8131MED - GMS Introduction to bacterial pathogenesis.pdf

Introduction to bacterial pathogenesis Associate Professor Nicole Masters Mycobacterium tuberculosis by NIAID, licensed CC BY 2.0. Introductions Nicole Masters School of Health, UniSC – email: [email protected] – Research; –Human and animal microbiotas –Health-related water microbiology –POC (equi...

Introduction to bacterial pathogenesis Associate Professor Nicole Masters Mycobacterium tuberculosis by NIAID, licensed CC BY 2.0. Introductions Nicole Masters School of Health, UniSC – email: [email protected] – Research; –Human and animal microbiotas –Health-related water microbiology –POC (equiv) diagnostic tools for detection of microbes –Microbiota as surrogate indices for ecosystem health –Protective role of probiotics in the gut –Mitochondrial function: role of respiratory chain –Health curriculum: urgent care / anterior hip arthroplasty 2 Learning objectives LO: Outline bacterial pathogenicity in relation to: a) bacterial structure, and b) mechanisms used to avoid host defence systems and cause disease. 1) 2) 3) 4) 5) Introduction to microbiome and host interactions Bacterial morphology and methods of classification & detection Principles of disease and epidemiology Bacterial mechanisms of pathogenicity Fever pathophysiology: case study 3 Introduction to bacterial pathogenicity 1. Introduction to microbiome and host interactions 2. Bacterial morphology and classification 3. Principles of disease and epidemiology 4. Bacterial mechanisms of pathogenicity 5. Fever pathophysiology: case study Interesting readings and resources: - Online textbook: Chapter 15 Microbial Mechanisms of Pathogenicity: biolibretexts.org - Online resource: Introduction to Microbiology (relevant sections). - Great youtube channel short videos on micro/immuno diseases: RWJF Microbiology, Immunology & Infectious Diseases (Stanford Medicine) - ‘This podcast will kill you’ infectious diseases produced by two postgrads - Prof Martin Blaser Missing microbes presentation: https://www.youtube.com/watch?v=KwK_O0ahDKo - Henna-Maria Uusitupa TED talk (Sep 2019): How the gut microbes you’re born with affect your lifelong health - Kathleen McAuliffe TED talk (Feb 2023): Do gut microbes control your personality 4 1. Introduction to microbiome and host interactions Until recently… 5 1. Introduction to microbiome and host interactions Shifting (scientific) opinion and understanding… 6 1. Introduction to microbiome and host interactions A rapidly evolving mega-field of research… 7 IMAGE: https://worldmicrobiomeday.com/resources/ Superhuman, Superorganism! Who is in control? Each human is a complex ecosystem whose microbes play ecological roles. Friends with benefits - we hope! Commensal (resident or transient) Opportunistic (pathobiont) Pathogenic Symbionts: host - microbe Commensalism Mutualism Parasitism Microbe – microbe interaction Synergism, Protocooperation Competition Question: Summarise host – microbe and microbe – microbe interactions Predation 8 IMAGE: https://flowingdata.com/2012/10/09/history-of-earth-in-24-hour-clock/ 1. Introduction to microbiome and host interactions Complex microbial ecosystems 1. Introduction to microbiome and host interactions Co-evolution IMAGE: Rowan-Nash AD et al. 2019 Microbiol Mol Biol Rev DOI: 10.1128/MMBR.00044-18 Who are our co-inhabitors? Evolutionary relationships of wild hominids Host phylogeny Oshman et al. PLoS Biology 2010. https://doi.org/10.1371/journal.pbio.1000546 Gut microbiota phylogeny 9 1. Introduction to microbiome and host interactions Clostridium spp. S. aureus H. sapiens L. monocytogenes S. cerevisiae B. anthracis P. falciparum Phylogenetic tree of life Streptococcus spp. G. lamblia C. pneumoniae Pink = eukaryote Animals Shigella spp. Plants Fungi E. coli Protozoa Salmonella spp. Helminths Y. pestis Algae Blue = bacteria H. influenza Eubacteria Vibrio spp. Cyanobacteria Green = archaea Pseudomonas spp. Viruses, viroids, prions?? C. burneti B. pertussis WIKICOMMONS N. meningitis Mycobacteria spp. C. jejuni Who’s there? Composition What are they doing? Functionality IMAGE: https://www.nap.edu/read/24960/chapter/6 1. Introduction to microbiome and host interactions How to study complex microbial communities Mendez-Garcia et al. 2018 DOI: 10.1128/JB.00376-17 11 1. Introduction to microbiome and host interactions Different microbial communities @ different body sites Marsland and Gollwitzer. 2014 Nat Rev Immunol DOI: 10.1038/nri3769 Human Microbiome Project Huttenhower et al. Nature 486, 207-214 (2012) DOI: 10.1038/nature11234 Modified by: https://oncohemakey.com/the-human-microbiome-of-local-body12 sites-and-their-unique-biology/ 1. Introduction to microbiome and host interactions What is normal? When there is considerable differences between individuals Gilbert J et al. 2018 13 Nat Med. DOI: 10.1038/nm.4517 1. Introduction to microbiome and host interactions You (and your microbiota) are unique! But we have a core microbiota To date approximately 85% human microbiome mapped: Diversity = 25 phyla, 2,000 genera, 5,000 species and 316 M genes (Pasolli et al. 2019) Each person has approximately 500 – 1000 gut species Microbiota of family members more similar than unrelated individuals Monozygotic twins have similar variability to dizygotic twins → environmental factors contribute to microbiota composition = nature AND nurture Core microbiota (independent of gender, age, ethnicity and diet) Approximately 75 species common to >50% of individuals Conserved because they carry out essential homeostatic functions in the body 14 1. Introduction to microbiome and host interactions Initial microbial colonisation Stiemsma and Michels 2018. Pediatrics DOI: 10.1542/peds.2017-2437 Tanaka M and Nakayama J. 2017. Allergol Int. DOI: 10.1016/j.alit.2017.07.010 15 1. Introduction to microbiome and host interactions Co-maturation: microbiota and immune system Drago et al. 2019. J Clin Med. DOI: 10.3390/jcm8081206 Wopereis et al. 2014. Pediatr Allergy Immunol DOI: 10.1111/pai.12232 16 1. Introduction to microbiome and host interactions The gut-brain axis: exert systemic effect Signalling mechanisms gut microbiota ↔ brain Modulation of neuro/endo/immune processes SCFAs 2BAs Tryptophan metabolites Microbiota produce neuroactive molecules e.g. 5-HT (serotonin) Dopamine Norepinephrine Neuropeptides Signalling mechanisms brain ↔ gut microbiota Stress factors (little as 2 hours!) Changes in GI motility, and mucosal barrier Microbe produced neurotransmitters Martin C. et al. 2018. CMGH. DOI: 10.1016/j.jcmgh.2018.04.003 17 1. Introduction to microbiome and host interactions Disturbances in microbiota: impact of ABs Data from Rea et al. 2011, reported in; Cotter P. D. 2012. Discovery Medicine. Access here Francino M.P. 2016 Front. Microbiol. DOI: 10.3389/fmicb.2015.01543 18 1. Introduction to microbiome and host interactions Microbial competition host niches Mallon et al. 2015. https://www.cell.com/trends/microbiology/fulltext/S0966-842X(15)00176-6 2. Bacterial morphology and classification Bacterial morphology Question: Compare and contrast prokaryotic (bacterial) and eukaryotic (animal) cells 20 2. Bacterial morphology and classification Bacterial classification Image: https://i0.wp.com/microbeonline.com/wp-content/uploads/2022/07/Hierarchial-arrangements-of-bacteria.png?ssl=1 21 Morphological Staining: shape, cell wall composition Metabolic / biochemical Enzyme activity, substrate utilisation, ABR Genetic (DNA/RNA) PCR, sequencing, FISH Immunologic ELISA, agglutination test Mass Spectrometry MALDI-TOF 22 https://www.frontiersin.org/files/Articles/144398/fmicb-06-00791-HTML/image_m/fmicb-06-00791-t001.jpg www.medical-labs.net Image: Mariana Ruiz: https://commons.wikimedia.org/w/index.php?curid=738916 2. Bacterial morphology and classification Bacterial classification & identification 2. Bacterial morphology and classification https://www.nature.com/articles/nrmicro3480 2. Bacterial morphology and classification Clinically relevant microbes Cell wall composition Gram Positive Streptococcus (pneumonia, pyogenes, agalactiae, viridans) Enterococcus (faecalis, faecium) Staphylococcus (aureus, epidermidis) Bacillus anthracis Listeria monocytogenes Nocardia spp. Corynebacterium spp. (diptheria) Clostridia spp. (tetani, botulinum, difficile) Gram negative Borrelia burgodorferi Bordetella pertussis Pseudomonas aeruginosa Klebsiella pneumoniae Haemophila influenza Enterobacter spp. Moraxella catarrhalis Campylobacter spp. Salmonella spp. Shigella spp. Escherichia coli Yersinia pestis Vibrio cholera Neisseria spp. Acinetobacter baumannii Atypical bacteria Legionella pneumophila Mycobacteria (tuberculosis, leprae) Chlamydia psittaci Mycoplasma pneumoniae Chlamydophila pneumoniae Q fever (Coxiella burneti) Rickettsia spp. Ureaplasma spp. Fungi Candida spp. Aspergillus spp. Protozoa Cryptosporidium spp. Plasmodium spp. 3. Principles of disease and epidemiology Principles of disease and epidemiology Infectivity Ability to infect (enter, survive and multiply), infectious dose Aetiology – causative agent Prevalence & incidence – # cases (point in time), # new case (time period) Pathogenicity – number needed to cause disease Depends on characteristics, incl. ability to: gain entry to host, attach to host tissues and multiply evade host defences, damage tissue, produce disease symptoms E.g. ID50 : 1 Ebola virus, 10,000 spores of B. anthracis, 1 Giardia lamblia, 1-10 Norovirus, 1M V. cholerae (O139, 01) Virulence – the degree of pathogenicity Virulence factors i.e. toxins, biofilm formation, inhibit detection by host, resistance to ABs E.g. Rabies: 100% fatal (without vaccine), Ebola >80% fatal Sudan strain, HIV 100% fatal, Smallpox 33% fatal Communicable / non-communicable disease Infectious agents (microbe or microbial products) Endogenous Disturbance in the host microbiome Exogenous Introduced to host (direct / indirect / vector transmission) 25 3. Principles of disease and epidemiology Koch’s postulates: determining causative agent https://www.pathelective.com/micromeded/kochs-postulates-and-the-advent-of-modern-medical-microbiology (biorender) 26 3. Principles of disease and epidemiology Spread of infectious agent / disease Reservoirs Human Animal Non-living Disease transmission Contact Vehicles Vectors Virulence factors 27 Infection & disease in human body generally follows defined pattern of sequence of events Question: What are the different types of infections? https://www.cdc.gov/pertussis/clinical/features.html 3. Principles of disease and epidemiology Stages of disease development 4. Bacterial mechanisms of pathogenicity Pathogenic features of bacteria Bacterial capsule Endospore Lipopolysaccharide (LPS) and cell wall components (endotoxins) Adhesins / fimbriae Flagellum Siderophores – iron sequestration Toxins – endotoxin, exotoxin Protein SS ABR https://bio.libretexts.org: Chap 15.3 (bacterial virulence factors) 4. Bacterial mechanisms of pathogenicity Bacterial survival: antibiotic resistance Intrinsic (primary) resistance Resistant organism; to specific class of ABs by virtue of genetic makeup Strep resistant of aminoglycosides I.e. lacks target, innate efflux pumps, drug inactivation Genus or species level Extrinsic (secondary, acquired) resistance Mutation Micro-evolutionary change: SNP Macro-evolutionary change: inversions, duplications Acquisition – i.e. plasmid (extra chromosomal nucleic acids) Usually results in strain variants of species Allen et al. 2010. https://www.nature.com/articles/nrmicro2312 4. Bacterial mechanisms of pathogenicity Bacterial survival: antibiotic resistance Mutation: Mutation in bacterial genome and transfer to progeny Conjugation: Direct contact between cells. Acquisition of plasmids Transduction: Bacteriophage injects viral DNA which is integrated into the chromosome Transformation: Cell lyses and naked DNA is released and taken up by recipient cell Sanseverino et al. 2019: https://publications.jrc.ec.europa.eu/repository/bitstream/JRC114775/amr__jrc_technical__report_final_online_15jan.2019.pdf 5. Fever pathophysiology: case study Fever (pyrexia) pathophysiology Upward change in core temperature set point Thermoregulatory centre of hypothalamus Causes; Exogenous pyrogens: microbe, toxin Endo pyrogens: IL-1/6, TNF, MMS, IFN, Ag-Ab Other causes Autoimmune Rheumatic fever Lupus Malignant tumour Acute brain injury Drug fever ≠Hypothermia (no change in set-point) NO production 5. Fever pathophysiology: case study Case study: urosepsis 83 year old lady in a rest home complaining of frequency of urine and dysuria, nurses note mild confusion. The house call doctor is called and starts on trimethoprim and sends a mid-stream urine off to laboratory which generally takes 3 days to come back. In the 2 days following she develops a fever and left renal angle pain. The doctor is called back again finds her with a temperature of 39C, hypotensive and tachycardic, and left RA tenderness. Because of her T2DM she is sent to hospital via ambulance where she receives IV AB and fluids. 33 5. Fever pathophysiology: case study Urosepsis – UTI derived E. coli, P. aeruginosa, Klebsiella spp, Strep spp., Staph spp. & C. albicans ExPEC – UPEC strains Virulence factors: Whelan et al. Microorganisms 2023. https://doi.org/10.3390/microorganisms11092169 Surface polysaccharides: LPS, Lipid A Fimbriae, pili: attachment & translocation Flagella Intracellular biofilm production - IBCs Iron acquisition systems Haemolysin toxin Complicated UTI: pyelonephritis → sepsis Klein & Hltgren. Nature Reviews Microbiology 2020. DOI: https://10.3389/fmicb.2017.01566 Urosepsis pathology 5. Fever pathophysiology: case study Risk factors ≥65 yrs DM Immune suppression Prior UTI Clinical presentation Infection symptoms (e.g. UTI) Decreased BP ↓Mean arterial pressure (CO x SV), ↓ venous return ↓Myocardiocyte function ↑Vessel permeability Microvascular thrombus ↑Procoagulants Tachycardia Tachypnoea Dysuria Sepsis associated delirium (SAD) Costrovertebral tenderness / flank pain Fig 1. Dreger et al. 2015. Dtsch Arztebl Intl. DOI:https://10.3238/arztebl.2015.0837 35 Inhibit folate pathway Trimethoprim (TMP) Sulfonamides (SMX) Bacteriostatic Host immune system required to remove Dihydrofolate reductase has higher sensitivity to trimethoprim in bacteria than humans (x50K fold) TMP-SMX – synergism – broader spectrum Purines DNA, RNA Thymidine DNA Methionine Protein Image sourced: https://pedsinreview.aappublications.org/content/25/11/375/tab-figures-data. 5. Fever pathophysiology: case study TMP - mechanism of action 1.5 – 2 kg 60% w/w 37 How much do you know about your gut microbiota? 50 – 60 grams CHOs daily Fermentation https://www.hsph.harvard.edu/nutritionsource/carbohydrates/fiber/ https://www.perthnow.com.au/opinion/tom-percy/tom-percy-schooners-middies-or-pints-why-beer-glass-sizesare-a-big-issue-for-wa-bars-ng-c8eef5075be4c5be5931d447fe385e52 https://www.cosmopolitan.com/uk/body/news/a43021/doctor-advice-poo-bowels-poop/ https://ksiegarnia-edukacyjna.pl/product-pol-5389-Odwaznik-1-kg.html Gut trivia