Microbiology Quiz on Human Body Flora

Chapter 1: Introduction to Medical Microbiology

• The chapter covers the scope of medical microbiology, its historical background, the natural microflora of the human body, and diagnostic/clinical microbiology.

C. Natural Microflora of the Human Body

• Normal microbial populations begin to establish before birth (in utero).

• The placental microbiome is primarily Enterobacteriaceae and Propionibacterium.

• These are present in the newborn's intestine.

• Lactobacilli in the vagina multiply rapidly and become the predominant organisms in the newborn's intestine just prior to birth.

• Breathing and feeding introduce more microorganisms to the newborn's body from the environment, establishing the individual's personal microbiome.

• Microbes acquired from foods, people, and pets inhabit the large intestine throughout life.

• These microorganisms respond to environmental changes, potentially increasing or decreasing in number to contribute to health or disease.

• The normal adult body contains 3 x 10¹³ body cells and 4 x 10¹³ bacterial cells, primarily on its surface and inside other parts of the body.

• The Human Microbiome Project (2007) analyzed microbiomes that inhabit and live on the human body.

• The goal is to define the relationship between changes in the microbiome and human health and disease.

• The human microbiome is diverse.

• The body's normal microbiota establish themselves permanently and don't cause disease in normal conditions.

• Historically referred to as normal flora.

• Transient microbiota may be present for days, weeks, or months, and then disappear.

• Microorganisms are not found throughout the entire human body, rather localized in certain regions.

• Factors that dictate normal microbiota distribution and composition:

  • Nutrients: Different microbes utilize different nutrients as energy sources. Microbes are concentrated in body sites with the appropriate nutrients.
  • Physical and chemical factors:
    • Temperature, pH, oxygen, and carbon dioxide levels affect microbial growth and composition in different parts of the body. Sunlight also plays a role.
  • Host's defenses: The immune system defends against pathogens. Exposure to microorganisms in childhood helps the immune system develop. Insufficient early exposure to microbes may play a role in allergies and other immune disorders.
  • Mechanical factors: Areas subjected to mechanical forces influence microbial colonization, such as; chewing, tongue movements can dislodge microbes, flushing actions by urine to remove microbes and mucus trapping microbes.

• Relationships between the Normal Microbiota and the Host:

  • Microbial antagonism or competitive exclusion: Normal microbiota protect against colonization of potentially pathogenic microbes by competing for nutrients, producing harmful substances to invaders, and influencing pH and oxygen availability. Disease follows when this balance is upset.
    • Example: The normal bacterial microbiota in the vagina maintains a pH of about 4. The presence of normal microbiota inhibits the overgrowth of Candida albicans (yeast). If the bacterial population is altered (due to antibiotics), this leads to vaginitis (vaginal infection).
    • Example: E. coli cells produce bacteriocins, proteins that inhibit the growth of other bacteria (like Salmonella and Shigella), in the intestine.
    • Example: Normal microbiota of the large intestine effectively inhibits C. difficile (possibly by reducing host receptors, competition for nutrients, or producing bacteriocins). If the normal microbiota is eliminated by antibiotics, C. difficile can cause gastrointestinal infections.
  • Commensalism: One organism benefits while another is unaffected. Bacteria like Staphylococcus epidermis inhabit the skin's surface and bring no apparent harm or benefit to the host.
  • Mutualism: Both organisms benefit in some way. For instance, bacteria in the large intestine can synthesize Vitamin K and some B Vitamins. These vitamins are absorbed into the bloodstream and distributed to the body, and in return, the large intestine provides nutrients for the bacteria, maintaining their survival.
  • Parasitism: One organism benefits at the expense of the other, for example, disease-causing bacteria.

• Representative Normal Microbiota per Body Region:

  • Table 13.1 shows sites where normal resident microbes are found.
  • Table 13.2 shows sterile anatomical sites and fluids.

• Skin and Mucous Membranes:

  • Some microbes don't become residents in areas of direct skin contact; the skin's antimicrobial properties (from secretions of sweat and oil glands) and keratin barrier inhibit many microbes; along with low moisture content and pH.
  • Moist areas support a more diverse population of microbes-sebum-rich areas fewer diverse ones. Sebum contains nutritive compounds for certain microbes, while some lipids and fatty acids inhibit microbial growth. The normal microbiota inhibits colonization of transient microbes by producing antimicrobial substances.

• Eyes (conjunctiva): The conjunctiva contains the similar microbiota found on the skin. Tears and blinking eliminate microbes. The surface is colonized with coagulase-negative Staphylococci, and organisms found in the nasopharynx.

• Most Common Microbes That Colonize the Skin: This list shows a variety of bacteria and fungi from study.

• Most Common Microbes That Colonize the Upper Respiratory Tract: Showing a variety of bacteria, fungi, and parasites.

• Most Common Microbes That Colonize the Gastrointestinal Tract: Shows a lot of bacteria, fungi, and parasites.

• Most Common Microbes That Colonize the Genitourinary Tract: Showing some bacteria, fungi.

• Maintenance of the Normal Microbiota:

  • Microbes naturally replace themselves to maintain types and numbers, but changes like broad-spectrum antibiotics, changing diets, and underlying diseases can upset this balance.
  • Probiotics involve introducing known microbes into the body through ingestion or inoculation.

• Diagnostic/Clinical Microbiology:

  • Microbiologists identify bacteria using phenotypes, immunology, or genotypes.
    • Phenotypic includes morphology (microscopic or macroscopic), physiology, or biochemistry.
    • Immunological/Serological entails analysis of blood and other fluids, e.g., HIV testing to detect antibodies.
    • Genotypic involves genetic techniques (more precise).
  • Specimen Collection: Procedures for specimen collection, handling, and storage are crucial for accurate diagnosis; specimens are prone to deterioration and contamination and proper storage is important to prevent these issues.

Methods of Microbial Investigation

• Inoculation: The first stage in culturing – placing a sample in medium.
  • Methods for inoculation include the streak plate method, the spread plate technique, and the pour plate/loop dilution method.
• Incubation: Exposing inoculated medium to optimal conditions (a few hours to several days) to encourage microbial growth and create macroscopically visible growth.
• Isolation: Separating individual microbes in a pure culture.
• Inspection: Observing the macroscopic appearance of growth and the microscopic appearance of cells in the culture.
• Information gathering: Analyzing culture through biochemical, enzymatic, immunological, drug sensitivity, and genetic testing.
• Identification: Establishing the identity of microbes in the sample with various schemes.

Procedures for Identifying Pathogens and Diagnosing Infections

• Phenotypic: Analyzing cell's morphology, physiology, biochemistry.
• Immunological: Analyzing blood tests (serology) for antibody presence to confirm pathogens.
• Genotypic: Analyzing genetic material (more precise).

Rapid Diagnostic Tests

• Rapid diagnostic panels use small blood samples for identifying different species of microorganisms like Plasmodium (the malaria agent) or Antibodies to Hepatitis B and C viruses/HIV.

Phenotypic Characterization of Bacteria

• Microscopic Morphology: Observing cell shape, size, staining reaction (Gram and acid-fast), special structures (endospores, granules, capsules) using electron microscopy for additional details like cell walls, flagella, pili, and fimbriae.

• Macroscopic Morphology: Observing growth, texture, shape of colonies, pigment; reaction to differential media.

• Physiological/Biochemical Characteristics: Testing fermentation of sugars, capacity to digest/metabolize complex polymers, production of gas, enzyme presence/absence, and sensitivity to antimicrobial drugs.

• Oxidation-Fermentation Test: Differentiating bacteria based on metabolic pathway (oxidative or fermentative) of carbohydrates. Oxidative organisms convert carbs to CO2 and H2O, while fermentative bacteria produce organic acids, gas, or alcohol from pyruvate. An example is the biochemical test.

• Fermentation Test: This test helps identify fermentative organisms by observing the change in color, and presence/absence of gas during the conversion of a carbohydrate into acids and/or alcohol, as described by the biochemical reaction.

• Methyl Red Test/ Voges-Proskauer Test/ Catalase Test: These are biochemical tests for the presence of specific enzymes or metabolic products related to specific bacterial species (presence of enzymes like catalase, or products like methyl red or other substrates from fermentation).

• Antimicrobial Susceptibility/Disk Diffusion: Testing microorganisms' resistance to different antibiotics using disk diffusion tests to measure the zone of inhibition (diameter of zone surrounding antibiotic where bacteria don't grow) for evaluating an organism's resistance or susceptibility to a particular antimicrobial compound.

Important Families and Genera of Pathogenic Bacteria

• Categorizes different important families of pathogenic bacteria based on cellular structure (gram-positive or gram-negative), spore-formation, etc. Includes examples and characteristics.

Important considerations for specimen analysis

• Methods for specimen analysis may include direct testing (microscopic, immunologic, or genetic) to detect characteristics of microbes in the sample, and cultivation, isolation, and identification of pathogens using general and specific tests that may take several days for results.
• Different categories of data like presumptive data (classifying the isolate to a broad category) or confirmatory data (definitive evidence for a species) are obtained from different tests. Time required for each analysis may vary from minutes (for strep throat) to several days(for Tuberculosis).
• Disease can be identified without identifying microbes through serologic testing of specimens.