I. Introduction to basic physiology and concepts of pathogenesis II. Bacterial cell structures III. Growth and nutrition IV. Antibiotic resistance-mutation and genomic change V. Antibiotic resistance-gene exchange

I. Introduction to basic physiology and concepts of pathogenesis II. Bacterial cell structures III. Growth and nutrition IV. Antibiotic resistance-mutation and genomic change V. Antibiotic resistance-gene exchange

The major cellular targets of antibiotics Peptidoglycan synthesis Cycloserine Vancomycin Penicillins Cephalosporins Bacitracin DNA RNA polymerase Rifampin mRNA 30S 50S Cell membrane Polymixins Ribosome inhibitors Erythromycin Chloramphenicol Clindamycin

I. Introduction to basic physiology and concepts of pathogenesis II. Bacterial cell structures III. Growth and nutrition IV. Antibiotic resistance-mutation and genomic change V. Antibiotic resistance-gene exchange

Metabolism Glycolysis Fermentation TCA Cycle Respiration

I. Introduction to basic physiology and concepts of pathogenesis II. Bacterial cell structures III. Growth and nutrition IV. Antibiotic resistance-mutation and genomic change V. Antibiotic resistance-gene exchange

Genomes within bacteria Virus Genome Plasmid

I. Introduction to basic physiology and concepts of pathogenesis II. Bacterial cell structures III. Growth and nutrition IV. Antibiotic resistance-mutation and genomic change V. Antibiotic resistance-gene exchange

Genetic exchange

VI. Virulence-basic mechanisms of gene regulation VII. Virulence- mechanisms of adaptation VIII. Emerging infections IX. Regulation of virulence-Example of Salmonella X. Regulation of virulence-Example of Neisseria gonorrhea

Gene regulation P P Receptor senses the environment Protein controls gene expression P P DNA

VI. Virulence-basic mechanisms of gene regulation VII. Virulence- mechanisms of adaptation VIII. Emerging infections IX. Regulation of virulence-Example of Salmonella X. Regulation of virulence-Example of Neisseria gonorrhea

Adaptation

VI. Virulence-basic mechanisms of gene regulation VII. Virulence- mechanisms of adaptation VIII. Emerging infections IX. Regulation of virulence-Example of Salmonella X. Regulation of virulence-Example of Neisseria gonorrhea

VI. Virulence-basic mechanisms of gene regulation VII. Virulence- mechanisms of adaptation VIII. Emerging infections IX. Regulation of virulence-Example of Salmonella X. Regulation of virulence-Example of Neisseria gonorrhea

Regulation of virulence Stomach: Acid tolerance Small intestine: Invasion

VI. Virulence-basic mechanisms of gene regulation VII. Virulence- mechanisms of adaptation VIII. Emerging infections IX. Regulation of virulence-Example of Salmonella X. Regulation of virulence-Example of Neisseria gonorrhea

Regulation of virulence:pilus variation

Fundamental concepts in bacteriology Bacterial diversity and the microbiota Classification (diagnosis) Steps in pathogenesis: Infection involves multiple steps. Focus on an early step: adherence. A successful pathogen has adapted to survive host defenses and to cause disease.

Diversity of life The number of bacterial species is vast. 1000’s of species (a very very small subset of the bacteria) comprise the human microbiota. A much smaller number of species can actually cause disease in humans. Archea are not (yet) known to cause human disease. However, they have been discovered among the human microbiota.

Diversity of life

Most (probably all) animals harbor a complex bacterial community called the microbiota The human microbiota is extremely complex. It spans 1000’s of species including some archea. Most of these species remain unidentified. There are 10 times more bacterial cells than human cells in a person. The bacterial species in an individual’s microbiota varies with age, geography and lifestyle. The microbiota participate in organ development, digestion of food, and synthesis of vitamins. The microbiota are especially important in preventing bacterial infection. The microbiota and the immune system influence each other. Still, the impact of the microbiota on normal health is much more complex than currently appreciated.

The microbiota are present throughout the GI tract The geographical distribution of the microbiota is a new area of study. Locations of particular interest: GI tract, skin, respiratory tract, vagina, penis. Adapted from Leser and Molbak, Env. Microbiol 2009

Changing historical perspectives on bacteria and human health 1. Bacteria are, most importantly, agents of disease. However, some live in harmony with the host or even contribute to host well being. 2. Most bacteria are harmless. Only a few highly adapted bacteria cause disease. Probably, the bacteria normally found in a healthy host are needed to suppress disease. 3. Hosts possess enormous, highly complex bacterial communities that are essential for health. The composition and distribution of these organisms emerges from a complex homeostasis involving the bacteria, the host immune system, life style and other host and environmental factors. 4. The bacteria and the host have coevolved and continue to do so. The integration of their evolutionary histories makes them effectively inseparable.

A device to measure metabolism of sugars and other compounds

Growth on antibiotics

Gram stain: purple, Gram +; pink, Gram -

Additional methods for bacterial identification: 1. Determine the ability of bacteria to grow on a variety of chemically distinct media: the preferred growth medium can identify the organism. 2. Identify the sugars used during, and the organic products of, fermentation (only during anaerobic conditions). 3. Determine whether peroxidases or superoxide dismutatases are present; if so, the bacterium can likely perform oxidative metabolism. 5. Identify genes specific to a given pathogen.

Identify bacteria by genes specific for given pathogen Analyze DNA from an infection site to determine whether pathogen-specific DNA is present. This requires knowledge of genes unique to a given pathogen. This requires significant basic science analysis.

PCR can identify specific DNA sequences Bacterial DNA ` Oligonucleotide probes

Diagnostic tests are only as reliable as the collection and culture methods Be sure to avoid contamination from organisms present at the collection site. Beware of downstream contamination (blood banks). Be suspicious of blood drawn from indwelling central venous catheters. Be knowledgeable about the real local pathogens. Be suspicious of infections by organisms not known to be in the environment. Be meticulous about your own sanitation (hands, equipment, vaccination). Stay home when you are sick.

EXPOSURE to pathogens ADHERENCE to skin or mucosa INVASION though epithelium COLONIZATION and GROWTH production of virulence factors SPREAD TOXICITY DISEASE

Steps in B. pertussis pathogenesis There can be many consequences to adhesion and invasion!

Steps in pathogenesis How might a bacterium cause significant disease WITHOUT invading or even adhering? Is this even possible?

Barriers to entry and adherence

Examples of pathogen adherence V. cholera, w/o capsule, rabbit brush boarder EPEC (E. coli), w/capsule, calf brush boarder

Direct consequences of pathogen adherence Activation of the immune system: adaptive and innate immunity Adapted from Bhavsar et al. Nature 2007

Direct consequences of pathogen adherence Uptake into a specialized, double membrane intracellular compartment Adapted from Bhavsar et al. Nature 2007

Direct consequences of pathogen adherence Cytoskeletal rearrangement, formation of a specialized lesion and entry into the host cell Adapted from Bhavsar et al. Nature 2007

Direct consequences of pathogen adherence Cytoskeletal rearrangement, formation of a specialized lesion and some degree of entry into the host cell Adapted from Bhavsar et al. Nature 2007

Preferred niches of certain pathogens

Normal flora These are commensal interactions!

Normal flora in the wrong place What happens when a commensal bacterium enters a location in the body that it does not normally occupy (as can happen during surgery)?

Fundamental concepts in bacteriology Bacterial diversity and the microbiota Classification (diagnosis) Steps in pathogenesis: Infection involves multiple steps. Focus on an early step: adherence. A successful pathogen has adapted to survive host defenses and to cause disease.