Introduction to Medical Microbiology and Virology 2023

INTRODUCTION TO MEDICAL MICROBIOLOGY AND VIROLOGY 2023 LECTURE OBJECTIVES By the end of the lecture the learner should be able to:  To understand differences between bacteria, viruses, fungi, parasites  To differentiate commensal microbes from pathogens  To understand common terminologies used fo...

INTRODUCTION TO MEDICAL MICROBIOLOGY AND VIROLOGY 2023 LECTURE OBJECTIVES By the end of the lecture the learner should be able to:  To understand differences between bacteria, viruses, fungi, parasites  To differentiate commensal microbes from pathogens  To understand common terminologies used for infections such as pathogens, contamination, virulence, colonization, epidemics, pandemics, source, reservoir etc.  To have a basic understanding of the characteristics of different bacteria, viruses, fungi, parasites OUTLINE  Introduciton  Definitions  Pathogenecity  Nomenclature  Bacteria  Fungi  Parasites  Viruses INTRODUCTION  Medical / Clinical Microbiology and Virology is the study of microscopic living forms  Some can live only in other cells (e.g. all viruses and some bacteria)  Others include macroscopic forms in their life cycles (e.g. fungal moulds, parasitic worms)  Major classes of micro-organisms in terms of ascending size and complexity include viruses, bacteria, fungi and parasites such as protozoa and helminths INTRODUCTION Some are eukaryotes while others are prokaryotes Eukaryotic cells contain a true nucleus with the genetic material [ DNA ] & chromosomes surrounded by a nuclear membrane  Humans, animals, plants, parasites, fungi Prokaryotic cells contain nuclear material that is NOT surrounded by a nuclear membrane  All bacteria INTRODUCTION  Viruses are not cells at all. They must take over machinery of another living cell(eukaryote/prokaryote) to replicate  Bacteria have a cell wall but lack the organelles of eukaryotic cells  Fungi are eukaryotic and have a rigid external wall that makes them seem more like plants than animals  Parasites exist as single (unicellular) or multicellular structures with the same compartmentalized eukaryotic cell plan including a nucleus and cytoplasmic organelles like mitochondria INTRODUCTION  This module includes the study of the interaction of micro-organisms with the human host which results in disease  The resultant diseases are termed infectious diseases Micro-organism = BUG Host = MUG Antibiotic = DRUG INTRODUCTION The presence of micro-organisms on or in humans is normal Humans harbour 10x the number of microbial cells than human cells Micro-organisms play a role in both human health and disease  Microorganisms play a USEFUL ROLE:  Commensal/ Normal flora  Degeneration of organic matter  Biotechnological areas – medicines, vaccines  Production of cheese, yogurt, beer and wine DEFINITIONS  Commensal organisms = Normal flora = Microbiota  These are microorganisms that are frequently found colonizing various body sites in healthy individuals  Constituents and numbers vary in different body areas and sometimes at different ages and physiologic states  Their morphologic, physiologic, and genetic properties allow them to  colonize and multiply under the conditions that exist in particular sites  to exist with other colonizing organisms and to inhibit competing intruders DEFINITIONS Residents  These are strains that have an established niche at one of the many body sites, which they occupy indefinitely Transients Are acquired from the environment and establish themselves briefly, but tend to be excluded by competition from residents or by the host’s innate or immune defense mechanism Pathogens  Microorganisms that possess the ability to cause infections  They are associated with disease with varying frequency and severity DEFINITIONS Contamination  Presence of micro-organisms for short period (transient) without damage or invasion Colonisation  Continued presence of organisms for long periods (months, years) without causing damage or invasion  Contagious  Can spread between people DEFINITIONS Carrier state  When pathogenic organisms establish themselves in a host without manifestation of symptoms  The hosts-carriers are capable of transmitting the infection  May be chronic (Salmonella enterica ser. Typhi) / acute(Neisseria meningitidis)/ transient (inoculation of one’s hand with Staphylococcus aureus) Reservoir  Where organism/pathogen lives & multiplies e.g. humans, animals, soil, water DEFINITIONS Source  Site from which organism/pathogen spreads to host, e.g. soil is reservoir for parasites whilst vegetables contaminated with (ova, cysts) serve as a source for transmission to humans or animals Sometimes reservoir & source can be same e.g. Streptococcus pyogenes causing sore throat e.g. Staphylococcus aureus causing skin infections DEFINITIONS Infection  Damage or invasion of host tissues by organisms  Occurs with Primary/ Professional pathogens or Opportunistic pathogens  Can be life-threatening  Many are treatable with anti-infective agents  Prevention is possible for many infectious diseases with vaccines DEFINITIONS Epidemics  Increase, often sudden, in the number of cases of a disease above what is normally expected in that population  Pandemics  Is the worldwide spread of a new disease. E.g., Corona virus PATHOGENICITY Pathogenicity  Ability of an organism to cause disease in a susceptible individual Pathogens may be:  Primary/ Professional pathogens  Cause infections in patients with normal immunity  Yersinia pestis, Bacillus anthracis  Opportunistic pathogens  Cause disease in patients with depressed immunity  Also occurs when their habitat is damaged, disturbed or changed  Haemophilus influenzae, Staphylococcus epidermidis PATHOGENICITY Virulence  Refers to the degree of damage caused by a microbe to its host  Multiple factors called virulent factors are required for an organism to attach, persist, cause disease and escape to repeat the cycle  Some such as capsules and toxins are used by many organisms  Others are specialized and specific to one particular organism- tissue tropism of the gonococcus PATHOGENICITY Attachment / adherence and persistence  Involves specialized surface molecules / structures that correspond to receptors on human cells  May be enough for some toxin producing organisms to cause disease  Secretory antibody, lactoferrin, and lysoz yme all are produced by the host as a way to protect against infection  Lactoferrin competes with bacteria for free iron  Adhesions – fimbriae (pili) , surface polysaccharides PATHOGENICITY Invasion into or beyond the surface mucosal cells  Ability to penetrate and grow in tissues  May be localized / may involve deep tissues  Invading organisms should be able to adapt to the new environment  Very essential for viruses since they cannot replicate on their own PATHOGENICITY Evasion of the immune system  Phagocytosis evasion / phagocytic cell killing  Inhibit activation of complement pathway  Polysaccharide capsule / Protein A / leukocidins Dissemination  Spread to distant sites, e.g. hematogenous NOMENCLATURE Giving of names to specific taxonomic groups, based on published guidelines The most general sequence of classification is:  Kingdom  Phyla or Divisions  Class  Order  Family  Genus  Species NOMENCLATURE Binomial system is used for micro-organisms:  Genus and Species  Genus: Similar for different species  Species: Most basic taxonomy group which characterize bacteria based on phenotypic and genotypic differences Examples: 1) Escherichia (genus) coli (species) 2) Staphylococcus (genus) aureus Staphylococcus (genus) epidermidis NOMENCLATURE Genus name starts with a capital letter Species name written in small letters Written in italics or underlined  Staphylococcus aureus  Staphylococcus aureus  Cryptococcus neoformans = yeast  Enterobius vermicularis = parasite BACTERIA Prokaryotic – No nuclear membrane, true nucleus, endoplasmic reticulum, mitochondria or Golgi bodies Unicellular organisms Gram negative, Gram positive bacteria Cell wall – provides rigidity & important for staining BACTERIA Gram staining  Crystal violet (the primary stain, 1 minute)  Iodine (the fixative, 1 minute)  Alcohol or an alcohol acetone solution (the decolorizer, quick on and rinse)  Safranin (the counterstain, 30 seconds) Rinsing with water between each step is important BACTERIA Gram staining  The bacteria are initially stained purple by the crystal violet, which is bound to the cell wall with the aid of iodine  When decolorizer is applied to bacteria with a Gramnegative type of cell wall structure, the crystal violet washes out of the cells, which take up the pink counterstain, safranin BACTERIA Gram staining  Therefore, Gram-negative bacteria appear pink / red under the light microscope  Bacteria with a Gram-positive cell wall retain the primary crystal violet stain during the decolorizing treatment and appear purple/blue Other stains:  Ziehl-Neelsen(ZN) for Mycobacterium tuberculosis - Acid fast BACTERIA:GROWTH AND METABOLIC REQUIREMENTS  Obligate aerobes require oxygen for growth Nocardia species. Require 15-21% O2  Obligate anaerobes cannot grow in the presence of oxygen. Require 0% O2. E.g., Most Bacteroides spp.  Aerotolerant anaerobes can survive in the presence of oxygen but do not use oxygen in metabolism (e.g., certain Clostridium spp.). Require reduced concentrations of O2 BACTERIA:GROWTH AND METABOLIC REQUIREMENTS  Facultative anaerobes can grow either with or without oxygen - Escherichia coli  Capnophilic organisms grow best when the atmosphere is enriched with extra carbon dioxide (5 to 10%) – Haemophilus influenzae  Microaerophilic bacteria require a reduced level of oxygen(5%) to grow - Camp ylo bacter species BACTERIA:SHAPES Coccus/cocci Bacillus/bacilli/ rods Curved bacillus/bacilli Cocco-bacillus/ short rods BACTERIA:SHAPES Spirochaete Filamentous bacteria BACTERIA:ARRANGEMENT COMMON BACTERIA:NAMES GRAM POSITIVE COCCI Staphylococci Streptococci Enterococci GRAM POSITIVE BACILLI Corynebacterium Nocardia Bacillus COMMON BACTERIA:NAMES GRAM NEGATIVE BACILLI ENTEROBACTERIACEAE NON FERMENTATIVE BACILLI Escherichia Pseudomonas Klebsiella Acinetobacter Citrobacter Burkholderia Enterobacter Morganella Proteus Salmonella Shigella Yersinia COMMON BACTERIA:NAMES ATYPICAL BACTERIA ANAEROBES Rickettsia Clostridium Coxiella Bacteroides Chlamydia Actinomycetes Mycoplasma Ureaplasma FUNGI Eukaryotic – nuclear membrane, endoplasmic reticulum, mitochondria, Golgi bodies Forms/groups: Unicellular = yeast Multicellular = Moulds [Filamentous form ] Thermally dimorphic = Exist as both forms: yeast @ 37 C or mould @ 25 C cryptococcus candida mould FUNGI Unicellular fungi (yeast)  E.g. Cryptococcus  E.g. Candida Multicellular fungi (moulds)  E.g. Aspergillus and Fusarium Thermally dimorphic fungi (yeasts & moulds)  E.g. Histoplasma capsulatum and Sporothrix schenkii YEASTS Cryptococcus neoformans Meningitis Cryptococcal choroiditis Candida spp. Candidiasis: skin, Candida albicans is mucosa, systemic the most common infection cause of fungal Hematogenous infections, however dissemination of non Candida albicans Candida species to the species are on the rise eyes CHRONIC DACROCYSTITIS MOULDS Microsporum species Trichophyton spp. Epidermophyton spp. = Dermatophytes Infections of the skin, hair and nails, e.g. ringworm, athlete’s feet – even healthy people Aspergillus spp. KERATITIS Lung infections in immunocompromised Mucor, Rhizopus, Absidia Rhino-cerebral mucormycoses Severe ORBITAL INFECTIONS THERMALLY DIMORPHIC FUNGI 25°C: moulds 37°C: yeasts Sporothrix schenkii Histoplasma capsulatum Coccidioides immitis Sporotrichosis (subcutaneous infection) Granulomatous conjunctivitis Respiratory infection; systemic infection POSTERIOR UVEITIS (CHORIORETINITIS) Malaria PARASITES  All parasites - Eukaryotic  Protozoa = unicellular  Helminths = worms multicellular (not really microbes) T. vaginalis  Complex life cycles  Infective forms – cysts, ova, larvae  May involve vectors e.g. mosquitoes, flies etc. PARASITES Unicellular parasites = Protozoa  Amoebae  Ciliates  Sporozoa (Coccidia )  Flagellates Multicellular parasites = Helminths  Nematodes (round worms)  Cestodes (tapeworms)  Trematodes (flukes) PROTOZOA Subgroups* Examples Type of infection(s) Flagellates Giardia lamblia Trichomonas vaginalis Diarrhoea Trichomoniasis (a sexually transmitted infection) Amoebas Entamoeba histolytica Dysentry [bloody diarrhoea] Naegleria fowleri Meningo-encephalitis KERATITIS KERATITIS Toxoplasmosis CHORIORETINITIS (POSTERIOR UVEITIS) Coccidia Acanthamoeba Toxoplasma gondii Haemosporidia Plasmodium species Ciliates Balantidium coli *Not essential to know this Malaria (can also have ophthalmic signs and symptoms) ? Diarrhoea HELMINTHS Cestodes (tapeworms) Taenia solium Gastrointestinal symptoms Trematodes (flukes) Fasciola hepatica Liver infections Nematodes (roundworms) Ascaris lumbricoides Gastrointestinal infections Enterobius vermicularis Gastrointestinal infections Peri-anal pruritis (itching) Toxocara canis Toxocara cati Visceral larva migrans CHORIORETINITIS (POSTERIOR UVEITIS) VIRUSES Smallest infectious particles  Nucleic acid = DNA or RNA  Protein shell = capsid  May have lipid membrane enclosing capsid = Enveloped virus  No lipid membrane enclosing capsid = Naked virus  Infection – leads to cell destruction or long term latent infection Prions  Virus-like particles, no DNA or RNA TYPE OF NUCLEIC ACID DNA Viruses EXAMPLES TYPE OF INFECTION(S) Variola virus Smallpox Herpes simplex type I (HSV I) Fever blisters (oral herpes) Herpes simplex type II (HSV II) Keratitis Genital herpes (Sexually transmitted infection) Varicella-zoster virus (VZV) Chickenpox, Shingles Conjunctivitis / Keratitis Cytomegalovirus (CMV) Eye infection (e.g. Retinitis) Ebstein-Barr virus (EBV) Infectious mononucleosis Adenovirus Sore throat, URTI Conjunctivitis Human papilomavirus (HPV) Warts Certain tumours e.g. cervix Hepatitis B virus (HBV) Hepatitis (Liver infection) Jaundice TYPE OF NUCLEIC ACID RNA Viruses EXAMPLES TYPE OF INFECTION(S) Enterovirus Poliomyelitis Haemorrhagic conjunctivitis Rhinovirus Common cold Coxsackie virus Chorioretinitis, Posterior uveitis Influenza virus (A,B,C) Influenza (“flu”) Hepatitis A Jaundice Measles, mumps and Measles, mumps, German rubella virus measles Common childhood diseases HIV (Human immuno- AIDS deficiency virus) VIRAL REPLICATION Main steps in viral replication:  Adsorption (attachment)  Penetration  Exposure of the viral nucleic acid  Eclipse phase (molecular events)  Assembly (maturation)  Release