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Questions and Answers
Amoeboid protozoans reproduce only sexually.
False
Helminths include nematodes, trematodes, and cestodes.
True
Arthropods act directly as human pathogens.
False
Prion diseases are caused by small hydrophobic glycoproteins with no nucleic acid.
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The microbiome consists of organisms that never form relationships with hosts.
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Bacterial pathogenicity is a scientific concept incorporated into clinical microbiology teaching.
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Candida albicans is classified as a virus.
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Antimicrobial stewardship is one of the major components of clinical microbiology.
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The basic categories of microbes include bacteria, viruses, fungi, and molecules.
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Genotype refers to the observable features of an organism.
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The bacterial cell possesses a single chromosome and plasmids.
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Fungi are more closely related to human cells than bacteria.
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Viruses can replicate on their own without a host.
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Species within a genus are unrelated organisms.
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Antibiograms are used to determine antibiotic susceptibility of microorganisms.
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Pneumonia is a major infection by system covered in clinical microbiology.
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All higher animal species are free from protozoan species.
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PCR is a technique used for genotypic characterization.
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Nucleic acid and capsid constitute the complex structure of viruses.
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Fungi have treatment options that are more abundant than for bacteria.
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Protozoa are multicellular organisms belonging to the eukaryotes.
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Prolonged use of antibiotics can disturb the normal flora.
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Cloistridioides difficile infections are primarily caused by viral pathogens.
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Faecal microbiota transplant is a recognized method for restoring a dysfunctional microbiome.
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A compromised host has a higher resistance to infections.
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The human microbiome is not essential for health.
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The skin can support diverse bacterial species due to its moist environments.
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The oral cavity hosts around 10 organisms per gram.
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The large intestine is an anoxic environment that predominantly supports anaerobes.
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Lactobacillus is the predominant organism found in the male genital tract.
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The vagina has a high pH environment favorable for all types of bacteria.
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Candida albicans is considered a beneficial organism within the female genital tract.
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The density of bacteria in the GI tract can reach up to 10,000 organisms per gram.
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Streptococci and lactobacilli are predominant microbes found in the oral cavity.
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Microbiology is the study of microscopic organisms such as viruses, bacteria, and fungi.
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The human microbiome develops in the same way throughout a person's life.
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Bacterial pathogenicity is a focus in clinical microbiology education.
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Protozoa are categorized as multicellular organisms in microbiology.
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Prolonged use of antibiotics can restore normal flora balance in the microbiome.
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The vagina has an acidic environment that supports the growth of beneficial bacteria.
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The density of bacteria in the gastrointestinal tract can exceed 10 million organisms per gram.
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The oral cavity hosts fewer microorganisms than other parts of the human body.
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Viruses have a complex structure consisting of nucleic acid and a protein shell called a capsid.
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Fungi are prokaryotic organisms that require treatment options similar to bacteria.
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All protozoans are free-living and do not exhibit any parasitic behavior.
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Genotypic characterization methods include techniques such as PCR and whole genome sequencing.
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Aspergillus fumigatus is a type of bacteria commonly grown on agar.
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Antibiograms are a method used to determine the susceptibility of microorganisms to different antibiotics.
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Viruses can replicate independently without the use of a host organism.
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Eukaryotic microorganisms, including fungi, have similar metabolic processes to human cells.
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Pathogenic microbes are typically present in higher numbers than harmless microbes in a healthy microbiome.
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Faecal microbiota transplant involves the transfer of donor stool to restore a healthy microbiome.
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Individuals with a compromised immune system are at a decreased risk of infections due to their enhanced defenses.
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Cloistridioides difficile infections are greatly influenced by the routine use of probiotics.
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A healthy microbiome is essential for optimal human health.
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Colonization refers to microorganisms damaging the host tissue.
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Mutualistic relationships benefit both organisms involved.
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Transient microorganisms permanently reside on the surface of the body.
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The human microbiome contains approximately ten times more microbial cells than human cells.
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Antagonistic relationships in symbiosis benefit both organisms.
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The human mycobiome consists mainly of human viruses.
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Diet, genetics, and age are factors that can affect the diversity of the microbiome.
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Pathogenic bacteria derive no benefit from their host.
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The skin supports up to 10^12 bacteria, including mainly coagulase negative Staphylococci.
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Aerobes are the predominant species found in the gingival crevices of the oral cavity.
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The large intestine predominantly supports aerobic bacteria like E. coli and Klebsiella aerogenes.
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Candida albicans is an opportunistic organism that may be present in the female genital tract.
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The upper genitourinary tract, including the kidneys and bladder, is typically free of microorganisms.
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Oral biofilms on the tooth surface require mechanical removal to prevent disease.
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The vagina has a neutral pH environment that supports a wide range of bacteria.
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The oral cavity hosts around 10^10 organisms, thriving in diverse microenvironments.
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Archaea are classified as eukaryotes due to their complex cellular structure.
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Hand hygiene is considered a major component of infection prevention and control.
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The binomial system of classification uses both the genus and kingdom of an organism.
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Prokaryotic cells, such as bacteria, contain membrane-bound organelles.
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Phenotype refers to the genetic makeup of an organism.
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Plasmids are considered extrachromosomal DNA in bacterial cells.
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Candida albicans belongs to the category of bacteria.
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Antimicrobial stewardship aims to promote the appropriate use of antibiotics to combat resistance.
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Flagellated protozoans primarily use cilia for locomotion.
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Prion diseases can be linked to the formation of amyloid-like plaques in the brain.
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Viruses are able to produce their own metabolic energy.
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Arthropods directly transmit diseases by acting as human pathogens.
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Protozoans can swim through water using cilia or flagella.
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Cestodes are categorized as parasitic worms that include organisms like tapeworms.
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Serotyping is a method used to characterize the genetic makeup of a microorganism.
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The microbiome is characterized only by transient microorganisms that do not establish long-term relationships.
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Fungi have treatment options that are less limited than those for bacteria.
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Phage typing involves testing microorganisms for their susceptibility to antibiotics.
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MALDI-TOF is used for phenotypic characterization rather than genotypic characterization.
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Eukaryotic microorganisms display metabolic processes that are entirely different from human cells.
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All viral particles have an envelope encasing their protein shell.
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Colonization refers to the presence of microorganisms on a body surface without causing damage to the host.
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In a mutualistic relationship, only one organism benefits at the expense of the other.
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The human microbiome comprises about 10 times as many viral cells as human cells.
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Fungi, such as Saccharomyces and Malassezia, are the predominant components of the human virome.
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Factors affecting the content and diversity of the microbiome include genetics and diet.
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The relationship defined as antagonistic means that both symbionts are positively affected.
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The term 'commensal' describes a relationship where one symbiont benefits and the other is harmed.
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The large intestine is an environment that predominantly supports aerobic bacteria.
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The human skin can support diverse bacterial species due to its acidic pH ranging from 3 to 5.
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The oral cavity contains more organisms than the large intestine on average.
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Anaerobic conditions in the large intestine primarily support aerobic microorganisms.
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Lactobacillus is the predominant organism found in the upper urinary tract.
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The predominant microbial species in the female genital tract is Bifidobacterium bifidum.
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The GI tract environment is characterized by a higher proportion of anaerobic bacteria compared to aerobic bacteria.
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Only aerobic bacteria can thrive in the moist and nutrient-rich oral cavity.
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Streptococci and lactobacilli are among the predominant microbes found on skin.
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Study Notes
Microbes
- Bacteria, viruses, fungi, protozoa, and arthropods are the four basic categories of microbes.
- Microorganisms can be differentiated based on their phenotypic and genotypic characteristics.
- Bacteria and archaea are single-celled organisms with no membrane-bound organelles.
- Fungi and protozoa are eukaryotes, meaning they have a nucleus and other membrane-bound organelles.
- Viruses are not cells and cannot replicate on their own. They are obligate intracellular parasites.
- Parasites include protozoa, helminths, and arthropods.
- Protozoa are single-celled eukaryotic organisms that can be free-living or parasitic.
- Helminths are parasitic worms categorized as nematodes, trematodes, and cestodes.
- Arthropods are invertebrates that often act as vectors for infectious agents, transmitting diseases such as malaria and Lyme disease.
The Binomial System
- The binomial system uses genus and species names to identify organisms.
- This system is used in all aspects of biology, including clinical microbiology.
The Bacterial Cell
- Bacterial cells have a single chromosome, plasmids, cytoplasm, ribosomes, a cytoplasmic membrane, a cell wall, flagellae, and pili/fimbriae.
Classification
- The classification of microorganisms relies on their phenotypic and genotypic characteristics.
- Genotype refers to the genetic makeup of an organism.
- Phenotype refers to the observable characteristics of an organism.
- Biotyping utilizes biochemical tests to differentiate strains.
- Serotyping identifies surface antigens.
- Antibiograms analyze antibiotic susceptibility patterns.
- Phage typing assesses susceptibility to viruses.
Fungi
- Fungi are eukaryotes, making them more closely related to human cells than bacteria.
- This makes treatment options for fungal infections more limited than for bacterial infections.
Viruses
- Viruses are not cells and cannot produce their own metabolic energy.
- They are obligate intracellular parasites, meaning they require a host cell to replicate.
- Viruses have a simple structure consisting of nucleic acid and a capsid, and some have an envelope derived from the host cell.
The Microbiome / Normal Flora
- The microbiome refers to the mixture of organisms regularly present at various anatomical sites.
- Microorganisms often form relationships with potential hosts, often existing in a symbiotic relationship.
Anatomical Sites
- The skin, oral cavity, gastrointestinal tract, upper respiratory tract, and vagina are all sites with significant microbial populations.
- The skin supports a diverse array of bacterial species, with moist areas like the axilla, groin, and between toes having higher microbial densities.
- The oral cavity is a rich environment for microorganisms, supporting a diverse population that includes both aerobic and anaerobic species.
- The large intestine is the site of the densest population of microorganisms in the human body, with a predominantly anaerobic environment due to the lack of oxygen.
- The upper genitourinary tract is typically free of microorganisms, while the female genital tract, particularly the vagina, houses a predominantly Lactobacillus population.
Damage Caused by Disruption of the Microbiome
- The microbiome can be disrupted by factors such as antibiotics, underlying health conditions, and trauma.
- This disruption can create an environment where opportunistic pathogens can thrive and cause infection.
Clostridioides Difficile
- C.difficile is a spore-forming, toxin-producing anaerobic bacterium.
- It can be carried asymptomatically.
- Antibiotics are a major risk factor for C.difficile infection (CDI).
- CDI can cause diarrhea ranging from mild to colitis.
- Recurrent CDI is a significant problem.
Faecal Microbiota Transplant (FMT)
- FMT is a therapeutic strategy used to manage recurrent CDI.
- It involves transferring screened donor stool into the recipient's gut to replace a dysfunctional microbiome.
- FMT is a recognized and potentially life-saving treatment option for recurrent CDI.
Summary
- The human microbiome is crucial for health.
- The microbiome is influenced by the different environmental conditions present at various anatomical sites.
- Disruptions to the microbiome can create opportunities for opportunistic pathogens to cause infection, such as C.difficile.
Clinical Microbiology Overview
- Studies microscopic organisms such as viruses, bacteria and fungi, though some are visible to the naked eye.
- Clinical Microbiology is concerned with microbes that cause common or serious diseases
- Antibiotic resistance is a critical concern in clinical microbiology.
- Many infections can be prevented such as tetanus, sexually transmitted infections, and cholera
Microbiology For Medical Students
- The subject in medicine is applied microbiology
- Clinically oriented to facilitate patient management
- More important to know the common causes of diseases rather than the details of the microbial cells
Microorganism Analysis
- The analysis of phenotypic characteristics is used to separate strains and confirm identification
- Phenotypic characteristics include biotyping, serotyping, antibiotic resistance, and phage typing
Genotype and Proteotype Analysis
- Analyses the genetic and protein components of microorganisms
- Techniques include: MALDI-TOF, PCR, and Whole Genome Sequencing
Fungi
- Eukaryotes with a nucleus, chromosomes, and mitochondria
- More closely related to human cells than bacteria
- Treatment options are limited as it is difficult to develop chemotherapy selectively toxic to fungal cells
Viruses
- Not technically cells, cannot create their own metabolic energy or replicate on their own
- Obligate intracellular, requiring a host cell
- Simple structure: nucleic acid + capsid +/- envelope (host cell derived)
Parasites
- Includes Protozoa, Helminths and Arthropods
- Protozoa are single celled eukaryotic microorganisms that are either free-living or parasitic
- All higher animal species are infected with one or more species of Protozoa
Microbe Relationships
- Colonization is the presence of microorganisms on a body surface without causing damage
- Resident colonizers live on the body permanently, transient colonizers may live on the body finitely or may come and go
- Infection is the invasion of body tissue by a microorganism
- Symbiosis is an association between two or more species and defines a range of different relationships:
- 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 Microbiome
- Composed of the collective genomes of microbes that live within and on the human body
- Made up of bacteria, bacteriophage, fungi, protozoa, and viruses
- Human cells are outnumbered ten to one by microbial cells
- Most studies focus on the bacterial component but the role of fungi and viruses is becoming more understood
- The Human Virome includes human viruses (e.g.Enteroviruses) + bacteriophages
- The Human Mycobiome is the fungal component of the microbiome, with Saccharomyces, Malassezia, and Candida being the most abundant fungi
Factors Affecting The Microbiome
- Age, Sex, Genetics, Diet, Other factors (eg stress, antibiotics, immunocompromised state)
Benefits of the Microbiome
- For microorganisms: Supply of nutrients + stable environment
- For the human host: Nutritional benefits, stimulates immunity, prevents overgrowth of pathogens
Anatomical Sites of Microbiome
- Skin (1012)
- Oral Cavity (1010)
- GI tract (1014)
- Upper respiratory tract
- Vagina
Skin Microbiome
- Adult humans have 2m2 of skin that supports 1012 bacteria
- Diverse microenvironments support diverse bacterial species
- Moist environments such as the axilla, groin, and between toes are more densely populated
- Sweat is salt rich therefore salt tolerant organisms are favored
- The pH of the skin is acidic (pH 3 to 5)
Oral Cavity Microbiome
- Up to 1010 microorganisms
- Diverse microenvironments: tooth surface, mucosa, gingival crevices
- Organisms that can resist mechanical removal are favored
- Individuals differ in the efficiency of salivary flow
- Aerobes are common on tooth surfaces while anaerobes are found in gingival crevices
- Favorable environment: nutrients, moisture, temperature
- Oral biofilms (dental plaque) on tooth surface require physical removal
- Predominant microbes: Streptococci, lactobacilli, neisseria, staphylococci, corynebacteria
Large Intestine Microbiome
- The most densely populated site: 1012 organisms/gm wet weight
- Major importance for health
- Anoxic environment supports anaerobes
- Predominant species: Anaerobic Bacteroides and anaerobic lactic acid bacteria - Bifidobacterium bifidum
- Also E.coli.Klebsiella aerogenes, proteus sp.(aerobic/anaerobic)
- Population in the intestine is similar to that in feces
- Proportions of different species is related to diet
Genitourinary Tract Microbiome
- Upper Tract (Kidney, bladder, ureters) is usually free of microorganisms
- Female genital tract has a low pH environment due to glycogen metabolism by lactic acid bacteria
- Lactobacillus predominates during reproductive years
- Candida albicans is an opportunistic organism that may be present
Disruption of The Microbiome
- Pathogenic microbes are normally outnumbered by harmless microbes
- Disruptions to the microbiome may create an environment in which opportunistic pathogens cause infection.
- Compromised hosts are at increased risk of infection due to low resistance
- May be caused by underlying causes such as malnutrition, cancer, diabetes, immunosuppression, trauma from surgery etc.
- Prolonged use of antibiotics can disturb the normal flora
Clostridioides Difficile (C. difficile)
- Spore-forming, toxin-producing anaerobic bacterium carried asymptomatically
- Common healthcare infection (HAI)
- Antibiotics are the main risk factor for infection
- C. difficile infection (CDI) is a toxin-mediated disease
- Diarrhoea (ranges from mild infection to colitis)
- May be recurrent
- Faecal microbiota transplant (FMT) is a therapeutic strategy used to manage recurrent CDI
- Involves the transfer of carefully screened donor stool via colonoscopy, enema, or a pill to replace a dysfunctional microbiome
Summary
- The human microbiome is critical to health
- Different environments of anatomical sites support the local microbiome
- Disruptions to the microbiome may create an environment in which opportunistic pathogens can cause infection, eg. C. difficile .
Clinical Microbiology Themes
- Bacterial pathogenicity, antibiotic resistance mechanisms, and clinically relevant pathogens like Staphylococcus aureus and Candida albicans are important topics in clinical microbiology.
- Understanding major infections classified by body system (e.g. pneumonia) and their diagnostic and therapeutic approaches is crucial for clinical practice.
- Preventing infection in both the community through vaccination and healthcare settings through standard and transmission-based precautions are key components of clinical microbiology.
Professionalism
- Developing professional values, behaviors, and attitudes is essential for building trust with patients and enhancing safety in healthcare.
The Major Components Of Clinical Microbiology
- Infection prevention and control, including practices like hand hygiene.
- Antimicrobial stewardship.
Classification of Microbes
- Microorganisms are broadly classified into four basic categories: bacteria, viruses, fungi, and protozoa.
- Arthropod vectors also play a role in disease transmission.
- Microorganisms can be differentiated based on their phenotypic and genotypic characteristics.
Binomial System
- The binomial system uses genus and species to name organisms, for example, Homo sapiens, Staphylococcus aureus, Candida albicans, and Plasmodium falciparum.
- Species within a genus are similar and can interbreed.
Bacteria and Archaea
- Bacteria and archaea are prokaryotes, meaning they lack a nucleus and other membrane-bound organelles.
Fungi and Protozoa
- Fungi and protozoa are eukaryotes, having a nucleus, mitochondria, Golgi apparatus, and endoplasmic reticulum.
The Bacterial Cell
- Bacterial cells are characterized by their single chromosome, plasmids (extrachromosomal DNA), cytoplasm, ribosomes, cytoplasmic membrane, cell wall, flagellae, and pili/fimbriae.
Classification of Microorganisms
- Phenotypic characteristics encompass observable features like morphology, physiology, and biochemical reactions.
- Genotypic characteristics refer to an organism's genetic makeup, including its DNA sequence.
Analysis of Phenotypic Characteristics
- Separating strains or confirming identification of an isolate can be done using techniques like biotyping, serotyping, antibiograms, and phage typing.
Analysis of Genotypic or Proteomic Characteristics
- Molecular techniques like MALDI-TOF (proteomic) and PCR or whole-genome sequencing (genotypic) are used for microbial characterization.
Fungi
- Fungi are eukaryotes more closely related to human cells than bacteria, making them difficult to target selectively with chemotherapy.
- Examples include Aspergillus fumigatus and Candida albicans.
Classification of Fungi
- Fungi are classified based on their morphology, life cycle, and reproductive structures.
Viruses
- Viruses are not cells and cannot replicate on their own.
- They are obligate intracellular parasites, meaning they need a host cell to reproduce.
- Viruses consist of nucleic acid (DNA or RNA) enclosed within a protein coat called a capsid.
- Some viruses also have an envelope derived from the host cell membrane.
Parasites
- Parasites include protozoa, helminths, and arthropods.
- Protozoa are single-celled, eukaryotic microorganisms that can be free-living or parasitic.
- Helminths are parasitic worms, categorized as nematodes, trematodes, and cestodes.
- Arthropods, such as arachnids and insects, act as vectors for infectious agents, transmitting diseases like malaria and Lyme disease.
Prions
- Prions are infectious agents composed of misfolded proteins.
- They lack nucleic acid and cause spongiform encephalopathies, such as Creutzfeldt-Jakob disease (CJD), Kuru, scrapie, and bovine spongiform encephalopathy (BSE).
The Microbiome/Normal Flora
- The microbiome refers to the collection of microorganisms living in or on the human body.
- It includes bacteria, bacteriophages, fungi, protozoa, and viruses.
- The microbiome is essential for human health, contributing to nutrient absorption, immune system development, and protection against pathogens.
- Colonization is the presence of microorganisms on a body surface without causing harm to the host.
- Transient microorganisms may be present for a limited time, while resident microorganisms colonize permanently.
- Changes in circumstances can lead to infection, where microorganisms invade body tissues.
Symbiosis
- Symbiosis describes interactions between different species, including commensalism, mutualism, parasitism, and antagonism.
The Microbial Components of the Human Microbiome
- The human gut microbiome, in particular, plays a significant role in health and disease.
- Factors influencing the microbiome include age, sex, genetics, diet, stress, antibiotics, and immune status.
Benefits of the Microbiome
- The microbiome provides benefits to both microorganisms and the human host.
- Microorganisms benefit from a supply of nutrients and a stable environment.
- Humans benefit from the microbiome's contributions to digestion, nutrient absorption, immune system development, and pathogen inhibition.
Anatomical Sites of the Microbiome
- The human microbiome is distributed across various anatomical sites, with varying densities of microorganisms. These sites include:
- Skin
- Oral Cavity
- Gastrointestinal tract
- Upper respiratory tract
- Vagina
Skin
- Skin is a diverse environment, with moist areas like the axilla, groin, and between toes supporting higher microbial density.
- Sweat's high salt content favors salt-tolerant organisms.
- The skin's acidic pH (3-5) influences the resident microbial community.
- Skin's resident microbes include coagulase-negative Staphylococci, Staphylococcus aureus, corynebacteria, micrococci, and Cutibacterium acnes.
Oral Cavity
- The oral cavity supports up to 10^10 organisms per ml of saliva.
- Diverse environments on tooth surfaces, mucosa, and gingival crevices influence microbial diversity.
- Organisms resistant to mechanical removal are favored, and salivary flow efficiency plays a role.
- Aerobes predominate on tooth surfaces, while anaerobes are more common in gingival crevices.
- Oral biofilms, like dental plaque, require regular removal to prevent oral disease.
- Predominant microbes include Streptococci, Lactobacilli, Neisseria, Staphylococci, and Corynebacteria.
Large Intestine
- The large intestine has the highest density of microorganisms (10^12 organisms per gram of wet weight).
- Its anoxic environment favors anaerobic bacteria, including Bacteroides species and Bifidobacterium bifidum.
- Aerobic/anaerobic bacteria like Escherichia coli, Klebsiella aerogenes, and Proteus species are also present.
- Intestinal microbial populations closely resemble those found in feces.
- Dietary factors influence the proportions of different microbial species.
Genitourinary Tract
- The upper genitourinary tract (kidney, bladder, ureters) is typically free of microorganisms.
- The female genital tract has a low pH due to lactic acid production by Lactobacillus species, which dominate during reproductive years.
- Candida albicans, an opportunistic organism, may be present.
Importance of the Microbiome
- The microbiome is critical for human health.
- Disruptions in the microbiome can lead to various complications, including:
- Gastrointestinal disorders like inflammatory bowel disease (IBD)
- Immune system dysregulation and allergies
- Metabolic disorders like obesity and diabetes
- Neurological and psychiatric conditions
- Understanding the microbiome's role in health and disease is crucial for developing effective therapies and preventative strategies.
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Description
This quiz explores the basic categories of microbes, including bacteria, viruses, fungi, and protozoa. It also covers the binomial system used for classifying organisms. Test your knowledge on the characteristics and classifications of various microorganisms!
