RCSI Classification of Microbes and The Microbiome and Health PDF

Leading the world to better health Classification of Microbes and The Microbiome and Health Dr Aoife Kearney (PhD) Clinical Lecturer Department of Clinical Microbiology Royal College of Surgeons in Ireland  RCSI Royal College of Surgeons in Ireland Coláiste Río...

Leading the world to better health Classification of Microbes and The Microbiome and Health Dr Aoife Kearney (PhD) Clinical Lecturer Department of Clinical Microbiology Royal College of Surgeons in Ireland  RCSI Royal College of Surgeons in Ireland Coláiste Ríoga na Máinleá in Éirinn Classification of Microbes and The Microbiome and Health Class Year 1 Course Undergraduate Medicine Lecturer Dr Aoife Kearney Date 16th October 2024  LEARNING OUTCOMES 1. Classify microorganisms as being bacteria, viruses, fungi, protozoa or arthropods 2. Differentiate microorganisms on the basis of their phenotypic and genotypic characteristics 3. Define important terms related to the human microbiome e.g. colonised, transient, symbiosis etc. 4. Discuss the various microbial components of the human microbiome i.e. bacteria, fungi and viruses and explain how the microbiome develops over time 5. Associate the microorganism with the anatomical site in which it usually resides 6. Discuss the importance of the microbiome to human health and complications that can arise when it is disrupted 7. Describe how the microbiome can be restored following disruption  Department of Clinical Microbiology – A brief overview MEET TEAM CLINICAL MICROBIOLOGY MORE ABOUT US… https://www.rcsi.com/dublin/about/faculty-of-medicine-and-health-scien ces/academic-departments/clinical-microbiology WE ARE NOT BRAVE ENOUGH FOR TIKTOK Instagram – @rcsi_micro Twitter – @RCSI_Micro  WHAT IS MICROBIOLOGY? THE STUDY OF MICROSCOPIC ORGANISMS ALTHOUGH A FEW ARE VISIBLE WITH THE NAKED EYE  WHAT IS CLINICAL MICROBIOLOGY? MICROBES THAT CAUSE COMMON OR SERIOUS DISEASES IN HUMANS. The undergraduate subject in medicine is applied microbiology Clinically orientated to facilitate patient management Infection + antimicrobial resistance = common & important worldwide (WHO Top 10 Threats) Many infections are preventable Biological diversity & evolution; new pathogens emerging (e.g. SARS-COV-2) Overlaps with other disciplines (e.g. Helicobacter pylori & peptic ulcer disease)  THEMES INCORPORATED INTO CLINICAL MICROBIOLOGY TEACHING Clinically relevant pathogens (e.g. Staphylococcus aureus, Candida albicans, etc) Scientific concepts & principles (e.g. bacterial pathogenicity, antibiotic resistance) Major infections by system (e.g. pneumonia  diagnosis & therapy) Preventing infection: – Community  vaccination – Healthcare-associated infections standard and transmission-based precautions PROFESSIONALISM Becoming a doctor involves forming values & developing behaviours and attitudes which foster professional relationships, promote public trust & enhance patient safety 2 major components in Clinical Microbiology 1. Infection Prevention & Control 2. Antimicrobial stewardship  LEARNING OUTCOMES 1. Classify microorganisms as being bacteria, viruses, fungi, protozoa or arthropods 2. Differentiate microorganisms on the basis of their phenotypic and genotypic characteristics BINOMIAL SYSTEM –SURNAME/NAME Genus & Species, e.g. – Homo sapiens – Staphylococcus aureus – Candida albicans – Plasmodium falciparum Species are similar, inter-breeding organisms within a genus Bacteria Single chromosome (genome) No cell organelles Fungi & Protozoa Nucleus (chromosomes) Mitochondria Golgi apparatus Endoplasmic reticulum  THE BACTERIAL CELL Single chromosome Plasmids (extrachromosomal DNA) Cytoplasm Ribosomes Cytoplasmic membrane Cell wall Flagellae Pili/Fimbriae More in: Overview of the Prokaryotic cell  CLASSIFICATION Based on: Phenotype = the observable (micro + macroscopic) features of an organism Genotype = the genetic make-up of an organism S aureus,. S. pyogenes, S. pneumoniae, N. gonorrhoeae, N. meningitidis  ANALYSIS OF PHENOTYPIC (PHYSICAL) CHARACTERISTICS Separating one strain from another (typing) or confirming the identification of an isolate – Biotyping (biochemical tests) – Serotyping (surface antigens) – Antibiograms (antibiotic susceptibility) – Phage typing (susceptibility to viruses) ANALYSIS OF GENOTYPIC OR PROTEOMIC (MOLECULAR) CHARACTERISTICS Proteotypical characterisation – e.g. MALDI-TOF Genotypic characterisation – e.g. PCR, Whole Genome Sequencing More in Appropriate Use of the Microbiology Laboratory  FUNGI Eukaryotes – nucleus, chromosome, mitochondria, etc. More closely related to human cells than bacteria Treatment options more limited than for bacteria – Difficult to develop chemotherapy selectively toxic to fungal vs human cells Aspergillus fumigatus on agar (Nottingham HPA) Budding yeasts on microscopy (Nottingham HPA) More in ‘Introduction to Fungi’  VIRUSES Viruses are NOT strictly speaking cells – Cannot produce their own metabolic energy – Cannot replicate on their own – Obligate intracellular Simple structure – Nucleic acid + capsid (nucleocapsid) – +/- envelope (host cell derived) More in ‘Introduction to viruses’  PARASITES Include protozoans, helminths & arthropods Protozoa Single-celled, eukaryotic microorganisms. – free-living (aquatic, freshwater, seawater) – parasitic (ectoparasites or endoparasites) Most are free living Cells contain the typical internal structures of an animal cell. Some can swim through water by the beating action of short, hair-like appendages (cilia) or flagella. Some can ingest food, while others can photosynthesise.  CLASSIFICATION Amoeboid Hair-like One-to-many One-celled, non- movement via organelles (cilia) whip-like flagella motile, parasitic temporary 1. motility spore-forming. cellular -shorter and in 2. attachment -complex projections larger numbers 3. Feeding lifecycles with (pseudopods) than flagella. sexual and asexual phases Amoeboid Ciliated Flagellated Sporozoans protozoans protozoans protozoans (Plasmodium (Entamoeba (Balantidium (Trypanosom falciparum) histolytica) coli) a cruzi)  PARASITES Helminths Parasitic worms Include 3 categories: – Nematodes (e.g. roundworm) – Trematodes (e.g. flukes) – Cestodes (e.g. tapeworms) Arthropods Invertebrate animals such as arachnids and insects Usually act as vectors for infectious agents – Malaria & mosquitoes – Ixodes species & Lyme disease (Borrelia burgdorferi) Do not act directly as human pathogens  PRIONS Spongiform Diseases: encephalopathies – CJD Small hydrophobic – Kuru glycoprotein closely related to human protein – Scrapie – No nucleic acid – BSE Pathogenesis (see also neuropathology) not clear Interaction of prion protein with human homologue may lead to amyloid-like plaque formation ‘Spongiform brain’ (Humphreys & Irving)  LEARNING OUTCOME 3. Define important terms related to the human microbiome e.g. colonised, transient, symbiosis etc.  THE MICROBIOME / NORMAL FLORA The mixture of organisms regularly present at any anatomical site Some microorganisms can live completely independently but usually they must form relationships with potential hosts. These associations are called symbiosis Colonization is the presence of microorganisms on a body surface (eg skin, mucosal membranes) without causing damage to the host – Some microorganisms are resident colonizers and live on the body permanently (Skin - Staphylococcus epidermidis) – Some are transient and may live on the body finitely or may come and go (Skin – Staphylococcus aureus) Changes in circumstances may result in Infection - the invasion of the body tissue by the microorganism  SYMBIOSIS An association between two or more species, may encompass a range of different relationships defined by their mutual effects on each other. Commensal - One symbiont benefits while the other is neither harmed nor helped. Mutualistic - both organisms benefit from each other. Parasitic - the host is harmed while the symbiant benefits. Antagonistic – The relationship harms both symbiants  LEARNING OUTCOME 4. Discuss the various microbial components of the human microbiome i.e. bacteria, fungi and viruses and explain how the microbiome develops over time  THE MICROBIOME Composed of the collective genomes of the microbes (composed of bacteria, bacteriophage, fungi, protozoa and viruses) that live inside and on the human body. We have about 10 times as many microbial cells as human cells. Most studies of the microbiome focus on the bacterial component but learning more about role of fungi and viruses also. – Human Virome made up of human viruses (e.g. Enteroviruses) + bacteriophages – Human Mycobiome is the fungal component of microbiome, Saccharomyces, Malassezia, and Candida most abundant  The whole body is normally sterile immediately before birth but the surfaces become rapidly colonized after delivery Environment and diet contribute to the dynamic development of the microbiome, eg different for vaginal delivery Vs Caesarian. breast fed Vs bottle fed and the introduction of solid food Age, Genetics, Other factors (eg stress, antibiotics, immunocompromised state) also contribute  WHAT’S IN IT FOR THEM AND US? Benefits for microrganisms – Supply of nutrients – Stable environment (constant temperature, protection) Benefits for human host – Nutritional benefits – Stimulates immunity – Prevents overgrowth of pathogens  LEARNING OUTCOME 5. Associate the microorganism with the anatomical site in which it usually resides  ANATOMICAL SITES Skin (1012) Oral Cavity (1010) GI tract (1014) Upper respiratory tract Vagina In general, micro-organisms can live on sites that have some exposure to the outside environment.  SKIN Adult humans – 2m2 skin - 1012 bacteria Diverse microenvironments support diverse bacterial species. Moist environment of occluded sites such as axilla, groin, between toes more densely populated. Sweat = salt rich environment = salt tolerant organisms. pH of skin is acidic pH 3 to 5 Examples Resident and transient microbes supported on skin Coagulase negative Staphylococci up to 90% Less common S. aureus, corynebacteria, Cutibacterium acnes.  ORAL CAVITY Up to 1010 organisms. Diverse microenvironments: – tooth surface, mucosa, gingival crevices. Aerobes - tooth surface: anaerobes, gingival crevices Organisms that can resist mechanical removal favoured. Individuals differ in the efficiency of salivary flow. Favourable environment, eg. nutrients, moisture, temperature. Oral biofilms-dental plaque on tooth surface, require physical removal to avoid disease. Predominant microbes include Streptococci  LARGE INTESTINE Site of most dense population: 1012 organisms/gm wet weight Anoxic environment supports anaerobes Anaerobic Gram - and Gram + – Predominant species - anaerobic Bacteroides and anaerobic lactic acid bacteria - Bifidobacterium bifidum. – Also E. coli. Klebsiella aerogenes, Proteus sp. Proportions of different species is related to diet.  GENITOURINARY TRACT Upper tract (Kidney, bladder, ureters), usually free of micro- organisms Female genital tract - Low pH environment of the vagina is the result of glycogen metabolism by lactic acid bacteria During reproductive years Lactobacillus predominates Candida albicans opportunistic organism may be present  LEARNING OUTCOME 6. Discuss the importance of the microbiome to human health and complications that can arise when it is disrupted 7. Describe how the microbiome can be restored following disruption BENEFITS 1. Colonisation resistance Prevention of colonisation by pathogens by competition for attachment and nutrients. colonization strategies that exclude potential pathogens – in this scenario ‘good’ bacteria keep ‘bad’ bacteria in check. Production of bacteriocins and other chemicals to kill/inhibit other bacteria. – Production of lactic acid by lactobacilli in the vagina prevent growth of pathogens – Corynebacteria on the skin produce fatty acids that inhibit colonization with pathogens 2. Host immunity Induction of immune competency. Bacteria of the normal flora act as antigens, recognise by our immune system and stimulates production of cross-reactive antibodies which are protective against some pathogens. Shown in germ-free animal studies. 3. Nutritional benefits Production of vitamin K (blood clotting), vitamin B12(co- factor for enzymatic reactions) 4. Digestion Microbes are very good at degrading complex carbohydrates that would not otherwise be easily digested. Provides further sources of energy for the host. DAMAGE CAUSED BY DISRUPTION OF THE MICROBIOME Pathogenic microbes may be present but normally outnumbered by harmless microbes so status quo maintained However under certain circumstances this can change, eg. breach of mucosal surfaces, impaired host defences Compromised host at increased risk- low resistance to infection. May be due to underlying causes such as malnutrition, cancer, diabetes, immunosupression, trauma from surgery etc. Prolonged use of antibiotics can disturb the normal flora.  CLOSTRIDIOIDES DIFFICILE Normal resident of bowel but kept in check by healthy gut flora. May overgrow after broad spectrum antibiotic use Toxin producing strains can cause infection (CDI) In Europe: Common healthcare infection (HAI): one in twenty HAI (48% of gastrointestinal HAI) C. difficile infection (CDI): Toxin-mediated disease – Diarrhoea (ranges from mild infection to colitis) – May be recurrent (risk increases with each recurrence)  Cochrane Database Syst Rev. 2023 Apr 25;4(4):CD013871. Faecal microbiota transplant (FMT) Well-recognised, accepted, and potentially life-saving therapeutic strategy, for the management of recurrent CDI Involves the transfer of carefully screened donor stool via colonoscopy, enema, or a pill for the purpose of replacing a dysfunctional microbiome Rigorous donor screening and testing is conducted. https://theconversation.com/stool-transplantation-shows-promise-treating-cancer-therapy- side-effect-106657  Other examples of colonizers causing infection when microbiome is disrupted S. aureus Colonizer of approx. 30 % of healthy people but can cause skin infections Skin flora keep it in check but breaches to skin can create opportunities for infection. Wound infections and cellulitis – often after trauma or surgery – edema, erythema, pain, accumulation of purulent material. Bloodstream infection – and may lead to sepsis Candida albicans May colonize oral cavity, vagina in healthy people but numbers kept low by microbiome Changes in oral/vaginal environment may result in outgrowth and infection Oral, vaginal thrush Eg hormonal changes, antibiotic use, dentures  SUMMARY Human microbiome critical to health Different environments of anatomical sites support the local microbiome Disruptions to the microbiome may create environment in which opportunistic pathogens cause infection, eg C. difficile. YEAR 1 STUDENTS IN NEED OF ASSISTANCE RCSI Student Assistance Programme – If you need urgent emotional support contact our student assistance programme available 24/7/ 365. 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