species) [蛔蟲(蛔蟲屬)] reside in the gastrointestinal tract of human, which the hoist providing food and protective environment. However, the worms cause health problems. (Chee et al., 2020) Microbes – Size in Micron Micron (µm) also known as micrometer is a length of measurement equal to one millionth of a meter. (1,000µm is equal to 1mm. ) (Aryal, 2015; US EPA, 2023) Microbes Classification Phenotypic observable characteristics include behaviour, morphology (includes 表現型 colony shape, size, and surface features); biochemical properties (staining properties, serotyping, antibiograms, cultural characteristics) Analytic We will talk it in the forthcoming lectures Genotypic Video - Microbes Size Comparison - 3D https://www.youtube.com/watch?v=h0xTKxbIElU Medical Microscopy Use for Microbiology Bright-field microscopy – commonly use model, uses light to illuminate a sample and create an image. The resolution of a light microscope is around 0.2 μm ie 200 nm Ocular lens Objective lens Objective lens X Ocular lens Blood smear from a patient = Total magnification Preparing Blood Smears with malaria; arrows show Plasmodium falciparum parasites infecting some red blood cells. Electron Microscope Unit o An electron microscope is a microscope that uses a beam of electrons as a source of illumination o A scanning electron microscope (SEM) is a type of electron microscope that produces images of a sample by scanning the surface with a focused beam of electrons. The resolution of electron microscope is around 0.1 nm, which compares to about 200 nm for light microscopes image of 229E coronavirus, 1975. Electron micrograph of a bacteriophage Electron Microscope Unit Credit: Fred Murphy, 1975, CDC. What Are Light And Electron Microscopes? - How Do They Work? https://www.youtube.com/watch?v=cQuX8tfwlYA Colony Morphology Bacterial (or fungal) colony morphology refers to the visual appearance of colonies on an agar plate Gram-positive bacterium, Bacillus anthracis, which were cultured on sheep blood agar (SBA) medium colonies of Gram-negative, Proteus mirabilis bacteria, grown on a xylose- lysine-deoxycholate (XLD) agar plate Bacterial Morphology By Shape / Bacterial Arrangements (1 of 2) Bacteria are classified into following groups and they can exist as single cells, in pairs, chains or clusters. Coccus (plural = cocci) Bacillus (plural= bacilli) Spirillum (plural= spirilla) Spherical-shaped Rod- shaped spiral-shaped Coccus / cocci Diplococci Bacillus / bacilli Diplobacilli Spirochete (螺旋體) (球菌) (雙球菌) (桿菌) (雙桿菌) Spirilla / Spirillum 螺旋菌 Tetrad Sarcina Staphylococci (Helical-shaped/Corkscrew form) Streptobacilli (鏈桿菌) (四聯球菌) (八疊球菌) (葡萄球菌) Streptococci (鏈球菌) Vibrio (弧菌) Coccobacilli Palisades 栅状 (球桿菌) (Aryal, 2023; Kaiser, 2022) Bacterial Morphology By Shape / Bacterial Arrangements (2 of 2 ) – for reference only Filamentous Pleomorphic Appendaged bacteria that are bacteria that do bacteria that long, thin, and not have a produce a unique filament-shaped. specified shape structure like pillus are included in or fimbriae are this group. called appendaged bacteria. Actinomyces israelii Mycoplasma pneumoniae Neisseria gonorrhoeae Box-shaped/ Rectangular Star-shaped Triangular-shaped bacteria are bacteria that look rectangular in like stars or are bacteria that are shape and star-shaped are triangular in shape. resemble a box. included in this group. Haloarcula marismortui Stella humosa Haloarcula japonica Biochemical Properties – Identify Bacteria By Gram Stain o A Gram stain is a common laboratory test that can help diagnose the presence of a bacterial infection quickly. o prompt identification types of bacteria causing infection and to commence treatment ASAP. Bacteria cell wall mainly made of Stain RED peptidoglycan Stain Purple The Ziehl-Neelsen stain, also known as the acid-fast stain, is a bacteriological staining technique used to identify acid-fast bacteria under microscopy, Gram-negative bacteria Gram-positive bacteria particularly members of the Thin and single layer cell wall Thick and multi layers of cell wall with Mycobacterium genus. with peptidoglycan AND WITH peptidoglycan but WITHOUT outer membrane outer membrane (Division of Laboratory Systems CDC, n.d.; Hussey & Zayaitz, 2008) Details for Biochemical Properties - staining properties, serotyping, antibiograms, cultural characteristics, will talk later Virus (plural: viruses) o Virus infect every form of life on Earth, including but not limited to human, animals and plants, but also bacteria, protozoa, fungi, algae; even bacteria suffer from viral infections ie Bacteriophages o capsomere is a subunit of the capsid, an outer covering of protein that protects the genetic material of a virus, forming the capsid Electron micrograph of a bacteriophage (Aryal, 2018; Cleveland Clinic, 2023) Virus Shape Helical Viral Genome Spike Protein (DNA/RNA) (glycoprotein) Capsid Capsid Viral Genome capsomere (DNA/RNA) capsomere mastadenovirus Tobacco Mosaic Virus Complex Spherical combine more than one shape Viral Spike Protein Genome Icosahedral (glycoprotein) (DNA/RNA) (Head) Capsid Capsid Helical Envelope (Tail sheath) Viral Genome (DNA/RNA) Coronaviruses Electron micrograph of a bacteriophage. Source: Molecular (Tail sheath) Tool http://www.bio.davidson.edu/Courses/Molbio/ MolStudents/spring2003/Keogh/plasmids.htm Images: CDC Public Health Image Library(PHIL) (Wells, 2018) Viral Structure o Viral Genome / Genome - Viruses contain nucleic acid Viral Genome as either RNA or DNA, called DNA virus or RNA virus, (DNA/RNA) respectively; vast majority of viruses have RNA genomes. Capsid DNA/RNA Single - or Double - Linear Circular (protein shell) stranded stranded Non-enveloped Virus (naked viruses) eg. norovirus Spike Protein (glycoprotein) o Spike Protein is a viral fusion protein on the outer virus that plays Envelope a critical role in viral infection by recognizing host cell receptors (phospholipid bilayer) and mediating the fusion of viral and host cell membranes Envelope Virus (lipid-enveloped viruses) eg. SARS-Cov-2 (Course Hero, n.d; The LibreTexts libraries, 2024) Bacterial Structure (1 of 2) Capsule Pillus Mesosome o Bacterium (plural: bacteria) Cell wall o prokaryotic, unicellular microorganism Plasma Nucleoid o Capsule - outer polysaccharide layer of some bacterium Membrane o Cell wall - mainly made of peptidoglycan; it is a polymer Ribosome of sugar and amino acids that forms a mesh-like layer Cytoplasm o Plasma Membrane - Composed primarily phospholipid Fimbriae and protein o Nucleoid (meaning Nucleus-like) - an irregularly shaped Inclusion Plasmid region contains all or most of the genetic material, usually contains only one chromosome. Flagellum / Flagella o Cytoplasm - gelatinous liquid that fills the inside of a cell, composed of water, salts, and various organic molecules o Plasmid – A small circular DNA molecule, plasmid DNA would cellular components are move from one cell (donor species) to another cell (recipient called cell organelles species) through direct contact. (Salton & Kwang, 1996) Bacterial Structure (2 of 2) Pili Capsule o Ribosome - made of both RNA and protein, and it is the Mesosome site of protein synthesis in the cell. Cell wall o Flagellum ( 鞭毛 ) - (plural flagella) for bacterial Plasma Nucleoid locomotion Membrane Ribosome o Mesosome - These extensions help in the synthesis of the cell membrane, replication of DNA, and protein Cytoplasm synthesis Fimbriae o Inclusions - various nutrients or pigments that can be Plasmid Inclusion found within the cell, non-living substances, do not have activity like other organelles. Flagellum / o Pili - (single: pilus) are hair-like structures on the cell surface of prokaryotic Flagella cells; more often involved in adherence to surfaces, which facilitates infection, and is a key virulence characteristic; transfer DNA (plasmid) between bacteria during conjugation. o Fimbriae - are short pili enable bacteria stick to each other and to surfaces. (Salton & Kwang, 1996) Fungal Structure o Fungus (plural: Fungi) o Fungi are neither plants nor animals, and belong to fungi kingdom o Eukaryotic; non-phototrophic; chemoheterotrophs o cell walls have chitin. This is the same material as the hard outer shells of insects and other arthropods. however, plants do not make chitin Heterotrophs are organisms that consume other organisms for energy. Animals, fungi, and many protists and bacteria are heterotrophs Mushrooms are the multicellular reproductive structure produced by some fungi Molds are fungi form in multicellular fibers called hyphae Yeats are fungi growing as unicellular (The LibreTexts libraries, 2021; The LibreTexts libraries, 2023) Protozoan (plural: protozoa)原蟲 o Protozoa belongs to the kingdom Protista. o Unicellular eukaryotic organism; no cell wall o Can be free-living or parasitic in nature o Most protozoa are microscopic in size; only a few would be visible to naked eye o Protozoa have the ability to move through their environments, allowing them to locate and find food. o Classified into 4 groups based on mode of movement Amoeba Flagellates Ciliates Sporozoa which move using temporary with tail-like structures which move by beating multiple intracellular parasites cell body projections (Flagellum / Flagella) hair-like structures called cilia called pseudopods that flap around to Plasmodium falciparum Entamoeba histolytica move them Balantidium coli 惡性瘧原蟲溶組織內阿米巴 Giardia duodenalis 大腸纖毛蟲十二指腸賈第蟲 (Australian Society for Parasitology, n.d.; Yaeger, 1996) Medically Important Protozoa (example) Urogenital Tract - Intestinal- Tissue- Blood - Protozoa Protozoa Protozoa Protozoa Trichomonas vaginalis Entamoeba spp. Toxoplasma gondii Plasmodium spp. Trichomoniasis Amebiasis Toxoplasmosis Malaria 陰道滴蟲病阿米巴性痢疾弓形蟲感染症瘧疾 Images: DCDC Public Health Image Library(PHIL) (MSF, n.d.) Algae (藻類) o Algae (singular, alga), Eukaryotic (True Nucleus) o Plant-like protists found in water (sea/fresh) and soil; do not have roots, stems, or leaves; some would move with pseudopods or flagella o composed of chlorophyll pigment, make food by photosynthesis, ie autotrophic o Are algae in green colour? The answer is no. They can be of other colours like red (red algae), brown (brown algae), olive green etc o word algae means 'seaweeds' in Latin. Algae have been part of the human diet, eg 紫菜, 昆布, 海带, 髪菜 o Most species of algae do not cause threats to the environment and human - algae are classified as one of the microscopic organism of phytoplankton (浮游植物), the foundation of the aquatic food web algae produce oxygen via photosynthesis, responsible for approximately 70% of all atmospheric oxygen. Diatoms Dinoflagellates (硅藻) (甲藻) unicellular algae (example) Other forms of algae are multicellular (example) (EABA, n.d.) Algal Blooms o Algal bloom can change the color of the water—for example to green, blue, brown, or red; local called as “Red Tide 紅潮” o 81 species are associated with local algal blooms, however, only 22 are classified as toxic algae, majority - dinoflagellates (甲藻) are classified under the Class Dinophyceae. Diatoms (硅藻) are classified under the Class Bacillariophyceae. o harmful algal blooms (HABs) may cause Harmful Algal Blooms (HAB) Associated Illness, causing mild to life-threatening symptoms in people and animals, and fish kill, medical important poisoning types are - Ciguatera Fish Poisoning 雪卡毒魚類中毒 Paralytic Shellfish Poisoning 麻痺性貝類毒素 https://www.youtube.com/watch?v=icexVKhfeo8 Percentage of red tide incidents caused by different phytoplankton groups (Law, 2018; YAU, 2018; YAU, 2021) Helminth (plural: Helminths)蠕蟲 o Multicellular eukaryotic organism, kingdom animalia, invertebrates o cause Helminthiasis (蠕虫病)- a medical condition characterized by the infestation of parasitic worms in human (affecting almost 2 billion people) and other animals body o Infections can occur through ingestion of contaminated food or water, contact with infected soil or transmission by insect vectors. o Ova seen in microscope, generally visible to the naked eye in their adult stages o long, flat or round bodies, size ranging from 1 mm to 25 m (longest tapeworms) in length o Some are monoecious (雌雄同株), having both male and female reproductive organs in a single individual, while others are dioecious (雌雄異體) (OpenStax Microbiology, n.d.) Medically Important Helminths (example) Roundworms Pinworms Hookworms Tapeworms Liver flukes 蛔蟲蟯蟲鈎蟲縧蟲肝吸蟲 Clonorchis sinensis Angiostrongylus sp. Enterobius vermicularis Ancylostoma duodenale Taenia saginata 中華肝吸蟲 round in shape round in shape flat in shape flat in shape flat, leaf-shaped Nematodes Nematodes Cestodes Cestodes Trematodes 綫蟲綱綫蟲綱絛蟲綱絛蟲綱吸蟲綱 male worm, Adult males measure up to Adult hookworms measure adult worm is ~ 4 meters (Photo: Dr. Samson S.Y. Wong, 2.5 mm long by 0.1-0.2 in length. Department of Microbiology, approximately 4.25 mm in approximately 8—12 mm University of Hong Kong length, mm wide Images: DCDC Public Health Image Library(PHIL) (CHP, 2023; OpenStax Microbiology, n.d.) Clonorchiasis (中華肝吸蟲感染症) Eggs (蟲卵) Clonorchis sinensis (中華肝吸蟲) Miracidia (尾/毛動幼蟲) Sporocysts (胞動幼蟲) Rediae (雷氏幼蟲) Cercariae (尾動幼蟲) Free swimming cercariae Metacercariae (囊狀幼蟲) (CDC, 2019;中華民國比較病理學會, et al., n.d.) Sexual & Asexual Reproduction Producing Offspring Asexual Reproduction generates offspring that are genetically identical to a single parent Sexual Reproduction two parents contribute genetic information to produce unique offspring, ie fertilization is required. Reproduction of Bacteria - Binary Fission Binary Fission - a type of asexual reproduction where a parent cell divides, resulting in two identical cells, each having the potential to grow to the size of the original cell. The word asexual describes a reproduction that occurs without involving sex cells (gametes). https://www.youtube.com/watch?v=s4p-H5bk9xI Reproduction of Fungi - Mold A mushroom is the reproductive structure o Most molds can reproduce both asexually and sexually. produced by some fungi. o Asexual reproduction can occur by fragmentation—if the mycelium (菌絲體) is physically separated, many of the pieces will continue to grow. o Another form of asexual reproduction involves spores. https://www.youtube.com/watch?v=IaZrt3CvNR4 spores (GeeksforGeeks, 2024) What is Spore (孢子)? o Spores are reproductive units produced by some fungi, plants, and bacteria. o unicellular or multicellular. o Spores have thick walls. They can resist high temperatures, humidity, and other harsh environmental conditions. o Only sterilization would kill spore; even high-level chemical disinfectants, it can kill spores from Bacillus bacteria, but not spores. anthracis bacteria Major Spore-forming Bacteria Bacillus anthracis 炭疽桿菌 Clostridium tetani 破傷風梭菌 Bacillus cereus 蠟樣芽孢桿菌 Clostridium perfringens 產氣莢膜梭狀芽孢桿菌 Clostridium botulinum 肉毒桿菌 Image – CDC Public Health Image Library (PHIL) (Basta & Annamaraju, 2023) What is Budding? Budding is an asexual mode of producing new organisms Budding in Yeast Budding in Hydra (Biologysir, 2023; Career Power School, 2023) Reproduction of Virus – Viral replication SARS-CoV-2 cell lysis Budding (Oiseth, Jones & Maza, 2022) Bacteriophages (Phages)(噬菌體) o "bacteriophage" literally means "bacteria eater“; are viruses that infect bacteria https://www.youtube.com/watch?v=mdKpHtVP19s&t=3s Examples of RNA viruses are influenza, SARS, MERS, COVID-19, Examples of DNA viruses are herpes, smallpox, Dengue virus, hepatitis C, hepatitis E, West Nile fever, Ebola virus hepatitis B, adenoviruses, and warts disease, rabies, polio, mumps, and measles. RNA viruses have a higher mutation rate when compared to DNA viruses. Also, their genetic diversity makes it difficult to produce effective vaccines against them. (@osmosis, 2020) Population Growth Curve Although bacteria are capable of replicating geometrically as a result of binary fission, in reality this only occurs as long as their is space to grow, sufficient nutrients, and a way to dispose of waste products. Because these factors limit the ability to replicate geometrically, over time in a closed growth system a bacterial population usually exhibits a predictable pattern of growth - its growth curve - Growth Curve https://www.youtube.com/watch?v=JpnH_6kqvdw Growth curve The growth of microbes undergoes different phases Lag phase - Microbes are adapting the new environment - Not yet multiplying at their maximum rate Exponential growth phase (Log phase) - Cells reach the maximum rate of cell division Stationary phase - The division rate is going down due to depleting nutrients and accumulating metabolic by- products - Rates of cell birth and cell death are more or less equal Death phase - Nutrients exhaust and microbes die at an exponential rate (Bruslind, 2021) Microbial Growth Temperatures - Minimal temperature: Lowest temperature that permits a microbe’s continued growth and metabolism - Maximum temperature: Highest temperature at which growth and metabolism proceed - Most medically important microorganisms are mesophiles (嗜温生物) ie organisms that can grow best in human body temperature at around 37°C - Psychrophile (嗜冷生物): organisms that grow over the range of subzero to 20˚C, with an optimum range of 10- 15˚C. - Psychrotroph ( 低温性生物 ): organisms that can grow at temperatures between 0˚C and 7˚C (Parker et al., 2021) Microbial Growth – Oxygen Obligate Aerobes Obligate Anaerobes Facultative Anaerobes Aerotolerant Anaerobes Microaerophiles 專性好氧菌專性厭氧菌兼性厭氧菌氧耐厭氧菌微需氧菌 Cannot growth Cannot survive with Do not require oxygen Do not utilize oxygen but Are harmed by normal without oxygen oxygen; lack of for metabolism but use can survive and grow in its atmospheric enzyme processing it when it is present presence concentrations of oxygen toxic oxygen but require a small amount of it in metabolism (EdUHK, n.d.; Westin, 2020) Microbial Growth Temperature o mesophiles (“middle loving”) - microbes are adapted to moderate temp, with optimal growth temp ranging from room temp (about 20 °C) to about 45 °C. o Sychrotrophs - microbes prefer cooler environments, from a high temp of 25 °C to refrigeration temp about 4 °C o Psychrophiles - microbes that can grow at 0 °C and below, have an optimum growth temp close to 15 °C, and usually do not survive at temp above 20 °C. Nutrients o Non-fastidious: Does not require specific nutrients o Fastidious: Require specific nutrients pH o Neutrophilic - Most microbes are neutrophiles, meaning they grow optimally at a pH within one or two pH units of the neutral pH of 7 o Alkaliphilic - microbes that grow at high pH of 8 or higher o Acidophilic - microbes that grow at low pH below 3–4. Osmotic pressure o Non-halophilic: do not prefer high salt concentration Blood Agar chocolate Agar Nutrient Agar o Halophilic: prefer higher concentration of salt (Irshad et al., 2014; Parker et al., 2021) Formation of Biofilms (1 of 2) o Biofilms (生物膜) are commonly found in nature, eg the slippery coating on rocks near rivers. o However, biofilms related to healthcare would increase infection risk, eg accumulation of dental plaque would cause oral diseases such as tooth decay and gum disease; bacteria attach to other cells bacteria secrete matrix bacteria in biofilm communicate through signaling and surfaces through hair-like consisting of extracellular molecules called autoinducers that are produced structures on their surface polymeric substances in response to changes in cell-population density. called pili and fimbriae (EPS) made up of This mechanism of cell-to-cell communication is proteins, lipid, called “quorum sensing” polysaccharides, and DNA act as cementing materials Bacteria reversibly Irreversible attachment Microcolony Biofilm maturation: Dispersal attach to surface and formation of formation of bacteria increased cell density; extracellular polymeric intercellular signaling substances (EPS) Cycle repeat (Basic Science Series, 2019; Sharma et al., 2023) Formation of Biofilms (2 of 2) Biofilm is extremely hard to detect and eradicate, because biofilm protects bacteria from being ingested by immune cells and being killed by antibiotics; commonly formed in - Urinary catheter would cause Catheter-Associated Urinary Tract Infections (CAUTI) IV catheter would cause Associated Blood Stream Infections (CABSI) water piping causing accumulation of Legionella would cause Legionnaires' disease (LD) https://www.youtube.com/watch?v=VJ1QsM9z6sI https://www.youtube.com/watch?v=97vX_jDhSqM (Basic Science Series, 2019; Sharma et al., 2023) The End Click Here for reference list

Tung Wah College NUR1016 Microbiology and Pharmacology Lecture (L01) 2024/2025 PDF

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