Microbes and The Microbiome

Classification of Microbes and The Microbiome

Introduction to Microbiology

Microbiology - the study of microscopic organisms.

Clinical microbiology - applied microbiology in medicine that focuses on microbes that cause common or serious disease in humans.

• Infection + antimicrobial resistance = a global health concern

• Many infections are preventable through…

  • vaccination    

  • proper sanitation

  • education

  • hygiene practices

• New pathogens are emerging; evolution

Themes Incorporated into Clinical Microbiology Teaching

• Clinically relevant pathogens (e.g., Staphylococcus aureus, Candida albicans).

• Scientific concepts and principles (e.g., bacterial pathogenicity, antibiotic resistance).

• Major infections by system (e.g., pneumonia).

• Preventing infection:

  • Community → vaccination

  • Healthcare-associated infections → standard and transmission-based precautions

Professionalism

• Becoming a doctor involves forming values & developing behaviors and attitudes which foster professional relationships, promote public trust & enhance patient safety

  1. Infection Prevention & Control

  2. Antimicrobial stewardship

Classification of Microorganisms

Binomial System

• Genus & Species, e.g.

  • Homo sapiens

  • Staphylococcus aureus

  • Candida albicans

  • Plasmodium falciparum

• Species are similar, inter-breeding organisms within a genus.

Types of Microorganisms

• 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

Classification Based On:

• Phenotype = observable features of an organism

• Genotype = 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: MALDI-TOF

• Genotypic characterisation: PCR, Whole Genome Sequencing

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

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)

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 of Protozoa

• Ciliated protozoans (Balantidium coli) - Hair-like organelles (cilia)

• Flagellated protozoans (Trypanosoma cruzi) - One-to-many whip-like flagella

• Sporozoans (Plasmodium falciparum) - One-celled, non-motile, parasitic spore-forming

• Amoeboid protozoans (Entamoeba histolytica) - Amoeboid movement via temporary cellular projections (pseudopods)

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 encephalopathies

• Small hydrophobic glycoprotein closely related to human protein

  • No nucleic acid

• Pathogenesis (see also neuropathology) not clear

• Interaction of prion protein with human homologue may lead to amyloid-like plaque formation

• Diseases:

  • CJD

  • Kuru

  • Scrapie

  • BSE

The Microbiome / Normal Flora

• The mixture of organisms regularly present at any anatomical site

• Symbiosis: associations between microorganisms and hosts

• Colonization: presence of microorganisms on a body surface without causing damage to the host

  • Resident colonizers: live on the body permanently (Staphylococcus epidermidis on the skin)

  • Transient: live on the body finitely or may come and go (Staphylococcus aureus on the skin)

• Infection: 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

The Human Microbiome

• Composed of the collective genomes of the microbes (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

Benefits of the Microbiome

• For microorganisms:

  • Supply of nutrients

  • Stable environment (constant temperature, protection)

• For the human host:

  • Nutritional benefits

  • Stimulates immunity

  • Prevents the overgrowth of pathogens

Anatomical Sites and Their Microbiome

• Skin:

• Oral Cavity

• GI tract

• Upper respiratory tract

• Vagina

• In general, micro-organisms can live on sites that have some exposure to the outside environment.

Skin

• Adult humans – 2m^2 skin - 10^{12} 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 10^{10} organisms.

• Diverse microenvironments: tooth surface, mucosa, gingival crevices.

• Aerobes - tooth surface: anaerobes, gingival crevices

• Organisms that can resist mechanical removal favored.

• Individuals differ in the efficiency of salivary flow.

• Favorable 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: 10^{12} 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 are 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

Importance of the Microbiome to Human Health

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, recognize 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 defenses

• 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

  • Diarrhea (ranges from mild infection to colitis)

  • May be recurrent (risk increases with each recurrence)

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 are conducted.

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.

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