2.6.1 Bacteria

Introduction to Bacteria 🧫

Bacteria are a central part of USMLE microbiology and appear in both basic science and clinical questions. In this chapter you will focus on what makes bacteria unique as microorganisms, how they are classified, and which structural and physiologic features are clinically important. Details of individual species, antibiotics, and immune responses are covered in other chapters, so here the emphasis is on the general principles that let you recognize and reason about any bacterial question.

Basic Bacterial Cell Structure 🧪

Bacteria are prokaryotic cells. They lack a true nucleus and membrane bound organelles. Their genetic material is a single circular double stranded DNA molecule that lies in a region called the nucleoid. Ribosomes are present but are of the 70S type, with 30S and 50S subunits, which is a key difference from human 80S ribosomes and is exploited by many antibiotics.

Bacterial cytoplasm contains metabolic enzymes, DNA, RNA, and ribosomes, but no mitochondria, endoplasmic reticulum, or Golgi apparatus. The cell membrane is a phospholipid bilayer with proteins, but unlike human cells it is also the site of the electron transport chain and ATP production. There is no mitochondrial membrane, so oxidative phosphorylation occurs at the plasma membrane.

Outside the membrane, most bacteria have a rigid cell wall composed of peptidoglycan. This structure is critical for cell shape and resistance to osmotic stress and is a major antibiotic target. Some bacteria also possess additional outer structures such as capsules, flagella, fimbriae or pili, and specialized outer membranes.

Gram Positive and Gram Negative Bacteria 🎨

The Gram stain is fundamental for bacterial classification and clinical decision making. It separates bacteria into two main groups based on cell wall structure. This structural difference leads to distinct staining, typical antibiotic sensitivities, and typical virulence properties.

In the Gram stain procedure, bacteria are first stained with crystal violet, then treated with iodine, decolorized with alcohol, and counterstained with safranin. Gram positive bacteria retain the crystal violet iodine complex and appear purple. Gram negative bacteria are decolorized then take up the pink counterstain.

The structural basis of this difference is the composition and organization of the cell wall. Gram positive organisms have a thick peptidoglycan layer external to the cell membrane. Gram negative organisms have a thin peptidoglycan layer and an additional outer membrane containing lipopolysaccharide.

These differences explain many clinically relevant features. Gram negative bacteria often cause endotoxin mediated effects due to LPS. Gram positive bacteria are more directly targeted by drugs that disrupt peptidoglycan cross linking, since this is the dominant structural component of their cell wall.

The Bacterial Cell Wall and Peptidoglycan 🧱

Peptidoglycan is a polymer of sugar chains cross linked by short peptides. The sugar backbone is made of alternating N acetylglucosamine (NAG) and N acetylmuramic acid (NAM). Attached to NAM residues are short peptide side chains that cross link with neighboring chains, forming a mesh like structure.

This cross linked network provides rigidity and shape. In Gram positive bacteria, this structure is thick and multilayered. In Gram negative bacteria, it is thin and lies in the periplasmic space between the inner and outer membranes.

Beta lactam antibiotics target the enzymes that catalyze cross linking of peptidoglycan, the transpeptidases. Without proper cross linking, the cell wall becomes weak and the bacterium can lyse. Some bacteria produce enzymes such as beta lactamases that can inactivate these drugs. Structural variations in peptidoglycan and associated proteins are therefore closely tied to antibiotic susceptibility and resistance.

Teichoic Acids and Lipopolysaccharide 💥

Certain cell wall associated molecules are important virulence factors.

In Gram positive bacteria, teichoic acids are polymers of glycerol or ribitol phosphate anchored in the peptidoglycan. They can extend through and sometimes beyond the cell wall. Teichoic acids can trigger immune responses and help bacteria adhere to host cells. They are specific to Gram positive organisms and are absent in Gram negatives.

In Gram negative bacteria, the outer membrane contains lipopolysaccharide, also called endotoxin. LPS has three main components: lipid A, a core polysaccharide, and an O antigen side chain. Lipid A is responsible for the toxic effects of endotoxin and activates immune cells, which release cytokines such as TNF and IL 1. Excessive release can lead to fever, hypotension, and septic shock.

The O antigen portion varies between strains and is useful for serologic classification. Because LPS is part of the outer membrane, Gram negative infections frequently have prominent systemic manifestations mediated by endotoxin.

Capsules, Slime Layers, and Biofilms 🧴

Many clinically important bacteria are surrounded by a capsule or produce a less organized surface coat. A capsule is a well organized, usually polysaccharide outer layer that firmly surrounds the cell. It provides protection from phagocytosis by interfering with opsonization and complement mediated killing, and often contributes to bacterial virulence.

Some bacteria instead produce a loosely attached, amorphous glycocalyx or slime layer. This facilitates adherence to surfaces, including medical devices, teeth, and mucosal surfaces. When bacterial communities form on a surface and are embedded in a self produced extracellular matrix, the result is a biofilm.

Biofilms have major clinical implications. Bacteria within biofilms can be much more resistant to antibiotics and to host immune responses. They can persist on catheters, prosthetic heart valves, joint prostheses, and other devices, leading to chronic or recurrent infections that resolve only when the device is removed. Biofilms can also block penetration of some antibiotics, creating concentration gradients inside the matrix.

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Bacteria in biofilms are significantly more resistant to antibiotics and host defenses than free living (planktonic) bacteria.

Flagella, Pili, and Fimbriae 🧬

Some bacteria possess external appendages that are critical for motility and adherence. Flagella are long, whip like structures that rotate and move the bacterium through liquid media. They are composed of the protein flagellin and are anchored in the cell membrane and wall. Motility can be an important trait on microscopy or in laboratory testing, and many motile bacteria are chemotactic, moving toward nutrients or away from toxins.

Pili and fimbriae are shorter, hair like projections made of pilin protein. They usually function in adherence to host cells and to surfaces. This adherence can be the first step in colonization of mucosal sites and in pathogenesis of infection. Specialized sex pili participate in conjugation, a mechanism by which bacteria transfer plasmids, including antibiotic resistance genes, from one cell to another.

Bacterial Genetic Material and Plasmids 📚

The primary bacterial chromosome is a single circular molecule of double stranded DNA. It contains the essential genes for survival and typical metabolic functions. This chromosome is supercoiled and located in the nucleoid region without a surrounding membrane.

Many bacteria also harbor plasmids. These are small, circular, double stranded DNA molecules separate from the main chromosome. Plasmids replicate independently and often carry genes that provide selective advantages such as antibiotic resistance, toxin production, or specialized metabolic capabilities.

Because plasmids can be transferred between bacteria, especially through conjugation, they are central to the rapid spread of resistance traits in clinical settings. Some plasmids are conjugative, meaning they encode the machinery required for transfer, including sex pili. Others depend on conjugative plasmids for mobilization.

Bacterial Growth and Nutrition 🌱

Bacteria reproduce by binary fission, which is a form of asexual reproduction. One cell grows, replicates its DNA, and divides into two genetically identical daughter cells. If conditions are favorable, this process yields exponential growth.

On a growth curve in a closed system, four phases are typically identified. In the lag phase, bacteria adapt to the environment and synthesize necessary enzymes, but cell numbers do not increase significantly. In the log or exponential phase, cells divide at a constant maximum rate. This is the phase in which many antibiotics acting on cell wall synthesis or protein synthesis are most effective because they target actively growing cells. In the stationary phase, nutrient depletion and waste accumulation slow growth and the rate of cell division equals the rate of cell death. In the death or decline phase, cells die at a faster rate than they divide.

Nutritionally, bacteria can be classified by their requirement for oxygen and by their energy sources. Some are obligate aerobes and require oxygen as a terminal electron acceptor. Others are obligate anaerobes and are harmed by oxygen, often due to lack of enzymes such as superoxide dismutase or catalase that detoxify reactive oxygen species. Facultative anaerobes can use oxygen when it is present but can also ferment or use other electron acceptors in its absence. These oxygen requirements affect where bacteria can survive in the host and how they are cultured in the laboratory.

Spore Formation 🌾

Certain Gram positive bacteria can form endospores. An endospore is a highly resistant, dormant structure that forms within the bacterial cell. It contains a copy of the bacterial chromosome, minimal cytoplasm, and a multilayered coat rich in dipicolinic acid and calcium.

Endospores are extremely resistant to heat, desiccation, radiation, and many disinfectants. They allow bacteria to survive harsh environmental conditions for long periods. When conditions become favorable again, the spore can germinate and return to a metabolically active, vegetative state.

Spore formation is not a form of reproduction because one vegetative cell produces one spore, which eventually produces one vegetative cell. Clinically, the environmental persistence of spores is important for infection control and sterilization. Ordinary cleaning procedures or low level disinfection may not destroy spores, so higher level sterilization techniques are required for instruments that contact sterile body sites.

Key Laboratory Identification Concepts 🔬

In practice, bacteria are identified with a combination of staining, culture, biochemical tests, and sometimes molecular methods. From a USMLE perspective, you should recognize which general properties guide this process rather than the full catalog of tests for each organism.

Initial distinction between Gram positive and Gram negative, along with cell shape, is usually the starting point on a lab report. Bacteria can be cocci, which are spherical, or bacilli, which are rod shaped. Some species have characteristic arrangements, such as chains, clusters, or pairs. In addition to Gram stain, some organisms require special stains or do not stain well due to lack of a typical cell wall.

After staining, growth characteristics on specific media are useful. Many bacteria have preferences for certain nutrients, pH ranges, or atmospheric conditions. Hemolysis patterns on blood agar, lactose fermentation on selective media, and response to oxidase or catalase tests are examples of common biochemical features. These tests, along with susceptibility patterns to certain antibiotics, form characteristic profiles used to identify species.

Bacterial Pathogenesis and Toxins 🧨

Bacteria cause disease through several mechanisms. Some directly damage tissues through invasion and multiplication, others primarily trigger harmful immune responses, and many produce toxins. Toxins are usually divided into exotoxins and endotoxin.

Exotoxins are actively secreted proteins, often by Gram positive but also by some Gram negative bacteria. They have specific enzymatic activities and targets such as blocking protein synthesis, disrupting cell membranes, or interfering with signal transduction. Exotoxins are usually heat labile and can often be converted into toxoids by formaldehyde treatment. Toxoids retain antigenicity but lack toxicity and can be used in vaccines.

Endotoxin refers mainly to the lipid A component of LPS in Gram negative outer membranes. It is not secreted but is released when bacteria die or multiply. It activates immune cells through pattern recognition receptors and leads to production of cytokines that can cause fever, hypotension, and disseminated intravascular coagulation in severe cases.

The ability of bacteria to adhere to host tissues, invade between or through cells, evade phagocytosis, resist complement, and vary their surface antigens also contributes to virulence. Many of these traits are encoded on plasmids or mobile genetic elements and can spread between strains.

Horizontal Gene Transfer 🔁

Bacteria can acquire new genetic material not only by mutation but also by horizontal gene transfer. This allows rapid spread of traits such as antibiotic resistance and toxin production. The detailed mechanisms are covered elsewhere, but it is useful here to recognize the general concept.

In conjugation, DNA is transferred directly between bacteria through cell to cell contact, often mediated by sex pili and plasmids. In transformation, bacteria take up free DNA from the environment, for example from lysed cells. In transduction, bacteriophages transfer bacterial DNA from one cell to another during their replication cycles.

These processes accelerate bacterial evolution and can create sudden changes in pathogenicity or drug resistance. As a result, clinical patterns of resistance can change quickly and may differ significantly between hospitals or regions.