Microbiology

Respi
Microbiology
SYLLABUS
Introduction to respiratory system infection: (P. 1047)
Normal flora (P. 1047): List
Pathogenic Microorganisms: List
Respiratory Tract Infection: Classification of respiratory diseases (P. 1047), list common pathogens causing
respiratory diseases (rhinitis, pharyngitis, laryngitis, sinusitis, community acquired pneumonia, hospital
acquired pneumonia, ventilator associated pneumonia etc.) (P. 1048)
Approach to diagnosis of respiratory pathogens: (P. 1049)
Procedure of sample collection, storage, transport, and processing and laboratory diagnosis (P. 1049) of
common respiratory pathogens
Bacteria as respiratory pathogen: (P. 1050)
Streptococcus pyogenes (P. 1050) (streptococcal sore throat and consequences), streptococcus pneumonia (P.
1052) and other streptococi, staphylococcus (P. 1055), hemophilus influenza (P. 1057), corynebacterium
diptheriae (P. 1059), bordetella pertusis (P. 1062), organisms causing hospital acquired pneumonia including
ventilator associated pneumonia (P. 1065) (e.g. klebsiella (P. 1066), pseudomonas etc ), atypical pneumonia
(P. 1067) (legionella (P. 1067), Chlamydia (P. 1069), mycoplasma (P. 1068), ureaplasma), mycobacterium
tuberculosis (P. 1069) and MOTT (P. 1072) IV
Fungi as respiratory pathogens: (P. 1073)
Histoplasma capsulatum (P. 1073); candida albicans (P. 1075), aspergilus fumigates (P. 1076); Cryptococcus
neoformans (P. 1077)–morphology ,pathogenesis and diagnosis
Viruses as respiratory pathogens: (P. 1079)
Orthomyxo (P. 1079) and paramyxo viruses (P. 1081), adenovirus (P. 1083), rhinovirus (P. 1084), SARS (P. 1084)
Parasites as respiratory pathogens: (P. 1085)
Pneumocystis jerovicci (P. 1085), paragonimis westermani (P. 1086): Morphology, life cycle and laboratory
diagnosis.
FAST TRACK BASIC SCIENCE MBBS -1045-

Microbiology
IV
-1046- FAST TRACK BASIC SCIENCE MBBS

Respi
MICROBIOLOGY
INTRODUCTION TO RESPIRATORY 3. Role of antibiotics:

SYSTEM INFECTION - Use of broad spectrum antibiotic, disrupt the
Past Questions: composition of normal flora.
List of normal flora of respiratory tract
1. Define normal flora. Explain, in brief, normal
flora of upper R.T. (1+4+5 = 10) [09 July] [05, 09]
2. List five normal and five common pathogenic - Normal flora are generally found in upper
organisms of respiratory tract infection. respiratory tract.
(2.5+2.5=5) [05 June] Sites of URT Normal flora
3. List four bacterial flora of respiratory tract. I. Nose - Diphtheroids
Describe the methods of laboratory diagnosis of - staphylococci, streptococci
bacterial pneumonia. (2+8=10) [10 July] - Haemophilus (occasionally)
4. Explain streptococcal throat infection. II. Nasopharynx - Corynebacterium species
(2) [10 July] (Predominantly)
5. List bacterial pathogens of U.R.T (2) [08] - Haemophilus
6. Name the various agents causing upper - Moraxella sp,Nesseria
respiratory tract infection (2) [09 July] III. Pharynx - Bacterioids pneumosintes
7. Explain upper respiratory tract infection (2)[05] - Candida
- Peptostreptococcus sp IV
Normal Flora [09] haemophilus parainfluenzae
 It is defined as mixture of organism which IV. Nasal sinuses - Generally sterile but upon
regularly inhabits any anatomical site. blockage of sinus containing
 It consists of bacteria, eukaryotic fungi and mucopolysaccharides
protista. contain some viruses.
 Normal floras are not pathogenic in their normal Respiratory Infections

anatomical site but become pathogenic in site - Infection of respiratory tract by various
other than normal anatomical site. pathogenic agent is characterized by various
Role of normal flora clinical sign and symptom.
1. Beneficial role - The Infection of respiratory tract is broadly
- Infection resistance divided into 3 groups.
- Nutrient source i. Upper respiratory tract infection (URTI)

ii. Lower respiratory tract infection (LRTI)
- Stimulation of immune system
iii. Infection of middle ear and sinuses
- Stimulation of epithelial turnover
2. Disease production - Upper respiratory tract infection
- Act as opportunistic pathogens if resistance of  Rhinitis

host is lowered.  Tonsilitis,
- Act as pathogen in tissue outside their habit.  Adenoiditis

Microbiology
 Pharyngitis Causative organism of various

 Gingivo-stomatitis respiratory diseases
 Epiglottitis 1. Rhinitis
 Laryngitis - It is characterized by sneezing, rhinorrhea,
- Lower respiratory tract infection obstruction of nasal passages, conjuctival,
nasal and pharyngeal itching and carination.
 Tracheaitis
Etiology:
 Emphysema  Dust
 Bronchitis  Pollens
 Pleuritis  Molds spores
 Bronchiolitis  Dermatophagoides farinae
 Pleural effusion 2. Pharyngitis
 Pneumonia - Acute inflammation of pharyngeal mucosal
submucosa and lymphatic tissues.
 Interstitial pneumonia
- Etiology:
 Lung abscess Bacteria:
- Infection of middle ear and sinuses  S. pyogen
 Otitis media  C.diphtheriae
 Sinusitis  N.gonorrhoea
Etiology of respiratory infection Virus:
- Viral: Obligate pathogen  Epstein Barr virus
- Bacterial: Secondary invaders  Adenovirus
- Fungal: Oppurtunistic Pathogens  Influenza A, B
IV  Coxsackie A
- Parasitic: Multiple organism infection
 Parainfluenzae
Pathogenesis
Pattern
Entry of pathogenic organism
 <3yr  100% viral

 5–15 yrs  15  30% of Group - A 
Cell attachment
Hemolytic Streptococcus
  Adult  10% of Group - A  Hemolytic
Toxin production Streptococcus
 3. Laryngitis
Cell invasion, destruction - Acute inflammation of larynx leading to edema
 of laryngeal mucosa & underlying structures
Phagocytosis resistance - Etiology
  Virus:
Inflammatory response  Epstein Barr virus
 Bacteria:

 S. pyogenes
Tissue damage
 Diphtheria

 Mycobacterium tuberculosis -
Repair
tuberculous laryngitis

Respi
4. Sinusitis 7. Ventilator associated pneumonia

- Inflammation of sinuses - Etiology
 Bacteria:
- Etiology:
 Klebsiella
 Viral is more common than bacterial cause
 Pseudomonas
 Virus:
 Rhinovirus
APPROACH TO DIAGNOSIS OF
 Parainfluenza
RESPIRATORY PATHOGENS
 Influenza Diagnosis of Respiratory Infections [05]
 Bacteria: Laboratory investigation
1. Specimen Collection
 S. Pneumoniae
- URI (Upper respiratory infection)
 Non typable H. influenza i. Specimen:
 Moraxella catarrhalis - Local secretion
 Staphylococus aureus - Membrane
5. Community Acquired pneumonia - Tissue, serum
- Etiology: ii. Procedure of sample collection:
 Virus: - Throat swab
- Washing
 RSV
- Scrapping
 Parainfluenza - Aspiration
 Measles - LRI (Lower respiratory infection)
 Adenoviruses i. Specimen:
 Cytomegalovirus - Sputum, secretions
 Bacteria: - Tissue, pleural fluid, blood. IV
ii. Method of collection:
 Secondary to viral infection:
- Active sputum, morning sample in
streptococcus pneumoniae
wide mouthed sterile container
 H. influenza
- Endoscopic aspiration
 Chlamydia - Washing
 Legionella pneumophilla - Biopsy, pleural tap
 Mycoplasma - The specimen thus collected is stored or
6. Hospital Acquired pneumonia transported to laboratory for further
investigation.
- Etiological
2. Demonstration:
 Bacteria:
- Light microcospy
 Staph – MRSA - Electron microscopy
 Streptococci 3. Isolation of organism:
 Klebsiella pneumoniae - Culture
 Virus:  Tissue culture
 RSV  Egg inoculation
 Animal studies
 Adenovirus
4. Immune response:
 Rhinovirus
- Humoral, CMI
 Influenzavirus 5. Histopathological changes
 Parainfluenza 6. Antigen detection
Microbiology
BACTERIA AS RESPIRATORY 14.Describe the pathogenesis and lab diagnosis of

PATHOGENS pulmonary tuberculosis.
Past Questions: (4+4=8, 5+5=10) [03 Dec, 08 Jan]
15.Explain atypical mycobacteria. Describe lab
1. Describe the methods of laboratory diagnosis of
diagnosis of tuberculosis. (3+5=8) [06 Dec]
bacterial pneumonia. (2+8=10) [10 July]
16.Define bacterial pneumonia. List four bacteria
2. Explain streptococcal throat infection. Describe
causing pneumonia in children. Describe the
the laboratory diagnosis of streptococcus
pathogenesis and laboratory diagnosis of
pyogenes. (2+8=10) [10 July]
Streptococcus pneumoniae. (2+2+6=10) [11 July]
3. Describe types of haemolytic streptococcus.
17.List four respiratory pathogens. Describe sample
Explain briefly lab Diagnosis of sore throat.
collection & laboratory diagnosis of bacterial
4. Describe the colony character of Pneumococcus. pneumonia. (2 + 4 + 4= 10) [07 July]
Describe briefly the laboratory diagnosis of
18. Write short notes on
Pneumococcus pneumonia. (2+2+4=8) [03 June]
a. Streptococcus pyogenes (5) [07 July]
5. Describe the laboratory diagnosis of
b. Streptococcus pneumonia
Corynebacterium diphtheriae. (2×5=10) [08]
(5) [07 June, 06 June, 05 Dec, 05 June, 04 June]
6. Explain upper respiratory tract infection.
c. Beta hemolytic streptococcal infection.
Describe the laboratory diagnosis of
Corynebacterium diphtheria. (25=10) [08 July] (5) [04 Dec]
d. Differences between pneumococci and
7. Name the causative organism of diphtheria.
viridians streptococci. (5) [10 Jan]
Write about the morphology and cultural
characteristics, pathogenesis and lab diagnosis? e. Bordetella pertusis (5) [06 Dec, 05 Jan]
IV (10) [05 June] f. Pertusis toxin (5) [05 June]
g. C. diphtheria (5) [05 Dec]
8. Explain diphtheroid. Write lab diagnosis of C.
diphtheriae. (2+6=8) [06 June] h. Pathogenesis of staphylococcus aureus
9. Write about morphology, cultural characteristics, (5) [04 Dec]

pathogenesis and laboratory diagnosis of 19.Discuss laboratory diagnosis of pulmonary
Tuberculosis (10) [05 June] tuberculosis [3][013]
10.Enumerate Mycobacteria causing lung infection 20.Discuss morphology of influenza virus [2][013]
in man. How do you proceed to establish lab Streptococus pyogenes
diagnosis? (3 + 5 = 8) [05 Dec]  It is the pathogenic bacteria which belongs to
11.Describe the pathogenesis of pulmonary group A –hemolytic streptococci.
tuberculosis. Write in detail the lab diagnosis. Morphology [10]
(4 + 4 = 8) [08 Jan]
- Individual cocci are spherical or oval.
12.Discuss the morphology and cultural characters
- Streptococci are gram positive bacteria.
of mycobacterium tuberculosis. Give a brief
- Non flagellate, non motile, non sporing
account of the lab diagnosis of pulmonary
tuberculosis. (2 + 2 + 4 = 8) [02 Dec] - Arranged in chain of varying length due to
different rate of division in one plane only.
13.Write the lab diagnosis of pulmonary
tuberculosis. (8) [04, 05 June] - Capsulated (made up of hyaluronic acid)

Respi
Culture characteristics iii. Colony morphology

i. Aerobic and facultative anaerobes - Blood agar:
ii. Culture media  Small, circular, low convex, semitransparent
- Enriched media  –hemolysis around colony
- Glucose broth/serum broth:
- Blood agar
 Circular deposit forms at the bottom
 10% CO2 promote growth and hemolysis
Virulence factors:
Virulence factors Pathogenic role
i. Capsular hyaluronic acid - Nonimmunogenic, antiphagocytic
ii. Group specific polysaccharide antigen - Responsible for non suppurative sequelae of
streptococcal infection
iii. Type specific protein antigen
a. M-protein (on surface) of cell in association with - antiphagocytic, degrades C3b
fimbriae
b. T and R proteins - No relation with virulence
iv. Cell surface proteins.
a. Protein F (Fibronectin binding protein) - Mediate adherence to epithelial cells.
b. Protein G - Bind with IgG via “Fe” region and may hinder
antibody binding and prevent effective phagocytosis
v. Exotoxins
a. Erythrogenic toxin (Pyrogenic exotoxins) - Mediate pyrogenicity, enhancement of delayed
hypersensitivity, cytotoxicity, Immuno- suppression IV
of  cell function, production of scarlariform rash 
b. Exotoxin A - Responsible for streptococcal system
c. Exotoxin B (Cysteine protease) - Responsible for heart & liver failure
vi. Hemolysin
a. Streptolysin O - i) Lyses WBC, RBCs and platelets ii) Immunogenic iii)
Stimulates release of lysosomal enzymes
b. Streptolysin S - Lyses WBCs, RBC & platelets, non immunogenic
vii. Enzymes (Spreading factor)
a. Streptokinase (Fibrinolysin) - Promote lysis of human blood
b. Streptococcal deoxyribonuclease - Responsible for liquefying the highly viscous DNA
c. Nicotinamide adenine dinucleotidase (NADase) - Antigenic, exerts leucotoxic effect
d. Hyaluronidase - Splits hyaluronic acid, favour spread of infection.
e. Lipoproteins - Serum opacity factor
f. Other extracellular - Serum opacity factor
Product:
DNase
Neuraminidase
Esterase
Amylase

Microbiology
Lesion  Incubation period 3 – 5 days

i. Suppurative  Spread by saliva or nasal secretion
ii. Non Suppurative Clinical feature
Biochemical reaction Mild case/early case
- Does not ferment ribose, positive Pyrase test - Redness of tonsil and pharynx
- Production of Acid but No gas - Classical picture: Infection and edema of
- Catalase –negative fauces of soft plate with exudates- Acute
follicular tonsillitis
- Bile insoluble
- Tinny, reddish-brown spots as back of
PYR: L – Pyrrolidoryl  napthylamidase
throat
Laboratory diagnosis - Swollen lymph nodes and tongue.
i. Sample/specimen Severe case:
- Throat swab, pus swab, pus, blood - Septic complication such as peritonsillar
ii. Microscopy abscess, sinusitis, otitis media
- Gram staining - Throat infection is accompanied by
- Gram+ve, spherical or oval cocci erythematous rash (scarlet fever)
- Arranged in short or long chain Note:
iii. Culture: refer above - Streptococcus pyogenes after sequel of sore throat
iv. Biochemical test: Mentioned above can cause rheumatic fever, rheumatic heart
disease and glomerulonephritis.
v. AST: Bacitracin sensitive
vi. Serological test Laboratory diagnosis: [09, 10, 11]
- ASO titer - Specimen: Throat swab
IV - Fluorescent AB technique - Culture: Blood agar incubated aerobically and
anaerobically
- Anti DNAase B
- Identification:
Types of hemolysis:
i. Colonies – small, dry, beta-hemolytic
i. α hemolysis:
ii. Lancefield grouping
- Partial hemolysis - Latent period: 2-3 weeks but upto 6 week after
- E.g. streptococcus pneumoniae, strept. throat infection.
Viridans - Serology: ASO titre 200 or more.
ii. β hemolysis: Streptococcus pneumoniae
- Complete hemolysis  Also called pneumococcus
- E.g. s. pyogenes, staph. Aureus Morphology [07]
iii.  hemolysis: - Gram +ve lanceolate diplococcus, Non acid
- No hemolysis fast.
- E.g. enterococcus - Lanceolate shaped diplococci with broad ends
in opposition.
Streptococcal sore throat [10, 11]
- Tissue form: Capsulated
 It is defined as acute infection of pharynx, tonsil - Grown on artificial media: non capsulated.
and larynx caused by Gr. A -hemolytic - Non sporing, non flagellated and non motile.
streptococci (KU 2012 ) - India ink preparations shows clear halo around
 Children of 5–8 years old  more susceptible capsule

Respi
Culture characteristic Pathogenesis

- Aerobe and facultative anaerobe - Source of infection: Human, upper respiratory
- Culture media: Enriched. tract
- Optimum temperature: 37°C (25°C–42°) - MOT: Respiratory droplets
- Optimum pH: 7–8 (6.52 – 8.3) Pneumococci
- Growth is improved by 5–10% of CO2. 
Colony morphology [03] Attached to epithelial cell receptor of nasopharynx
i. On blood agar: through surface adhesion
- After incubation for 18 hour, colonies are 

small dome shaped with hemolysis (zone Nasopharyngeal colonization
of green discoloration) 
- Old colonies: Rough surfaces with raised Infection of middle ear, paranasal sinuses and
margin, central depressions and concentric respiratory tract by direct spread and other organs
ring (Draughtman colony) by contiguity or through blood
ii. On chocolate agar: Colonies produce well 
marked green discolouration In Immunocompromised condition, cocci multiply
iii. Loeffler's serum: Discrete moist colonies and penetrate the bronchial mucosa
iv. Glucose broth: Uniform turbidity 
Biochemical test Damage to respiratory epithelium and excessive
- Catalase –ve secretion
- Optochin sensitivity +ve  IV
- Oxidase –ve Outpouring of edema fluid followed by red cells and
leucocytes into alveoli
- Inulin fermentation +ve

- Bile solubility +ve
Consolidation of portion of lung
Antigenic structure
I. Capsular polysaccharide Clinical syndromes
- Type specific and immunologically distinct - Pneumonia (lobar form mostly)
II. Somatic M protein - Otitis media
III. Cell wall carbohydrate - Sinusitis
Virulence factors - Meningitis

i. Polysaccharide capsule - Septicemia
ii. IgA protease - Empyema
iii. Protein adhesion - Tracheobronchitis
iv. Cell wall constituents Predisposing factor
- Techoic acid i. Abnormalities of respiratory tract
- Peptidoglycan ii. Impaired immune response
- Pneumolysin iii. Loss of splenic function

Microbiology
Laboratory diagnosis [03, 07] Note:

i. Specimen: Quellung reaction [04]
- It should be collected from site of infection. - It is also called as Neufeld's phenomenon as it
- Sputum, pus, CSF, blood, laryngeal swab was first described by Neufeld's.
and pleural exudates etc. - Principle: When capsulated organism
ii. Microscopy (Pneumococcus) in a specimen of sputum are
- Gram staining: Shows gram positive lancet exposed to their corresponding type specific sera
shaped diplococci and loop full of methylene blue solution, there is
iii. Culture capsular swelling. This phenomenon is called
- Blood agar quelling reaction.
- Chocolate agar – See above - Organism showing quellung reaction:
iv. Biochemical test – See above i. Pneumococcus
v. Optochin sensitivity test +ve ii. H. influenza
vi. Capsular swelling test (Quellung test)  +ve iii. Klebsiella
vii. Serological test iv. Pseudomonas
- Indirect hemagglutination test
Significance
- Indirect Fluorescent Antibody test
i. Used as a quick diagnostic test
- Counter immune electrophoresis
ii. Helps in determining the serotypes
- Radioimmunoasay (RIA)
Differential properties of pneumococcus and streptococcus viridians [10]
Features Pneumococcus Streptococcus viridians
1. Morphology
IV
- Shape - Lanceolate or flame shaped cocci - Round oval cocci
- Capsule - Capsulated - Non capsulated
- Arrangement - Diplococci - In chain
2. Cultural features
i. On solid medium - Dome shaped,  – hemolytic -  –hemolytic colonies
transparent, later gives draughtman
appearance
ii.On liquid media - Uniform turbidity - Granular turbidity
3. Biochemical features
i. Bile solubility - Positive - Negative
ii.Inulin fermentation - Positive - Negative
iii. Optochin sensitivity - Positive - Negative
4. Quellung reaction - Positive - Negative
5. Animal pathogenicity - Fatal infection - Non pathogenic
(Intraperitoneal inoculation
in mice)

Respi
Other streptococci Staphylococcus aureus

Group  streptococci Morphology:
Eg. Streptococcus agalactiae - Gram positive, nonsporing, non motile, usually
- It often colonise nasopharynx, oral cavity, non capsulated, aerobic and normally
intestinal tract. facultatively anaerobic cocci.
- It is an important causative agent of Bovine - Characteristically arranged in cluster.
mastitis - Cluster formation result from sequential
- Bacteraemia & pneumonia  most common division of bacteria in three perpendicular
manifestation caused by Gr. streptococci in planes (3 dimension)
1st week of life. Cultural characteristics
- Hydrolyse sodium hippurate and gives +ve - Grows readily in ordinary culture media under
cAMP reaction. aerobic or anaerobic condition at temp. 10–42°
Group C streptococci - Following culture media can be used
i. Nutrient agar
- It is distinguished biochemically in four species:
 Colony morphology: Round, smooth,
 Streptococcus equisimilis Most
raised, shiny opaque and often
commonly isolated from throat of human
pigmented.
 Streptococcus dysagalactiae
 Staphylococcal pigment is carotenoid
 Streptococcus zooepidemicus ii. Blood agar
Group F and G Streptococcus  Colony are similar to nutrient agar
- Commensal of throat of man, moneky.  Produce  hemolysis
Group D Streptococci iii. Liquid medium
- Heterogeneous group of streptococci  Uniform turbidity is produced IV
(enterococci) iv. Selective media
- Lancefield Gr. D. v. Mac-Conkey's agar:
Group R & S Streptococci  Pinhead size & pink to lactose
- S. Suis (serotype – 1)  posses S. antigen fermentation
vi. Mannitol salt agar
- S. Suis (serotype – 2)  Posses R. antigen
 Yellow color colonies
Viridans streptococci
Biochemical reaction
- Streptococcus mitior - S. aureus ferments glucose and mannitol
- S. sanguis producing acid but no gas.
- S. mutans - Are catalase positive
- S. salivarius - Most strains hydrolyse urea, reduce nitrates to
Properties: nitrites, liquefy gelatin and are MR, VP positive
but indole –Ve.
- Microaerophilic
Identification:
- Grow in protein rich medium
- The main distinctive diagnostic features of S.
- No group specific cell wall antigen
aureus are
Clinical disease:
i. Coagulase positive
i. Dental caries ii. Protein A
ii. Endocarditis

Microbiology
iii. Phosphates production in phenolphthalein  Test for coagulase is done by

diphosphate. i. Tube test
iv. Deoxyribosenuclease test +ve ii. Slide test
v. Ferment mannitol - Both coagulase positive and negative
vi. Reduction of potassium tellurite to staphylococci produce a no. of bacteriocins.
tellurium Pathogenesis [04]
Antigenic structure - Sources of infection: Nasal mucosa and skin of
i. Staphylococcal cell wall having antigenic patients or carrier
polysaccharides and protein peptidoglycan. - Portal of entry
ii. Protein A  Spread via sneezing
iii. Capsule: Bound coagulase lacking strain of S.  Surgical wounds
aureus possess capsule.
 Ingestion of pre formed toxin (food
iv. Techoic acid poisoning)
Determinates of pathogenicity Pathogenesis include
I. Exotoxins 
a. Pryogenic exotoxins  
- Enterotoxin A Staphylococcal infection Intoxication
 Responsible for food poisoning  
- Enterotoxin B Cocci enter via damaged Toxin cleaves the stratum
- Toxic shock syndrome toxin – 1 (TSST – 1) tissue (skin, mucosa) granulosum of epidermis
IV b. Leukocidin:  
- Kill polymorphonuclear WBC & macrophages. Gets adhered to cells/ECM Lysis of intercellular
c. Exofoliatins: and undergoes attachment between
- Split stratum corneum colonization cells.
- Types A  Coded by chromosomal gene  

Weaken the host defense Exfoliation dermatitis
- Type  Coded by plasmid
mechanism
II. Haemolysin (, ,  and )

III. Protein A
Tissue damage
- Surface protein
- Aids in septic shock syndrome Note:
IV. Enzymes i. Cytolytic toxins: Damage cells
- Coagulase, phosphatase, deoxyribonuclease, ii. TSST: Cause toxic shock syndrome
hyaluronidase, staphylokinase iii. Enterotoxins: Cause food poisoining
- Coagulase iv. Exfoliatins: Causes in staphylococcal scalded skin
 Enzyme like protein syndrome (SSS) and bullous formation (common in
 Causes clotting of human or rabbit plasma neonates and infant which is also called Reiter's
 Exist in two form (i) free (ii) Bound form syndromes- not in adult)

Respi
Clinical manifestation 5. Identification:

- Coagulase enhances virulence of S. aureus by a. Coagulase test positive
inhibiting phagocytosis and forming a wall of b. AST, biotyping, phage typing
fibrin clot around the lesion. Note: Staphylococcus intermedius
- Clinical manifestation can be categorized into: - The organism with characters intermediate between
S. aureus and epidermidis are called S. intermedius.
Infection
Coagulase - negative staphylococci
Superficial Deep Toxin - 1. S. epidermidis
infection infection mediated - Universal skin commensal
Skin: 1 Bone/joint 1 Toxic food - Act as opportunistic pathogen in prosthetic
- Folliculitis - Osteomyelitis poisoning device e.g. prosthetic heart valves etc, and in
- Boil - Septic arthritis 2 Skin immunocompromised patient.
- Impetigo 2 Respiratory tract exfoliation
- Pemphigus - Tonsilitis 3 Toxic shock 2. S. Saprophyticus
Neonatorum - Pharyngitis syndrome - Acts as opportunistic pathogen with defective
- Pneumonia (TSS) resistance.
- Lung abscess
- Empyema - Can be distinguished from S. epidermidis in its
3 Cardiac resistance to novobiocin
- Endocarditis
4 CNS
Haemophilus influenzae
- Meningitis Morphology
5 Blood - H. influenzae is small, gram negative, nonacid
- Septicemia
fast.
Laboratory diagnosis - Pleomorphic short rod (coccobacillus) IV
1. Specimen: - Non motile, nonsporing, aerobic and
- It is collected depending on nature of lesion, facultative anaerobe.
Pus - From suppurative lesions Note:
CSF - In meningitis - Long filamentous forms are predominant in CSF in
Blood - In septicemia meningitis
Sputum - In respiratory infection - Strains isolated from acute infection are of capsulated
Faeces /vomit - In from food poisoning Cultural characteristics
Urine - from UTI patient - Aerobic and facultative anaerobe
2. Microscopy - Culture media
- Gram staining of smear of pus and other i. Chocolate agar
specimen shows gram positive cocci in cluster.  H. influenzae grow well in this media.
3. Culture  Factor X and factor V (protoporphyrin
i. Blood agar and nicotinamide adenine dinucleotide
ii. Selective media with 7% sodium chloride respectively) are incorporated in media.
iii. Mannitol salt agar  Colony  most smooth and gray on
Colony morphology refer above overnight incubation at 37°c
4. Biochemical reaction: Refer above  Only freshly prepared medium supports H.
influenzae growth because V factor is labile.
Microbiology
ii. Special media Clinical manifestation

1. Levanthal agar - It is considered in two groups:
2. Filde's peptic digest agar i. Invasive infection
- Both are useful for capsule ii. Non invasive infection
demonstration i. Invasive infection
- H. influenzae show satellitism phenomenon on - Meningitis
regular blood agar medium with S. aureus. - Acute epiglottitis
Biochemical reaction - Bacteraemia
- Catalase positive - Suppurative lesions
- Oxidase positive - Pneumonia
- Ferment glucose and xylose with acid ii. Non- invasive infection
production. - Produces local infection:
- Reduces nitrate to nitrite  Otitis media
- Divided into (I – VII) biotype biochemically.  Sinusitis
Determinant of pathogenicity  Chronic obstructive airway disease
I. Capsular polysaccharide exacerbation.
- In H. influenzae (type b), capsular Laboratory diagnosis
polysaccharide consist of phosphoribosyl I. Specimen collection
ribotol phosphate (PRP). - Depending upon type of lesion
- Capsular PRP has antiphagocytic properties. - Nasopharyngeal swabs, pus, blood, CSF,
- Prime virulence factor of H influenza (Type b) sputum, throat swab
II. Membrane lipooligosaccharide II. Microscopy
IV - Gram staining: Gram -ve coccobaccili
- Responsible for bacterial attachment,
- Quellung reaction  For capsular
invasiveness, paralysis of ciliated respiratory 
epithelium. - Direct immunofluorescence  swelling
III. IgA protease III. Culture
- Inactivates secretory antibodies. - Refer above
IV. Biochemical Test
Pathogenesis
- Refer above
- Portal of entry: Respiratory tract, nasopharynx.
V. Serology
- Dissemination:
- Immunofluorescence
H. influenzae
- Direct precipitation
Penetrates nasopharyngeal epithelium - PCR.
HACEK Group bacteria
Disseminate
- Refer to a group of fastidious bacteria,
normally resident in mouth, but can sometimes
Either via blood or spread directly to causes severe infection such as endocarditis.
stream meninges - The group contain Haemophilus Sp.
(Parainfluenzae, aphrophilus, paraphrophilus),
Enzyme & toxin production
Actinobacillus, Actinomycetes, Cardio
Clinical manifestation bacterium hominis, Eikenella and kingella.

Respi
Satellitism [09] Cultural characteristics:

- Regular blood agar medium contains factor 'X' - Facultative anaerobe and aerobic
but inadequate concentration of factor 'V' due - Culture media: Enriched
to presence of intact red blood cells in i. Serum broth
medium.
 Show turbidity and pellicle formation
- Hence, colonies of H. influenzae in blood agar
ii. Loeffler's inspissated serum medium
are small.
 Colony: Small circular, granular, creamy
- Thus, enhancement of growth can be obtained
& glistening.
by supplementing medium with NAD or
iii. Blood tellurite agar medium
streaking an organism that secretes excess of
'V' factor at 37°C (Eg. Staph. aureus). This leads - Colony greyish or black colonies due to
to large and well developed colony of H. reduction of potassium tellurite to
influenzae around staphylococcus aureus, metallic tellurium.
whereas further away from S. aureus streak are Biochemical reaction
smaller. This phenomenon is called as - Catalase: +Ve
satellitism. - Oxidase: -Ve
Determinant of pathogenicity
- C. diphtheriae is not an invasive organism but
systemic manifestation results from exotoxin
production.
- Diphtheria toxin
 It is phage mediated produced exotoxin.
 Protein in nature IV
 Mol. wt.  62,000
 Structural similarity with cytochrome b.
Diptheria Toxin
Synthesis of Diphtheria toxin:
- Structural gene for toxin is part of genome of
Corynebacterium diphtheria
beta bacteriophage.
Morphology [05]
- Phage causes lysogenic conversion
- Thin, slender, gram-positive rods
- Toxin synthesized as a single polypeptide chain.
- Are clubbed shaped due to the presence of
- Low iron concentration induces synthesis.
metachromatic (volutin) granules at one or
Structure:
both ends.
Exotoxin consist of two moieties:
- Non capsulated, nonsporing, nonmotile and
non acid fast. i. Fraction: A  Active moiety
- Also called polar bodies as granules are often ii. Fraction: B  binding moiety that mediates
situated at the poles of bacilli. binding to a receptor.
- Are arranged in angular fashion like Chinese Pathogenesis [06]
letter or cuneiform arrangement due to - Source of infection: Carrier
incomplete separation of daughter cells after - Mode of transmission: Aerosolized
binary fission. nasopharyngeal secretion/skin contact

Microbiology
- Diphtheria is primarily a pediatric disease. 2. Advanced case:

Infection - Arrythmia
 - Dysphagia
  - Difficulties in vision
Local invasion of Toxin production
- Cervical lymphoid enlarged (bull neck)
tissue 
appearance
 Translation process
Colonization and is arrested 3. Complication
proliferation  i. Local
 Cell death - Laryngeal diphtheria
Formation of pseudo - Asphyxia
membrane
ii. Systemic

Extension into - Diphtheritic myocarditis
trachea/ larynx - Polyneuropathy
- Degenerative changes
Toxin has 'A' and 'B' components Laboratory diagnosis of diphtheria[05, 06, 08]
 1. Specimen collection
Toxin binds to target cell via binding of component 'B' - Two swabs are taken from site of lesion
to HB (Heparin binding) receptor - Swab from, throat, nose and larynx
 - One for smear examination and other for
Entire molecule is endocytosed and 'A' is released culture.
into cytoplasm 2. Microscopy
IV  - Gram staining: Gram +ve rod
Subunit A then catalyse adenosine diphosphate- - Neisser/Albert staining  Show typical Chinese
ribolysation of elongation factor 2 (EF-2), there is no – letter pattern.
movement of nascent peptide chains on ribosomes 3. Culture: swab inoculated on culture media
 (enriched)
Inactivation of elongation factor-(EF2) - Loeffler's serum slope
  Colony: Small circular, granular, moist,
Protein synthesis stops creamy glistening with irregular edges
 - Blood tellurite agar: Grey black colony due to
Cell death redn of potassium tellurite to tellurium.
Note: One molecule of toxin can kill one cell. - Serum broth: Show turbidity and pellicle
formation.
Clinical manifestation:
4. Biochemical test
1. Initial symptoms:
- Refer above
- Pharyngitis and laryngitis
5. Virulence test (Toxigencity)
- Pseudomembrane formation
- In vivo test
- Clinically, diphtheria is
 Animal inoculation test
i. Anterior nasal diphtheria (mild)
i. Subcutaneous test
ii. Pharyngeal diphtheria (Pseudomembrane)
ii. Intracutaneous test
iii. Nasopharyngeal diptheria
Respi
- In vitro test v. Parallel to this streak, a known toxigenic

i. Elek's agar -gel precipitation test strain of C. diphtheriae (positive control) is
ii. Tissue culture test streaked on one side of test strain and non-
toxigenic strain (negative control) on the
Elek's Agar gel precipitation test [07]
other side.
- This test was first described by Elek
vi. The plate is incubated at 37°C and
- Principle: It is based on the precipitation of
examined after 24 and 48 hrs.
antigen - antibody.
- Observation
- Procedure
 Toxin produced by bacterial growth diffuse
i. A rectangular filter paper strip is soaked in
in agar medium and produces line of
diphtheria antitoxin.
precipitation where it meets antitoxin
ii. It is placed on the surface of a serum agar molecules (dispersed from filter paper) in
plate containing 20% of horse serum while optimum concentration.
medium is still in fluid form.
- Application
iii. As the agar sets, the surface is dried.
 Virulence test in Diphtheria
iv. Testing strain is streaked across the plate at
right angles to the filter paper strip.
IV
Schick test Diphtheroids [06]

- Intradermal susceptibility test to demonstrate - C. xerosis
immunity to diphtheria (antitoxin C. hofmannii
demonstration) - Some corynebacteria normally present in skin
Other corynebacterium species and mucus membranes which resemble
- C. ulcerans  Bovine mastitis morphologically C. diphtheriae and they are
- C. PseudotuberculosisGranulomatous mistaken for diphtheria bacilli are called
lymphadenitis. diphtheroids.
- C. urealyticum  UTI - Diphtheroids are non pathogenic

Microbiology
Features C. Diphtheriae Diphtheroids Biochemical reaction

1. Morphology i. Weakly GPB i. Strongly GPB - B. Pertussis is biochemically inactive
ii. Meta- chromatic ii. Less/ absent - Oxidase "+ve"
granule more - Catalase  "+ve"
iii. Pleomorphism iii. Very little - Nitrate reduction –ve
present pleomorphism
present Virulence factors
iv. Chinese letter iv. No such - Two major virulence factors governed by two
pattern arrangement sets of gene.
arrangement i. Adhesins
2. Culture Grows on enriched Also grows on ii. Toxins
media ordinary media
Note: Genes are inactive at 25°C and active at 37°C.
3. Biochemical Ferment glucose only Ferment both
rex
n
and does not ferment glucose and I. Adhesins:
sucrose sucrose - Specific to Genus and species
4. Toxigenicity Toxic Non -toxic - Essential for pathogenesis of the organism and
Bordetella Pertussis is mediated by capsular fimbriae or
agglutinogen.
Morphology
- The most important adhesion is filamentous
- Small, nonmotile, nonsporing, ovoid, Gram -
haemagglutinin.
negative coccobacillus
Note: Out of total 14 agglutination factors, factor 7 is
- Strict aerobe and fastidious
found in all human species of Bordetella.
- Capsulated but become uncapsulated on
repeated cultivation. Uses
IV - Promotes virulence by helping bacteria to
- Bipolar metachromatic granules seen on
staining with toludine blue. attach to respiratory epithelial cell.
Cultural characteristics - Useful for serotyping & epidemiological typing.
- It is strict aerobic II. Toxins
- Optimum temperature is 35°C a. Pertussis toxin
- Does not grow on common laboratory media. b. Adenylate cyclase toxin
So, it is fastidious and thus requires selective c. Tracheal cytotoxin
media. d. Lethal toxin (Dermonecrotic toxin)
- Culture media e. Heat – Labile toxin
i. Bordet Gengou (Potato–blood–glycerol) e. endotoxin LPS
agar. f. Peractin
 Shows slow growth g. Filamentous hemagglutinin antigen (FHA)
 Colonies: a. Pertussis toxin [06]
 Small, smooth, opaque, grayish, - Is colonizing factor and exotoxin
white, refractile, resembling bisected - It is cell bound and extracellular
pearls or mercury drops. - Hexamer protein in mol.wt. 117,000.
ii. Charcoal–Blood agar medium - Has Antiphagocytic effect and causes
 Used for isolation (Primarily) lymphoid hyperplasia.

Respi
Structure: - Alters both AMI (Antiobody mediated

- It consists of two components, A & B immunity) and CMI (Cell mediated
bacterial exotoxin. immunity) so explain high frequency of
secondary infection in pertussis
i. Component 'A'
- Is an ADP ribosyl transferase Note:
Common secondary infections in pertussis are:
- Has enzymatic activity
- Pneumonia
ii. Component 'B'
- Otitis media
- Is five polypeptide subunits.
b. Adenylate cyclase toxin
- Responsible for binding to target cell
(Specific carbohydrates) on the cell - Invasive toxin
surface. - Activated by host cell calmodulin
Mechanism of action of pertussis toxin - Impairment of immune effector cells.
- Not produced by bordetella avium.
Pertussis toxin is transported from site of growth of
the Bordetella to susceptible cell and tissues of the c. Tracheal cytotoxin
host - Toxic for ciliated respiratory epithelium i.e.
stops cilia from beating.

- It is not protein and derived from
"A' subunit gains enzymatic activity after inserted
peptidoglycan.
into cytoplasm by direct entry and transfers the
- Stimulate release of cytokine. IL–1, and
ADP ribosyl moiety of NAD to the membrane bound
causes fever.
regulatory protein G. that normally inhibits the
d. Lethal toxin (Dermonecrotic toxin)
IV
eukaryotic adenylate cyclase
- Consist of 4 subunits

- Inflammation and local necrosis
"Gi" protein is inactivated and cannot perform its
normal function to inhibit adenylate cyclase. e. FHA
- Present on surface of the bacillus and

adhere to the cilia of respiratory epithelium
The conversion of ATP to cyclic AMP cannot be & RBC.
stopped and thus es in intracellular cAMP level f. Endotoxin (LPS):
 - Heat stable present in all bordetella
Disrupt cellular function, by decreasing phagocytic g. Peractin:
activity such as chemotaxis, engulfment, oxidative - Outer membrane protein
burst and bactericidal killing
Whooping cough
Systemic effects
 Also known as pertussis and is 100 days cough.
- Lymphocytosis
 Major cause of childhood fatality prior to
- Alteration of hormonal activities. vaccination.
- sed insulin production (hypoglycemia) Portal of entry
- Responsible for anaphylaxis - Air borne droplets

Microbiology
Pathogenesis Notes: Whoop

Entry into host by air - borne droplets - Characteristic audible sound at the end of
 paroxysm which occur upon rapid inspiration
  against a closed glottis
Adhesion of bacteria to Systemic effects:
Complication
ciliated epithelium of - Lymphocytosis
respiratory tract by - More common in infants and young children
- Hypoglycemia
filamentous and include
- Hormonal imbalance
haemaglutinin  Hypoxia
 (Histamine, serotonin
insulin)  Subconjunctival hemorrhage
Colonization and toxin
production - Macrophage infiltration  Apnea
  Pneumonia
Exert antiphagocytic  Seizures
activity, P cell inactivation
 Encephalopathy

Peribronchial and  Malnutrition
tracheobronchial lymph  Death in unvaccinated children
node hyperplasia
Laboratory diagnosis [05,06]

Necrosis, desquamation i. Clinical specimen
of epithelium - Nasopharyngal aspirate: Collected by
  Cough plate method
Diffuse
Bronchopneumonia  Postnasal swab (peroral)
 Pernasal swab
IV Clinical features
- Incubation period: 4 – 21 days ii. Transport media:
- Consist of 3 stages - 1% acid hydrolysed casein, amine charcoal
i. 1st stage – catarrhal stage (1 – 2 weeks) medium
ii. 2nd stage – paroxysmal stage (1 – 6 weeks) iii Microscopy
iii. 3rd stage – Convalescent stage (weeks – - Stained with toluidine blue shows bipolar
months) metachromatic bordet granules
Catarrhal Paroxysmal Convalescent iv. Culture:
- Last for 1 to 2 - Repetitive - Vomiting and Culture media:
weeks cough with whooping
a. Bordet gengou medium
whoops cough cease
first - Colony morphology (Refer above)
- Mild cough - Cough is dry -  in cough b. Charcoal blood agar

and harsh around the 6th v. Biochemical test:
week - Rise of antibody titre can be demonstrated in
- Low grade - Child vomit - Whooping paired serum sample by agglutination, gel
fever with the cough can last precipitation or complement fixation test.
coughing and upto several - Ag detection by direct fluorescent antibody.
appear to be weeks and can vi. Blood picture
strangling on lead to - Marked leukocytosis
the vomit pneumonia - Absolute lymphocytosis

Respi
Bacterial pneumonia - Culture

Pneumonia  Culture media:
- It is defined as acute inflammation of lung  Blood agar
parenchyma characterized by homogenous  Chocolate agar
consolidation of lung portion.  MacConkey agar
- Major bacterial pathogens includes  Anaerobic culture
i. Streptococcus pneumoniae Note: Blood culture is particularly done for
ii. Mycobacterium tuberculosis pneumococcal pneumonia
ii. Bordetella pertussis - Biochemical test
iv. Haemophilus influenza  Bile solubility
Laboratory diagnosis: [10, 11]  Inulin fermentation test
- Specimen collection  Optochin sensitivity test: Positive for
i. If patients who expectorate, sputum streptococcus pneumonia
specimen collected from is considered  Capsular swelling test
ideal - Serology
- Ideal sputum will have neutrophils  Ag detection by direct
and alveolar macrophage. immunofluorescesce test
ii. If a patient doesnot expectorate,  Antibody demonstration
following method is applied. - Total and differential leucocyte count
- Sputum production is induced by  Leucocytosis with a high percentage of
administrating nebulized hypertonic polymorphonuclear leucocytes
saline. (neutrophils) IV
- Percutaneous transtracheal aspiration - Radiology
of secretions.  Plain chest x–rays shows area of
- Fibreoptic bronchoscopy with consolidation
bronchoalveolar lavage and bruisings.
Organisms causing hospital associated
- Diagnostic open lung biopsy (only in
pneumonia (HAP) & Ventilator
selected patient as it carries high
associated pneumonia
risk).
 Hospital – acquired pneumonia/Nosocomial
- Percutaneous transthoracic needle
pneumonia refers to any pneumonia contracted
aspiration preferably under CT
by a patient in a hospital at least 48–72 hrs after
guidance.
being admitted.
iii. Other specimens like blood (for
 It is usually caused by a bacterial infection rather
pneumococcal culture), Pleural fluid can
than a virus.
be taken
 Nosocomial pneumonia includes
- Microscopy
i. Ventilator–associated pneumonia (VAP)  Sub
a. Gram staining
type of nosocomial pneumonia which occurs in
b. Ziehl–Neelsen staining. people who are receiving mechanical
 Helps in identification of bacterial ventilation after 48 to 72 hrs.
morphology ii. Postoperative pneumonia

Microbiology
iii. Health care–associated pneumonia: Criteria

pneumonia acquired by patients in health care i. Clinical: Fever, cough with purulent sputum.
facilities such as chronic care facilities, dialysis ii. Radiographic: New or progressive infiltrates
centers and infusion center.
iii. Blood cell count: Leukocytosis
 Nosocomial pneumonia is second most common
iv. Microbiologic:
infection (1st common is urinary tract infection)
- Gramstain, sputum culture, tracheal
 HAP typically lengthens a hospital stay by 1–2 wks.
aspirates, bronchial brushing, pleural
Etiologic agents fluid.
- Enterobacteriacea - Quantitative culture
- S. aureus
Ventilator associated pneumonia (VAP)
- P.aeruginosa
 The main difference between VAP and HAP is
- Acinetobacter sps.
return to dependence on expectorated sputum to
- Polymicrobial microbiologic diagnosis of VAP.
- Anaerobic bacteria  Etiologic agent
- Legionella
Streptococcus pneumoniae, Actinobacter spp.
- Aspergillus sps.
H. influenza, Enterobacter spp.
- Viral
Pseudomonas aeruginosa
- Fungal (<1%)
Klebsiella pneumonia.
Sign and symptom
 Pathogenic mechanism for ventilator associated
- New or progressive infiltrate on chest X–ray
pneumonia include.
with one of following:
i. Fever > 37.8°C (100°F) i. Oropharyngeal colonization with pathogenic
IV bacteria
ii. Increased tracheal secretions (purulent
sputum) ii. Elimination of normal flora
iii. Leucocytosis iii. Gastroesophageal reflux
iv. Poor oxygenation iv. Bacterial overgrowth of stomach
Risk factor Klebsiella pneumonia
- Mechanical ventilation Morphology
- Decreased filtration of inspired air - Gram negative bacilli, short plump.
- Neurologic diseases - Nomotile and capsulated
- Trauma, surgery, medication Culture:
- Poor –hand washing
i. MacCokey's agar
- Inadequate disinfection of respiratory device.
ii. Ordinary media
Pathogenesis
Biochemical:
- Microaspiration of upper airway secretions.
- Indole production (I) : –ve
- Macroaspiration of oesophageal or gastric
material is known to result in HAP. - Methyl red test (MR) : –ve
- Gram–negative bacilli infection. - Voges–prausker (VP): '+'
Diagnosis - Citrate (C) : '+'
- Difficult to diagnosis accurately @IMViC : – – + +

Respi
Virulence factor - Virus

i. Capsule i. RSV
ii. Plasmid exchange ii. Influenza A and B
iii. Antibiotic resistance iii. Para influenza
iv. Toxins iv. Adenovirus
Clinical syndrome v. SARS
i. Pneumonia vi. Measles
ii. UTI
Clinical Features
iii. Wound infection
- Chills, fever, lassitude, anorexia
iv. Epidemic diarrhoea
- Headache, confusion, sweating, muscle ache
Laboratory diagnosis
- Dyspnoea on exertion
- Specimen: Urine, pus, sputum, pleural fluid
- Cough (non productive), chest pain,
Microscopy:
hemoptysis
- Gram staining
- Rash (mycoplasma)
Culture:
i. MacConkey agar
Legionella pneumophila
ii. Blood agar General properties
Biochemical: - Live within amoeba in nature, fresh water,
- Refer above ponds, protected from chlorination
- Source: Cooling towers
Atypical pneumonia
 Atypical pneumonia is milder form of pneumonia
- Die at 60°C IV
that is caused by atypical pathogens. Morphology
 It is characterized by - Gram negative rod
- Walking pneumonia - Pleomorphic flagellated, nonsporing, non

capsulated
- Nonlobar pneumonia
- Best stained in tissue with Dieterler's silver
- Interstitial pneumonia
stain culture
- Extra pulmonary clinical features
- Fastidious bacteria, facultative intracellular
- Patients are more severe than they appear parasite.
- No leucocytosis - Cultured on buffered charcoal Yeast Extract
Causative pathogens (BCYE) Agar.
- Bacteria: Biochemical test
i. Legionella pneumophila - Oxidase positive
ii. Mycoplasma pneumonia - Catalase positive
iii. Chlamydia pneumonia - Produce –lactamase
iv. Chalamydia psittaci Determinant of pathogencity
v. Coxiella burnetti i. Adhesion: Mediated by outer membrane
vi. Francisella tularensis protein
Microbiology
ii. Ability to survive intracellular: the factor Clinical features:

responsible for resistance to intracellular killing - Predisposition
are: - Systemic features (GIT, CNS and Kidney
a. A peptide toxin involvement is common)
b. Catalase  detoxifies residual H2O2 - Cough (non productive)
- Chest pain, hemoptysis.
c. Phagolysosome formation inhibiting factor.
Laboratory Diagnosis
iii. Inhibition of CMI:
- Direct fluorescent antibody test
- By down–regulation of MHC–I & MHC II - Agglutination for bacterial Ag in urine
expression in phagolysosome in infected - DNA probes
macrophage - Antibody detection
iv. Toxin  Hemolysin, cytotoxin - Systemic evaluation
Clinical syndromes: Legionellosis Mycoplasma pneumonia
- Incubation period: 2 to 42 days General properties
- Mode of transmission: Air – borne aerosols - It is called as 'Eaton's agent'.
containing microorganism - It is pleomorphic.
- Spread from initial site takes place via - Takes Giemsa stain.
 Endobronchial - Cell wall–lack peptidoglycan.
- It is resistant to  lactamase.
 Haemtogenous
- Cell membrane consist of sterol compound
 Contagious invasion - Smallest known genome 816 kbs. like
- Legionellosis consist of two important mitochondria
syndrome: - It is an obligate parasites.
IV
i. Legionnaries' disease (pneumonia) Morphology
ii. Pontiac fever (Influenza like illness) - Gram negative bacteria with no true cell wall.
Legionnaries' disease - Non motile, non capsulated, non sporing,
aerobic organism.
- It is a pneumonic illness which begins with
abrupt prodrome of malaise, headache, Culture:
myalgia and weakness. - Facultative anaerobe
- Pathogenesis - It is cultured on Enriched media i.e. media
containing 20% serum and yeast extract.
Virulent strain of legionella (Sero group 1 and 6)
- Fried egg appearance.

- Biochemical: Produce H2O2.
Uncontrolled conditions allow bacteria to multiply
Clinical feature

- Symptomatic/Asymptomatic
Contaminated water is discharged into
- Gradual onset
atmosphere as aerosol
- Prodrome of 'flu-like' symptom.

- Other
Sufficient droplets are deeply inhaled by
susceptible people  Headache
  Malaise
Symptoms appear  Fever

Respi
Laboratory diagnosis Morphology of M. tuberculosis [05, 07]

1. Microscopy - Thin, straight or slightly curved.
- Not useful as bacteria do not possess cell wall. - Acid fast and gram positive.
2. Culture - Non motile, non sporing and non capsulated
- Culture takes long time (2-6 weeks) and is - With ZN stain: It looks curved rod with beaded
insensitive. or barred appearance.
- Also not available in most laboratories - Arranged either singly or in groups.
3. Serology: - Have thick, complex, lipid rich waxy cell wall.
i. Antigen: Detected by direct immunofluorescent Cultural characteristics
test, counter immunoelectrophoresis (CIEP) - Obligate aerobe, slow growing bacilli.
ii. Specific DNA: Defected by PCR - Culture media
iii. Antibody: Detected by CIEP, ELISA, indirect IFT A. Sold media
iv. Non specific test: a. Egg contain medium
 Streptococcus MG agglutination test i. LJ medium
 Cold agglutination test ii. Dorset egg medium
Chlamydia pneumoniae iii. Petragnani medium
General characters b. Blood containing medium
- Obligate intracellular organism with inclusion i. Tarshis medium
bodies. ii. Loeffler's serum slope
- Small, cocoid, gram negative bacteria that c. Potato based media pawlosky medium
resemble rickettsiae. B. Liquid media
Clinical Features - Used for mycobacterial Ag for vaccine
- Mostly asymptomatic preparation and antibiotic susceptibility IV
- Can cause prolonged, acute bronchitis with test.
productive cough. - Commonly used liquid media
- Hoarseness, headache is common features i. Soloac's solution
- Fever relatively uncommon ii. Dubos medium
- Sinusitis iii. Middlebrook's and Beck's medium
- Otitis media
Note:
- New onset asthma
L–J medium
- Myocarditis
- Used for routine culture
Mycobacterium Tuberculosis (TB) - Constituents:
 Tuberculosis is chronic infection, the majority of  Coagulated whole egg
which is caused by M. tuberculosis and also  Asparagines
caused by M. bovis, which is acquired by drinking
 Malachite green – selective agent
unpasteurized milk from infected cows.
 Mineral salts
 M. tuberculosis complex includes
 Glycerol/sodium pyruvate
i. M. tuberculosis – Human type
- Colonies: Rough, Tough and Buff colony.
ii. M. bovis – bovine type  Rough: due to dry raised with wrinkled surface.
iii. M. africanum  Tough: Tenacious and not easily emulsified.
iv. M. microti  Buff: Pale yellow color.

Microbiology
Biochemical reaction Activated macrophages

i. Niacin test positive. 
ii. Catalase – peroxidase activity  +ve  
- Formation of TNF, Chemokine
iii. Amidase test +ve
phagolysosome - Requirement of
iv. Neutral red test +ve
-  nitric oxide + free monocyte that
v. Nitrate reduction test: +ve differentiate into
radical
vi. Aryl sulphate test: –ve epithelioid from

Determinant of pathogencity
 Kills and digest tubercle - Accompanied by tissue
i. Cording factor (Glycolipid derivative of mycolic
bacilli without causing destruction due to
acids)
further tissue caseation and
ii. Cell surface glycolipid destruction cavitation
iii. Antibacterial resistance due to mutation 
Pathogenesis of tuberculosis [03] Epitheloid glanuloma
- Mode of transmission Types of TB
a. Droplet nuclei - On the basis of duration of infection, it is
b. Respiratory droplet mainly divided into two type:
- M. tuberculosis, a intracellular organism that I. Primary TB
donot produce exotoxin or endotoxin however - When a healthy person get infected 1st time
damage occur due to hypersensitization of with M tuberculosis.
immune system. - This is characterized by Ghon focus and Ghon
complex.
Inhalation of droplet nuclei having M. tuberculosis
- Ghon focus consist of foci of tuberculus

pneumonia in the lung parenchyma.
IV Engulfed by alveolar macrophage by blocking
- Ghon complex: The Ghon focus along with
fusion of phagosome and lysosome (This is due
involvement of hilar lymph node, is called
to sulfatides that impairs Ca2+/Calmodulin
pathway) Ghon complex/primary complex.
 II. Secondary TB
Multiplication of bacteria in macrophage after 3 - This may develop either by
week i. Progression of primary infection or
 ii. Reactivation of quiescent of primary
Release of chemoattractant infection (Latent infection)
- Risk factor:

i. Poor socioeconomic condition
Recruitment of immature monocyte desired
macrophage and dendritic cells ii. Poverty
iii. Malnutrition

- Entire pathogenesis consists of 5 stages
Also recruitment of Antigen presenting cell, thus
presentation of mycobacterial Antigen to T i. Stage I
lymphocyte in lymph node  Inhalation of Aerosolized droplet
  Smaller droplet reach alveoli
Activation T cell ii. Stage II
IL-12  7–21 days post infection
TH1 (active)  Unrestricted multiplication of bacilli.
 Gama–IFN  Macrophage brust and release of bacilli.

Respi
iii. Stage III - Fluorscent staining

 Lymphocytes begin to infliltrate  Fluorescent stain such as auramine–
 T cell recognition and its activation. rhodamine is used
 Production of IFN–γ and macrophage  Bacilli appear bright rods against dark
activation background under ultraviolet light.
 Vigorous CMI response  Used for rapid and mass screening.
 Granuloma/ Tubercle formation begins III. Culture:
Solid media
vi. Stage IV
a. Lowstein and Jensen medium
 Replication of bacilli in poorly activated
b. Dorset egg medium
macrophage at periphery of tubercle.
c. Pawlowsky
 Invasion of bronchus
Liquid medium
v. Stage V:
a. Dubos medium
 Liquefaction of caseous center b. Middle brook
 Escape of tubercle Colony morphologies:
 Cavitation of tubercle. On solid media
 Dissemination of bacilli throughout a. LJ medium: Refer above
body. On liquid media
Laboratory diagnosis [03, 05, 07]  Growth begins at the bottom
I. Specimen:  A prominent surface pellicle which
- Sputum, pleural fluid in cases of tubercular may extend above medium.
pleural effusion IV. Biochemical test
 Sputum: - Refer above IV
 3 samples VI. Nuclei acid amplification
- Polymerase chain reaction (PCR)
 First on the spot, second early morning
sample and third on the spot next day. - Ligase chain reaction (LCR)
VII. Animal inoculation test
 Concentration of sputum smear:
- In guinea pigs
 By petroff's method
VIII. Mantoux test (PPD skin test)
 N-acetyl-L-cysteine method
- Positive result indicates infection (initial) but
 Immunomagnetic separation of M-TB not necessarily active disease.
Petroff's method Mantoux test [012 PBQs]
 Sputum is mixed with 4% NaOH and Principle:
incubated at 37°C for 20 minutes, then
- This is tuberculin test based on delayed or type
centrifuged at 300 rpm for 20 minutes.
IV hypersensitivity reaction.
Finally sediment is neutralized with
Method:
N/10 HCl and used for smear culture
- 0.1ml of PPD (Purified protein derivative) is
and animal inoculation.
injected intradermaly counting 5 tuberculin
II. Microscopy
units in flexor aspect of fore arm.
- Zeihl Neelson staining
Result:
 Acid test bacilli appear at pink brightened
- Site of injection is examined after 48–72 hrs for
rods.
zone of indurations.
Microbiology
Classification of tuberculin reaction False negative

1. 5-10mm – weak reaction - Technical flaws
Positive:  Inadvertent subcutaneous injection
- HIV-positive person  Improper storage, insufficient dose
- Patients with organ transplants and other - Severe TB disease
immunosuppressed patients - HIV (if CD4 count < 200 cells/ml)
- Recent contacts of TB case - Renal failure
- Persons with nodular or fibrotic changes on - Imunosuppressive drugs
chest x-ray consistent with old healed TB - Diabetes
2. 10–15 mm – moderate reaction - Sarcoidosis
Positive: - Extremes of age -old age or newborn infants
- Residents and employees of high-risk Limitations
congregate settings
- Not very useful in this part of world because
 Prisons
a. BCG vaccination
 Nursing homes
b. Infection is endemic in these area. Positive
 Hospitals results does not always indicate recent
 Homeless shelters infection
- Persons with clinical conditions that place c. Requires multiple visit–affecting the compliance
them at high risk
Mycobacteria other than tuberculosis
 Diabetes
(MOTT)
 Prolonged corticosteroid therapy
 All mycobacteria species except those that cause
 Leukemia
IV  End-stage renal disease
TB and leprosy are called MOTT.
 Other names: Atypical environmental
 Malabsorption syndromes
opportunistic mycobacteria.
 Low body weight
 General character [03]
- Mycobacteriology lab personnel
- Lives in water soil, food and animals.
- Injection drug users
- Aerophilic bacteria
- Children less than 4 years of age, or
children and adolescents exposed to adults - Temperature growth range: 28–45°C
in high-risk categories - Relatively resistant to chlorination & ozonization.
3. 15 mm or more – strong reaction  Classification [03]
Positive: - Classified by Runyon in 1954 into 4 group.
 Persons with no known risk factors for - Runyon classification is based on
TB 1. Rate of growth
 A tuberculin test conversion is defined as 2. Production of yellow pigment: whether this
an increase of 10 mm or more within a pigment was produced in dark or only after
2-year period, regardless of age – is exposure to light.
considered positive i. Photochromogens
False positive ii. Scotochromogens
- Previous administration of BCG vaccine iii. Nonchromogens
iv. Rapid Growers
- Infection with nontuberculous mycobacteria

Respi
Runyon's group Rate of growth Pigment produced Organism

Group I Photochromogens Slow growing Produce yellow-orange pigment in light M. Kansasii
M marinum
Group II Scotochromogens Slow growing Produce yellow– orange – red pigment in M. Scrofulaceum
light or dark M. Gordonae
M. Szulgai
Group III Non chromogens Slow growing Do not produce pigment M.avium-intracellulare
M. Xenopi
M. terrae
M. Ulcerans
Rapid grower Rapid growing Do not produce pigment M. Fortuitum
M. peregrinum
M. chelonae
M. abscessus
Species Diseases produced by them 5. Laboratory diagnosis of fungal chest infection.

i. M. kansasii - Pulmonary disease [10 Jan]
6. Candida albicans [03 June]
ii. M. marinum - Swimming pool granuloma
7. Dimorphic fungi [05 June]
iii. M. scrofulaceum - Lymphadenitis in children
8. Cryptococcus neoformans [06 Dec, 08 Jan]
iv. M. ulcerans - Buruli ulcer [KU-2012]
v. M. chelonoe - Superficial and systemic Fungal pneumonia [10]
disease - It is defined as acute infection of lung IV
Risk Factors: parenchyma caused by fungal pathogens.
- Causative pathogens of fungal pneumonia:
- Immunosuppression
i. Aspergillus fumigatus
- Aging
ii. Pneumocystis jirovecii
-  BCG vaccination iii. Candida albicans
- Cystic fibrosis iv. Coccidioides immitis
v. Histoplasma capsulatum
FUNGI AS RESPIRATORY Histoplasma Capsulatum
PATHOGENS
Morphology [03, 07]
Past Questions: - H. Capsulatum is dimorphic fungus
1. Histoplasma capsulatum - Growth:
(3) [08 July, 07 June, 03 Dec]  Grow as separate mycelium in soil and
artificial culture at 25–30°C
2. Respiratory dimorphic fungal pathogen.
 As intracellular yeast in animal tissues
(3) [09 July] - In culture, mycelia phase  Produces 2 types
3. Morphology and lab diagnosis of Cryptococcus. of unicellular asexual spores.
(4) [02 June] i. Large round tuberculate  Macroconidia
(8–14 m)
4. Laboratory diagnosis of a cryptococcosis.
ii. Smaller elliptical microconidia (2–4m
(3) [02 Dec] diameters)
Microbiology
Note: - Clinical outcomes resemble pulmonary

Yeast phase can also be grown in blood agar at 37°C. tuberculosis.
- But chest radiograph shows bilateral
Pathogenesis
interstitial infiltrates (absent in TB) and later
- H. capsulatum  Responsible for disease of gets calcified.
reticuloendothelial system & respiratory
III. Disseminated disease
system.
- Occurs occasionally
- Mode of transmission: Inhalation of organism,
conidia or hyphae fragments. - An acute progressive form of the disease with
Inhalation of organism widespread involvement of reticuloendothelial
system.

- Usually, occurs in old patients and infant with
Taken up by alveolar macrophages
underlying disease (Malignancy) or immune

suppression.
Undergoes survival and proliferation as the H.
IV. Ocular histoplasmosis
capsulatum behaves as facultative intracellular
organism & causes infection - Seen in endemic area
 - Is hypersensitivity reaction which is not a true
  retinal infection by fungus.
The infection may remain May spread to other Laboratory diagnosis [07, 08]
asymptomatic (In majority organ of
I. Specimen:
of case) reticuloendothelial cells
(like bone marrow, liver & - Sputum
Spleen) - Biopsy material from pulmonary diseases.
IV  - Bone marrow aspirates
In the presence of high - Biopsy of Lymph nodes.
load of fungal spore
II. Microscopy
exposure or underlying
disease or in - On staining the smear of sputum or pus with
Immunocompromised Giemsa or wright stain, H. capsulatum appears
state as small, oval yeast cells packed within
 macrophages or monocytes.
Occurrence of clinical III. Culture
manifestations - Culture media
Clinical Manifestations: i. Sabouraud's dextrose agar
I. Acute pulmonary histoplasmosis ii. Brain heart infusion (BHI) having
- Is acute influenza like, self-limited illness with cycloheximine & chloramphenicol.
fever and non-productive cough. - Colony:
II. Chronic pulmonary disease i. White cottony mycelium, aerial hyphae
- Mostly occurs in adult Albino type when incubated at 25°C.
- Manifested by cavitiy formation in lung either ii. Brown type: Flat, dark brown color at 25°.
due to primary lesions or reactivation of - When cultured at 37°C, yeast forms appears,
apparently healed old lesion. that produces Whitish tan colonies.

Respi
IV. Histoplasmin skin test Habitat:

- Similar to tuberculin test. - Inhabitant of intestine as normal flora (40–
- Histoplasmin is a culture filtrate antigen of 80%). Also can be isolated from oral cavity,
mycelial phase of H. Capsulatum. vagina, rectal area of healthy people.
- Positive test: Indicates past or present Pathogenesis:
infection but do not differentiate active & past - Candidiasis is an opportunistic endogenous
infection. infection.
V. Serological test - Predisposing factors:
- Complement fixation (CFT) test  Diabetes mellitus
- Precipitation test
 Immunodeficiency
- Latex agglutination tests
 Malignancy
Note:
 Prolonged administration of antibiotics
i. Antigen used is histoplasmin.
 Intravenous catheters
ii. CFT is positive in about 95% case.  Pre-mature babies.
VI. Histopathology test Clinical manifestation
- On staining tissue with H & E, and Giemsa stain - Lesion produced by C. albicans can be
 H. Capsulatum (yeast form) can be seen categorized into two group:
within mononuclear cells. a. Superficial lesion
Treatment b. Systemic candidiasis
i. DOC is Amphotericin  a. Superficial Lesion
1. Mucosa:
ii. Mild pulmonary histoplasmosis: Ketoconazole IV
a. Oral thrush: Infection of mucous
Candida albicans
membrane of mouth
 Candida albicans is responsible for most (90%) of b. Vulvo-vaginitis
human mycotic infection.
c. Balanitis
 Infection caused by C. albicans is called 2. Skin:
candidiasis/moniliasis where there may be
- Infection of skin usually occur in sites
superficial or deep infection.
that may become abnormally moist and
 C. albicans has two serotypes on the basis of warm like, axilla, groin, perineum, sub
differences between mannose component of the mammary folds.
cell wall. 3. Nail:
Morphology - Infection of finger, webs, nail fold and
- Spherical or ovoid budding cells of yeast or Y nails occur as reddened swelling
form. resembling pyogenic paronychia.
- Elongated filamentous cells, joined end to end, - Most often infection is associated with
resembling hyphae (pseudohyphae), producing frequent immersion of hands and feet in
buds blastospores in tissue and culture. water.
4. Chronic mucocutaneous candidiasis:
Note: C. glabrata never forms pseudo mycelium.
- Sign of deficient CMI.

Microbiology
b. Systemic candidiasis  When portion of colony is incubated

- Urinary tract infection with normal human serum at 37°C for 2
- Gastrointestinal candidiasis: It is frequent to 4 hrs and observed as wet
sequel to oral antibiotic therapy and preparation, it shows long tube like
present as diarrhea. projection extending from yeast cell K/A
- Pulmonary candidiasis germ tube.
- Endocarditis 4. Biochemical test

- Meningitis - Sugar assimilation and fermentation
- Septicemia - Ferments glucose, maltose but not sucrose

and lactose.
Laboratory diagnosis [03]
- Assimilates sucrose, lactose, galactose,
1. Specimen collection:
cellobiose, etc.
- Specimens are collected on the basis of site
5. Serology
involved.
- Confirms two serotype of C. albicans which
 Scraping from lesion of skin
is serotype A and serotype .
 Nail, mucus membranes.
- Antigen detection: ELISA, RIA
 Sputum culture, lung biopsy 6. Skin test
2. Microscopy: - Candida test shows universal positivity and
i. Potassium hydroxide (KOH) Preparation is useful as an indicator of competent CMI.
 Wet mount preparation Aspergillus fumigatus
 Observation of yeast, budding and
 Aspergillus fumigatus is mainly an opportunistic
pseudohyphae.
pathogen.
IV ii. Gram stain
Morphology
 Show gram positive budding yeast and
- KOH mount show non pigment mycelium with
pseudohyphae.
characteristic dichotomous branching and
iii. Histopathological sections: irregular outline.
 The slide is stained with H and E, and Pathogenesis
PAS stain and observed for yeast,
- Aspergillosis is caused by inhalation of
budding pseudohyphae.
Aspergillus conidia or mycelia fragments.
3. Cultural characteristics
- Aspergillosis develops when host defense is
i. Routine media compromised & in anticancer therapy.
ii. Sheep blood agar: Colony – white with foot 1. Respiratory aspergillosis
like extension from margins.
2. Disseminated (invasive) aspergillosis
iii. Sabouraud's dextrose agar: Colonies are
3. Superficial infection
smooth, creamy white with a yeast odour.
1. Pulmonary aspergillosis (Respiratory aspergillosis)
iv. Corn meal agar: Used for species
identification. a. Aspergillus asthma
v. Nickerson's medium: Glistening black b. Aspergilloma
colonies. c. Allergic bronchopulmonary aspergillosis
vi. Germ tube formation: d. Chronic necrotizing aspergillosis
 Also K/A Reynolds-Braude phenomenon e. Invasive pulmonary aspergillosis

Respi
a. Aspergillus asthma II. Microscopy

 It is hypersensitivity state due to a. KOH mount:
aspergilla.  KOH mount of sputum shows non
b. Aspergilloma pigmented septate mycelium of fungus
with characteristic dichotomous
 Called fungus ball
branching and irregular outline.
 Develops in preexisting lung cavity
b. H & E and PAS staining of biopsy show
c. Chronic necrotizing aspergillosis (= characteristic hyphae.
semiinvasive aspergillosis) III. Culture
 Develop in moderately immune - Sabroud Dextrose agar: Without
compromised hosts. cycloheximide and incubated at 25°C.
 CXR shows infiltrate in upper lobes or  Colony: A velvety to powdery surface
superior segment of lower lobes. and cloudy.
d. Invasive pulmonary aspergillosis  A. fumigateshas green colour colonies.
 Develops in hematologic malignancy, IV. Skin test:

solid organ transplantation and HIV - Intradermal skin test to Aspergillus antigen
extract is used for patients with suspected
 Present with pleuritic chest pain and
allergic bronchopulmonary aspergillosis,
hemoptysis (from pulmonary infraction)
atopic dermatitis.
e. Broncho pulmonary aspergillosis
V. Serology
 Fungus grow in lumen of bronchioles - Serum antibodies to A. fumigatus can be
 Produces plug of mycelium and mucus determined by precipitation or IV
that occlude the lumen. immunodiffusion test.
2. Disseminated aspergillosis Cryptococcus neoformans
- Disseminates to brain, kidney, heart and other  Cryptococcus neoformans is capsulated which
organ. causes subacute or chronic infection called
3. Superficial infection: cryptococcosis.
- A flavus and A.fumigatus colonise in part of Morphology [09]
nasal sinuses (sinusitis), external ear - Capsulated yeast
(otomycosis) - Spherical budding cell excluding the capsule.
Laboratory diagnosis - Has prominent polysaccharide capsule.
1. Radiograph - Reproduces by budding.
2. Clinical history Note:
3. Microbiologic diagnosis as follows: Cryptococcus is fungus with capsule not
histoplasma capsulatum [MCQs 2012 KU]
I. Specimen collection
- Sputum Habitat
- Bronchoalveolar lavage - Found in environment especially dust
containing excreta of person.
- Biopsy
- In flowers of Eucalyptus camaldulensis.

Microbiology
Antigenicity: Laboratory diagnosis [02, 06, 08, 09]

- Antigenically, C. neoformans are of four types I. Specimens:
(A, B, C, D) - CSF, sputum, biopsy material and urine.
i. Infection due to serotype A and D occur in II. Microscopy
birds - Negative stain by using indian ink/nigrosin
ii. Serotypes B & C are found in Eucalyptus - Gram stain: Show gram positive budding
camaldulensis. yeast cells.
- Calcofluor white: Also can be used to
Note: Birds are not infected due to high body
demonstrate fungus by fluorescent
temperature.
microscope.
Pathogenesis III. Culture characteristics
- Determinant of pathogenecity - Culture media
i. Antiphagocytic polysaccharide capsule:  SDA
major virulence factor.  Blood agar
ii. Melanin: produced by fungus is deposited  Nigar seed agar, Birdseed agar
in cell wall there by protect itself from - Two slants of SDA are inoculated and
oxidant released by phagocytic cells. incubated at 37°C and 25°C and observed
Mode of transmission for period of 4 week.
- Infection occurs from the environment usually - Colony morphology (on SDA): Highly
mucoid, creamy colonies are observed.
by inhalation, specially of dust containing
excreta of pigeons. IV. Biochemical tests
- Urease: +ve
IV Clinical manifestation
- Assimilation of nitrate
- Cryptococcosis is usually a primary and
- Assimilation of inositol
symptomless granuloma of the lung.
V. Serology
- Form of crytococcosis
a. Detection of Ag: Later agglutination test
1. Pulmonary form
most useful in detection of cryptococcal
 Respiratory route act as portal of entry polysaccharide antigen.
for Cryptococci.
b. Serum antibodies can be detected by
 Particularly occur in immunocompromised agglutination and immunofluorescence.
host.
VI. Histopathological examination
 Reactivation of old healed lesion may
- Section stained with H & E, PAS shows
occur.
budding yeast cells.
2. Crytococcal meningitis
Laboratory diagnosis of fungal pneumonia
 Found in small proportion
I. Specimen collection
 Hematogenous spread results in
- Sputum
subacute or chronic meningitis or
- Bronchial lavage
meningoencephalitis.
- Biopsy material
3. Cutaneous form
- Aspirated fluid
 Skin, LN are involved
Respi
II. Microscopy Classification:

a. KOH mount of sputum Family: Orthomyxoviridae
- Non pigmented septate mycelium Genus:
(Aspergillus sps) i. Influenza virus A, B
- Yeast cells (Cryptococcus)
- Influenza A virus
- Budding yeast cells (candida)
b. Giemsa stain - Influenza B virus
- Small oval yeast cells within macrophages ii. Influenza virus C
(Histoplasma capsulatum) - Influenza C virus
III. Culture
- Sabouraud dextrose agar Viral morphology (of influenza virus)[02, 05]
IV. Serology - Spherical, filamentous
- Antigen detection by - Capsid: helical
a. Latex agglutination
- Genome: '–ve' sense, single stranded RNA with
b. ELISA
7 or 8 segment.
V. Molecular method: PCR
VI. Chest X-ray: - Presence of:
- Suggestive of cavitation I. A viral RNA dependent RNA
- Consolidation polymerasefor infectivity.
- Lung nodules II. Envelope nucleocapsid with two layers:
a. Outer layer Lipid layer (derived from
VIRUSES AS RESPIRATORY
host cells) [MCQs 012 KU]
PATHOGENS (RESPIRATORY
VIROLOGY) b. Inner layer protein layer
IV
Past Questions: III. Envelope glycoproteins
1. Short notes on:  Haemagglutinin (H)triangular in cross

section.
a. Structure of Influenza virus (2) [05 June, 02 June]
b. Antigenic shift and drift of influenza virus  Neuraminidase (N)Mushroom shaped
(3) [2012] & less in number.
c. Respiratory viruses [08 July]
d. Viruses causing respiratory infections [05 June]
e. Respiratory syncytial virus [06 Dec., 03 June]
f. Influenza virus [07 July, 03 Dec]
Orthomyxo viruses
 Orthomyxoviruses are spherical or filamentous
with single stranded and segmented RNA genome.
 Orthomyxo = Orthom+ Myxa
"
(free) "
(Mucin)
 Pleomorphic
 Influenza types A, B & C and Thogoto virus
 Cause Febrile, respiratory illness with systemic
symptoms.

Microbiology
IV. Antigens - Complication:

Type specific antigen Subtype specific  Pulmonary complication
antigens  Primary influenza pneumonia
- Nucleoprotein (RNP) - Hemagglutinin: H1– H13
 Secondary bacterial infection
-Matrix protein (M1) -Neuraminidase: N1 – N9
 Nonpulmonary complication
Antigenic variation [KU 2012]  Myositis
i. Antigenic shift  Cardiac complication
- Undergoes reassortment  Encephalopathy
- Results in changes of H & N antigen  Reyes syndrome
- Major change Features of influenza A, B & C virus
- Occur with influenza A only Influenza A virus Influenza B Influenza C
- Pandemic & epidemic virus virus
ii. Antigenic drift - Flu symptoms - Less severe - Mild coryza
- Change in the amino acid sequence of the H – - GI symptom: - Epidemic - Sporadic URT
antigen. Vomiting form illness
- Occurs in both influenza A & B - More in
adolescent
- Periodic epidemics
and school
- Minor Change age children
Mode of transmission: - Acute Laryngo- - GI symptom: - Rarely
- Airborne respiratory droplets (100,000 – tracheobronchi Common associated
IV 1,000,000 virions/Droplet) tis (in <1 yr old) with severe
- Incubation period: 18 – 72 hrs LRT illness
- Site of infection: Epithelial cells of respiratory Laboratory diagnosis:

tract. I. Specimen:
Pathogenesis - Throat swab, throat gargle
Entry of influenza virus via respiratory tract II. Culture:
 a. Amniotic cavity of 11–13 days old eggs
Viral neuraminidase causes mucosal destruction  After incubation at 35°C for 3 days,
and desquamation amniotic fluids are tested for
 hemagglutinin using guinea pig & fowl
Viral attachment to mucosal epithelial cells & cells.
attack ciliated cell b. Primary monkey kidney or human embryo
 kidney
Causes acute inflammation, edema  Virus growth can be identified by
 hemadsorption with human ‘O’ blood
group or guinea pig erythrocytes.
Clinical symptom
 Rapid results can be obtained by
Clinical Features
demonstrating virus antigen in infected
- Chills, headache, dry cough, fever, muscle
cell cultures by immunofluroescence.
ache, malaise, anorexia.

Respi
III. Serology Parainfluenza viruses

a. Ag demonstration - Parainfluenza viruses are ubiquitous and cause
 Immunofluorescence common respiratory illness of varying severity
in all age group.
 ELISA
- Transmission: droplet
 RIA
- Type 1, 2 and 3 are particularly considered
b. Four fold or greater rise of antibody titer in major pathogens of severe respiratory tract
paired sera can be detected by infection in infants an young children.
 Complement fixation test - But type 4 does not cause severe disease even
 Heamagglutination inhibition test on primary infection.
Clinical manifestations:
Vaccine
- Incubation period 2 to 6 days.
- Because of rapid change of antigens, vaccines
- Primary infection in young children usually
are less successful
result in
- Trivalent influenza vaccine (TIV): Contain
 Rhinits
purified and inactivated material from three
 Pharyngitis
viral strains.
- However, primary infection caused by
Paramyxo viruses serotypes 1, 2 and 3 may cause serious illness.
I. General Properties  Laryngotracheobronchitis
1. Shape and size:  Bronchiolitis & pneumonia mainly type 3
- Roughly spherical enveloped particles of (age < 6 month)
heterogeneous sizes. Laboratory diagnosis
2. Genome: I. Isolation
IV
- ssRNA as a single piece. Specimen: Mouth wash, throat swabs
3. Glycoprotein: - Sample collected from posterior pharynx or
- Neuraminidase, haemagglutinins nasopharynx yield better result.
4. Syncytial formation: - The sample thus collected is inoculated in
monkey tissue culture.
5. Sensitive to lipid solvents
II. Identification
II Classification
- Virus in infected cell is identified by
- Family paramyxoviridae
Haemadsorption with guinea pig red cells.
Genus Human Pathogen III. Direct demonstration:
- Morbillivirus Measles virus - Viral antigens can be demonstrated by
ELISA, immunofluorescence
- Paramyxovirus Parainfluenza viruses 1
IV. Serology
to 4 mumps virus
- Detection of rising antibody titer by ELISA
- Pneumovirus Respiratory syncytial
- CFT is helpful in diagnosis
virus
Respiratory syncytial virus (RSV)
- All members initiate respiratory tract infection
- It belongs to genus pneumovirus of
but parainfluenza and RSV remain limited to paramyxoviridae family
respiratory epithelium.
Microbiology
- Morphology - Laboratory diagnosis

 Size: 150–300 nm I. Isolation
 Diameter of nucleocapsid: 13 nm  Specimen: Nasopharyngeal secretion or
nasal washing.
 Negative sense and ssRNA
 Culture: Sample is inoculated in Human
 No haemagglutinin or neuraminidase (HeLa, HEP – 2) or monkey cell cultures.
 Contain G (Glycoprotein) and F (Fusion) that II. Direct demonstration
induces fusion of cells in to large  Rapid diagnosis of RSV infection can be
multinucleated syncytia. done by immunofluorescence.
- Pathogenesis III. Serology
 Incubation period: 4–6 days  Not much helpful
 Severe infant infection  Rise in Ab titre in serum is detected by
 Mode of transmission: ELISA, CFT.
Difference between the ortho &
 Large droplets
paramyxoviruses
 Contaminated hands and surface
Features Orthomyxo Paramyxo
 Nosocomial infection viruses viruses
Entry of virus into respiratory tract 1. Size of virion - 80–120 nm - 100–300 nm
 2. Shape - Spherical, - Pleomorphic
Virus undergoes multiplication initially in epithelial filamentous
cell of nasopharynx 3. Genome - Segmented, 8 - Single piece
pieces of of ssRNA
IV 
ssRNA
Viruses then spread to lower respiratory tract via
4. Nucleocapsid - 9nm - 18 nm
secretion (diameter)
 5. Site of - Nucleus - Cytoplasm
Clinical symptom ribonucleo
- Clinical manifestation protein
synthesis
1. Lower respiratory tract infection
6. genetic - Common - Absent
 Bronchitis (60% by RSV) recombinatio
 Pneumonitis (30% by RSV) n
 Above manifestation occur in infant 7. DNA- - Necessary for - Not required
dependent multi-
between 1 to 6 month of age when
RNA synthesis plication
maternal antibody level falls.
8. Rate of - High - Low
2. Upper respiratory tract infection antigenic
 Asymptomatic or febrile rhinitis or change
common cold 9. Hemolysin - Absent - Present
3. Complications 10. Diseases - Influenza - Para influenza
types A, B & C 1–4 infection,
 Otitis media
RSV diseases
 Myocarditis
Respi
Adenovirus II. Incubation period: 5–7 days

Classification III. Infections type: Serotype 1 to 7 (mostly)
- Family: Adenoviridae IV. Type of infection: Produces 3 types of infection
- Genus a. Lytic infection
i. Aviadenovirus  After infection, virus replicates actively
ii. Mastadenovirus and progeny virions are released by
- Species (sub–genera) 6, A  F: Divided on the rupture of cell membrane causing cell to
basis of: die.
 Their haemagglutination of red cells of b. Latent infection
Monkey, Rat
 The virus remain latent (types 1, 2, 5 & 9)
 Guanine and Cytosine content of DNA and
in lymphoid tissue (adenoid tissue tonsils)
oncogenic potential
- Species B has been divided into B1and B2  Can be reactivated in immune
subspecies suppressed state
- Total human adenovirus serotypes: 47 c. Transforming infection
- All adenovirus share a common complement  Transform cells by integration of viral
fixing antigen. DNA in host DNA, however
Morphology transformation of human cells not been
- Adenovirus is naked. observed.
- 70–90 nm in diameter with an icosahedral Clinical manifestation
capsid
i. Acute febrile pharyngitis and pharyngo –
- dsDNA
conjunctival fever. IV
- Capsid consist of 252 capsomers (240 hexons,
ii. Acute respiratory tract disease – fever, cough
12 pentons) which is arranged as icosahedron
pharyngitis, cervical lymphadenitis.
with 20 triangular facets and 12 vertices. The
12 pentons are located at each of the vertices, iii. Conjunctivitis and epidemic keratitis
contain a penton base and a fibre. iv. Gastroenteritis and diarrhea
Replication v. Systemic infection in immunocompromised
- Viral DNA replication: Occurs in nucleus
- Include pneumonia and hepatitis
- Capsid proteins are produced in the cytoplasm
and transported to nucleus. Laboratory diagnosis
Transmission i. Specimen: Throat swab, nasopharyngeal
aspirate, bronchial lavage, corneal scraping and
- Resistant to drying, detergents and GI
secretions. biopsy.
- Spread person to person contact by aerosol ii. Microscopy:
droplet or by faeco-oral contact. - Viral particles from respiratory tract can be
- Ocular infection spread by hand to hand demonstrated by immunofluorescence
contact. using monoclonal antibodies.
Pathogenesis - Viral particles in stool seen by electron
I. Portal of entry: Adenovirus infects epithelial microscopy.
cells lining respiratory and enteric organs.
Microbiology
iii. Culture: Cultured in Entry of Rhinovirus

- Clinical specimen in tissue cultures such as 
HeLa, Hep – 2, KB and human embryo Grow in cooler environment of nasal mucosa
kidney cells.

- Identification: By immunofluorescence, CFT
Cause the infection of URT including throat
and haemagglutination test.

- Typing: by Neutralization
Clinical symptom
iv. Latex agglutination test: Detect enteric
adenovirus Clinical manifestations
v. PCR: - Common cold
- Detect Antigen  Rhinorrhea

- Rapid method for detecting all human  Sore throat
serotypes.  Minimal cough
vi. Serology: Rise in titer of Ab should be  Low grade fever
demonstrated. - Complication
Rhinovirus  Asthma / COPD exacerbations
- Rhinoviruses cause common cold and are  Chronic bronchitis
isolated commonly from nose and throat.  Sinusitis
- It is so named because of their special  Otitis media
adaptation to grow in the nose (Rhine). Laboratory diagnosis
IV Morphology i. Isolation of virus:
- Can be isolated from nose throat swab or
- Resembles other picornavirus with an nasopharyngeal washings.
exception that they are destroyed at pH 3–5
- Specimen is inoculated or human & monkey
and more heat stable, Icosahedral symmetry. lines & incubated at 33°C.
- Non–enveloped ii. Demonstration of Ag: By ELISA
- Non – segmented positive (+) RNA iii. Demonstration of RNA: Demonstrated by PCR.
- More than 100 serotypes are known. iv. Serology: Not useful due to multiplicity of
serotypes.
- Almost 80% of virus has common receptor
ICAM – 1 (a member on epithelial, fibroblast,  Prevention & Treatment:
lymphoblastoid cells) - Proper and washing
- Rhinovirus is inhabitant of upper respiratory - Pleconaril
tract. Severe Acute respiratory syndrome
Pathogenesis: (SARS)
- Incubation period: 2–5 days - Severe acute respiratory syndrome (SARS) is
- Transmission: viral respiratory disease in humans.
- Infection with the SARS virus causes acute
 Aerosol (Sneezing)
respiratory distress and sometimes death.
 Direct transmission (fomites)

Respi
- SARS-Cov is a variant of coronavirus.

- It causes serious form of pneumonia.
PARASITES AS RESPIRATORY
PATHOGENS
Morphology of virus:
Past Questions:
- Spherical or pleomorphic medium sized.
- Enveloped RNA virus. 1. List two viral pathogens of respiratory tract.
Describe the pathogenesis and laboratory
- Has petal or clubbed shaped peplomer on the
diagnosis of pneumocystis carini.
surface.
(1+4+5=10) [10 Jan]
Mode of infection
2. Describe in brief the pathogenesis and laboratory
- SARS spread by inhalation of virus present in
diagnosis of: [11 July]
respiratory secretion of patient.
a. Cryptococcus neoformans (5)
- Incubation period
b. Paragonimus westermanii
 10 days or less c. Pneumocystis carinii
Symptoms [07 June, 06 June, 05 Dec, 05 June, 03 June]
- Cough Parasitic pneumonia
- Difficulty in breathing
 Varieties of parasites localize to lungs or involve
- Fever greater than 100.4° F the lung at some stage of their development.
- Chills  Parasites involved in pneumonia.
- Headache a. Trematoda
- Myalgia - Paragonimus westermani (adult and ova)
Laboratory diagnosis - Ectopic schistosome ova
b. Nematoda (visceral and Migratory larvae)
i. Specimen:
- Ascaris lumbricoides
IV
- Nasopharyngeal swab or aspirate throat
- Strongyloides stercoralis
swab.
- Hookworms
- Serum: Collected for Ab detection. c. Cestoda
ii. Culture: Vero cell lines - Echinococcus granulosus
iii. PCR: d. Protozoa
- Entamoeba histolytica
- Reverse-transcriptase PCR has been used
for early diagnosis
Pneumocystis Jirovecii
 Pneumocystic Jerovicii is an opportunistic fungus
iv. Ab detection that belong to ascomycetes, however it was
- The rise in tire of Ab in paired serum thought to be a protozoan.
samples can be demonstrated by ELISA or  P. Jiroveciii is a human species and P. carinii is
indirect immunofluorescent. found only in rats, but nowdays both are
v. A chest x–ray considered same.
Morphology
- Shows pneumonia like changes.
- P. Jiroveciii has two stages
vi. Blood:
i. Trophozoites (1m)  Thin walled
- WBC and platelet counts are often Low
ii. Spherical cysts (4 – 6m)
- Neutrophilia  Thick walled, sporocyst
- Lymphopenia  Contain 4 to 8 nuclei

Microbiology
Life cycle Clinical manifestation

- Definitive host: Human beings - P. Jerovicii infection occur in
- Intermediate host: Not required  Immunocompromised individual (AIDS)
Inhalation of freshly released trophozoite deep  Premature and debilitated infants
into lung (by Droplet infection)  Antimalignant therapy

 Patient receiving corticosteroid therapy
Lives in lung alveoli attached to alveolar
epithelium - Clinical disease:
  Interstitial pneumonia
Trophozoites divide by binary fission  Fever
  Nonproductive cough
Some Trophozoites secrete thick cyst wall and
 Respiratory distress
become cyst
 Laboratory diagnosis [10]
Undergoes nuclear and cytoplasmic division i. Specimen
 - Bronchial alveolar lavage
Maturation of cyst & becomes mature cyst which - Lung biopsy
contain sporozoites - Sputum (less significant)

ii. Microscopy
On rupturing of cyst wall, sporozoites are released
 - Giemsa stain
Sporozoites converted into trophozoites - Methamine silver technique
 - Fluorescent Antibody staining: Stains cysts
Initiation of fresh cycle in sample
IV
Note: Both cyst and trophozoites are found in iii. Culture
infected alveoli. iv. Serological test
- Indirect fluorescent Ab test: detect specific
Pathogenesis: [10]
antibody
Entry of organism
- A four fold  in Ab titer strongly suggest

infection.
Binding of P. Jiroveciii to alveolar epithelial cell
mediated by gpA, a glycoprotein v. PCR based method:
 - Detect, P. Jirovecii antigen
gPA bind to SPA (major lectin like surfactant vi. Blood examination
apoprotein) & augment SPA's ability to inhibit - Anemia
surfactant phospholipid secretion by Type – II
- Leucopenia
alveolar epithelial cells
 - ESR
Multiplication of organism is accompanied by a - CRP
hyaline or foamy alveolar exudates which Paragonimus westermani
contain inflammatory cells, lymphocytes,
plasma cell, macrophages - It is also called oriental lung fluke which causes
 paragonimiasis, a chronic infection of lungs of
Reduced respiratory function human.

Respi
Morphology Miracidium in snail develops through the stages

- Adult worm: of sporocyst, first generation redia and 2nd
 Thick, Fleshy, reddish brown (when freshly generation redia, which finally develop into
passed) cercariae
 Shape: Egg shaped 

Cercariae escape from snail in water and enter
 Size: 7.5 – 12 mm in length, 4.6mm breadth
into second intermediate host, the crab or cray
and 4–5 mm in thickness.
fish and develop into metacercaria which are
 Has two suckers: Oral near anterior end
infective to human beings
and ventral near middle of the body.
Pathogenesis
 Life span: 6–7 yrs
- Pathogenic effect results from
 Has excretory vesicle, intestinal caeca and
reproductive organ. i. Migratory larval form
- Egg ii. Adult
 Colour  Yellow iii. Egg
 Shape  oval, size 80 × 60 I. Larval effect
 Shell  Thick – shelled, operculated  During migratory phase, once the larvae
 Content  unsegmented ovum with mass reach the peritoneal cavity, they begin to
of yolk cells migrate through organ, tissues, produces
Life cycle haemorrhage.
- Definitive host: human beings II. Effect due to adult flukes
- Intermediate host:  Causes inflammatory reaction in lung,
i. 1st intermediate host: Fresh water snails of causing cough, fever and increased sputum.
genus Melania  Destruction and cavitations occur IV
ii. 2nd intermediate host: Fresh water crab or
 Sputum becomes bloody dark with egg so
cray fish.
called rusty sputum.
Infection occurs by ingestion of raw or
III. Effect due to egg
undercooked infected crab or cray fish
 Evoke foreign body granulomatous reaction

that may undergo softening in the Center
Excystation of metacercaria occurs in duodenum
producing cavities, the wall of which is
liberating young worms, which penetrate the
composed of fibrous granulation tissue.
gut wall and reach peritoneal cavity and
 Hemorrhage occurs from cavities.
penetrate through the diaphragm into thoracic
cavity to reach lungs Clinical manifestation
 - The disease caused is K/A Paragonimiasis
Develop into egg–producing adult worm - It occurs as:
 i. Pumonary paragonimiasis
Adult worm liberate eggs, which are passed in ii. Extrapulmonary paragonimiasis
sputum and faces I. Pulmonary paragoniomiasis
  Characterized by chronic granulomatous
Eggs develop into larvae (miracidium) in water reaction because of encystment eggs in
and enter into first intermediate host, the snail deeper layer of lungs and are about 1cm in
diameter.

Microbiology
 The lesion shows blood mixed thick - Empyema

purulent fluid, which consist of golden - Cerebral paragonimiasis
brown eggs. Laboratory diagnosis (KU2011)
 The cyst may rupture in bronchiole i. Specimen:
releasing eggs, which are then found in
- Sputum, lung biopsy, feces
sputum.
ii. Microscopy
 Clinically, it presents: fever, cough, with
- Demonstration of egg in sputum and rarely
rusty sputum, dyspnea, chest pain,
in stool by saline and iodine preparation.
hemoptysis and recurrent attack of
- Egg: Oval, brown and operculated.
bacterial pneumonia.
iii. Intradermal test:
II. Extrapulmonary
- Intradermal injection of saline extract of
 It may involve abdominal, hepatic, cerebral
adult P. westermani (Antigen) gives an
or subcutaneous tissue.
immediate sensitivity reaction.
 Diarrhea, abdominal pain & urticaria due to
iv. Serology
invasion of intestine and subsequent
migration of larvae. i. CFT
 Egg entering in circulation may reach to ii. ELISA

various organ. v. Radiology
Complications - Chest x-ray reveals abnormal shadows.
- Lung abscess vi. Blood examination
- Pleural effusion - Eosinophilia is constant finding.
IV

Respi
SPECIAL POINTS FOR MCQs

1. Sore throat is essentially an acute tonsillitis or pharyngitis.
2. Viruses are more common cause of sore throat (2/3rd)
3. S. pyogens is the most common bacterial cause of sore throat.
4. Pneumonia is inflammation and consolidation of lung substance.
5. S. pneumonia is most important bacterial causes of pneumonia.
6 S. Pyogens
- "C" carbohydrate is used for Lancefield classification.
- "M" protein is mainly responsible for pathogenecity.
- Gram positive cocci arranged in chain.
- S. pyogenes belong to Lancefield Gr.A.
- Crystal violet blood agar is a selective medium used for isolation of streptococci.
- Toxin produced by S. pyogens is Hemolysin & pyrogenic exotoxins.
- Non suppurative sequelae of local infection by S. pyogens include acute glomerulonephritis
and rheumatic fever.
- Streptococcus pyogens is main cause of cellulitis.
- S. pyogens show B–hemolysin.
- S. Pyogenes causes
 Erysipelas, cellulitis
 Impetigo, scarlet fever, Rheumatic fever, Acute Glomerulonephritis.
7. Hemolysis
– hemolysis is shown hemolysis is shown by hemolysis is shown IV
by by
- S. pyogens - Strep.Pneumonia - Enterococcus
- Strept. agalactiae - Strep.Viridans
- Staph. aureus - Strep. Mutins
- Listeria - Strep sanguis
monocytogens
- Bacillus subtilis
8. Streptococcus aglactaciae
- Belong to Gr. B streptococci, gram positive
- –hemolytic
- Bacitracin resistant
- Hydrolyses hippurate
- CAMP test positive
- Causes neonatal meningitis, neonatal sepsis.
9. The serotypes mostly cause Rheumatic fever  5, 18, 24
10. Significant titre for ASO Rheumatic fever is >300 in children's and >200 in adults.
11. Commercially, streptokinase is obtained from strep equi.
12. Rash of scarlet fever is due to erythrogenic toxin.
13. Hyaluronic acid capsule is present in Gr. A and Gr. C streptococci.

Microbiology
14. Staphylococcus Aureus

- Gram positive, cluster forming cocci.
- Notimotile, non sporeforming, facultative lactic acid.
- Fementation of Glucose produces mainly lactic acid.
- Ferments mannitol Distinguishes from S. spidermidis.
- Catalase +ve, coagulase +ve
- Coagulase is responsible for pathogenicity.
- Golden yellow colony on agar.
- Normal flora of human found on nasal passage, skin and mucous membrane.
- Food poisoning is due to preformed endotoxin and occurs within 6 hr. of food intake.
- Panton valentine leucocidin is seen in staph infection.
- Specially, diary products are involved in poisoning.
- Causes:
 Acute osteomyelitis  Furnclulosis, carbuncle
 Acute mastitis  Acute endocarditis
 Botromycosis  Sycosis barbe
 Staphylococcal scalded skin syndrome  Tropical polymyositis
 Toxic shock syndrome (TSS)
15 TSS is caused by any of several related exoproteins produced by S. aureus.
i. TSST –1 is toxin most frequently implicated
ii. Staphylococcal enterotoxin 2nd most frequent
16. TSST toxin is super antigen
17. Methicillin resistant staph aureus (MRSA) main, cause outbreaks of hospital infection.
IV 18. Staph. saprophyticus is novobiocin resistant which distinguishes it from staph. epidermidis and
staph. aureus.
19. Penicillin resistant staphycococci may be due to production of –lactamase (penicillinase) which is
plasmid coded and transmitted by transduction.
20. Streptococcus pneumonia
- Gram positive capsulated, diplococci
- Most virulent type is Type C
- Shows Draughtman colonies on blood agar in prolonged incubation.
- Vaccine is prepared from capsule
- Lanceolate, flame shaped diplococcus
- Bile soluble
- Optochin sensitive
- Virulence is due to capsule
- Show -hemolysis
- Quellung reaction is associated with capsular delineation
- Ferment inulin
21. Haemophilus
- Are non motile, nonsporing, Gram negative bacilli and required both two accessory growth
factor (X and V present in blood).
- H. influenzae and H. ducreyi are major pathogens in genus Haemophilus.
- Grows on chocolate agar

Respi
- Capsulated
- Required factor X & V
- Shows satellitism
- Chancroid is caused by H. ducrey.
- School of fish appearance shown by H. ducreyi.
- Haemophilus influenza biotype Aegyptius causes a highly contagious form of conjunctivitis.
22. Corynebacterium diphtheria
- Is gram positive, non motile, non sporing, non capsulated.
- Usually seen in angular fashion resembling the letters V or L, called Chinese letters.
- Contains  Babes ernest/volutin granules/ Metachromatic grarules.
- Loeffler's serum slope, Tellurite media is used for growth.
- Eleks get precipitation test is used (Immunodiffusion tests).
- Incubation period is 2–6 days.
- Faucial (tonsillar) diphtheria is the commonest type of diphtheria.
- Pseudomembrane formation is a feature.
- Bulls neck (cervical lymphadenopathy) occur in diphtheria.
- The pathogencity is due to production of a very powerful extoxin.
- Toxin is () phage mediated
- Diphtheria toxin acts by inhibiting protein synthesis. It inhibitis polypeptide chain elongation
by inactivating the elongation factor EF–2.
- Triple vaccine (DPT) is used for active immunization.
- This vaccine contains diphtheria toxoid, tetanus toxoid and pertussis vaccine.
- Commensal corynebacterium present normally in throat, skin, are mistaken for C. diphtheria and
are called Diphtheroids.
- Diphtheroids posses few or no metachromatic granules. IV
- Diptheroids are arranged in palisades (parallel rows) rather than in Chinese letter pattern.
- E.g. of Diphtheroids: C. xerosis and C. Pseudodiphtheriticum.
- Corynebacterium parvum  immunomodulater.
- Corynebacterium pseudotuberculosis  is Nocards bacillus
- Ehrilichs phenomenon is seen in diphtheria (toxin antitoxin reaction)
- C. diptheriae gravis  Show Daisy head colony.
- C.diptheriae intermedius  Show frogs egg colony.
- C. diptheriae mitis  Show poached egg colony.
- Corynebacterium is club Shaped due to presence of metachromic granules. In Albert staining,
Bacilli look green and volutin granules look Bluish-black.
- Shick's test is used to determine  Susceptibility to C. diphtheria.
23. Bordetella pertussis
- Gram negative cocco bacillus
- Important 3 species of Bordetella are B. pertussis, B parapertussis and B. bronchiseptia.
- B. Pertussis main causative agent of whooping cough
- It is small, ovoid, non motile, coccobacillus
- Bordet Gengou (glycerol potato blood agar) is commonly used medium.
- Regan–Lowe (RL) medium is charcoal blood agar used for growth of B pertussis.
- B. pertussis is oxidase positive
- Produce pertussis toxin a exotoxin.

Microbiology
- Incubation period pertussis is 1–2 week.

- Thumb printing appearance in culture films.
- Erythromycin prevents spread of disease in children.
- Whooping cough caused by B. pertussis is also called 100 day cough disease.
- Pertussis toxin causes anaphylaxis and Hypoglycemia.
- DPT vaccine is given at 6, 10, 14 weeks.
- Pertussis toxoid contains toxoid strain 1, 2 and 3. The strain to be removed at last is strain 2.
24. Mycobacterium tuberculosis
- Discovered by Robert Koch
- Obligate aerobe
- Acid fast
- Acid fastness is due to mycolic acid and cell wall
- Is slightly curved rod
- LJ medium is used to culture.
- Usually affect apical and posterior segments of upper lobes.
- Lung is main organ involved.
- Tubercular lymphadenitis is the main extra pulmonary TB.
- Rapid diagnosis is done by Auramine Rhodamine stain.
- Production niacin is an important feature.
- Cord factor promotes virulence.
- Mycobacterium para–tuberculosis is Johnes bacillus.
- Morphology:
i. On Z.N. stain: It looks bright red (Acid test) in blue back ground.
ii. With Auramine O, rhodamine (Fluorescent dye) It appears  Yellow luminous bacilli
under fluorescent microscope.
iii. On L J medium: Colony  dry, cough, buff colored, raised with a wrinkled surface.
IV - Show luxuriant growth (Eugonic growth) whereas M. bovis show sparsely growth (Dysgonic
growth)
- Niacin test and Nitrate reduction test  important test for identification of M.TB.
- Tuberculin test is delayed or type – IV hypersensitivity reaction.
- PCR is a rapid method in diagnosis of TB.
- For prophylaxis, BCG vaccine is given. BCG is live attenuated vaccine and is given
intradermally.
- Guinea pig  used for animal inoculation test in M.TB.
- ELISA  Most commonly used in detection of antimycobacterial antibodies in patients serum.
- Blood is not a useful sample for tuberculosis.
25. Atypical Mycobacteria (MOTT)
- Normally exists as saprophytes of soil and water.
- Occasionally causes opportunistic infection.
- Classified by Runyon as follow:
i. Gr. I – Photochromogen: M. Kansasi
ii. Gr. II – Scotochromogen: M. scrofulaceum
iii. Gr. III – Non photochromogens: M.avium intracellulare.
iv. Gr. IV – Rapid Grower: M. smegmatis
- Buruli ulcers caused by M. ulcerans. [KU 2012]
- Swimming pool granuloma/fish tan granuloma is caused M. Marinum.
- Lung involvement occurs in all typicalmycobacteria infection except in M. marinum.
- M. szulgai is a photochromogen at 25°C and scotochromogen at 37°C (Dual Atypical mycobacteria).
Respi
26. Histoplasma capsulatum

- It is a dimorphic fungus
- Hyphae bear both large and small pores, which are used for identification.
- H. capsulatum grows as small budding yeast in host tissue and on enriched agar. Such as
blood cysteine glucose at 37°C.
- The fungus is not encapsulated.
- Grow in bird/bat enriched soil.
- Telemorph or the perfect state are seen in culture, the Ajellomyces capsulatus is used.
- Causes Histoplasmosis.
- Most common fungus of reticuloendothelial system.
27. Candida albicans
- Causes candidiasis, commonly called yeast infection or thrush, also K/A as
candidosis/Moniliasis/oidiomycosisis
- Candida albicans infection is most common fungal infection.
- It is endogenous infection.
- Appear as shorter, pseudohyphae in association with budding yeast form.
- It is main fungal infection in Neutropenic patients.
- Presence of Pseudohyphae.
- Shows Reynolds Braude Pnenomenon: ability to form germ tubes with in 2 hr when
incubated in human serum at 27°C.
- Hepatosplenic candidiasis manifests as Bull eye Lesion.
- Systemic infection (Candidemia): Meningitis, endocarditic.
- On Nickerson's medium: Show Glistening black colonies.
28. Aspergillus fumigates
- It is the most common cause of aspergillosis but A.flavus, A.niger, and several other species IV
can also cause disease.
- One of the most common opportunistic fungal sinusitis in immunocompromised.
- Has branching hyphae (Septate)
- Main disease: Otomycosis
- Aspergillus is a mold with septate hyphae.
- Portal of entry: Lungs.
- Aspergillomas:
 Ball of hyphae within cysts of cavities usually in the upper lobe, may reach several cm in
diameter and may be visible on chest X-ray.
 Tissue invasion doesnot occur.
- Allergic bronchopulmonary aspergillosis denotes condition of patients with pre existing
asthma who have eosinophilia IgE Ab to Aspergillus and fleeting pulmonary infiltrates from
bronchial plugging.
29. Cryptococcus Neoformans
- Crytococcus is monomorphic yeast.
- Has a polysaccharide capsule. [MCQs 012 KU]
- The environmental source is soil enriched with pigeon dropping.
- Prediliction for brain.
- Acute pulmonary infection are common in pigeon breeders.
- Cryptococcal meningitis is dominant in AIDS and cancer patients.

Microbiology
- It is Urease positive.
- Indium in 111 – labeled leukocyte Scans 'used in detection of cryptococcal meningitis.
30. Influenza virus
- Belong to orthomyxovirus group
- Enveloped RNA virus
- Type A: Causes all pandemics and most epidemics
- Type C: Causes Reyes Syndrome
- Haemaglutinin and Neuraminidase is strain specific.
- Antigenic variation seen as
i. Antigenic drift (minor change)
ii. Antigenic shift (major change)
- Bird flu virus: H5N1 is "Avian flu influenza virus". [MCQs 012 KU]
- H5N1 – transmits vertically and is highly pathogenic.
- Risk factor for Bird flu is handling of poultry.
- Swine flu "H1N1” virus.
31. Adeno virus
- Non enveloped virus, DNA virus
- Main manifestation is URTI in children.
- Main manifestation RDS in adult.
- Causes: Diarrhoea, Haemorragic cystitis, Epidemic Keratoconjuctivitis.
32. SARS: Severe acute respiratory syndrome.
- It caused by SARS corona virus (SARS – Cov)
- Was 1st identified in 2003 Feb.
33. RSV
IV - Causes most of bronchiolitis
- F glycoprotein of respiratory syncytial virus induces syncytia formation.
- It is paramyxovirus.
- Malaise and fatigue sed "atypical" lymphocytes and a reactive neutrophil Ab test is most
commonly caused by EBV.
34. Paragonimus westermani
- Also called oriental lung fluke.
- Has 3 host.
- Definitive host: Man
- 1st intermediate host: Snail of Genus Melania.
- 2nd intermediate host: Crayfish/crab
- Infective agent: Metacercaria
- Portal of entry: Digestive tract
- Site of localization: Lungs
35. Pneumocystis Jerovicii
- Opportunistic fungus
- Belong to ascomycetes
- No intermediate host
- Causes interstitial pneumonia

Microbiology

Uploaded by

Copyright:

Available Formats

You might also like

Microbiology

Uploaded by

Document Information

Original Description:

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Microbiology

Uploaded by

Copyright:

Available Formats

Respi

FAST TRACK BASIC SCIENCE MBBS -1045-

-1046- FAST TRACK BASIC SCIENCE MBBS

INTRODUCTION TO RESPIRATORY 3. Role of antibiotics:

 Normal floras are not pathogenic in their normal Respiratory Infections

- Nutrient source i. Upper respiratory tract infection (URTI)

- Act as opportunistic pathogens if resistance of  Rhinitis

FAST TRACK BASIC SCIENCE MBBS -1047-

 Pharyngitis Causative organism of various

-1048- FAST TRACK BASIC SCIENCE MBBS

4. Sinusitis 7. Ventilator associated pneumonia

BACTERIA AS RESPIRATORY 14.Describe the pathogenesis and lab diagnosis of

9. Write about morphology, cultural characteristics, (5) [04 Dec]

-1050- FAST TRACK BASIC SCIENCE MBBS

Culture characteristics iii. Colony morphology

FAST TRACK BASIC SCIENCE MBBS -1051-

Lesion  Incubation period 3 – 5 days

-1052- FAST TRACK BASIC SCIENCE MBBS

Culture characteristic Pathogenesis

- After incubation for 18 hour, colonies are 

II. Somatic M protein - Otitis media

III. Cell wall carbohydrate - Sinusitis

Virulence factors - Meningitis

FAST TRACK BASIC SCIENCE MBBS -1053-

Laboratory diagnosis [03, 07] Note:

-1054- FAST TRACK BASIC SCIENCE MBBS

Other streptococci Staphylococcus aureus

FAST TRACK BASIC SCIENCE MBBS -1055-

iii. Phosphates production in phenolphthalein  Test for coagulase is done by

- Types A  Coded by chromosomal gene  

-1056- FAST TRACK BASIC SCIENCE MBBS

Clinical manifestation 5. Identification:

ii. Special media Clinical manifestation

-1058- FAST TRACK BASIC SCIENCE MBBS

Satellitism [09] Cultural characteristics:

FAST TRACK BASIC SCIENCE MBBS -1059-

- Diphtheria is primarily a pediatric disease. 2. Advanced case:

- In vitro test v. Parallel to this streak, a known toxigenic

Schick test Diphtheroids [06]

FAST TRACK BASIC SCIENCE MBBS -1061-

Features C. Diphtheriae Diphtheroids Biochemical reaction

-1062- FAST TRACK BASIC SCIENCE MBBS

Structure: - Alters both AMI (Antiobody mediated

FAST TRACK BASIC SCIENCE MBBS -1063-

Pathogenesis Notes: Whoop

- Mild cough - Cough is dry -  in cough b. Charcoal blood agar

-1064- FAST TRACK BASIC SCIENCE MBBS

Bacterial pneumonia - Culture

FAST TRACK BASIC SCIENCE MBBS -1065-

iii. Health care–associated pneumonia: Criteria

-1066- FAST TRACK BASIC SCIENCE MBBS

Virulence factor - Virus

- Walking pneumonia - Pleomorphic flagellated, nonsporing, non

ii. Ability to survive intracellular: the factor Clinical features:

-1068- FAST TRACK BASIC SCIENCE MBBS

Laboratory diagnosis Morphology of M. tuberculosis [05, 07]

FAST TRACK BASIC SCIENCE MBBS -1069-