Microbiology Revision Notes PDF

Contents General Microbiology  1 Hospital Infection Control  7 Immunology  10 Laboratory Diagnosis of Infections : Bacterial and Fungal  15 Laboratory Diagn...

Contents General Microbiology  1 Hospital Infection Control  7 Immunology  10 Laboratory Diagnosis of Infections : Bacterial and Fungal  15 Laboratory Diagnosis of Infections : Viral and Parasitic  18 Central Nervous System  23 Cardiovascular System : Infections of Heart  27 Cardiovascular System : Bloodstream and Lymphatic Infections  30 Respiratory System  38 Gastrointestinal and Hepatobiliary System  45 Genitourinary System  51 Skin, Subcutaneous and Musculoskeletal System  53 Miscellaneous Infections  60  General Microbiology 1 GENERAL MICROBIOLOGY ----- Active space ----- Kary B Mullis : Invented PCR (Molecular) : Detects gene. Eva Engvall (Along with Peter Perlman) : Developed ELISA (Immunological) : Detects Ag/Ab. Microscopy & Staining 00:09:58 MICROSCOPY Detection of organism Morphology : Staining (Killed). Motility : Hanging drop (Live). Types of Microscopes to Visualize Motility : Bright field microscope (Light) Darkfield microscope Phase contrast microscope Features M/c used Darkfield (Special condenser) > Phase contrast (Phase plate) Bright organism with bright Characteristics background Bright organism with Dark organism with dark background bright background Motility Thin organisms motility visualized All except thin organisms Observed (Spirochetes : Corkscrew motility) Darkfield microscope : Contains dark field condensor. Phase contrast microscope : Contains phase plate. Microbiology Revision v4.0 Marrow 8.0 2024  2 Microbiology ----- Active space ----- STAINING Violet : Gram Positive Gram Stain : Pink : Gram Negative Smear preparation : Primary staining : Crystal violet/Gentian/Methyl violet Organisms (1 min) stain violet Wash Add mordant : Gram’s Iodine Organisms (1 min) remain violet Wash Add decolourization (Critical step) : Acetone (2-3 secs)/ Decolorize - : Retain 1O stain. (Few seconds) Alcohol (20-30 secs) Decolorize + : Colorless. Wash Counter staining : Saffranin/Dilute carbol fuschin Violet : Gram + (Thick cell wall) (1 min) Pink : Gram - (Thin cell wall) Acid Fast Stain/Ziehl-Neelsen Stain : Blue background Pink : Acid fast No pink : N  on-acid fast Smear Preparation : Primary staining + Mordant : Concentrated Carbol fuchsin (Pink) (5 min) + Intermittent heating Wash Decolorization (Critical step) : H2SO4 (1 min) Decolorize - Pink Decolorize + Colourless Wash Acid fast organism Pink Counter staining : Methylene blue (Cell wall : Mycolic acid) Non-acid fast organisms Blue (Not visible against same blue background) 20% : M. Tb Note : 5% : M. leprae. Concentration of H2SO4 1% : Nocardia & parasites. Microbiology Revision v4.0 Marrow 8.0 2024  General Microbiology 3 Culture & Molecular Methods 00:31:51 ----- Active space ----- Culture Media (CM) : Simple/Basal CM : Nutrient agar (Straw-colored). Appearance : White-grey colonies. Exceptions : Golden yellow pigment Bluish-green pigment White-grey colonies Staphylococcus aureus Pseudomonas aeruginosa Enriched Media : Blood agar. Normal Appearance : No zone surrounding colonies. No zone Exceptions : a-hemolysis (Partial) : b-hemolysis (Complete) : Double zone/Target hemolysis : Greenish-grey zone Clear zone Complete followed by partial hemolysis a-hemolysis b-hemolysis Pneumococcus Staphylococcus Clostridium perfringens Differential Media : McConkey agar : CLED (Cystine-lactose-electrolyte deficient) agar : Only gram -ve organisms grow. Gram - , Gram + & Candida grows. Pink colonies : Lactose fermenters (LF) Yellow colonies (LF) E. coli, Klebsiella Pale colonies : Non-lactose fermenters (NLF) Blue colonies (NLF) Many organisms Microbiology Revision v4.0 Marrow 8.0 2024  4 Microbiology ----- Active space ----- Enrichment CM : Use : Inhibit commensals in stool sample. Types : Selenite F broth Tetrathionate broth Alkaline peptone water Colour of CM Light brown Bluish green Straw colour Pathogen Salmonella, Shigella Vibrio Note : NALC-NaOH method : Inhibits commensals in sputum sample N-Acetyl-L-cysteine : Liquefies sputum. NaOH : Inhibit commensals. Transport Media : Transport of Stool Sample Cary Blair media (Best) : Buffered glycerol saline : For all stool pathogens. For all except Vibrio & Campylobacter. Anaerobic CM : Robertson cooked meat (RCM) : Best Thioglycollate broth : Aerobic growth Only anaerobic growth Meat particles Anaerobic growth Culture Identification : Biochemical Tests : Catalase Test Oxidase Test Urease Test Bubble No bubble No blue colour Blue colour Pink color : Urease +ve Features No pink color : Urease -ve Catalase -ve : Oxidase +ve : Urease +ve : Streptococcus Vibrio Helicobacter Organisms Pneumococcus Pseudomonas Proteus Enterococcus Campylobacter Helicobacter Microbiology Revision v4.0 Marrow 8.0 2024  General Microbiology 5 MOLECULAR METHOD ----- Active space ----- PCR : Steps : Nucleic acid extraction : Enzyme method (Add Lysozyme). Nucleic acid amplification in thermocycler Denaturation (95°C) : ds to 2 single strands. Annealing (55°C) : Primer attachment. Extension (72°C) : Primer extension. Nucleic acid detection : Gel electrophoresis/Fluorescent method. Uses : Diagnostic test : Detects gene. Prognostic test : To monitor Rx response. - Gives organism load. - If PCR + : If ↑CT (Cycle Threshold) value ↓Organism ↑Prognosis. Modifications : Conventional PCR : Detects only DNA. Real-time RT (Reverse Transcriptase) PCR : - Detects DNA & RNA. - Semiautomated. Automated Realtime RT-PCR : CBNAAT (Cartridge based) & TruNAT (Chip based). Multiplex Realtime RT-PCR : Detects multiple organisms. Antimicrobial Susceptibility Testing (AST) 01:00:40 Phenotypic Method : Culture method. Kirby Bauer disk diffusion : M/c. E-strip : Mueller Hinton Agar (MHA). MHA. Zone of inhibition Present : Antibiotic sensitive. MIC obtained. Absent : Antibiotic resistant. Minimum Inhibitory Concentration (MIC) Zone of inhibition : Antibiotic sensitive of antibiotic not obtained. Zone of inhibition MIC Antibiotic disk Antibiotic strip Microbiology Revision v4.0 Marrow 8.0 2024  6 Microbiology ----- Active space ----- Broth dilution : Gold standard. Mueller Hinton Broth (MHB). MIC obtained. Clear (No turbidity) : Sensitive. Genotypic Method : Molecular method. PCR : Detects resistant gene If present : Antibiotic resistant. If absent : Antibiotic sensitive. Example : CBNAAT detects M. Tb rpo-B gene (If + : Rifampicin resistance). Microbiology Revision v4.0 Marrow 8.0 2024  Hospital Infection Control 7 HOSPITAL INFECTION CONTROL ----- Active space ----- Hand Hygiene & PPE 00:00:42 Hand Hygiene : Methods : 1. Hand wash 2. Hand rub Better method. If visibly soiled : Not acceptable. Soap & water used. Disinfectant used. Steps : 1 2 3 4 Rub hands palm to Rub hand’s back Rub palm to palm, rub backs of fingers to palm. with other palm, fingers interlaced. opposing palms, hands fingers interlaced. clasped 5 6 7 Rub tips of fingers Rub each thumb with Rub each wrist onto palm in a rotational motion. circular motion. 5 Moments for hand hygiene : Before & after touching patient. Before & after procedures & fluid exposure. After touching patient surroundings. Personal Protective Equipment (PPE) : Essential PPE : Gown, gloves, mask, goggles & faceshield. Two Methods : 1. Donning 2. Doffing Action Putting PPE on Removing PPE Sequence Gown Mask Goggles/Face shield Gloves. Gloves Goggles/Face shield Gown Mask Microbiology Revision v4.0 Marrow 8.0 2024  8 Microbiology ----- Active space ----- Biomedical Waste Management (BMW) 00:11:40 Method of segregation & disposal of waste contaminated with microorganisms. Yellow Bag Red Bag White Bag Blue Bag Cotton, Linen Plastic : Metals Type of Tissues, culture media Urine bag Glass Metallic Sharps Waste Chemicals, medicines Rubber Blood bags (Plastic) Na hypochlorite Autoclave Na hypochlorite Disposal F/b Shredding/Pack Incineration Method Recycling in puncture proof Recycling. containers then bury Sterilization 00:20:41 Sterilization vs Disinfection : Including spore form : Sterilization. Complete killing of all forms of microorganisms Excluding spore form : Disinfection. Sterilization > Disinfection. Types of Methods : Moist Heat Dry Heat H2O2/Plasma Ethylene oxide (ETO) Example Autoclave Hot air oven - - 121°C for 15 min under M/c method 15 lbs pressure 160°C for 2 hours - - Bacillus subtilis/ Bacillus subtilis/ Bacillus Bacillus Control Bacillus atrophaeus/ Bacillus atrophaeus/ Stearothermophilus stearothermophilus Clostridium tetani Clostridium tetani Materials Sterilized : Materials Method Surgical instruments except sharps (Eg : Linen, sutures without needle) Autoclave > H2O2 > ETO Plastic & rubber materials (Eg : Syringe, gloves) Glass & sharps (Eg : Flasks, scalpels) Autoclave > Hot air oven All culture media (CM) Autoclave Exceptions in CM : Serum CM (Loeffler’s serum slope) Inspissation > Tyndallization Egg CM (Lowenstein-Jensen medium) Oily & powdery materials Hot air oven (Eg : Liquid paraffin, glove dust powder) Microbiology Revision v4.0 Marrow 8.0 2024  Hospital Infection Control 9 Disinfection 00:33:50 ----- Active space ----- Types : High level (HLD) : Intermediate level (ILD) : Low level (LLD) : Aldehyde. 1% Na hypochlorite. Alcohol. Better : kills some spores. Test for Disinfectant : Chick martin (Better) : Rideal walker : Kelsey sykes : Maurer’s Inuse : Efficacy tested. Efficacy tested. Capacity tested. Contamination tested. Materials Disinfected : 1. Endoscopes : Aldehyde (Glutaraldehyde > Orthophthalaldehyde) > H2O2> ETO. 2. Blood spill : 1% Na hypochlorite. 3. Thermometer/Hand rub : Alcohol. Spaulding’s Classification of Medical Devices : Level of Medical devices disinfectant Enter sterile site Critical HLD Eg : Surgical instruments, implants Contact with mucous membrane Semi-Critical HLD Eg : Endoscopes Contact with intact skin Non-Critical ILD/LLD Eg : Stethoscopes, Sphygmomanometers Microbiology Revision v4.0 Marrow 8.0 2024  10 ----- Active space ----- IMMUNOLOGY Superantigen & Antibody 00:01:50 SUPERANTIGEN AG Presented by APC (MHC-II) to T cell (TCR). APC Super Ag binds to β-chain of receptor laterally MHC-II α β Polyclonal activation TCR Exaggerated response. α β Normal Ag binds to Ag binding groove b/w α & β chains T-cells Eg : Immune response. B-cells - TSST/pyrogenic exotoxin (TSS) : S. aureus (M/c), S. pyogenes. Ab - Enterotoxin (GE) : S. aureus. TSST : Toxic shock syndrome toxin ; GE : Gastroenteritis Exaggerated immune response ANTIBODY Proteins Detectable > 7 days of symptoms. Produced by plasma cells. Features Monomer. IgG 2 : Highest serum concentration. - Does not cross placenta. Subclass : IgG1 IgG2 , IgG3 , IgG4. - Major antibody against capsulated organisms. Ig G Function : IgG 4 : Does not fix complement. - Fixes the complement : Acquired immunity. - Provides immunity to baby : cross placental. Serum IgA : Secretary IgA : Monomer. Dimer. Ig A From plasma cells. From mucus cells. Present in blood. Present in RT, GIT, GUT, breast milk. Fixes compliment : Acquired immunity. Local immunity to RT, GIT, GUT. Pentamer. Ig M Highest molecular weight. Function : Fixes compliment (Acquired immunity). Monomer. Ig D Can be present as receptor on B cells. Monomer. Ig E Elevated in : Type 1 hypersensitivity, parasitic infections. Microbiology Revision v4.0 Marrow 8.0 2024  Immunology 11 Antigen-Antibody Reactions 00:13:56 ----- Active space ----- Test Organism Slide flocculation : VDRL, RPR. Treponema Precipitation Tube/ring : Ascoli thermo ppt Bacillus anthracis reaction Plate : Elek’s gel ppt Corynebacterium diphtheria Neutralization Toxin neutralisation : Naeglers reaction Clostridium perfringens reaction Widal agg Salmonella Agglutination Standard agg Brucella reaction Microscopic agg Leptospira Weil felix agg Rickettsia AGGLUTINATION Only when concentration of Ag = Ab. Serial dilution of sample (Ab) with NS & add fixed quantity of Ag. 1 : 20 1 : 40 1 : 80 1 : 160 1 : 320 Prozone phenomenon Ab = Ag. Post zone phenomenon Ab excess Agglutination. Ag excess (Initial dilution). (Later dilution). No agglutination. No agglutination. Immunity 00:21:52 Innate : Minor, present by birth. Ist line : within 3-4 hrs. Non specific. No memory. Acquired : Major, after entry of the organism. 2nd line after 5-7 days. Specific Memory present. CMI (Cell mediated immunity) or Ab/HI(Humoral immunity). Microbiology Revision v4.0 Marrow 8.0 2024  12 Microbiology ----- Active space ----- ACQUIRED APC : Dendritic m/c /Macrophage/B cells. Main receptor : MHC. Co-receptor : B-7. T cells : 3 signals to activate response. Main receptor : MHC TCR. Co-receptor : B-7 CD-28 Cytokine : IL 1 CD4 ; IL 2 CD8 Antigen Organism MHC I APC MHC II W W W TCR B-7 TCR W W IL - 2 CD8 CD4 IL - 1 T - cells CD28 T - cells W W Cytotoxic cells Helper IL - 12 Cells IL - 4, 5 Release perforins & Granzymes Th1 CD4 Th2 CD4 T cells T cells Cytolysis (CMI) B - cells IFN - γ Activates Plasma cells Macrophages, NK cells Antibodies (Ab) Cytolysis Bind to antigen (Ag) (CMI) Initiates classical complement pathway Cytolysis : Main receptor signal (HI) : Co - Receptor signal : Cytokine signal Microbiology Revision v4.0 Marrow 8.0 2024  Immunology 13 Immunodeficiency Disorders 00:37:06 ----- Active space ----- Disease Mutation Effect Humoral 1DD Bruton’s tyrosine kinase deficiency : Brutons disease X-linked : BTK gene B-cells not formed. Cellular IDD Presentation mneumonic : CATCH 22 Autosomal dominant : Conotruncal cardiac defect. Ch 22q11 deletion Di George Abnormal facies (Narrow jaw) syndrome Thymus aplasia (No T cell maturation) Abnormal development of Clept lip & palate. 3rd, 4th pharyngeal pouch Hypocalcemia Combined IDD X-linked : ILR gene m/c. IL deficiency. SC1D AR : ADA gene. ADA deficiency. Wiskott Aldrich X-linked : WAS gene No WASP protein syndrome Ataxia ATM gene mutation DNA repair defect telengiectasia Phagocytic 1DD NADPH oxidase deficiency. High risk of catalase positive organism Chronic infection (S. aureus). granulomatous X-linked : CYBB/Phox gene Tests : disease - Nitro blue tetrazolium. - Dihydro Rhodamine. Peroxidase + giant granules in leucocytes Chediak-Higashi AR : LYST gene disease Defect in fusion of phagosome-lysosome Albinism : Skin & eye. Microbiology Revision v4.0 Marrow 8.0 2024  14 Microbiology ----- Active space ----- Hypersensitivity & Transplant Immunology 00:48:34 Hypersensitivity Reactions : Type 1 Type 2 Type 3 Type 4 Immunity Allergic Cytotoxic Immune complex Delayed A/w Allergy RBC Ag-Ab complex Intracellular Ag Allergic : Glomerulonephritis - Rhinitis Blood transfusion Tuberculin test. Rheumatoid arthritis. - Bronchitis reaction. Mantoux test. Examples Arthus reaction. - Dermatitis AIHA (Auto Immure Lepra 1 reaction. Serum sickness. - ABPA Hemolytic Anemia). Lepromin test. Lepra 2 reaction. Anaphylaxis Transplant Immunity : Graft rejection (HVGD) Graft vs. Host Disease (GVHD) Host rejects graft. Graft rejects host. Any allograft Bone marrow & thymus allografts CMI : Type 4 HS Hyperacute : Acute : Chronic : Mins to hrs. Week to months. Months to years. HI : Type 2 CMI : Type 4 > CMI : Type 4 > (Preexisting Ab). HI : Type 2 HI : Type 2 Microbiology Revision v4.0 Marrow 8.0 2024  Laboratory Diagnosis of Infections : Bacterial and Fungal 15 LABORATORY DIAGNOSIS OF INFECTIONS : ----- Active space ----- BACTERIAL & FUNGAL Bacteria 00:02:22 Classification : Gram positive : Cocci : Bacilli : Staphylococcus Bacillus Spore containing. Streptococcus Clostridium Pneumococcus Corynebacterium Enterococcus Mycobacterium Actinomyces Filamentous. Nocardia Listeria : Differential motility. Gram negative : Cocci : Bacilli : Meningococcus Gonococcus Coccobacilli : Enterobacterales : Spirochetes : Haemophilus Escherichia Treponema Brucella Klebsiella Borrelia Bordetella Salmonella Leptospira Acinetobacter Shigella Yersinia Proteus Special groups of gram negative bacteria : Citrobacter Oxidase positive Non-cultivable Atypical pneumonia Miscellaneous Vibrio Rickettsia Mycoplasma Pseudomonas HACEK group Chlamydia Legionella Campylobacter Gardnerella vaginalis T. pallidum Chlamydia Helicobacter Note : Mycobacterium is also non cultivable. High Yield Points : Capsulated : Anaerobic : Intracellular : Pneumococcus Clostridium Neisseria Meningococcus Actinomyces Mycobacteria Hemophilus influenzae G. vaginalis Rickettsia Bacillus anthracis Chlamydia G. vaginalis Microbiology Revision v4.0 Marrow 8.0 2024  16 Microbiology ----- Active space ----- Lab Diagnosis : Microscopy : Gram stain, special stain. Culture : Selective culture media. Test : Special biochemical/Immunological test. Fungus 00:17:34 Classification : 1. Yeast : 2. Yeast like : Replicate by budding. Both yeast cells & hyphae simultaneously. Organism : Cryptococcus. Organism : - Candida. - Malassezia 3. Mold - Trichosporon. Filamentous cell, have hyphae. Aseptate mold : Obtuse & Septate mold right angle hyphae. Rhizopus Irregular hyphae Acute angle & Absidia Mucormycetes Dermatophytes dichotomous hyphae : Mucor Madurella mycetomatis Aspergillus. Dematiaceous (Pheoid) 4. Dimorphic Sample : Always yeast. Yeast at 37°C On culture. Hyphae (Septate) at 25°C Organism : - Histoplasma. - Paracoccidioides. - Blastomyces. - Sporothrix schenckii. - Coccidioides. - Talaromyces marneffei. Lab Diagnosis : Sample microscopy & Sample microscopy & Culture tests Culture Microscopy (LPCB) Sample microscopy : Check form of fungi on KOH wet mount Yeast & yeast like Mold & dimorphic Culture microscopy :Check spores on SDA agar with LPCB stain - + SDA : Sabouraud Dextrose Agar. LPCB : Lactophenol Cotton Blue. Note : Sample microscopy : Can also use PAS stain/GMS stain. Microbiology Revision v4.0 Marrow 8.0 2024  Laboratory Diagnosis of Infections : Bacterial and Fungal 17 High yield Points : ----- Active space ----- Important aseptic molds (Mucormycosis) : Rhizopus Absidia Mucor Important dimorphic fungi : Histoplasma Paracoccidioides Blastomyces Sporothrix schenckii Coccidioides Talaromyces marneffei Important markers for invasive mycosis : Beta-D-Glucan : Candida, Aspergillus, Pneumocystis Galactomannan : Aspergillus Microbiology Revision v4.0 Marrow 8.0 2024  18 ----- Active space ----- LABORATORY DIAGNOSIS OF INFECTIONS : VIRAL & PARASITIC Virus 00:00:13 CLASSIFICATION DNA : ds RNA : ss Enveloped Non-enveloped Enveloped Non-enveloped Hepadna : HBV. Papova virus : Retrovirus : HIV. Picornavirus : Herpes : HHV. - HPV. Flavivirus : - HAV. Pox : Biggest. - JC. - HCV. - Polio. - BK. - JE. - Coxsackie. Adenovirus. - YF. - Entero. Parvo virus : - KFD. Calicivirus : - ssDNA. - Dengue. - HEV. - Smallest. - ZIKA. - Sapo. Toga virus : - Noro. Chikungunya. Reo virus : ds RNA Matona : Rotavirus. Rubella. Other RNA enveloped viruses : Orthomyxo Arena Rhabdo Influenza Lassa fever virus Rabies Filo Bunya Delta Ebola Hanta virus HDV Marburg virus CCHF virus Paramyxo Corona Nipah Mumps - Measles Microbiology Revision v4.0 Marrow 8.0 2024  Laboratory Diagnosis of Infections : Viral & Parasitic 19 LAB DIAGNOSIS ----- Active space ----- Molecular Methods : Immunological Methods : PCR (M/c). Ag/Ab. Identification of Diagnostic Test : ≤7 days : Duration from >7 days : PCR > Ag detection > symptoms known Ab detection. Microscopy, culture. Duration unknown PCR : Ag detection : Ab detection : Herpes : Lesion swab. Hepatitis : Blood. Most of the Influenza Naso pharyngeal &/or Polio other viruses. Stool. Corona oro pharyngeal swab. Rota Rabies : Skin (Nape of neck) (Ag-DIF). Key Points For Identification of Virus : 2 copies of RNA : HIV. Spike receptors Segmented nucleic acid : (Long petal shaped) - Rota (dsRNA) : 11 segments. - Influenza : 8 segments. Adeno virus Corona virus Circular nucleic acid : - HBV : Partially ds. - HPV : Completely ds. Characteristic shape : Rabies virus Ebola/Marburg virus - Pox : Box. DNA. - Adeno : Satellite. - Rabies : Bullet. - Ebola : Filamentous. RNA. - Corona : Crown. HBV HPV Pox virus HIV virus Influenza virus Rota virus Microbiology Revision v4.0 Marrow 8.0 2024  20 Microbiology ----- Active space ----- Inclusion Bodies : Intranuclear (Cowdry Type A) : Intracytoplasmic : HSV : Lipschutz. Rabies : Negri bodies. CMV : Owl eye appearance. YFV : Torres bodies. Virus Culture Methods : Viral Assays : Animal inoculation. Pock assay : Embryonated egg Embryonated egg culture. culture. Tissue cell culture (M/c). Plaque assay : Tissue culture. Cytopathic Effects : Measles virus : Syncytium formation. Adeno virus : Granular clumping. HSV : Ballooning. Entero V : Crenation. Parasites 00:33:42 PROTOZOA Classification : Ciliates Amoeba Flagellates Sporozoa/Coccidia (Cilia) (Pseudopodia) (Flagella) (Non-mobile) Intestinal : Intestinal : Intestinal : Intestinal : Balantidium Entamoeba Giardia lamblia. - Cryptosporidium. coli. histolytica. Vaginal : - Cyclospora. Free-living : Trichomonas - Cysto-isospora. - Naegleria. vaginalis. Blood and tissue : - Acanthamoeba. Blood & tissue : - Plasmodium. - Balamuthia. - Leishmania. - Babesia. - Sappinia. - Trypanosoma. - Toxoplasma. Lab Diagnosis : Microscopy : Intestinal protozoa Free-living protozoa Vaginal protozoa Blood & tissue protozoa Form Trophozoite & cyst Trophozoite Different forms Sample Vaginal Stool CSF Peripheral blood smear tested discharge Microbiology Revision v4.0 Marrow 8.0 2024  Laboratory Diagnosis of Infections : Viral & Parasitic 21 HELMINTHS ----- Active space ----- Classification : Cestodes : Trematodes : Nematodes : (Round worms) (Tape worms) (Flukes) Intestine : Intestine : Blood : - Strongyloides stercoralis : - Taenia solium : Schistosoma. Parthenogenic. Pork tapeworm. Intestine : - Ancylostoma duodenale Hook - Taenia saginata : Fasciola buski. - Necator americanus worm. Beef tapeworm. Liver : - Ascaris lumbricoides : - Hymenolepis nana : - Fasciola hepatica. Round worm. Dwarf tapeworm. - Clonorchis sinensis. - Enterobius vermicularis : - Diphyllobothrium latum : - Opisthorchis. Pin worm. Fish tapeworm. Lung : - Trichuris trichiura : Tissue : Paragonimus Whip worm. Echinococcus granulosus : westermani. Tissue : Dog tapeworm. - Filarial worm. - Trichinella spiralis : Spiral worm. - Dracunculus medinensis : Guinea worm. Lab Diagnosis : Microscopy : Oviparous helminths Ovoviviparous helminths Viviparous helminths Morphological Egg Larva Larva form Sample Stool Stool Tissues Filarial worm Organisms All other helminths Strongyloides Trichinella spiralis Dracunculus medinensis Identification of Parasites 00:54:06 Morphology & Transmission : Morphological forms : Infective forms : 2 forms : Worm & larva 3 forms : Worms, Egg : Larvae : Filarial worm. egg & larva E. granulosus. Remaining all Trichinella spiralis. H. nana. Dracunculus medinensis. Remaining. Ascaris. Trichuris. Transmission : E. vermicularis. Skin penetration : Schistosoma. Strongyloides. Ancylostoma/Necator. Microbiology Revision v4.0 Marrow 8.0 2024  22 Microbiology ----- Active space ----- Causative Organisms : Opportunistic infection : Auto infection : Giardia. T. solium. Cestodes. Cryptosporidium H. nana. Cyclospora Protozoa. Enterobius. Nematodes. Cysto-isospora Strongyloides. Toxoplasma. Strongyloides (Helminth). Anemia : Megaloblastic : D. latum. Carcinoma : Iron deficiency : Bladder : Schistosoma hematobium. - Ancylostoma & Necator. Colon : Schistosoma japonicum. - Trichuris trichiura. Cholangio Ca : Clonorchis sinensis. Larva migrans : Animal nematodes (M/c) : Human nematodes (Rare) : - Ancylostoma braziliensis. - Strongyloides stercoralis. Cutaneous - Ancylostoma caninum. - Ancylostoma duodenale. - Toxocora canis (M/c). Visceral - Ascaris lumbricoides. Loeffler’s pulmonary eosinophilia/Loeffler’s syndrome : All larvae migrans causing. Visceral (M/c) > Cutaneous. Tropical pulmonary eosinophilia/Weingarten’s syndrome : Filarial worm. Eggs : Non-bile stained : Float in saturated salt solution : Operculated : Necator americanus. Trichuris trichiura. Clonorchis. Enterobius vermicularis. Enterobius vermicularis. Opisthorchis. H. nana. H. nana. P. westermani. Ancylostoma duodenale. A. duodenale/N. americanus. D. latum. Ascaris lumbricoides (Fertilized). Fasciola hepatica. Fasciola buski. Microbiology Revision v4.0 Marrow 8.0 2024  Central Nervous System 23 CENTRAL NERVOUS SYSTEM ----- Active space ----- Common organisms causing CNS infections : Meningitis : Bacterial. Encephalitis : Viral, parasitic. Myelitis : Viral. Others : Bacterial neurotoxin related diseases. Meningeal irritation signs : Neck rigidity. Brudzinski’s sign : Trying to flex neck Involuntary flexion of leg. Kernig’s sign : Trying to flex neck Difficulty in extension of legs. Acute Bacterial/Pyogenic Meningitis 00:04:50 Etiology : Pneumococcus Group B streptococci Meningococcus In adults. E. coli In neonates. H. influenza b Listeria Lab Diagnosis & Rx of Pyogenic Meningitis in Adults : Lab diagnosis : Rx : CSF : ↑↑↑ neutrophils & ↓↓↓ glucose. Empirical : Vancomycin + ceftriaxone. Pneumococcus Meningococcus H. influenzae b A/w rashes Features M/c in adults Demography : Northern india Children Bacilli Neutrophil Coccobacillus Microscopy Cocci Gram + cocci in pairs, Gram - cocci in pairs, lens, lens shaped, capsulated capsulated, intracellular Gram - , pleomorphism S. aureus Growth Culture Blood agar : α Hemolysis Thayer martin medium Blood agar : Satellitism Optochin sensitivity Tests Bile solubility Maltose fermenter - Inulin fermentation Microbiology Revision v4.0 Marrow 8.0 2024  24 Microbiology ----- Active space ----- Pyogenic Meningitis In Neonates : Group B streptococcus (S. agalactiae) E. coli Listeria Gram + bacilli. M/c : World. Differential motility M/c : India. Gram + , long chains. Gram - bacilli. cAMP test +. 22˚ C 37˚ C Tumbling Non-motile Lab diagnosis : Rx : CSF : ↑↑↑ neutrophils & ↓↓↓ glucose. Empirical : Ampicillin + ceftriaxone. Chronic Bacterial Meningitis 00:19:52 Etiology : Mycobacterium tuberculosis (M/c). Lab diagnosis : Microscopy : Other tests : - Interferon gamma release assay (IGRA). - Mantoux test (Type 4 hypersensitivity). - LJ culture (1 - 2 months). Acid fast, non-filamentous (Weakly gram positive) CSF : ↑↑↑ proteins (Cobweb formation). Molecular tests : CBNAAT (PCR) : MTB with rpo-B gene (Rifampicin resistance). Rx : 2 months HRZE + 10 months HRE. Viral Encephalitis 00:25:50 Charactestic clinical feature is seizures. Etiology : Rabies. Japanese encephalitis : M/c organism (Overall). HSV-1. Measles. Nipah. JC virus. Microbiology Revision v4.0 Marrow 8.0 2024  Central Nervous System 25 ----- Active space ----- Rabies Measles Rabies encephalitis. Measles disease Fever. World : Bat. M/c animal 7 - 10yrs after recovery Koplik spots. India : Dog. Hyperactive bizzare behaviour. Subacute sclerosing Rash. Diseases Hydrophobia (Laryngospasm). panencephalitis ↓ School performance & myoclonus. Skin : Nape of neck m/c. Specimen Saliva. CSF CSF. Test Ag : Direct immunofluorescence > PCR. IgG Ab : ELISA. PEP (Post exposure prophylaxis) : Wash wound : Soap & water (15min). Live vaccine : Treatment Antiseptic. Edmonston - Zagreb strain. Injection IG : Locally. Given with rubella (MR). killed vaccine : Deltoid. Japanese Herpes Nipah v John Cunnigham (JC) encephalitis simplex v Fruit bats Progressive multifocal M/c. (Direct contact). leukoencephalopathy (PML) Temporal lobe Features Children : 5-15yrs. 40-70% mortality. (White matter). encephalitis. Northern India. West bengal & Only in immunocompromised Kerala. patients. Test Ab-ELISA > PCR PCR > Ab-ELISA PCR PCR Vaccine : Vaccine/ Live : SA-14-14-2. Rx - Rx : Acyclovir - Killed : kolar strain. Parasitic Encephalitis 00:44:06 Etiology : - Naegleria m/c Free living amoeba (Locomotion : Pseudopodia). - Acanthamoeba Infected while swimming. - Sappinia Can also cause meningitis. - Balamuthia Microbiology Revision v4.0 Marrow 8.0 2024  26 Microbiology ----- Active space ----- Labaratory Diagnosis & Rx : Naegleria Sappinia Acanthamoeba Balamuthia Type Acute Chronic Chronic Chronic Granulomatous amoebic Primary amoebic Sappinia Disease encephalitis (GAE) GAE meningoencephalitis (PAM) encephalitis Contact lens keratitis Microscopy : Trophozoites Lobe like Bilobed nucleus Spike/thorn Branching pseudopodia Normal pseudopodia like pseudopodia pseudopodia Rx Liposomal Amphotericin B None None None Viral Myelitis & Bacterial Neurotoxin Related Diseases 00:55:44 Viral Myelitis (Poliomyelitis) : Clinical features : Asymptomatic/flu like symptoms : 99%. Meningitis : 1%. Acute flaccid paralysis : 0.1% Lab diagnosis : Stool : Ag-ELISA > PCR. Prophylaxis : Live : OPV (Sabin) Birth, 6w, 10w, 14w, 16-24w. Both vaccines taken Killed : Fractional IPV (Salk) 6w, 14w. Bacterial Neurotoxin Related Diseases : Clostridium botulinum Clostridium tetani Toxin Botulinum Tetanospasmin Inhibits excitatory neurotranstmitter (↓Ach) Inhibits inhibitory neurotransmitter (↓GABA & glycine) Pathology ↓ Muscle contraction ↓ Muscle relaxation Flaccid paralysis (Botulism) Spastic paralysis (Tetanus) Robertson cooked Meat (RCM) culture (Anaerobic). Diagnosis Toxin : ELISA Rx Antitoxin ± Metronidazole. Microbiology Revision v4.0 Marrow 8.0 2024  Cardiovascular System : Infections of Heart 27 CARDIOVASCULAR SYSTEM : ----- Active space ----- INFECTIONS OF HEART Infections of the heart : Infective endocarditis. Acute rheumatic fever. Blood & systemic infections : Viral : HIV disease. Viral haemorrhagic fever. Parasitic : Blood and tissue flagellates : Blood and tissue sporozoa : Helminths : - Leishmaniasis. - Malaria. - Schistosomiasis. - Trypanosomiasis. - Babesiosis. - Filariasis. - Toxoplasmosis. Infective Endocarditis  00:04:36 Inflammation of endocardium Valvular damage Regurgitation. Clinical Features : Vascular Immunological Janeway lesions Osler’s nodes Roth’s spots (Bleeding spots : Palms & soles) (Painful nodes : Palms & soles) (Bleeding spots in retina) Etiology : Native valve : Staphylococcus aureus (M/c). Prosthetic valve : Early (1 yr of surgery) : Streptococcus viridans (M/c). Microbiology Revision v4.0 Marrow 8.0 2024  28 Microbiology ----- Active space ----- Diagnosis : Modified Duke’s criteria : Major criteria (2) : 1. Positive blood culture : Typical organism Atypical organism 2 separate + ≥2 + cultures. 3 or 4 separate culture. Except Coxiella : blood cultures. (12 hrs apart) (lst & last sample taken Single + blood culture. ≥1 hr apart) 2. Evidence of endocardial involvement : On ECHO - Valvular abcess or cardiac mass or new partial dehiscence of valves. - New valvular regurgitation. Minor criteria (5) : a. Fever : ≥38˚C. b. Predisposing factor : Cardiac valvular disease. c. Vascular phenomenon : Haemorrhage (Janeway leisions)/infarct /emboli. d. Immunological phenomenon : Osler’s nodes, Roth’s spots. e. Microbiological evidence : Blood culture + not meeting major criteria. Serological evidence. For Diagnosis : 2 major/ 1 major + 3 minor/ 5 minor. Treatment : Penicillin If allergic Vancomycin Native valve (2) : Gentamycin Prosthetic valve (3) : 4-6 weeks. Rifampicin 6 weeks. Acute Rheumatic Fever  00:17:56 Non-suppurative complication of Group A streptococcal pharyngitis. Clinical Features : Pancarditis : Regurgitation murmur or prolonged PR interval. Arthritis : Migratory polyarthritis. Sydenham’s chorea : Involuntary movement of head & neck. Subcutaneous nodules : Painless mobile nodules. Erythema marginatum : Rash with red margins and pale centre. Microbiology Revision v4.0 Marrow 8.0 2024  Cardiovascular System : Infections of Heart 29 Diagnosis : ----- Active space ----- Modified Jone’s criteria : Based on risk for ARF High risk Both low & high risk Low risk Major criteria Pancarditis Monoarthritis Arthritis Polyarthritis /Polyarthralgia Sydenham’s chorea Subcutaneous nodules Erythema marginatum Minor criteria ≥38°C Fever ≥38.5°C Monoarthralgia Arthralgia Polyarthralgia ≥30 mm/hr ESR ≥60 mm/hr CRP ≥ 3 mg/dL Prolonged PR interval For Diagnosis : 2 major/ 1 major + 2 minor/ 3 minor + Past h/o ARF. Treatment : DOC : Penicillin/Amoxicillin If allergic Erythromycin. Microbiology Revision v4.0 Marrow 8.0 2024  30 ----- Active space ----- CARDIOVASCULAR SYSTEM : BLOODSTREAM AND LYMPHATIC INFECTIONS HIV Disease 00:40:00 2 receptors Structure : Family : Retrovirus. WHO Staging : Stage 1 : Asymptomatic. Generalised lymphadenopathy. Stage 2 : Cutaneous candidiasis. 2 RNA : Herpes zoster/shingles. Identification feature Stage 3 : Stage 4 (AIDS defining illness) : Oral candidiasis (Candida, Removed Oesophageal candidiasis. on rubbing) Wasting syndrome. Oral hairy leukoplakia (EBV, Cannot Extra pulmonary TB. be removed). Kaposi sarcoma. Pulmonary TB. Other opportunistic infections. Fever >1 month. Diarrhoea Opportunistic Infection Investigations Based on CD4 Count : Antibody detection : ELISA. Western blot. CD4 count/mm3 Opportunistic infection Rapid tests (Reading on 3 tests) : Pulmonary TB m/c > bacterial pneumonia - Criteria for Dx : Oral Candidiasis NACO Aedes albopictus. Microbiology Revision v4.0 Marrow 8.0 2024  32 Microbiology ----- Active space ----- Clinical features : Primary infection Re-infection : Severe d/t ADE (Mild) (Antibody dependent enhancement) Classical dengue fever. Dengue haemorrhagic fever. Dengue shock syndrome (DSS). Probable Dengue Dengue with warning signs Severe dengue Severe plasma leak : Fever + any 2 : Abdominal pain Retro-orbital headache Persistent vomiting - DSS Rashes Mucosal bleed Severe bleeding : Nausea & vomiting Fluid accumulation. - Hemodynamic instability Leukopenia & ↓platelets Hepatomegaly >2 cm Severe organ damage : Torniquet test positive Rapid ↓ platelets - AST & ALT ≥1000 IU/ml - Impaired consiousness Diagnosis : ELISA : IgM Ab > PCR > NCI Ag. Vaccine : Live : CYD - TDV (Not in India). Yellow Fever Virus : Vector : Aedes aegypti > Aedes albopictus. Complication : Viral haemorrhagic fever with hepatitis. Area : Central & south america (Not India). Diagnosis : ELISA - IgM Ab > PCR. Vaccine : - Live : 17D strain. - Killed : Dakar strain. Other Viruses Causing VHF : Lassa fever Hanta CCF Ebola & Marburg Family Arena Bunya Bunya Filo Reservoir Rat Ixodid tick Fruit bat Vector None Ixodid tick None Area Not seen in india Gujarat Not India Complication pneumonia Pneumonia Shock Diagnosis ELISA - IgM Ab > PCR Vaccine Not available Microbiology Revision v4.0 Marrow 8.0 2024  Cardiovascular System : Bloodstream and Lymphatic Infections 33 Blood and Tissue Flagellates  00:39:50 ----- Active space ----- LEISHMANIASIS Agent : Leishmania Has kinetoplast & rk 39 Ag. Vector : Sand fly (Phlebotomous). Clinical Features : Cutaneous/Oriental Mucocutaneous/ Visceral/Kala azar sore/Delhi boil Espundia Species L. tropica L. braziliensis L. donovani Hepatomegaly Clinical Can progress to Papule Ulcerative lesions feature Post kala azar dermal leishmaniasis (Nodules on face) Microscopy : Rx : Peripheral blood smear : Lipo Amphotericin B : DOC. Paramomycin. IV Pentamidine. Kinetoplast Sitamaquine. Amastigote form Miltefosine (Oral). in macrophage Leishmania donovani body TRYAPANOSOMIASIS American African Disease Chagas disease Sleeping sickness Agent Trypanosoma cruzi Trypanosoma brucei Vector Reduvig bug (Triatomine bug) Tse-tse fly Chagoma : S/c nodules (At entry site). Trypanosomal chancre : Inflammatory lesion (At entry site). Clinical Romana S sign : Eyelid edema. Winter-bottom sign : Posterior cervical LN. Megaly : Esophagus, colon, heart. Somnolence : Insomnia + daytime sleeping spells. Folded flagella Microscopy Spindle shaped Trypomastigote form Rx Benznidazole Suramin Microbiology Revision v4.0 Marrow 8.0 2024  34 Microbiology ----- Active space ----- Blood and Tissue Sporozoa 00:51:35 MALARIA Agent : Plasmodium (P. falciparum M/c > P. vivax). Vector : Anopheles mosquito. Clinical Features : Fever, chills, hepatosplenomegaly. Complications : Cerebral malaria. Acute tubular necrosis : P. falciparum. Black water fever. Nephrotic syndrome : P. malariae. Algid malaria. Diagnosis & Rx : P. vivax P. falciparum Single ring Ring forms Single ring forms Multiple ring accole forms (Ring attached to inner surface of RBC) Amoeboid/round Present but not seen. Schizont (Firmly attached to capillary endothelium) Banana Gametocytes Round shaped Dots & pigments Schüffner’s dots; brown pigment Maurer’s cleft; black pigment Ag PLDH (Plasmodium LDH) PLDH & HRP-2 Ag Microbiology Revision v4.0 Marrow 8.0 2024  Cardiovascular System : Bloodstream and Lymphatic Infections 35 ----- Active space ----- P. vivax P. falciparum Other areas : Artesunate Weakly Chloroquine Pyrimethamine + Sulfadoxine gametocidal Rx + Primaquine (Kills gametocyte) Primaquine (Prevent relapse by vivax) North-east India : Pregnancy : Artemether 1st trimester : Quinine Lumefantrine 2nd & 3rd trimester : Artesunate Note : Pregnancy contraindicated drugs Pyrimethamine : Inhibit folate NTD. Sulfadoxine & Primaquine : Hemolysis (Also in G6PD deficiency). BABESIOSIS Agent : Babesia. Vector : Ixodid tick. Clinical Features : Diagnosis : Fever, chills, myalgia. Peripheral smear microscopy : CHF. ARDS. Hepatosplenomegaly. Renal failure. Maltese cross Rx : Single ring forms Merozoites Atovaquone + Azithromycin. TOXOPLASMOSIS Agent : Toxoplasma Transmission : Feco-oral Oocyst stool Sporulation of oocyst Cat Sporozoite in soil route Human. (Infective form) Clinical Features : Fever, cervical lymphadenopathy. Congenital : Immunocompromised : Chorioretinitis - Muscle involvement : Myalgia (Muscular toxoplasmosis). - Retinitis : Blurred vision (Ocular toxoplasmosis). Hydrocephalus Diffuse brain - Encephalitis : Seizures calcifications (Neural toxoplasmosis) Microbiology Revision v4.0 Marrow 8.0 2024  36 Microbiology ----- Active space ----- Diagnosis : Microscopy : PBS. Immunological : - Sabin-Feldman dye test : Detect IgG (Gold standard). - IgG avidity test. High avidity Low avidity Tachyzoites : Spindle shaped Chronic infection Acute infection Rx : DOC : Pyrimethamine + Sulfadiazine. DOC in pregnancy : Spiramycin. Helminths 01:10:48 SCHISTOSOMIASIS/KATAYAMA FEVER/SWIMMERS ITCH Agent : Schistosoma/blood fluke (Ovoparous). Causes entry site dermatitis. S. hematobium S. mansoni S. japonicum Symptom Haematuria Diarrhea Diarrhea Cystitis Gastroenteritis Gastroenteritis Disease Blood stream infection Blood stream infection Blood stream infection Ca Bladder squamous cell Ca No Ca Colorectal Ca Sample Urine Stool Stool Microscopy Terminal spine Lateral spine Lateral knob Rx Praziquantel Microbiology Revision v4.0 Marrow 8.0 2024  Cardiovascular System : Bloodstream and Lymphatic Infections 37 FILARIASIS ----- Active space ----- Vector : Culex mosquito. Area : North east India. Agents : Filariasis Lymphatic : Subcutaneous : Swelling Elephantiasis Subcutaneous nodules Wuchereria bancrofti. Onchocerca volvulus : River blindness. Brugia malayi. Loa loa : Calabar swelling. Diagnosis : Peripheral blood smear : IOC. Blood collection : At night/If filarial Ag + : Direct blood collection & smear. During day/If filarial Ag - : DEC provocation test. DEC tablet 30-60 min Collect blood & then smear. Microscopy : Microfilaria larvae. W. bancrofti B. malayi Onchocerca Loa loa Microscopy Tail tip None 2 nuclei No nuclei Multiple nuclei Sheath Present Present Absent Present Rx : DEC for all except Onchocerca (Ivermectin). Microbiology Revision v4.0 Marrow 8.0 2024  38 ----- Active space ----- RESPIRATORY SYSTEM URTI : Diphtheria. LRTI : Tuberculosis, whooping cough, typical & atypical pneumonia. Diphtheria, Tuberculosis & Whooping Cough 00:02:28 PTBA : Potassium Tellurite blood agar LSS : Loeffler Serum slope LJ : Löwenstein-Jensen Diphtheria Tuberculosis Pertussis Etiology Corynebacterium diphtheriae Mycobacterium tuberculosis (M. Tb) Bordetella pertussis Pulmonary : Pseudo membrane (M/c) : - Evening ↑ of fever. Clinical Tonsillar/faucial area. - Cough >2 weeks. Whooping cough manifestations Bull neck lymphadenopathy - Weight loss. Complication : Myocarditis. Meningeal : Neck rigidity. Albert’s stain : Chinese letter Acid fast stain : Acid fast Gram stain : Gram negative pattern with metachromatic/ non-filamentous bacilli. cocco bacilli with thumbprint volutin/Babes Ernst granules. appearance. Metachromatic Staining granules Bacilli CBNAAT (PCR) : - M. Tb Selective media : Culture/ - rpo-B gene PTBA (Best) + Bordet-Gengou media Molecular LSS : E arly diagnosis ELISA : Antibody testing tests M. tb rifampicin-resistant (within 6 hours) IGRA LJ culture Toxin demonstration : ELEk’s gel Other tests Mantoux Test - precipitation test. Antitoxin Pulmonary : 2 HRZE + 4 HRE Rx Azithromycin Penicillin/Erythromycin Meninges : 2 HRZE + 10 HRE Microbiology Revision v4.0 Marrow 8.0 2024  Respiratory System 39 Post Exposure Prophylaxis for Diphtheria : ----- Active space ----- Antibiotic : Erythromycin/Penicillin for 10 days. Vaccine : Based on immunization status. ≥3 doses : Complete immunization ≤3 doses : Partial immunization Complete Td series Last dose within last 5 years Last dose ≥5 years ago No vaccine Td Td booster : Every 10 years. Typical/Lobar Pneumonia 00:18:16 Affects alveoli. Clinical manifestations : Consolidation, cough, dyspnea. Important organisms (Bacteria) : Pneumococcus/Streptococcus pneumoniae (M/c cause of CAP). Staphylococcus : M/c cause of HAP. Pseudomonas. Acinetobacter. Burkholderia. Bacillus anthracis. Pneumococcus Staphylococcus aureus Gram +ve cocci in pairs Morphology Lens shaped, capsulated Gram +ve cocci (Clusters) a hemolysis (Greyish- b hemolysis green zones) (Clear zone) Lab Diagnosis Blood agar Blood agar Optochin sensitive Bile soluble Coagulase + Inulin fermenter MSSA : Penicillin Rx Amoxicillin/Ceftriaxone MRSA : Vancomycin VRSA : Daptomycin/Linezolid Microbiology Revision v4.0 Marrow 8.0 2024  40 Microbiology ----- Active space ----- Pseudomonas Acinetobacter M/c cause of ventilator- Pathogenicity M/c cause of Cystic fibrosis associated pneumonia Microscopic features Gram -ve bacilli Gram -ve coccobacilli Media Cetrimide agar Blood agar Treatment Ceftazidime/Meropenem Ceftazidime/Meropenem Burkholderia Bacillus Melioidosis : B. Pseudomallei (Soil & H2O) Pathogenicity Wool sorter’s disease Glanders disease : based on (Hemorrhagic pneumonia) : B. Mallei (Horse) species B. anthracis