Microbiology Module 6 PDF

MODULE 6│PHARMBIOSCI 5 MICROBIOLOGY MICROBIOLOGY BACTERIAL ENVELOPE study of microorganisms which are large and diverse group All concentric outer la...

MODULE 6│PHARMBIOSCI 5 MICROBIOLOGY MICROBIOLOGY BACTERIAL ENVELOPE study of microorganisms which are large and diverse group All concentric outer layers of microscopic organisms that can occur as either single cell Capsule or in cluster arrangement including viruses which are Outer Membrane microscopic but acellular Cell wall Cell Membrane BACTERIOLOGY Attachment protein Organ of locomotion IINTRODUCTION TO BACTERIOLOGY Capsule MORPHOLOGY Outermost layer, if present Encapsulated Bacteria: Coccus “Some Killers Have Pretty Nice Capsule” round/ circular Streptococcus pneumoniae Klebsiella pneumoniae Haemophilus influenzae Pseudomonas aeruginosa Neisseria meningitidis Cryptococcus neoformans (fungi) Virulence factor (VF): K antigen → prevents phagocytosis Mucoid and slimy polysaccharide layer Identification: India ink stain Outer membrane Major permeability barrier for Gram-negative bacteria Contains lipopolysaccharide (LPS) → endotoxin Bacillus Also present in Listeria spp. (Gram-positive) → not rod shaped converted to endotoxin (according to studies) Periplasmic Space: found between the outer membrane and cell wall Cell wall A.k.a. Peptidoglycan (PG) layer O antigen Present in all bacteria EXCEPT Mycoplasma spp. Gram-Positive Gram-Negative Gram reaction Blue/ violet Red/ pink PG layer Thicker (7-8) Thinner (1-2) Teichoic acid Present Absent Spirochetes Periplasmic space Absent Present spiral shaped Toxin Produces Exotoxin Endotoxin GRAM STAINING Most commonly used differential stain Steps (VIAS) Gram (+) Gram (-) Crystal Violet Primary Stain Gram’s Iodine Mordant Alcohol Decolorizer Pleomorphic Safranin O Secondary stain/ vary in shape Counter stain Gram Staining: General Rules All cocci are Gram-positive, EXCEPT NVM Neisseria Veillonella Moraxella All bacilli are Gram-negative, EXCEPT BANCEL MP Bacillus Actinomyces Nocardia Streptomyces Corynebacterium, Clostridium Erysipelothrix Listeria, Lactobacillus Mycobacterium Propionibacterium Module 6 – Microbiology Page 1 of 32 RJAV 2022  Bacteria that cannot be seen on Gram Staining Endospores Thin or absent cell wall Thick mycotic acid layer Main composition is calcium dipicolinate/ dipicolinic acid MCLRT CLINM Important for survival: resistance to heat, chemicals, Mycoplasma (absent) Cryptosporidium (protozoan) dehydration Chlamydia Legionella micdadei Identification: Malachite Green Staining Legionella pneumophila Isospora (protozoan) Green: Spore Rickettsia Nocardia (weakly acid fast) Red: Vegetative cell Treponema Mycobacterium (Gram-variable) Acid Fact Staining Carbol-Fucshin Fuchsia dye: Primary stain Carbolic acid: Chemical mordant Heat Physical Mordant Acid alcohol Decolorizer Methylene blue Secondary stain/ counterstain Ex. Bacillus, Clostridium STAGES OF MICROBIAL GROWTH Cell membrane Phospholipid bilayer embedded with protein Function: selective barrier for solutes, energy metabolism (ATP production) Attachment proteins Fimbriae – attachment to host cell Pili – attachment to another bacteria, conjugation (virulence Lag Phase factor) No replication, ↑ size, ↑ synthesis Organ of locomotion Log Phase/ Maximum Exponential Phase Axial filament – corkscrew motion of spirochetes ↑ replication, ↑ antibiotic susceptibility Flagella – forward locomotion of bacilli, H antigen Atrichous – no flagella Stationary Phase Monotrichous – one flagellum on one end Number of replications = Number of deaths Lophotrichous – tufts of flagella on one end Amphitrichous – flagella on both ends Death Phase/ Decline Phase Peritrichous – flagella all over the surface Number of deaths > Number of replications INTERNAL BACTERIA STRUCTURE Reasons for microbial death ↓ nutrients Nucleoid ↑ toxins Plasmid Ribosomes Physical Requirement: Endospores Temperature: Nucleoid Psychrophiles/ Cryophiles A.k.a. nuclear region/ nuclear body/ chromatin region/ Cold temperature chromatin body Listeria monocytogenes Not a true nucleus due to lack of nuclear membrane Mesophiles (“primitive nucleus”) Body temperature Circular double stranded (ds) DNA which contains essential Medically important bacteria] genetic formation Thermophiles Hot temperature Plasmid Sporeformers (Bacillus, clostridium) Extrachromosomal circular dsDNA which contains non- pH essential genetic formation: Acidophiles Resistance (R plasmid) Acidic pH Conjugation (F plasmid – Fertility) Lactobacillus acidophilus, Lactobacillus casein (Yakult®) Toxin production Neutrophiles Virulence Neutral pH (7.2-7.6) Transposons (jumping genes) Medically important bacteria Alkaliphiles/ Basophiles Methods of Gene Transfer Alkaline/ basi pH Vibrio cholera Transformation: free uptake of naked DNA in solution Transduction: bacteriophage-mediated (virus Osmotic Pressure Conjugation: via sex pili (F plasmid) Halophiles Transposition: via transposons ↑ salt content/ osmotic pressure Ribosomes Vibrio parahemolyticus (seafood/ oyster poisoning) Site of protein synthesis 70s = 30s + 50s → potential sites for antibacterial agents Module 6 – Microbiology Page 2 of 32 RJAV 2022 Nutritional Requirement Example For organisms that Blood Agar Plate (BAP) Require high nucleic acid content Energy source Milk agar Require high protein diet Phototrophs – light Chocolate Agar Plate (CAP) Require molybdenum from diet (present in hemoglobin) Chemotrophs – redox potential (medically important) Reducing Medium Carbon Requirement For growth of obligate anaerobes Heterotrophs/ Organotrophs – organic carbon (medically Thioglycolate broth: the ONLY reducing medium important) Simple Media using Candle Jar/ Gas Pak® → provides Autotrophs/ Lithotrophs – inorganic carbon anaerobic environment Selective Medium Oxygen Requirement Culture Media Selective For Obligate aerobes MCA, EMB Enterobacteriaceae Require O2 for survival Colistin-Nalidixic Agarbor (CAN) Gram-positive organisms PNBMC Thayer-Martin Neisseria spp. Pseudomonas Lowenstein-Jensen Mycobacterium tuberculosis Nocardia Loeffler’s Serum Medium, Tellurite Corynebacterium diphtheria Bacillus Medium Mycobacterium Campy BAP, Skirrow’s agar Campylobacter jejuni Corynebacterium Bordet-Gengou Medium Bordetella pertussis Thiosulfate citrate bile salts Vibrio spp. sucrose (TCBS) Obligate anaerobes Grow only in the absence of O2 ABCEFP Differential Medium Actinomyces Subdivided a big group of microorganisms into categories Bacteroides Blood Agar Plate – for Streptococcus spp. Clostridium Organisms Type of Hemolysis Zone of Hemolysis Eubacterium α-hemolytic Partial hemolysis Green Prevotella β-hemolytic Complete hemolysis Clear γ-hemolytic Non-hemolytic Red Microaerophiles Require ↓ O2, however ↑O2 concentration → toxic MacConkey agar (MCA) and Eosin Methylene Blue (EMB) – Campylobacter for Enterobacteriaceae Helicobacter Culture Lactose Fermenters Non-Lactose Aerotolerant Medium Fermenters Tolerates O2 but cannot replicate in its presence MCA Pink colonies Colorless LP EMB Purple black colonies Colorless Lactobacillus Propionibacterium E. coli: green metallic sheen Facultative anaerobes GRAM POSITIVE COCCI Could thrive with or without O2 THE REST Gram-Positive Cocci CULTURE MEDIA Catalase test Nutrient material for microbial growth in laboratory Composition Catalase (+) Catalase (-) Chemically Defined Medium Exact composition is known For growth of photoautotrophs and chemoautotrophs Staphylococcus Streptococcus Complex/ Not Chemically Defined Medium Exact composition is not known For growth of most medically important bacteria Staphylococcus Tissue Culture Coagulase test For growth of viruses Mannitol Salt Agar (MSA) Physical State Liquid – no solidifying agents (agar) POSITIVE NEGATIVE Staphylococcus aureus Semi-solid – 0.5 to 1.0% agar MSA: golden yellow colonies Solid – 1.5-3.0% agar Staphylococcus aureus Function/ Use Pathogenic VF: Simple Media Lipase: causes boils, furuncle, carbuncle (clusters) Designed for unfastidious organisms Exfloliatin: causes Staphylococcal scalded skin Nutrient agar/ broth syndrome (SSSS) Enriched Media Enterotoxin B: causes food poisoning, toxic shock Fortified with vitamins, nutrients, and other substances syndrome (SSSS + hypotension) needed for the growth of fastidious organisms β-lactamase/ penicillinase: antibiotic resistance Module 6 – Microbiology Page 3 of 32 RJAV 2022  Treatment: Anti-staphylococcal penicillin (Methicillin, Nafcillin, Streptococcus Oxacillin) For MRSA: Vancomycin Blood Agar Plate For VRSA: Linezolid, streptogramins NEGATIVE β-hemolytic Bacitracin Sensitivity Novobiocin Sensitivity GABHS GBS SENSITIVE: RESISTANT: SENSITIVE: RESISTANT: Staphylococcus Staphylococcus Streptococcus Streptococcus epidermidis saprophyticus pyogenes agalactiae Staphylococcus epidermidis Streptococcus pyogenes MSA: Porcelain white colonies Normal flora of the skin Suppurative Presentation: bacterial endocarditis in patients with Respiratory Tract: pharyngitis (Strep throat) Skin prosthetic heart valves (observe post-op) Cellulitis Impetigo: honey crusted lesions Staphylococcus saprophyticus Erysipelas: painful red rash with orange peel MSA: colorless colonies Normal flora of the vagina Non-Suppurative Presentation Urinary tract infection in women Exotoxin A Treatment: Fluoroquinolones Scarlet fever/ 2nd disease: sandpaper rash, strawberry tongue Toxic shock syndrome (less severe compared to Staphylococcus) Streptococcus M Protein (type III hypersensitivity): Rheumatic hear fever (RHF) Post-Streptococcal glomerulonephritis (PSGN) Blood Agar Plate Streptococcus agalactiae Normal flora of vagina Presentation: causes neonatal sepsis and meningitis α-hemolytic Treatment: Ampicillin + Gentamicin Quellung Reaction Optochin Sensitivity Streptococcus SENSITIVE: RESISTANT: Streptococcus Viridans pneumoniae Streptococcus γ-hemolytic Streptococcus pneumoniae 0.5% NaCl Pneumococcus Lancet-shaped diplococci VF: Capsule (Quellung reaction) Quellang Reaction POSITIVE: NEGATIVE: German word for “swelling” Enterococcus Streptococcus antibodies bind to bacterial capsule to make it spp. bovis more opaque Prevention: PCV Enterococcus MOST COMMON CAUSE OF Normal flora of GIT Community Acquired Pneumonia 2nd / 3rd generation cephalosporins Presentation: Nosocomial/ hospital-acquired infections: (CAP) + extended macrolides meningitis, endocarditis Meningitis in elderly 3rd generation cephalosporins Treatment Otitis media Penicillin Vancomycin For VRE: Linezolid, streptogramins Viridans Streptococcus S. mutans: normal flora of the mouth ESKAPE Pathogen: Associated with antimicrobial resistance Overgrowth may cause dental caries Enterococcus faecium Presentation: Subacute bacterial endocarditis in patients Staphylococcus aureus with prosthetic heart valves Klebsiella pneumoniae Acinetobacter baumanii Pseudomonas aeruginosa Enterobacter spp. Module 6 – Microbiology Page 4 of 32 RJAV 2022  GRAM POSITIVE BACILLI MOT Presentation Prevention Adult Ingestion of - Nausea, - Heat canned Sporeformers botulism performed toxins vomiting, diarrhea, good at 100°C Bacillus from infected flaccid paralysis for 20 minutes Clostridium canned goods - COD: paralysis of - discard respiratory defective/ muscles bulging goods Bacillus Infant Ingestion of Flaccid paralysis Avoid honey Obligate aerobe botulism spores from → floppy baby during the 1st Bacillus anthracis infected honey syndrome year of life Bacillus cereus All are motile, EXCEPT B. anthracis Clostridium perfringens Some members could be sources of antibiotics VF: Bacitracin: Bacillus subtilis Enterotoxin: Clostridial food poisoning Polymixin B: Bacillus polymyxa α toxin (lecithinase) ϴ toxin (hemolysin) necrotizing and hemolytic effects Bacillus anthracis produces target/ double hemolysis on BAP Manner of Transmission (MOT): entry of spores via ϵ toxin: neurotoxic (animal studies) → bioterrorism Injured skin → cutaneous anthrax Presentation Mucous membranes → gastrointestinal anthrax Clostridial Myonecrosis Respiratory tract → inhalational anthrax Severe muscular infection with gas gangrene Presentation Hemorrhage and red-black discoloration Cutaneous anthrax Papule → vesicle → necrotic ulcer → Usually seen in diabetic patients eschar Foul-smelling discharge: mixed infection Gastrointestinal anthrax Causes bowel ulceration → sepsis Complication: sepsis → death Inhalational anthrax Wool sorter’s disease Treatment Pulmonary hemorrhage (fetal) Penicillin Surgical debridement/ amputation Bacillus cereus Presentation: food poisoning Clostridium difficile Self-limiting (fluid replacement) Normal flora of the large intestines Emetic form Diarrheal form Associated with chronic antibiotic use: Implicated food Fried rice Meat, vegetables Clindamycin Symptoms Vomiting, Diarrhea, Amoxicillin, Ampicillin abdominal cramps abdominal cramps Presentation Pseudomembranous Colitis Overgrowth of C. difficile produces biofilm/ pseudo-membrane Clostridium → diarrhea Obligate anaerobe Treatment All are motile, EXCEPT C. perfringens Most important for management: stop the above Subterminal spores: C. perfringens (club shaped) antibiotics! Spherical and terminal spores: C. tetani (tennis racket/ Treatment: Metronidazole (DOC), Vancomycin drumstick appearance Clostridium tetani Non-sporeformers Clostridium botulinum Actinomyces Clostridium perfringes Nocardia Clostridium difficile Streptomyces Corynebacterium Clostridium tetani Erysipelothrix Spherical and terminal spore: tennis racket/ drumstick Listeria, Lactobacillus appearance Mycobacterium MOT: skin penetration from soil contaminated objects Propionibacterium (habitat) VF: Tetanospasmin Actinomyces & Nocardia: MOA: inhibits release of inhibitory neurotransmitter agents Actinomytes (glycine, GABA → important to initiate muscle relaxation → Formerly classified under Kingdom Fungi tetanic contraction → spastic paralysis Branching and Filamentous under microscope Presentation Anaerobic First sign: trismus/ lockjaw Triad: Actinomyces israelii Spastic paralysis Aerobic Opisthotonos (overarching of the back Nocardia asteroides Sardonic smile (grin with raised eyebrow) Actinomadura madurae Tetanus neonatorum: from cutting the umbilical cord with unsterile equipment (non-institutional/ home delivery) → spastic paralysis Actinomyces israelii Cause of death (COD): paralysis of respiratory muscles Anaerobic actinomycetes Treatment Normal flora of the skin and oral cavity Metronidazole, Penicillin Presentation Tetanus toxoid ± Tetanus antitoxin Actinomycosis/ Lumpy jaw Spasmolytic agents (Diazepam) Granulomatous abscess usually in the mandible Prevention: DPT Treatment Penicillin Clostridium botulinum VF: Botulinum toxin (Botox®) Nocardia asteroids MOA: inhibits release of acetylcholine from presynaptic Aerobic actinomyces neuron → flaccid paralysis Weakly acid fast Destroyed by heating at 100°C for 20 minutes Presentation: Nocardiosis (pneumonia) Clinical use: treatment of wrinkles Treatment: TMP-SMZ Actinomadura madurae Aerobic actinomyces Presentation: Mycetoma Bacteria: Actinomycetoma Fungi: Eumycetoma Module 6 – Microbiology Page 5 of 32 RJAV 2022  Causes blockade of lymphatic GRAM NEGATIVE COCCI Vessels → subcutaneous Swelling → Madura foot Neisseria Treatment: General Characteristics: Ketoconazole (bacteria) Kidney-shaped diplococci Amputation (fungi) Catalase positive Oxidase positive Streptomyces: Source of Antibiotics Differentiation: Carbohydrate utilization/ Fermentation test Organism Antibiotic N. gonorrhoeae – glucose only Streptomyces erythreus Erythromycin N. meningitidis – glucose and maltose Streptomyces griseus Streptomycin Streptomyces lincolnensis Lincomycin Isolation: Streptomyces orientalis Vancomycin For sterile specimen (ex. CSF): Chocolate agar plate (CAP) Streptomyces roseosporus Daptomycin → black colonies Streptomyces venezuelae Chloramphenicol For non-sterile specimen (ex. genital discharge): Thayer- Streptomyces orchidaceous Cycloserine Matin = CAP + VCN Streptomyces nodosus Amphotericin B Streptomyces noursei Nystatin Vancomycin – Gram-positive Colistin – Gram-negative Nystatin – fungi Corynebacterium: Modified Thayer Martin = CAP + VCN + Trimethoprim Corynebacterium diphtheriae (Proteus spp.) Non-moyile, club-shaped bacilli, Chinese character arrangement/ palisades Neisseria gonorrhoeae Identification (ID): Gonococcus Loeffler’s agar slant: for visualization metachromic VF: Babes-Ernst granules Pili BAP: gray colonies β-lactamase: PPNG (penicillinase-producing N. Elek Test gonorrhoeae) Diagnosis: Dacron swab Lipooligosaccharide: endotoxin VF: Diphtheria toxin Presentation MOA: Fragment A → inhibits protein synthesis by Genital Gonorrhea (tulo) inhibiting elongation factor 2 → cell death Males: penile discharge, dysuria, urethritis Presentation Females: asymptomatic → ascending infection Cutaneous Diphtheria Complication: Pelvic Inflammatory Disease → scarring → Necrotic skin lesion infertility Pharyngeal Diphtheria Dirty gray pseudo-membrane Treatment: May extend to larynx/ trachea (bull neck appearance) → Ceftriaxone IM single dose + Doxycycline BID for 7 days obstruction Doxycycline for contaminant Chlamydia infection Treatment: Erythromycin + Diphtheria antitoxin Also treat the asymptomatic partner Prevention: DPT Ophthalmia Neonatorum Acquired via passage through infected vaginal canal Erysipelothrix: Prophylaxis: Silver nitrate, Erythromycin Disseminated Gonococcal Infection Erysipelothrix rhusopathiae Arthritis, dermatitis H2S producing (Triple Sugar Iron medium) H2S – Negative: no black precipitate formed Neisseria meningitidis H2S – Positive: black precipitate formed Meningococcus Zoonotic infection VF: Greatest risk: fishermen, fish handlers, butchers (meat/ fish Capsule: A, C, Y, W – 135 (pathogenic subgroups) vendor disease) Lipooligosaccharide (very potent) Presentation Presentation Erysipeloid/ whale finger/ seal finger Meningitis raised violaceous lesion on the finger without pus Most common cause in teenagers and young adults Treatment Prevention: meningococcal vaccine (A, C, Y. W-135) Penicillin Meningococcemia Flu-like symptoms Listeria: Widespread thrombosis → Disseminated intravascular Listeria monocytogenes coagulation (DIC) → bleeding Waterhouse-Friedrichsen syndrome: hemorrhage to the adrenals ID: Shock (septic/ hypovolemic) → death Microscopy: tumbling motility Treatment: Penicillin, Chloramphenicol, 3rd generation Motility medium: umbrella growth pattern cephalosporins Important food-borne pathogen: can survive Prophylaxis: Rifampicin, Ciprofloxacin Refrigerator temperature Low pH GRAM NEGATIVE COCCOBACILLI ↑ salt content Presentation Haemophilus Adult Human Listeriosis Brucella Bacteremia (asymptomatic) Francisella Perinatal Human Listeriosis Pasteurella Early onset syndrome: Stillbirth Bordetella Neonatal sepsis (granulomatosis infantseptica) Late onset syndrome: neonatal meningitis Haemophilus Treatment: Ampicillin + Gentamicin “Blood loving” Isolation: Chocolate agar plate Nutrients needed are inside the RBC Haemophilus influenzae Haemophilus aegypticus Haemophilus ducreyi Module 6 – Microbiology Page 6 of 32 RJAV 2022 Haemophilus influenzae GRAM NEGATIVE BACILLI Pfeiffer’s bacillus MOT: respiratory droplets Enterobacteriaceae VF: Capsule type b → most pathogenic All are facultative anaerobes, oxidase negative Prevention: Hib vaccine All are motile, EXCEPT Shigella Presentation Klebsiella Community Acquired Pneumonia (CAP) 2nd or 3rd generation Yersinia cephalosporins + extended macrolides H2S producing (SPaCEd) Meningitis in infants and toddlers 3rd generation H2S – Negative: no black precipitate formed cephalosporins H2S – Positive: black precipitate formed Most common cause of Meningitis by Age group Salmonella Neonates GBS Proteus E. coli Citrobacter freundii L. monocytogenes Edwardsiella Infants and H. influenzae Toddlers Rapid Lactose fermenters (KrEE) Teenagers N. meningitidis Klebsiella and young Escherichia adults Enterobacter Elderly S. pneumoniae Otitis media Amoxicillin Lactose fermenters Acute bacterial epiglottitis 3rd generation Citrobacter cephalosporins (Ceftriaxone) Serratia Salmonella arizonae Haemophilus aegypticus Shigella sonnei Koch-Week’s bacillus Yersinia enterocolitica Presentation: Purulent conjunctivitis aegypticus = EYEgypticus Non-lactose fermenters Treatment: topical sulfonamide Pathogenic pathogens Salmonella arizonae Haemophilis ducreyi Shigella (except) sonnei Presentation: Chancroid → soft painful chancre (genital Yersinia enterolitica ulcer) Opportunistic pathogens vs. T. pallidum → hard, painless chancre Proteus “You cry with ducreyi” Providencia Treatment: Morganella Azithromycin PO single dose Edwardsiella Ceftriaxone IM single dose Escherichia: Brucella Escherichia coli Zoonotic infection Colon bacillus Brucella abortus: (most common: “Bruce the cow”) Most abundant aerobic flora of the colon Binds to fetal bovine protein erythritol → abortion Most common flora of the colon: anaerobes (not present in humans) (Bacteroides, Fusobacterium) Brucella melitensis: goat, sheep Common indicator of fecal contamination of water (water Brucella suis: pigs potability) Brucella canins: dogs EMB: green metallic MOT Presentation: most common cause of UTI Ingestion of unpasteurized dairy products Treatment: Nitrofurantoin, Fosfomycin, Fluroquinolones Direct contact (high risk butchers, veterinarians) Presentation: Brucellosis/ Bang’s disease/ Malta fever/ DIARRHEIC STRAINS Undulant fever ETEC Enterotoxigenic Traveler’s diarrhea Treatment: Tetracycline + Gentamicin EPEC Enteropathogenic Infantile diarrhea EIEC Enteroinvasive Produces Shigella-like dysentery EAEC Enteroaggregative Persistent watery diarrhea Francisella EHEC Enterohemorrhagic VF: Shiga-like toxin (STEC)/ verotoxin Francisella tularensis (VTEC) Zoonotic infection MOT: contact with rabbits (“Francis the rabbit”, bite of ticks O157:H7 strain → produces severe Presentation: Tularemia/ rabbit fever disease (Hamburger) Treatment: Streptomycin Presentation: Pasteurella Dysentery Hemolytic-uremic Pasteurella multocida syndrome (HUS): Renal Zoonotic infection failure, Anemia, MOT: dog or cat scratch Thrombocytopenia More common with cats, “Papa the cat” Presentation: Pasteurellosis/ Dog or cat scratch disease Treatment: Fluoroquinolones Treatment: Penicillin Salmonella Bordetella Salmonella typhi Bordetella pertussis Reservoir: poultry and dairy products VF: Pertussis toxin → lymphocytosis Diagnosis: Widal test, Typhidot Isolation: Bordet-Gengou media (Potato-Blood-Glycerol Presentation agar): pearl-like colonies Enterocolitis: most common manifestation (constipation/ diarrhea) Presentation: Whooping cough/ pertussis Enteric fever/ Typhoid fever Treatment: Macrolides Prolonged high-grade fever Rose spots – rose-colored rash on the torso (rare) Prevention: DPT Chronic carrier state: gallblader Module 6 – Microbiology Page 7 of 32 RJAV 2022  Treatment: Treatment: Ceftriaxone, Ciprofloxacin (Philippines) Triple Therapy: OCA/ OCM Chloramphenicol (international literatures) Omeprazole/ any PPI Clarithromycin Shigella Amoxicillin Medically important members: Metronidazole Shigella dysenteriae: Group A – most common Quadruple Therapy: TOMB Shigella flexneri: Group B – endemic in the Philippines Tetracycline/ Amoxicillin Shigella boydii: Group C Omeprazole/ any PPI Shigella sonnei: Group D – late lactose fermenter Metronidazole Bismuth salicylate VF: Shiga toxin Neurotoxic Seizure Campylobacter: Enterotoxic Dysentery Campylobacter jejuni Cytotoxic Tenesmus/ Painful defecation Oxidase positive Comma-, S-, or gull wing-shaped bacilli Treatment: self-limiting, if severe may give: Culture: Skirrow/ Butzler medium Ciprofloxacin (adults) Reservoir: dogs Azithromycin (children) Presentation Similar to Shigellosis Yersinia: Crampy abdominal pain Yersinia enterocolitica Bloody diarrhea MOT: Fecal-oral route Complication: Guillan-Barré syndrome Presentation: enterocolitis Sometimes mistaken for appendicitis Treatment: supportive Treatment: self-limiting, may give Doxycycline May give fluoroquinolones Yersinia pestis Pseudomonas: Zoonotic infection Pseudomonas aeruginosa MOT: bite of rat or flea (remember: “Yeye the rat”) Colonies emit a fruity smell Inhibits soil, water, vegetation Presentation VF: Bubonic plague Presence of enlarged suppurative lymph nodes Capsule in the groin and/ or axilla (buboes) Exotoxin A: major VF, inhibits protein synthesis Septicemic plague Hemorrhage, black gangrene (fingers, toes, Pigments: nose) → black death Pyocyanin: blue pigment, stimulates inflammatory Pneumonic plague Either from septic emboli or airborne response Pyoverdine: fluoresces in tissues Treatment: Aminoglycoside, Tetracycline Pyorubin: dark red pigment Pyomelanin: black pigment Other Gram-negative Bacilli Presentation: Vibrio Nosocomial infection: sepsis, meningitis Helicobacter Hot tub folliculitis (jacuzzi) Campylobacter Treatment: Pseudomonas Antipseudomonal penicillin and cephalosporins Calymmatobacterium Aminoglycosides Gardnerella Calymmatobacterium: Vibrio Calymmatobacterium granulomatis General characteristics: Formerly Klebsiella granulomatis Oxidase positive, motile Presentation: Donovanosis/ Granuloma inguinale Comma-/ curve-shaped Genital ulcer with beefy base Halophilic, EXCEPT V. cholerae Pseudobuboes – nonsuppurative enlarged lymph nodes Treatment: Azithromycin Organism TCBS Disease Vibrio cholerae Yellow Cholera ! NOTE: Donovanosis is not caused by Leishmania colonies donovani Vibrio parahaemolyticus Green Seafood/ oyster colonies poisoning ! Leishmania donovani: visceral leishmaniasis/ Vibrio vulnificus Blue-green Oyster poisoning kala-azar colonies Gardnerella: Vibrio cholerae Gardnerella vaginalis VF: cholera toxin → ↑ cAMP → ↑ movement of water and Normal flora of vagina sodium into the intestinal lumen → rice watery diarrhea → Presentation: Bacterial Vaginosis dehydration Foul smelling whitish vaginal discharge (fishy odor) Treatment: fluid replacement Diagnosis: clue cells (vaginal cells embedded with bacteria) May give Tetracycline to shorten infection Treatment: Metronidazole Helicobacter: BACTERIA NOT SEEN ON GRAM STAINING Helicobacter pylori Oxidase positive, motile Mycoplasma Spiral shaped bacilli Chlamydia VF: Urease → liberates ammonia → neutralizes gastric acid Legionella pneomophila Diagnosis: Urea breath test Rickettsia Presentation: Treponema Halitosis Mycobacterium (Gram-variable) Peptic ulcer disease (duodenal, gastric) Chronic gastritis Risk factor for gastric cancer Module 6 – Microbiology Page 8 of 32 RJAV 2022 Mycoplasma: Disease Vector Mycoplasma pneumoniae Spotted Fever No cell wall, pleomorphic Rickettsia rickettsi Rocky mountain Tick Smallest free-living organism (mollicutes) spotted fever Identification: Rickettsia akari Rickettsial pox Mite Microscopy: Diene’s stain → fried egg colonies Typhus Rickettsia prowazekii Epidemic typhus Louse Presentation: Atypical pneumonia/ walking pneumonia Rickettsia typhi Epidemic typhus Flea Mild symptoms only Scrub Typhus Treatment: Macrolides Orientia tsutsugamushi Scrub typhus Chigger mite Ureaplasma urealyticum Coxiella burnetti Non-gonococcal urethritis in males Previously under Rickettsia Salpingitis and post-partum fever in females Vector: ticks Associated with lung disease in premature infants of low birth Presentation: Q fever weight Fever, rashes, headache (similar to Rickettsia) Treatment: Tetracycline, Ciprofloxacin Chlamydia Obligate intracellular parasite Treponema Forms: Elementary body: Spirochetes: Treponema, Leptospira, Borrelia Extracellular Metabolically inert Treponema pallidum Infective form Treponema: Greek for “coiled hair” Reticulate body Intracellular reproductive form Stages of Syphilis Chlamydia trachomatis Primary Syphilis Chlamydia pneumoniae Hard, painless chancre Chlamydia psittaci Self-limiting Diagnosis: dark field microscopy Chlamydia trachomatis Secondary Syphilis Condylomata lata: wart-like lesions on the genitals Presentation Diagnosis: serological testing Eye Neonatal inclusion conjunctivitis: passage through Non-treponemal tests: used for screening infection infected birth canal VDRL: Venereal Disease Research Laboratory Adult inclusion conjunctivitis: acute infection RPR: Rapid Plasma Reagin Trachoma: chronic follicular conjunctivitis → blindness Genital Males: penile discharge, dysuria, urethritis Treponemal tests: confirmatory test infection Females: asymptomatic FTAA: Fluorescent Treponemal Antibody Absorption Lymphogranuloma venerum MHA: Micro hemagglutination Self-limited genital ulcer Swelling of inguinal lymph nodes Treatment: Penicillin (DOC), Erythromycin Jarisch-Herxheimer reaction: due to antigen released by dead Treatment: Doxycycline T. pallidum → neutropenia, hypotension Latent Syphilis Chlamydia pneumoniae Asymptomatic stage, last for around 10 years Formerly known as Taiwan acute respiratory (TWAR) agent Tertiary Syphilis Presentation: Rare mainifestation after the advent of penicillin Atypical pneumonia Gumma (Granulomatous lesions) Systemic manifestations: neurosyphilis, aortic aneurysm Risk factor for atherosclerosis 9recent studies) Treatment: Macrolides Congenital Syphilis Chlamydia psittaci Acquired during the 1st trimester of pregnancy MOT: inhalation from dried bird excrement Presentation: Presentation: Intrauterine death Psittacosis: parrots (parrot fever) Congenital abnormalities t birth: Ornithosis: other birds - Hutchinson’s triad: Hutchinson’s teeth, interstitial keratitis, CN VII Treatment: Macrolides deafness - Saber shin Legionella: - Scaphoid scapula - Saddle nose Legionella pneumophila Silent infection: may not be apparent until 2 years old MOT: droplet transmission May spread through air-conditioning units that use Leptospira: water cool air. Leptospira interrogans Presentation MOT: through mucous membrane or breaks in the skin Legionnaire’s Disease/ Legionellosis coming in contact to water with infected urine (rodents, cats, Atypical pneumonia Treatment: Macrolides dogs, humans) Pontiac fever Presentation Acute flu-like symptoms Leptospiremia, Leptospiruria Anicteric Leptospirosis: mild, flu-like symptoms Rickettsia Icteric Leptospirosis/ Weil’s disease: severe Meningitis, renal failure, liver failure Obligate intracellular parasite COD: Pulmonary hemorrhage Vector transmitted Prophylaxis: Doxycycline 200mg OD for 3-5days Diagnosis: Weil-Felix reaction Treatment: Presentation: triad of: Mild: Doxycycline Fever Moderate to Severe: Penicillin Rashes Headache Borrelia: Treatment: Tetracycline, Chloramphenicol Borrelia burgdorferi Vector: Ixodes tick Presentation: Lyme Disease Module 6 – Microbiology Page 9 of 32 RJAV 2022  Bull’s eye rash/ erythema chronicum migrans: No. of Bacilli ↓ Paucibacillary ↑ Multibacillary expanding rash Clinical presentation Hyposthetic Leonie facies, saddle hypopigmented skin nose, nodular skin lesions lesions Borrelia recurrentis Treatment Rifampicin + dapsone Rifampicin + Dapsone Presentation: relapsing fever (recurrent fever) + Clofazimine Endemic form: tick bite (rodent host) Epidemic form: body louse (human host) PARASITOLOGY Mycobacterium PROTOZOA Mycobacterium tubercolosis Mycobacterium avium-intracellulare complex Intestinal Protozoa Mycobacterium leprae Mycobacterium tuberculosis Giardia lamblia Koch’s bacillus Entamoeba histolytica #8 leading cause of morbidity in the Philippines (as of 2010) Cryptosporidium hominis VF: tuberculin and mycolic acid – stimulates type IV Cyclospora cayetanensis hypersensitivity/ cell-mediated immunity → immune system Balantidium coli causing damage to the body MOT: airborne transmission Giardia lamblia Also referred to as Giardia duodenales or Giardia intestinalis Pathogenesis MOT: ingestion of fecally contaminated water or food Primary infection: initial infection usually during childhood → bacilli containing Giardia cysts or by direct-fecal contamination walled by carinal lymph nodes Presentation: Secondary infection: Acute or chronic diarrhea Reactivation: immunocompromised state usually in adulthood Stools may be watery, semisolid, greasy, bulky and foul Pulmonary tuberculosis (PTB): classical apical infiltrates smelling Extrapulmonary (EPTB) Diagnosis: stool exam (cysts, trophozoites) - CNS: Tuberculous meningitis Treatment: Metronidazole or Nitazoxanide - Vertebral column: Pott’s disease Entamoeba histolytica Presentation MOT: main source of water food contamination is the Cough for ≥ 2 weeks: most Night sweats important clinical findings Easy fatigability asymptomatic carrier who passes cysts Hemoptysis Dyspnea Presentation Weight loss Chest/ back pain Asymptomatic infection Amebic colitis/ dysentery (mild severe, “flask-shaped” Diagnosis ulcer) Sputum Microscopy Extraintestinal infection (amebic liver abscess*, amebic Gold standard for fiagnosis hepatitis) 2 sputum samples: at least 1 out of 2 must be positive Diagnosis: Stool exam (cysts, trophozoites) Tuberculin Skin Test (TST)/ Purified Protein Derivative (PPD)/ Treatment: Mantoux Test Asymptomatic infection: luminal amebicide Positive result: wheal or erythema ≥10mm after 48-72hours Amebic colitis/ dysentery: tissue + luminal amebicide International literatures: ≥15mm is positive, but note that in endemic countries (Philippines) the cutoff is ≥10mm Extraintestinal infection: tissue + luminal amebicide Culture: Lowenstein-Jensen medium Free living amebae Amebae MOT Disease Naegleria fowwleri Invade the nasal Acute primary amebic mucosa → extend into meningoencephalitis the brain Acanthamoeba spp Starts with eye and - Granulomatous skin infection amebic encephalitis (GAE) - Acanthamebic keratitis (contact lens wearers) Cryptosporidium hominis Infect the intestine in immunocompromised persons (e.g., those with AIDS) Mycobacterium avium-intracellulare complex MOT: acquired from infected animal or human feces or form 2 combined species fecally contaminated food or water Presentation: causes TB in AIDS patients (AIDS-defining Presentation: water diarrhea, which is mild and self-limited illness: usually seen in patients with advanced HIV infection/ 91 to 2 weeks) in normal persons (prolonged in AIDS) immunocompromised or very young or old individuals) Treatment: Macrolides + RE Diagnosis: Stool exam (cysts) Treatment: no broadly effective therapy Mycobacterium leprae Hansen’s bacillus Cyclospora cayetanensis Obligate intracellular parasite with predisposition to cooler MOT: waterborne and foodborne infections from various parts of the body (ex: skin, nerves) types of fresh produce (raspberries, mesclun, and basil) Isolation: armadillo foot pad Presentation: diarrhea, anorexia, fatigue, and weight loss MOT: nasal discharge from untreated lepromatous leprosy Diagnosis: stool exam (oocysts, acid-fast positive) patients Treatment: Trimethoprim-sulfamethoxazole (TMP-SMZ) Leprosy Tuberculoid Lepromatous Balantidium coli Cell-mediated Strong Weak Only member of the ciliate group that is pathogenic for immunity humans Lepromin skin test Positive Negative MOT: outbreaks are associated with contamination of water (Same principle as supplies with pig feces TST) Presentation: Module 6 – Microbiology Page 10 of 32 RJAV 2022  Asymptomatic infection Mucocutaneous leishmaniasis (Espundia) – primary Watery stools with blood and pus lesion → spread to the nasal and oral mucosa → Round-shaped ulcer producing severe and disfiguring facial mutilation Diagnosis: Stool exam (cysts, trophozoites) Visceral leishmaniasis (Kala-azar) – of inoculation to Treatment: Tetracycline multiply → reticuloendothelial cells in spleen, liver, lymph nodes and bone marrow Sexually Transmitted Protozoa Diagnosis: detecting either the amastigotes in clinical specimens or the promastigotes in culture Trichomonas vaginalis Treatment: Na stibogluconate Most infections are asymptomatic or mild for both women and men Plasmodium spp. Infection is normally limited to the vulva, vagina, and cervix: it MOT: through the bite of an infective female Anopheles does not usually extend to the uterus. mosquito (definitive host) Presentation: Diagnosis: thick and thin films of blood Women: frothy yellow or cream-colored discharge, local Thick film: used to detect the presence of organisms tenderness, vulval pruritis, and burning Thin film: establishing species identification Men: thin, white urethral discharge, GUT infection - Best time is midway between paroxysms of chills and fever Diagnosis: microscopic examination of vaginal or urethral (greatest number of intracellular organisms is present) discharge Treatment: (refer to drugs for malaria) Treatment: Metronidazole (both partners should be treated) Plasmodium falciparum – most common, most virulent, most fatal Blood and Tissue Protozoa Malignant tertian malaria (36 to 48 hours) No selectivity in host erythrocytes; invades any RBC at any Trypanosoma spp. stage in its existence Shortest incubation period (7 to 10 days) Leishmania spp. Plasmodium spp. Produces daily (quotidian) chills and fever Toxoplasma gondii Mature gametocytes of P. falciparum are sausage-shape/ banana shape Babesia microti Trypanosoma spp.: Plasmodium vivax – 2nd most common Benign tertian malaria (48 hours) Trypanosoma brucei Trypanosoma brucei gambiense – West African Invades only young, immature erythrocytes trypanosomiasis Capable of hypnozoite stage Trypanosoma brucei rhodesiense – East African trypanosomiasis Plasmodium ovale – rarest spp. MOT: introduced through the bite of the tsetse fly (Glossina Benign tertian malaria (48 hours) Selectivity for young, pliable erythrocytes spp.) → multiply at the site on inoculation → induration and swelling (the primary lesion) Capable of hypnozoite stage Presentation: African Sleeping sickness syndrome Plasmodium malariae Lassitude, inability to eat, tissue wasting, unconsciousness, and death Infect only mature erythrocytes Winterbottom sign – swelling of the posterior cervical Longest incubation period (18 to 40 days) Quartan malaria (72 hours) lymph nodes Diagnosis: thick and thin blood films, in concentrated anticoagulated blood preparations from lymph nodes and Plasmodium knowlesi Malaria parasites of Old-World monkeys and pig-tailed concentrated spinal fluid Treatment: macaques Non-CNS: Pentamidine, Suramin Permissive in humans as well as in nonhuman primates No selectivity in host erythrocytes CNS: Eflornithine, Melasrsoprol Simian malaria or quotidian malaria (24 hours) Trypanosoma cruzi Toxoplasma gondii MOT: infective trypomastigote, which is present in the feces of a reduviid bug (“kissing bug”) → enters the wound MOT: created by the biting → introduced when infected bug feces Ingestion of improperly cooked meat (intermediate host) Ingestion of infective oocysts from contaminated cat are rubbed into the conjunctiva, the bite site, or a break in the skin. feces (definitive host) Presentation: American Sleeping disease (Chaga’s disease) Transplacental transmission Presentation: Site of the bite: chagoma, Romana’s sign (unilateral swelling of the eyelids) Asymptomatic (most common) Acute Chaga’s disease: asymptomatic Symptomatic Acute: chills, fever, headache, myalgia, Chronic Chaga’s disease: cardiomyopathy → arrhythmia lymphadenitis, and fatigue Chronic: lymphadenitis, occasionally a rash, Brazilian Chaga’s disease: megaesophagus, megacolon evidence of hepatitis, encephalomyelitis, and Diagnosis: thick and thin blood films or concentrated myocarditis Congenital infection: chorioretinitis (most common) anticoagulated blood early in the acute stage Treatment: Nifurtimox; Benznidazole and other CNC disorder Diagnosis: serologic testing (detecting ABYs) Treatment: Pyrimethamine + Sulfadiazine (DOC); Leishmania spp. Cutaneous leishmaniasis: L. tropica, L. Mexicana, L. major Pyrimethamine + Clindamycin (Alternative) Mucocutaneous leishmaniasis: L. brzilliensis Babesia microti Visceral leishmaniasis: L. donovani, L. chagasi MOT: transmitted by adult female sandflies belonging to MOT: human infection follows contact with an infected tick genera Phlebotomus and Lutzomyia (Ixodes dammini) Presentation: Presentation: Cutaneous leishmaniasis (Oriental sore, Delhi boil) – General malaise, fever without periodicity, headache, red papule, appears at the site of the fly’s bite → chills, sweating, fatigue, and weakness Advance infection: hepatomegaly, splenomegaly, enlarge and ulcerate hemolytic anemia, renal failure Diagnosis: blood smear Module 6 – Microbiology Page 11 of 32 RJAV 2022  Treatment: