Week 6: The Microbial World – Bacteria, Viruses, and Prions

Bacteria

Prokaryotic, Unicellular, Small, Absent Nucleus, Binary Fission

Archaea

Prokaryotic, Unicellular, Small, Absent Nucleus, Binary Fission

Eukarya

Eukaryotic, Multicellular, Large, Present Nucleus, Mitosis and Cytokines

Structure and Classification of Prokaryotic Organisms​

• Prokaryotes are classified based on shape, staining patterns, and genetic sequences.​

• Bacteria are traditionally grouped as gram-positive, gram-negative, or atypical based on cell wall properties.​

• Modern classification also includes categories like Proteobacteria and gram-positive bacteria with varying guanine-cytosine content.​

• Classification of prokaryotes continues to evolve with new discoveries.​

How Do We Classify Bacteria?

• By their scientific name​

• By their shape​

• By their need for oxygen​

• By their genetic makeup​

• By how we stain them

Naming Microbes and Bergey’s Manuals​

Binominal nomenclature​

• Developed by Linnaeus: Two-word naming system (genus and species).​

• Example: Escherichia coli (genus Escherichia, species coli).​

• Naming conventions: Genus capitalized, species not, both italicized.​

Naming Sources​

• Derived from Latin, Greek, or English.​

• Example: Staphylococcus aureus (genus Staphylococcus from Greek for "grape cluster,” species aureus from Latin for "golden").​

Cocci

The term "cocci" comes from the Greek word kokkos, which translates to berry or seed. Cocci refer to archaeon or bacteria that typically have a round, oval, or spherical shape

Bacilli​

The term "bacilli" is derived from the Latin word bacillus, meaning little rod. Bacilli refer to bacteria that are typically rod-shaped, ranging from short and stubby to long and filamentous forms.​

Other​

The "Other" category includes bacteria that do not conform to the typical shapes of cocci or bacilli.

Pleomorphic

Bacteria that can change their shape are known as pleomorphic.​

Obligate Aerobes (Oxygen Requirements of Microorganisms​)

Require oxygen for growth; use oxygen for cellular respiration (e.g., Mycobacterium tuberculosis).​

Obligate Anaerobes (Oxygen Requirements of Microorganisms​)

Cannot tolerate oxygen; growth occurs only in oxygen-free environments (e.g., Clostridium botulinum).​

Facultative Anaerobes (Oxygen Requirements of Microorganisms​)

Can grow with or without oxygen; prefer oxygen for energy production but can switch to anaerobic metabolism (e.g., Escherichia coli).​

Aerotolerant Anaerobes (Oxygen Requirements of Microorganisms​)

Do not use oxygen but can tolerate its presence; rely on fermentation (e.g., Streptococcus pyogenes).​

Microaerophiles (Oxygen Requirements of Microorganisms​)

Require low levels of oxygen (lower than atmospheric levels) for growth (e.g., Helicobacter pylori).​

G+C Content

• Measures the proportion of guanine (G) and cytosine (C) in the bacterial DNA.​

• High G+C vs. Low G+C content helps distinguish between different bacterial groups (e.g., Actinobacteria vs. Bacilli).​

16S rRNA Gene Sequencing:

• Analyzes the sequence of the 16S ribosomal RNA gene, a highly conserved region in bacterial genomes.​

• Used for identifying and classifying bacteria at the genus and species level.​

Whole Genome Sequencing (WGS)

• Involves sequencing the entire DNA of a bacterium.​

• Provides comprehensive information for precise classification, including strain-level differences.​

Classification by Staining​

In 1884, the Danish microbiologist Hans Christian Gram developed an effective method for distinguishing different types of bacteria based on their cell walls – the Gram Stain! (get it??).​

• Gram-positive, gram-negative, and atypical​

But why do these differences occur?​

• Based on the presence or absence of a cell wall, as well as the composition of the cell wall​

Gram positive (staining)

Thick layer of peptidoglycan and contains teichoic acids​

Gram negative (staining)

Thin layer of peptidoglycan and does not contain teichoic acids

Gram-Positive Bacteria

Cell Wall Structure​

• Thick peptidoglycan layer​

• Retains crystal violent stain, remains purple

Classification​

• Classified by guanine and cytosine nucleotide ​

• Content into low G+C and high G+C

Examples of Pathogens​

• Low G+C: Bacillus anthracis (anthrax), Clostridium tetani (tetanus), Listeria monocytogenes (listeriosis)​

• High G+C: Corynebacterium diphtheriae (diphtheria), Mycobacterium tuberculosis (tuberculosis)

Gram-negative Bacteria

Cell Wall Structure​

• Thin peptidoglycan layer​

• Does not retain crystal violet stain, appears pink/red after safranin

Classification​

• Classified into groups like ​

• Proteobacteria, CFB, and spirochetes

Examples of Pathogens​

• Proteobacteria: E. coli, Bordetella pertussis (whooping cough)​

• CFB: Bacteroides (part of normal gut microbiota)​

• Spirochetes: Treponema pallidum (syphilis)

The Gram Stain Procedure​

• Crystal violet is applied to a heat-fixed smear which turns all cells purple.​

• Gram's iodine is then added, which acts as a mordant to trap the crystal violet in cells with thick peptidoglycan layers.​

• A decolorizing agent, such as ethanol or an acetone/ethanol solution, is used. Cells with thick peptidoglycan layers retain the purple color, while those with thinner layers lose the dye and become colorless.​

• A secondary stain, typically safranin, is applied, staining the decolorized cells pink, while the purple-stained cells remain purple.

Other Staining Measures​

• Acid-Fast Stain: Differentiates bacteria with waxy cell walls (e.g., Mycobacterium species) using carbol fuchsin and methylene blue.​

• Capsule Stain: Negative staining technique that highlights protective capsules around bacteria by staining the background.​

• Endospore Stain: Uses malachite green and safranin to identify tough, dormant endospores within bacterial cells.​

• Flagella Stain: Thickens and stains bacterial flagella to make them visible under a light microscope, aiding in classification.

One Health and Bacteria​

“To realistically control infectious diseases, human, animal, and environmental factors need to be considered together, based on the One Health perspective”

Cat-Scratch Disease (Animal-Borne Zoonoses)

(Bartonella henselae): Transmitted through cat scratches or bites, causing skin lesions, fever, and swollen lymph nodes, with risks of severe complications in immunocompromised individuals.​

Pasteurella Infections (Animal-Borne Zoonoses)

Often result from dog or cat bites, leading to rapid infection at the bite site, with potential complications like cellulitis and abscess formation.​

Campylobacter Infection (Animal-Borne Zoonoses)

Campylobacteriosis, a common zoonotic bacterial disease, can be transmitted from animals to humans through the fecal-oral route. The risk of infection is significantly increased by feeding pets raw food diets, which can harbor the bacteria. ​

Salmonellosis (Farm Animal-Borne Bacterial Zoonoses)

This food-borne bacterial infection is often transmitted through consuming contaminated eggs, poultry, or other foods. It can cause severe diarrhea, sometimes with blood, and poses a particular risk to young children and the elderly, potentially leading to life-threatening complications or permanent kidney damage. ​

Bovine Tuberculosis (Farm Animal-Borne Bacterial Zoonoses)

This zoonotic disease, caused by M. bovis, primarily affects cattle but can be transmitted to humans through direct contact with infected animals or the consumption of unpasteurized dairy products. ​

Q Fever (Farm Animal-Borne Bacterial Zoonoses)

Spread by inhalation of particles from infected animals or through unpasteurized dairy products, causing flu-like symptoms that can persist for months.​

Lyme disease (Vector-Borne Bacterial Zoonoses​)

Transmitted by ticks, causing rash, joint pain, and potential neurological issues. Common in areas where humans and ticks coexist.​

Tularemia (Vector-Borne Bacterial Zoonoses​)

Spread through tick bites, handling infected animals, or inhaling contaminated dust, leading to symptoms that vary from skin ulcers to pneumonia.​

Proteobacteria (Gram-Negative Bacteria)

Gram-negative bacteria that can be found in the human microbiome and other pathogenic species​.

Are comprised of five distinct classes:​

• Alphaproteobacteria​

• Betaproteobacteria​

• Gammaproteobacteria​

• Deltaproteobacteria​

• Epsilonproteobacteria​

Alphaproteobacteria: The Oligotrophs​

• Alphaproteobacteria thrive in low-nutrient environments such as deep oceanic sediments, glacial ice, and soil.​

• Key genera include Rickettsia and Chlamydia.​

• Rickettsia rickettsii causes Rocky Mountain spotted fever, transmitted by tick bites.​

• Chlamydia trachomatis is a human pathogen responsible for trachoma and lymphogranuloma venereum (LGV).​

Betaproteobacteria: The Eutrophs​

• Betaproteobacteria require high levels of organic nutrients and often inhabit areas between aerobic and anaerobic zones.​

• Notable pathogens include Neisseria gonorrhoeae (gonorrhoea) and Neisseria meningitidis (bacterial meningitis).​

• Bordetella pertussis causes whooping cough, producing toxins that damage respiratory cells​

Gammaproteobacteria: The Diverse Group

• Gammaproteobacteria are the most diverse class, including many human pathogens.​

• Pseudomonas aeruginosa is an opportunistic pathogen which causes infections in wounds and respiratory tracts.​

• Escherichia coli includes both mutualistic strains and dangerous pathogens like E. coli O157, which causes severe gastrointestinal diseases.​

• Vibrio cholerae is responsible for cholera, leading to severe dehydration through profuse watery diarrhea.

Deltaproteobacteria: Sulfate Reducers and Predators​

• Deltaproteobacteria are known for their ability to reduce sulfate and sulfur.​

• Desulfovibrio orale is associated with periodontal disease.​

• Bdellovibrio species are parasites of other gram-negative bacteria, invading and consuming host cells.​

• Myxobacteria form multicellular fruiting bodies and myxospores, showcasing -complex social behavior.​

Epsilonproteobacteria: The Smallest Class​

• Epsilonproteobacteria are microaerophilic, requiring low oxygen levels.​

• Campylobacter jejuni is a common cause of food poisoning through contaminated poultry, leading to severe enteritis.​

• Helicobacter pylori survives in the acidic environment of the stomach and causes chronic gastritis, peptic ulcers, and is linked to stomach cancer.​

Gram-Negative Nonproteobacteria

• Nonproteobacteria are gram-negative bacteria that do not belong to the phylum Proteobacteria.​

• This group includes three primary classes: Spirochetes, the CFB group (Cytophaga, Fusobacterium, Bacteroides), and Planctomycetes.​

Spirochetes

• Long spiral-shaped bodies​

• Includes pathogens like Treponema pallidum (causes syphilis) and Borrelia burgdorferi (Lyme disease) ​

CFB Group

• Anaerobic species which includes Cytophaga, Fusobacterium, and Bacteroides—key players in human health and disease.​

• Bacteroides make up 30% of the gut microbiome​

Planctomycetes

Unique aquatic bacteria with unusual reproductive and metabolic features.​

Phototropic Bacteria

Phototrophic bacteria are a diverse group that harness sunlight for energy through photosynthesis.​

• Are generally not harmful to humans, with some exceptions (cyanobacterial blooms “blue-green algae” produce toxins which have been implicated in tumors of the liver and neurological disease). ​

Gram-Positive Bacteria Characteristics

• For gram-positive bacteria, technological advancements have introduced new methods for their characterization, including the analysis of guanine-cytosine (G+C) ratio in the bacteria DNA.​

• The proportion of two specific DNA building blocks, guanine (G) and cytosine (C), which helps differentiate between different types of bacteria.​

• Basically, this approach further classifies gram-positive bacteria into High C+G and Low C+G​

High G+C Gram-Positive Bacteria Characteristics (Actinobacteria)​

• The Actinobacteria species are one of the largest phyla of the bacterial kingdom and are a very diverse species​

• The bacteria vary in size (can be small or large) and shape (rods, coccobaccili)​

• G+C content greater than 50% (can be up to 70%)​

• Found in diverse environments (soil, water).​

• Cell walls contain multiple peptidoglycans.​

Mycobacterium​ (Actinobacteria Examples)

• Includes M. tuberculosis, which causes tuberculosis, and M. leprae, which causes leprosy.​

• Unique Feature: Waxy mycolic acid coat that resists Gram staining (instead, acid-fast staining must be used)​

Corynebacterium​ (Actinobacteria Examples)

• Notable species: C. diphtheriae, which causes diphtheria.​

• Morphology: V-shaped pairs (palisades).​

Bifidobacterium​ (Actinobacteria Examples)

• Commonly found in the human gut, vagina, and mouth.​

• Used as probiotics and in yogurt production.​

Streptomyces​ (Actinobacteria Examples)

• Found in soil and important for antibiotic production (e.g., streptomycin).​

• Filamentous, spore-forming bacteria.​

Low G+C Gram-Positive Bacteria Characteristics

• G+C content less than 50%.​

• Includes many pathogenic genera.​

• Diverse morphologies: Bacilli and cocci.​

• Important for human health and industry.

Clostridium (Rod-shaped, spore-forming anaerobes)​ (​​​Low G+C Gram-Positive Bacteria Examples)

C. perfringens

C. tetani

C. botulinum

C. difficile

C. perfringens

Causes gas gangrene and food poisoning.​

C. tetani

Causes tetanus, leading to muscle spasms.​

C. botulinum

Produces botulinum toxin, the most lethal biological toxin known.​

C. difficile

Common cause of hospital-acquired colitis.​

Low G+C Gram-Positive Bacteria Examples

Streptococcus

S. pyogenes

S. pneumoniae

S. agalactiae

Streptococcus

Spherical cocci, forming chains or pairs

S. pyogenes

Causes strep throat and necrotizing fasciitis.​

S. pneumoniae

Causes pneumonia and other respiratory infections.​

S. agalactiae (Group B Strep)

Can cause serious infections in newborns, pregnant women, and adults with chronic illnesses.

Low G+C Gram-Positive Bacteria Examples

Bacillus

B. anthracis

B. cereus

Bacillus

Rod-shaped, forms chains, spore-forming

B. anthracis

Causes anthrax, a severe disease affecting skin and lungs.​

B. cereus

Causes food poisoning; forms milky white colonies on blood agar.​

Low G+C Gram-Positive Bacteria Examples

Staphylococcus

S. aureus

S. epidermidis

Staphylococcus

Spherical cocci, clusters resembling grapes

S. aureus

Causes skin infections, food poisoning, and toxic shock syndrome.​

S. epidermidis

Common on human skin, can cause infections in immunocompromised patients.

Mycoplasmas

The Shape-Shifting Bacteria Without Borders!​

Mycoplasmas (Pleomorphic, Wall-Less Bacteria)​ Characteristics​

• Lack a cell wall; not stained by Gram-stain.​

• Extremely small, some as small as 0.2 μm.​

• Pleomorphic: Can change shape, resembling small animal cells.​

• Over 100 species identified.​

M. pneumoniae

Causes “walking pneumonia,” a mild, atypical pneumonia.​

The Laboratory Workflow (Broadly)​

• Specimen Receipt and Logging​

• Direct Examination​

• Specimen Inoculation​

• Incubation​

• Initial Plate Examination​

• Subculture and Isolation (if necessary)​

• Bacterial Identification​

• Antibiotic Susceptibility Testing​

• Results Reporting​

• Storage and Disposal​

Medical Errors in Laboratory Diagnostics

• Laboratory results influence up to 80% of clinical decisions​

• A study in British Columbia found that laboratory-associated errors accounted for nearly 5% of all hospital errors.​

• Laboratory errors are typically divided into three phases:​

• Pre-analytical (errors that occur before the specimen arrives in the lab)​

• Analytical (errors that occur during the analysis stage)​

• Post-analytical (errors that occur after the analysis of the specimen. For example, failure to report, improper data entry)​

What phase has the greatest error rate

pre-analytic

A Sample of Hospital-Related Laboratory Incidents​

• Samples without proper patient identification, such as missing or mismatched labels, are often rejected to prevent errors in diagnosis or treatment.​

• Using the wrong collection method, such as drawing blood from the wrong site or using the incorrect container​

• Submitting a sample with insufficient volume can prevent the lab from performing the required tests, leading to rejection.​

• Contamination during collection, such as using non-sterile equipment or improper handling​

• Failing to transport the specimen to the lab within the required timeframe, especially for time-sensitive tests​

• Storing samples at incorrect temperatures or inappropriately handling them before submission can lead to sample degradation and rejection.​

How Might Nurses Work to Reduce These Errors

• Familiarize Yourself with Policies and Procedures: Ensure you thoroughly understand and adhere to established protocols.​

• Seek Guidance When Needed: If you’re uncertain about how to perform a task, don’t hesitate to ask for help or request additional training.​

• Report Incidents Promptly: Reporting errors or near-misses contributes to the collective learning process and helps prevent future mistakes.​

• Enhance Communication: Foster clear, open communication with colleagues to ensure accurate and effective collaboration.​