Welcome!

1. MMI480B: Medical Microbiology Welcome! For questions about Bacteriology and Mycology: Renée Tsolis, Ph.D., co-IOR Office: 5519 Genome and Biomedical Sciences Facility rmtsolis@ucdavis.edu

2. Medical Microbiology components: Parasitology: Dr. S. Luckhart Virology: Dr. M. Mudryj Bacteriology and Mycology: Dr. R. Tsolis Objective of this course: to acquire knowledge about human pathogens that is relevant for patient care.

3. Reading material: Required text: Murray, 6th ed. Recommended by previous classes. Caveat! If information here contradicts the assigned text we will consider the information in the text to be correct.

4. Systems based organization of the course: Introductory section Respiratory tract infections Skin and soft tissue infections Infections of the gastrointestinal tract Infections affecting the CNS Urogenital tract infections Vectorborne and zoonotic infections Keep in mind that many pathogens affect more than one organ system!

5. Learning Objectives for Bacteriology • All of the bacteria listed on the next 2 slides • Clinical presentation • Tissue(s)/organ(s) affected • Pathogenic mechanisms • Epidemiology • Transmission • Laboratory Diagnosis • Treatment and/or prevention

6. Important bacterial pathogens and their clinical presentations Respiratory tract Streptococcus pneumoniae Haemophilus influenzae Mycoplasma pneumoniae Chlamydophila pneumoniae Mycobacterium tuberculosis Bordetella pertussis Legionella pneumophila Klebsiella pneumoniae Pseudomonas aeruginosa Staphylococcus aureus Acinetobacter baumanii Head/Neck Corynebacterium diphtheriae Streptococcus pyogenes Actinomyces Fusobacterium Skin/Soft tissue Streptococcus pyogenes Staphylococcus epidermidis Staphylococcus aureus Bacteroides fragilis Pasteurella multocida Rickettsia spp Borrelia burgdorferi Treponema pallidum Bacillus anthracis GI tract Vibrio cholerae Enterotoxigenic E. coli Enteropathogenic E. coli Enterohemorrhagic E. coli Campylobacter jejuni Shigella spp. Non-typhoidal Salmonella Salmonella typhi Clostridium difficile Helicobacter pylori Intoxication: Staphylococcus aureus Clostridium perfringens Bacillus cereus

7. Important bacterial pathogens and their clinical presentations CNS Streptococcus pneumoniae Neisseria meningitidis Escherichia coli K1 Streptococcus agalactiae Listeria monocytogenes Clostridium botulinum Clostridium tetani Treponema pallidum Eyes Chlamydia trachomatis Neisseria gonorrheae Pseudomonas aeruginosa Urinary tract Escherichia coli (UPEC) Staphylococcus saprophyticus Klebsiella pneumoniae Proteus mirabilia Enterococcus faecalis Enterohemorrhagic E. coli (HUS) Genital tract Chlamydia trachomatis Neisseria gonorrheae Treponema pallidum Haemophilus ducreyi Gardinerella vaginalis Mobiluncus spp. Blood/Lymphatics/RES Francisella tularensis Yersinia pestis Brucella abortus Rickettsia spp. Anaplasma spp.

8. What is an infection? • Colonization of body tissues or surfaces by pathogenic organisms that are able to multiply and cause injury, resulting in disease. • Some possible pathogenic mechanisms: • Release of toxins or toxic substances • Elicitation of host responses (inflammation or • autoimmunity) that are injurious • Intracellular multiplication leading to cell death

9. Classes of infectious agents: • Prions (single protein molecule) • Viruses • Bacteria (prokaryotes) • Fungi (eukaryotes) • “Parasites” (eukaryotes) • Protozoa: unicellular • Helminths: multicellular • Nematodes: multicellular

10. Eukaryotes vs. prokaryotes • Eukaryotes have a well-defined nucleus. • Eukaryotes have 80S ribosomes, while prokaryotes have 70S ribosomes. • Organelles such as Golgi apparatus, mitochondria, lysosomes and endoplasmic reticulum are unique to eukaryotes.

11. The eukaryotic cell ~15µm in diameter

12. The prokaryotic cell ~0.5 x 1-3 µm in diameter

13. Bacterial morphology • Bacteria are classified on the basis of microscopic appearance and biochemical characteristics. • Gram stain determines the type of cell wall that bacteria have. • The type of cell wall is important for determining characteristics such as antibiotic susceptibility.

14. Gram stain procedure • Streptococcus pyogenes • Staphylococcus aureus • Bacillus anthracis • Escherichia coli • Salmonella typhi • Neisseria gonorrhoeae http://pathmicro.med.sc.edu/fox/gram-st.jpg (see also Murray, Fig. 3-3)

15. Morphological characteristics: cocci Clumps of bacteria: Staphylococcus aureus (Gr.:staphyle=grapes; kokkos = berry) Chains of cocci: Streptococcus (derived from Greek term for “helix”) Diplococci: present in pairs e.g.Neisseria gonorrhoeae

16. Morphological characteristics: rods (bacilli) Rods or bacilli are longer than cocci. Bacillus anthracis is 1µm x 3-5µm In pink, a spore is visible. Gram stain of Bacillus anthracis http://textbookofbacteriology.net/Anthrax.html

17. Other types of rods (bacilli): Coccobacillus: Haemophilus influenzae http://textbookofbacteriology.net Coccobacillus: Brucella melitensis http://www.state.sd.us/doh/ LabBT/brucellaGram.htm

18. Other types of rods (bacilli): Rods with terminal endospores: Clostridium botulinum http://www.textbookofbacteriology.net/clostridia.html Curved rods: Vibrio cholerae (l) Campylobacter (r)

19. Spirochetes Treponema pallidum Leptospira interrogans

20. Diagnosis of Bacterial Infections: Clinical presentation http://mdchoice.com/pt/Photo/cptod0012.asp • Erythema migrans lesions typical of patients with Lyme disease caused by Borrelia burgdorferi.

21. Gram-positive diplococci surrounded by clear zone (suggesting a capsule) Diagnosis of Bacterial Infections: Gram stain and morphology PMN • Gram stain of sputum from a patient with pneumonia. Appearance is consistent with S. pneumoniae.

22. Diagnosis of Bacterial Infections: Specialized staining Sputum sample from a patient with tuberculosis stained with Ziehl-Neelsen acid fast stain.

23. Diagnosis of Bacterial Infections: Metabolic capabilities (biotyping) Triple sugar-iron agar slants inoculated with different bacteria. Species are differentiated by their ability to metabolize sugars. API identification strip for enteric bacteria.

24. Diagnosis of Bacterial Infections: Surface antigens Immunofluorescence assay (IFA) of mixed bacteria. • This test uses a commercial antibody to identify bacteria in patient samples.

25. Diagnosis of Bacterial Infections: Serology Enzyme-linked Immunosorbent Assay (ELISA) Agglutination of bacterial antigen by patient serum • These tests detect a pathogen-specific antibody response in patient samples

26. Diagnosis of Bacterial Infections: Colony morphology Staphylococcus epidermidis on Blood Agar (non-hemolytic) Staphylococcus aureus on Blood Agar (hemolytic) Images: www.microbelibrary.org

27. Diagnosis of Bacterial Infections: Phage typing http://www.bmb.leeds.ac.uk/mbiology/ug/ugteach/icu8/xinfect/phagetype.html Bacteriophage susceptibility test Bacteriophage (virus that infects bacteria) Used mostly for enteric bacteria and MRSA typing

28. Diagnosis of Bacterial Infections: PCR-based diagnostics Image:Nobelprize.org Specific kits are available based on DNA sequence of the organism to be tested. This technique is especially useful for slow growing organisms and viruses.

29. Take-home points: • Prokaryotes and eukaryotes have several important differences in cell structure. • Gram stain and morphology are used to classify bacteria • A combination of clinical observation and diagnostic tools is useful in determining bacterial causes of disease.

30. Online resources used • Murray, 6th ed. www.studentconsult.com • ASM Microbe Library: microbelibrary.org • Dennis Kunkel Microscopy: http://education.denniskunkel.com • Todar’s Online Textbook of Bacteriology: http://www.textbookofbacteriology.net/ • Microbiology and Immunology On Line: http://pathmicro.med.sc.edu/book/bact-sta.htm