1. Lab Diagnosis of
Infectious Diseases
Tsegaye A.
(assistant Professor of
Microbiology)
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2. Cont’d…
Laboratory diagnosis
• Requires the appropriate specimen is collected
• Delivered in the appropriate transport system, &
• Processed in a manner that will maximize detection of the most
likely pathogens.
Physician responsibility
• Collection of the proper specimen & its rapid delivery to the
clinical laboratory.
Clinical microbiologist responsibility
• Selects the appropriate transport systems & detection method (i.e.,
microscopy, culture, antigen or antibody detection, nucleic acid-
based tests).
• These responsibilities are not mutually exclusive.
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3. Cont’d…
• The microbiologist should be prepared to instruct the
physician about what specimens should be collected
if a particular diagnosis is suspected, &
• The physician must provide the microbiologist with
information about the clinical diagnosis so that the
right tests are selected.
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5. Blood culture
Transport System:
• Blood culture bottle with nutrient media/ Tryptosoya
Specimen Volume
• Adults: 20 ml/culture
• Children: 5-10 ml/culture
• Neonates: 1-2 ml/culture
Other Considerations:
• Skin should be disinfected with 70% alcohol followed by 2%
iodine.
• 2-4 cultures collected to avoid the contamination unless patient
is in septic shock or antibiotics will be started immediately.
• Two bottle is optimum
• Blood collections should be separated by 30-60 min.
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6. Possible pathogen
Gram positive
• S. aureus
• V. streptococci
• S. pneumoniae
• S. pyogenes
• E. faecalis
• C. perfringens
• Also M. tuberculosis
• Candida species,
• Cryptococcus neoformans
Gram negative
• S. Typhi
• Other Salmonella serovars
• Brucella species
• H. influenzae
• P. aeruginosa
• Klebsiella strains
• E. coli
• Proteus species
• N. meningitidis
• Y. pestis
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7. Commensals
• Blood does not have a normal microbial flora.
• Common skin contaminants include
CoNS
V. streptococci
Micrococci, &
Corynebacterium species
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8. Cerebrospinal fluid
Transport system
• Sterile screw-capped tube.
Specimen Volume
Bacteria culture
• 1-5 ml
Mycobacterial culture
• As large a volume as possible
Other consideration
• The specimen must be collected aseptically & delivered
immediately to the laboratory
• It should not be exposed to heat or refrigeration.
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9. Possible pathogen
Gram positive
• S. pneumoniae
• S. agalactiae*
• L. monocytogenes*
• M. tuberculosis
Fungí
C. neoformans
Histoplasma
• Blastomyces
• Coccidioides
• Candida
Gram negative
• N. meningitidis
• H. influenzae type b
• E. coli *
• P. aeruginosa*
• Proteus species
• Salmonella serovars
*Mainly isolated from neonates
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Tsegaye A (assistant Professor)
9
10. Body fluids
• Other normally sterile fluids (e.g., Peritoneal, Pleural ,
synovial, pericardial ).
Transport system:
• Small volume: sterile screw capped tube
• Large volume: blood culture bottle with nutrient
medium.
Other consideration:
• Specimens are collected with a needle & syringe.
• Swab is not used because the quantity of collected
specimen is inadequate.
• Air should not be injected into culture bottle because it
will inhibit growth of anaerobes.
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11. Possible pathogens in synovial fluid
Gram positive
• S. aureus
• S. pyogenes
• S. pneumoniae
• Anaerobic streptococci
• Also M. tuberculosis
Gram negative
• N. gonorrhoeae
• N. meningitidis
• H. influenzae
• Brucella species
• E. coli
• P. aeruginosa
• Proteus Spp
• Bacteriodes Spp
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12. Possible pathogens in Pleural &
Pericardial Fluids
Gram positive
• S. aureus
• S. pneumoniae
• S. pyogenes
• M. tuberculosis
Gram negative
• H. influenzae
• Bacteriodes Spp
• P. aeruginosa
• Klebsiella species
• Other enterobacteria
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13. Possible pathogens in ascitic fluid
• Gram positive
• Enterococcus species
• S. pneumoniae
• S. aureus
• S. pyogenes
• S. agalactiae
• V. streptococci
• C. perfringens
• M. tuberculosis
• Candida species.
Gram negative
• E. coli
• Klebsiella Spp
• Other enterobacteria
• P. aeruginosa
• Bacteroides
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14. Throat & Mouth specimen
Transport System:
• Swab immersed in transport medium
Specimen volume: N/A
Other consideration:
• The area of inflammation is swabbed
• Exudate is collected if present
• Contact with saliva should be avoided because it
can inhibit recovery of group A streptococci.
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15. Possible pathogen in throat
& mouth specimens
Gram positive
• S. pyogenes
• C. diphtheriae
• C. ulcerans
Gram negative
• Vincent’s organisms
(Borrelia vincenti)
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16. Commensals
Gram positive
• V. streptococci
• Non-haemolytic
streptococci
• S. pneumoniae
• S. epidermidis
• Micrococci
• Lactobacilli
• Diphtheroids
Gram negative
• M. catarrhalis
• Neisseria pharyngitidis
• Coliforms
• Fusobacterium
• H. influenzae
• Bacteriodes species
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17. Ear Discharge
Transport system:
• Capped, needleless syringe; sterile screw-capped tube.
Specimen Volume:
• Whatever volume is collected
Other consideration:
• The specimen should be aspirated with a needle &
syringe.
• Culture of the external ear has no predictive value for
otitis media.
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18. Possible pathogens
Gram Positive
S. aureus
S. pyogenes
S. pneumoniae
Candida spp
Gram Negative
E. coli
Proteus spp
P. aeruginosa
H. influenzae
Bacteriodes spp
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19. Eye
Transport system:
• Inoculate plates at bedside (seal & transport to laboratory
immediately).
Specimen volume:
• Whatever volume is collected
Other consideration:
• For infections on surface of eye, specimens are collected with a
swab or by corneal scrapings.
• For deep-seated infections, aspiration of aqueous or vitreous fluid is
performed.
• All specimens should be inoculated onto appropriate media at
collection; delays will result in significant loss of organisms.
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20. Possible pathogen
Gram positive
• S. aureus
• Beta-hemolytic
streptococci
• S. pneumoniae
Gram Negative
• H. influenzae
• P. aeruginosa
• N. gonorrhea
• C. trachomatis (D-K)
• Note: C. trachomatis best
stain with Giemsa stain
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21. Wounds (Abscess & Pus)
Transport system:
• Aspirate in sterile screw capped tube/sterile
anaerobic tube/vial.
Specimen volume:
• 1-5 ml of pus
Other consideration:
• Specimens should be collected with a sterile needle
& syringe;
• Swabbed specimens should be avoided.
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22. Possible pathogen
Gram positive
• S. aureus
• S. pyogenes
• Enterococcus species
• Anaerobic streptococci
• Other streptococci
• C. perfringens
• Clostridia
• M. tuberculosis
Gram negative
• P. aeruginosa
• Proteus species
• E.coli
• Bacteriodes species
• Klebsiella species
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24. Urine: midstream
Transport system:
• Sterile urine container
Specimen volume:
• Bacteria: 1ml
• Mycobacteria: ≥ 10 ml
Other consideration
• Contamination of the specimen with bacteria from the
urethra/vagina should be avoided;
• The first portion of the voided specimen is discarded;
organisms can grow rapidly in urine; so, specimens must
be transported immediately to the laboratory, held in
bacteriostatic preservative, or refrigerated.
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25. Urine: catheterized
Transport system
• Sterile urine container
Specimen Volume
Bacteria: 1ml
Mycobacteria: ≥ 10 ml
Other consideration
• Catheterization is not recommended for routine cultures (risk of
inducing infection)
• The first portion of collected specimen is contaminated with
urethral bacteria.
• So it should be discarded (similar to midstream voided specimen);
• The specimen must be transported rapidly to the laboratory.
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26. Urine: Suprapubic aspirate
Transport system: Sterile anaerobic tube or vial
Specimen volume:
• Bacteria: 1 ml
• Mycobacteria: ≥10 ml
Other consideration:
• This is an invasive specimen, so urethral bacteria are avoided;
• It is the only valid method available for collecting specimens for
anaerobic culture.
• It is also useful for collection of specimens from children or adults
unable to void uncontaminated specimens.
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27. Possible pathogen
Gram positive
• S. saprophyticus
• E. faecalis
• Enterobacter aerogenes
Gram negative
• E. coli
• Proteus species
• P. aeruginosa
• Klebsiella Species
• S. marcescens
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28. Genitals
Transport system:
• Specially designed swabs for N. gonorrhoeae & Chlamydia
probes.
Specimen volume: N/A
Other consideration:
• The area of inflammation or exudate should be sampled;
• The Endocervix (not vagina) and urethra should be cultured for
optimal detection.
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29. Possible pathogens
urethral swabs
• N. gonorrhoeae
• C. trachomatis (serovars D-K)
• occasionally Ureaplasma,
• Mycoplasma, &
• T. vaginalis.
From non-puerperal women
• N. gonorrhoeae,
• C. trachomatis (serovars D-K)
• S. pyogenes
• Herpes simplex virus
From women with
puerperal sepsis/septic
abortion:
• S. pyogenes
• S. aureus
• Enterococcus species
• Anaerobic cocci
• C. perfringens
• Bacteroides
• Proteus
• E. coli & other coliforms
• L. monocytogenes
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30. Feces (Stool)
Transport system:
• Sterile screw-capped container
Specimen Volume: N/A
Other consideration:
• Rapid transport to the laboratory is necessary to prevent
production of acid (bactericidal for some enteric
pathogens) by normal fecal bacteria
• It is unsuitable for anaerobic culture; because a large
number of different media will be inoculated, a swab
should not be used for specimen collection.
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31. Possible pathogen
Gram positive
• C. perfringens types A &C
• C. difficile
• B. cereus
• S. aureus
Gram negative
• Shigella species
• Salmonella serovars
• Campylobacter species
• Y. enterocolitica
• E. coli (ETEC, EIEC,
EPEC, EHEC, EAgEC)
• V. cholerae O1
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32. Sputum
Sputum for microbiological investigation:
• Give the patient a clean (need not be sterile), dry, wide-
necked, leak proof container, & request him to cough
deeply to produce a sputum specimen
Important
Must not be saliva.
Best collected in the morning soon after the patient
wakes & before any mouth wash.
Gastric washings/aspirate can be used for the isolation of
M. tuberculosis in children.
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Tsegaye A(assistant Professor)
33. Cont’d…
• If pneumonia/bronchopneumonia is suspected, deliver the
sputum to the lab with a little delay as possible, because H.
influenzae & S. pneumoniae require culturing as soon as
possible.
• If the specimen is for the isolation of M. tuberculosis, it should be
delivered to the lab within 2 hours or kept at 4 0C.
Note:-
S. pneumoniae & H. influenzae must never be refrigerated.
If pneumonic plague is suspected : deliver the sputum to the Lab
as soon as possible.
Should be marked as “HIGH RISK”
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34. Possible pathogen
Gram positive
• S. pneumoniae
• S. aureus
• S. pyogenes
• H. capsulatum
Gram negative
• H. influenzae
• K. pneumoniae
• P. aeruginosa
• Proteus species
• Y. pestis
• M. catarrhalis
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35. Commensals in sputum
Gram positive
• S. aureus
• S. epidermidis
• V. streptococci
• S. pneumoniae
• Enterococci
• Micrococci
• Lactobacilli
• Diphtheroids
• H. capsulatum
Gram negative
• Neisseria species
• M. catarrhalis
• H. influenzae
• Fusobacterium
• Coliforms
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36. Catheter
Transport System:
• Sterile screw-capped tube or specimen cup
Specimen volume: N/A
Other consideration:
• The entry site should be disinfected with alcohol.
• The catheter should be aseptically removed on receipt
of the specimen in the laboratory.
• The catheter is rolled across a blood agar plate & then
discarded.
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37. Bacterial detection &
identification
• Detection of bacteria in clinical specimens is
accomplished by five general procedures
• Microscopy
• Detection of bacterial antigens
• Detection of specific bacterial nucleic acids
• Culture, &
• Detection of an antibody response to the bacteria
(serology).
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38. Principles of Diagnosis
General Concepts
• The clinical presentation of an infectious disease
reflects the interaction between the host & the
microorganism.
• This interaction is affected by the host immune status
and microbial virulence factors.
• Signs and symptoms vary according to the site &
severity of infection.
• Diagnosis requires a composite of information,
including history, physical examination, radiographic
findings, & laboratory data.
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39. Microbial Causes of Infection
• Infections may be caused by bacteria, viruses, fungi,
and parasites.
• The pathogen may be exogenous (acquired from
environmental or animal sources or from other persons)
or endogenous (from the normal flora).
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40. Specimen selection
• Specimens are selected on the basis of signs &
symptoms
• Should be representative of the disease process.
• Should be collected before administration of
antimicrobial agents.
• The specimen amount & the rapidity of transport to the
laboratory influence the test results.
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41. Microbiologic Examination
Direct Examination(macroscopic) : Direct examination of
specimens reveals gross pathology.
Microscopy: can be used in wet mount & with staining
Staining
is the process of coloring of colorless object using stains
(dyes).
Uses of staining
To observe the morphology of bacteria.
To differentiate one group of bacteria from the other group.
Stain in Microbiology
Staining is possible due to the difference in the composition of
the dyes and the cellular components.
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42. Basic principle of staining
Acidic part of the cell negatively charged (nucleic
acid, & nucleoproteins of the nucleus) stains with basic
dye (methylene blue), &
Basic component of the cell positively charged
(cytoplasm) stains with acidic dyes (eosin).
Other structure stained by a combination of this two
(neutral stain).
Type of staining methods
1. Simple staining method
2. Differential staining method
3. Special staining method
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43. 1. Simple staining method
Only a single dye is used
Two kinds of simple stains
i) Positive staining
The bacteria or its parts are stained by the dye
E.g. Methylene blue, Crystal violent
ii) Negative staining
The dye stains the background and the bacteria
remain unstained.
E.g. India ink, Negrosin
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44. 2. Differential staining method
Multiple stains (dye) are used to distinguish different
group of bacteria.
Gram staining
Ziehl-Neelsen (acid fast staining technique).
A) Gram stain
Most bacteria are differentiated by their gram reaction
(Gram positive & Gram negative bacteria) due to
difference on their cell wall structure.
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48. B) Ziehl- Neelsen staining Method
is used to stain mycobacterium & other acid fast
organisms which cannot be stained with gram
stain.
Principle
Once the mycobacterium is stained with the primary
stain it can not be decolorized with acid.
So named as Acid fast bacteria
Acid fast bacilli (AFB)
Mycobacterium tuberculosis
Mycobacterium leprae
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50. C)Special Stains
a) Capsule Staining Method
b) Spore Staining Method
c) Flagella Staining
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51. Culture
• Isolation of infectious agents frequently requires
specialized media.
• Non-selective (noninhibitory) media permit the
growth of many microorganisms.
• Selective media contain inhibitory substances that
permit the isolation of specific types of
microorganisms.
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52. Non-selective culture media
• Blood agar: Recovery of bacteria & fungi
• Chocolate agar: Recovery of bacteria including
Haemophilus & Neisseria gonorrhea
• Mueller-Hinton agar: Bacterial susceptibility test
medium
• Thioglycolate broth: Enrichment broth for anaerobic
bacteria
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53. Selective, & differential
• MacConkey agar: selective for gram negative
bacteria; differential for lactose fermenting & non
fermenter species.
• Mannitol salt agar: selective for Staphylococci;
differential for Staphylococcus aureus vs CoNS.
• Xylose lysine deoxycholate agar: selective,
differential agar for Salmonella & Shigella in enteric
cultures.
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54. Cont’d…
• Lowenstein-Jensen medium: selective
for mycobacteria
• Middlebrook agar: selective for
mycobacteria
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55. Transport media
Amies transport media
• Is used for transportation of gonococci.
Cary Blair transport media
• Is used for preserving & transporting enteric
pathogens.
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56. Enriched media
• These media are required for growth of organism with
extra nutritional requirements such as H. influenza,
Neisseria spp, & some streptococcus species.
• An enriched medium increases the number of a
pathogen by containing all the necessary ingredients to
promote its growth.
E.g. Blood & Chocolate agar
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57. Enrichment media
• This term is usually applied to fluid
selective media
• E.g. Tryptosoya broth & Selenite F broth
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58. Basic media
• These are simple media that will support the growth
of micro organisms that do not have special
nutritional requirement
• E.g. Nutrient agar & Nutrient broth
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59. Microbial Identification
• Colony and cellular morphology may permit
preliminary identification
• Growth characteristics under various conditions
• Utilization of carbohydrates and other substrates
• Enzymatic activity
• Immunoassays, and genetic are also used.
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60. Serodiagnosis
• A high or rising titter of specific IgG antibodies or
• The presence of specific IgM antibodies may suggest
or confirm a diagnosis.
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61. Antimicrobial Susceptibility
• Microorganisms, particularly bacteria, are tested in
vitro to determine whether they are susceptible to
antimicrobial agents.
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62. Microscopy
Five general microscopic methods are used:
Bright field (light) microscopy
Darkfield microscopy
Phase-contrast microscopy
Fluorescent microscopy
Electron microscopy
Note: Read for detail information on Murray
Medical Microbiology book
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63. Lab. Diagnosing of
Viral Infections
• Cryptologic examination
• Electron microscopy
• Virus isolation and growth
• Detection of viral proteins (antigens & enzymes)
• Detection of viral genomes
• Serology
NB: read about specimen for viral diagnosis
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64. Lab Diagnosis for Fungal Disease
Conventional Microbiologic Methods
Direct microscopy
•Gram
•Giemsa, &
•Calcofluor white stains
•Lacto phenol blue
•10-20 % KOH
•Indian Ink
• Culture (SDA-Recovery of fungi)
•Identification
•Susceptibility testing
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69. Epidemiology of infectious diseases
Introduction
• Transmission from one host to another is fundamental to the
survival of infectious agent,
• since any host will eventually either clear the infection or die.
Infectious (Communicable) Diseases
• These are illnesses due to specific infectious agents or its toxic
products, which arise through transmission of the agent or its toxic
products from an infected person, animal or inanimate reservoir to
a susceptible host, either directly or indirectly through an
intermediate plant or animal host, vector or inanimate environment
69
70. Natural History of Diseases
• Refers to the progression of a disease process in an individual
over time, in the absence of intervention.
• The process begins with exposure to the causative agent capable
of causing disease.
• Without medical intervention, the process ends with recovery,
disability, or death.
• Most diseases have a characteristic natural history, although the
time frame and specific manifestations of disease may vary from
individual to individual.
• The usual course of a disease may be halted at any point in the
progression by preventive and therapeutic measures, host
factors, and other influences.
70
72. Sequence of Pathogenesis
Microbe must gain access to host
• Attachment to host tissues critical to gaining
access
Must also penetrate or evade host defenses
• Skin
• Immune cells
• Must compete with Normal Flora
Become established
Cause damage 72
73. Components of Infectious Disease
Process
Infectious diseases result from the interaction of
Infectious agent
Susceptible host
Environment
73
74. The epidemiologic triad or triangle is the traditional
model of infectious disease causation
74
75. 75
Host factors Agent factors Environmental
factors
Age
Sex
Previous disability
Behavior
Genetic
inheritance
Height
Weight
socioeconomic
status
Virulence of
organisms
Serotype of
organisms
Antibiotic resistance
Home
overcrowding
Air pollution
Workplace
hygiene
Weather
Water
composition
Food
contamination
Animal contact
Examples of causes of disease by host, agent &
environmental factors.
76. Chain of Infection
• This refers to a logical sequence of factors or link of
disease of a chain that are essential to the
development of the infectious agent & propagation of
disease.
• Infection implies that the agent has achieved entry
and begun to develop or multiply, whether or not the
process leads to disease.
76
77. Components of Chain of Infection
1. Causative Agent
2. Reservoir host
3. Portal of exit
4. Mode of transmission
5. Portal of entry
6. Susceptible host
77
78. A) Infectious agent
an organism that is capable of producing infectious
disease.
On the basis of their size etiological agents are generally
classified in to:
Metazoan (Multicellular organisms E.g. Helminths)
Protozoa (Unicellular organisms E.g. Amoebae)
Bacteria (E.g. Treponema palladium, Mycobacterium
tuberculosis, etc)
Fungus (E.g. Candida albican)
Virus (E.g. Chickenpox, Polio, etc.)
78
79. B) Reservoir of infection
• Any person, animal, arthropods, plant, soil or substance
(or combination of these) in which an infectious agent
normally lives and multiplies, on which it depends
primarily for survival and where it reproduces itself in
such a manner that it can be transmitted to a susceptible
host.
Types of reservoir
i) Man:- Human can be healthy carrier, convalescent
carrier.
• Measles, smallpox typhoid, meningococcal meningitis,
gonorrhea & syphilis.
• The cycle of transmission is from human to human.
79
80. Cont’d…
ii) Animal :- (Zoonosis)
from animal to man under natural conditions.
Bovine tuberculosis –cow to man.
Brucellosis –cows, pigs and goats to man.
Anthrax – cattle, sheep, goats, horses to man.
Rabies – Dogs, foxes and other wild animals to man
Plague from rats &
Typhus from rodent
80
81. Cont’d…
iii) Non-living things
Many of the agents are basically saprophytes
living in soil.
Soil:- can be source of different parasitic, fungal &
bacterial infections.
Eg
• Clostridium botulinum Botulism.
• Clostridium tetani Tetanus.
• Clostridium welchi gas gangrene.
81
82. Source of infection
It is a place from which infectious agent to human to cause
infection & disease.
I. Endogenous (Autogenous) infection
When the source of infection is from one’s own normal flora within the body.
II. Exogenous infection:
When the source of infection is from outside the body
Human patients
Human carrier
Animal zoonosis - Reservoir hosts
Insects (vectors) - Mechanical vector and Biological vector
arthropod borne disease
Water - Due to the presence of pathogen
– E.g. Vibrio cholera, Hepatitis A, Guinea Worm
Food poisoning:- Microbial, Toxic
Soil
82
83. C) Portal of exit
• Mode of escape from the reservoir
• This is the site through which the agent escapes from
the reservoir.
• Examples include:
GIT Typhoid fever, bacillary dysentery,
amoebic dysentery, cholera, ascariasis etc.
Respiratory tuberculosis, common cold, etc.
Skin & mucus membrane syphilis.
Genitourinary tracts - STD’s, UTI’s
Conjunctiva
83
84. D)Modes of Transmission of
Infectious Agents
• The mechanism by which an infective agent exits from a
reservoir host & enters into a susceptible host.
There are two major modes:
a) Direct Transmission- immediate transfer of the agent
from a reservoir to a susceptible host .
i)Direct Vertical – such as: transplacental transmission
of syphilis, HIV, etc.
ii)Direct Horizontal – Direct touching, biting, kissing,
sexual intercourse, droplet spread onto the conjunctiva
or onto mucus membrane of eye, nose or mouth during
sneezing coughing, spitting or talking 84
85. Cont’d…
b) Indirect Transmission
Vehicle-borne transmission:
Indirect contact through contaminated in contact
through contaminated inanimate objects (fomites) like
Bedding
Toys
Handkerchiefs
Soiled clothes
Cooking or eating utensils and
Surgical instruments
85
86. Cont’d…
Contaminated food & water
Biological Products
blood, serum, & plasma
The agent may or may not multiply or develop in the vehicle
before it is introduced in to man.
Vector borne transmission: occurs when the infectious agent
is conveyed by an arthropod (insect) to a susceptible host.
– Mechanical transmission: The arthropod transports the agent
by soiling its feet or proboscis, in which case multiplication of
the agent in the vector does not occur (e.g. common house fly)
– Biological transmission: This is when the agent multiplies in
the arthropod before it is transmitted, such as the transmission
of malaria by mosquito.
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87. Cont’d…
Air-borne transmission: Dissemination of microbial
agent by air to a suitable portal of entry, usually the
respiratory tract. Two types of particles are implicated in
this kind of spread dusts and droplet nuclei.
Dust - Small infectious particles of widely varying
size that may arise from soil, clothes, bedding or
contaminated floors and be resuspended by air
currents.
Droplet nuclei - Small residues resulting from
evaporation of fluid (droplets emitted by an infected
host). They usually remain suspended in air for long
periods of time.
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88. E) Portal of entry
• The site in which the infectious agent enters to the
susceptible host.
• For example:
o Mucus membrane
o Skin
o Respiratory tract
o GIT
o Blood
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89. F) Susceptible host (host factors)
A person or animal lacking sufficient resistance to a
particular pathogenic agent to prevent disease if or
when exposed.
Occurrence of infection & its outcome are in part
determined by host factors.
The term "immunity" is used to describe the ability
of the host to resist infection.
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90. How to control infectious disease
Environmental sanitation
Personal hygiene
Water treatment
Proper food handling
Killing of micro-organisms
Immunization
Use of personnel Protective equipment's
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