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BACTERIAL CLASSIFICATION AND DIAGNOSIS OF BACTERIAL DISEASE. Disease causing agent Bacterial, fungal, viral or other? Treatment Antibiotic sensitivity Source of infection Food, air or contact? Epidemiology Cholera, Diphtheria Prevention E. coli O157:H7 outbreak, Shigella, Listeria.
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BACTERIAL CLASSIFICATION AND DIAGNOSIS OF BACTERIAL DISEASE • Disease causing agent • Bacterial, fungal, viral or other? • Treatment • Antibiotic sensitivity • Source of infection • Food, air or contact? • Epidemiology • Cholera, Diphtheria • Prevention • E. coli O157:H7 outbreak, Shigella, Listeria
Site of sampling • Sterile sites • Blood • Cerebrospinal fluid (CSF) • Body fluids (Peritoneal and pleural) • Non-sterile (normal flora) • Respiratory tract • Ear, eye and mouth • Skin (wound and abscess) • Urine (mid-stream) • Feces
Bacterial classification • Wall structure • Gram + • Staphylococcus, Streptococcus, Clostridium, Bacillus • Gram - • Enteric, respiratory and others • Acid-fast • Mycobacterium • Wall-less • Mycoplasma • Unusual • Obligate intracellular • Rickettsia, Chlamydia Bacteria G+ G- AF WL IC
Bacterial classification • Cell morphology • Shapes • Rod • Cocci • Spiral • Associations • Individual • Diplo- • Staphylo- • Strepto- Bacteria G+ G- AF WL IC Rod Cocci Rod Cocci Spiral
Bacterial classification • Growth characteristics • Oxygen requirement • Aerobic • Anaerobic • Microaerophilic, aerotolerant • Facultative • Spore formation • Intracellular/extracellular • Fastidious/non-fastidious Bacteria G+ G- AF WL IC Rod Cocci Rod Cocci Spiral + +/- -O2 + spore -
Classification & Diagnosis • Type of colonies • Appearance • Color, shape, size and smoothness • On differential media • Blood, MacConkey, EMB • On selective media • MacConkey, Thayer-Martin
Classification & Diagnosis • Metabolism • Utilization of specific substrates • Lactose (Sal/Shi/Yer/)- • Citrate (E. coli-/Klebsiella+) • Production of certain end products • Fermentation end products • Acid (acetate, propionic acid, butyric acid etc.) • Acetoin • Alcohol • Amine • H2S
Classification & Diagnosis • Specialized tests • Immunological • O-, H- & K-Ag (serotype) • Precipitation, agglutination • Specialized enzymes • Catalase--- Staph+. vs. Strep-. • Coagulase---S. aureus+ vs. S. epidermidis- • Oxidase---Neisseria gonorrhoea+ • Urease---Proteus+, Helicobacter+ • Antibiogram pattern • Phage typing • Fatty acid profile
Conventional method • Depend on ability to culture • Treponema pallidum • Slow, esp. for fastidious species • Mycobacteriumspp. • Not always definitive
Molecular diagnosis • Ribotyping • Restriction fragment length polymorphism (RFLP) • DNA hybridization • PCR, RT-PCR and RAPD • Nucleic acid sequence analysis • Phage-GFP (TB)
RFLP GGATCC CCTAGG
PCR RT-PCR Rate of increase 2n
Reduce reliance on culture Faster More sensitive More definitive More discriminating Techniques adaptable to all pathogens Technically demanding Relatively expensive Can be too sensitive Provides no information if results are negative Molecular diagnosis
Bioterrorism • Pathogen detection • Fast and accurate • Mobile • Inexpensive • Source investigation
Differentiating Staphylococci from Streptococci • Gram stain and morphology • Both Gram + • Staphylococci: bunched cocci • Streptococci: chained cocci (S. pneumoniae form diplococcus) • Enzyme tests • Staphylococci: catalase + • Streptococci: catalase - • Growth • Staph.: large colonies (non-fastidious), some hemolytic • Strep.: small colonies (fastidious), many hemolytic (a or b)
Staphylococci • S. aureus: coagulase + • S. epidermidis: coagulase -
Differentiating the Gram- bacteria • Cocci • Neisseria • Rods • Type of disease they cause • Enteric Gram- rods • API test • Curved • Vibrio, Campylobacter, Helicobacter • Spiral Gram- organisms • Spirochetes
Gram negative Curved rods Straight rods Lactose+ Lactose- TCBS agar Yellow Oxidase+ Vibrio Campy blood agar 42oC+ 25oC- Campylobacter Citrate+ Citrate- H2S+ H2S- Klebsiella E. coli Salmonella Shigella
Bacteria Intra Cellular Wall Less Gram+ Gram- Acid Fast Cocci Rod Spiral Rod Cocci M.t. M.l. N.c. Rickettsia Coxiella Erlichia Chlamydia Mycoplasma Staph. Strep. Non-spore Spore Treponema Borrelia Leptospira Neisseria Moraxella Fil Rod +O2 -O2 Curve B.a. B.c. C.b. C.t. C.p. C.d. S. a. S. e. S. s. A B Pn Vir A.i. C.d. L. m. Straight Vibrio Campylobacter Helicobacter +O2 +/-O2 -O2 Other P.a. Enteric Bact. Resp. Zoo GU H. ducreyi Gardnerella Calymmatobacterium Yersinia Pasteurella Brucella Francisella Streptobacillus Bordetella. H. influenzae Legionella