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Lab Diagnosis of
Infectious Diseases
Tsegaye A.
(assistant Professor of
Microbiology)
4/21/2023 Tsegaye A(assistant Professor) 1
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.
4/21/2023 Tsegaye A(assistant Professor) 2
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.
4/21/2023 Tsegaye A(assistant Professor) 3
Specimen collection,
transportation, detection &
identification of
microorganism
4/21/2023 Tsegaye A(assistant Professor) 4
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.
4/21/2023 Tsegaye A(assistant Professor) 5
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
4/21/2023 Tsegaye A(assistant Professor) 6
Commensals
• Blood does not have a normal microbial flora.
• Common skin contaminants include
 CoNS
 V. streptococci
 Micrococci, &
 Corynebacterium species
4/21/2023 Tsegaye A(assistant Professor) 7
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.
4/21/2023 Tsegaye A(assistant Professor) 8
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
4/21/2023
Tsegaye A (assistant Professor)
9
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.
4/21/2023 Tsegaye A (assistant Professor) 10
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
4/21/2023 Tsegaye A(assistant Professor) 11
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
4/21/2023 Tsegaye A(assistant Professor) 12
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
4/21/2023 Tsegaye A(assistant Professor) 13
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.
4/21/2023 Tsegaye A(assistant Professor) 14
Possible pathogen in throat
& mouth specimens
Gram positive
• S. pyogenes
• C. diphtheriae
• C. ulcerans
 Gram negative
• Vincent’s organisms
(Borrelia vincenti)
4/21/2023 Tsegaye A(assistant Professor) 15
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
4/21/2023 Tsegaye A(assistant Professor) 16
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.
4/21/2023 Tsegaye A(assistant Professor) 17
Possible pathogens
Gram Positive
 S. aureus
 S. pyogenes
 S. pneumoniae
 Candida spp
Gram Negative
 E. coli
 Proteus spp
 P. aeruginosa
 H. influenzae
 Bacteriodes spp
4/21/2023 Tsegaye A(assistant Professor) 18
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.
4/21/2023 Tsegaye A(assistant Professor) 19
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
4/21/2023 Tsegaye A(assistant Professor) 20
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.
4/21/2023 Tsegaye A(assistant Professor) 21
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
4/21/2023 Tsegaye A(assistant Professor) 22
Commensals
Gram positive
• Staphylococci
• Micrococci
• V. streptococci
• Enterococci
• Diphtheroids
• Propionibacterium
acnes
 Gram negative
• E. coli
• Coliforms
4/21/2023 Tsegaye A(assistant Professor) 23
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.
4/21/2023 Tsegaye A(assistant Professor) 24
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.
4/21/2023 Tsegaye A(assistant Professor) 25
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.
4/21/2023 Tsegaye A(assistant Professor) 26
Possible pathogen
Gram positive
• S. saprophyticus
• E. faecalis
• Enterobacter aerogenes
 Gram negative
• E. coli
• Proteus species
• P. aeruginosa
• Klebsiella Species
• S. marcescens
4/21/2023 Tsegaye A(assistant Professor) 27
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.
4/21/2023 Tsegaye A(assistant Professor) 28
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
4/21/2023 Tsegaye A(assistant Professor) 29
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.
4/21/2023 Tsegaye A(assistant Professor) 30
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
4/21/2023 Tsegaye A(assistant Professor) 31
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.
4/21/2023 32
Tsegaye A(assistant Professor)
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”
4/21/2023 Tsegaye A(assistant Professor) 33
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
4/21/2023 Tsegaye A(assistant Professor) 34
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
4/21/2023 Tsegaye A(assistant Professor) 35
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.
4/21/2023 Tsegaye A(assistant Professor) 36
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).
4/21/2023 Tsegaye A(assistant Professor) 37
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.
4/21/2023 Tsegaye A(assistant Professor) 38
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).
4/21/2023 Tsegaye A(assistant Professor) 39
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.
4/21/2023 Tsegaye A(assistant Professor) 40
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.
4/21/2023 Tsegaye A(assistant Professor) 41
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
4/21/2023 Tsegaye A(assistant Professor) 42
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
4/21/2023 Tsegaye A(assistant Professor) 43
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.
4/21/2023 Tsegaye A(assistant Professor) 44
GP vs GN
4/21/2023 Tsegaye A(assistant Professor) 45
GP vs GN
 Gram positive
 Staphylococcus
 Streptococcus
 Clostridium
 Bacillus
 Corynebacterium
 Gram negatives
 Neisseria spp
 Shigella
 Haemophilus spp
 Vibrio
 Salmonella
 Klebsiella
4/21/2023 Tsegaye A(assistant Professor) 46
GP vs GN
4/21/2023 Tsegaye A(assistant Professor) 47
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
4/21/2023 Tsegaye A(assistant Professor) 48
AFB Positive
4/21/2023 Tsegaye A(assistant Professor) 49
C)Special Stains
a) Capsule Staining Method
b) Spore Staining Method
c) Flagella Staining
4/21/2023 Tsegaye A(assistant Professor) 50
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.
4/21/2023 Tsegaye A(assistant Professor) 51
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
4/21/2023 Tsegaye A(assistant Professor) 52
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.
4/21/2023 Tsegaye A(assistant Professor) 53
Cont’d…
• Lowenstein-Jensen medium: selective
for mycobacteria
• Middlebrook agar: selective for
mycobacteria
4/21/2023 Tsegaye A(assistant Professor) 54
Transport media
Amies transport media
• Is used for transportation of gonococci.
Cary Blair transport media
• Is used for preserving & transporting enteric
pathogens.
4/21/2023 Tsegaye A(assistant Professor) 55
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
4/21/2023 Tsegaye A(assistant Professor) 56
Enrichment media
• This term is usually applied to fluid
selective media
• E.g. Tryptosoya broth & Selenite F broth
4/21/2023 Tsegaye A(assistant Professor) 57
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
4/21/2023 Tsegaye A(assistant Professor) 58
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.
4/21/2023 Tsegaye A(assistant Professor) 59
Serodiagnosis
• A high or rising titter of specific IgG antibodies or
• The presence of specific IgM antibodies may suggest
or confirm a diagnosis.
4/21/2023 Tsegaye A(assistant Professor) 60
Antimicrobial Susceptibility
• Microorganisms, particularly bacteria, are tested in
vitro to determine whether they are susceptible to
antimicrobial agents.
4/21/2023 Tsegaye A(assistant Professor) 61
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
4/21/2023 Tsegaye A(assistant Professor) 62
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
4/21/2023 Tsegaye A(assistant Professor) 63
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
4/21/2023 Tsegaye A(assistant Professor) 64
Cont’d…
• Histopathologic Methods
• Routine stains (H & E)
• Spécial Stains:
•Gomori Methanamine silver (GMS)
•Periodic acid–Schiff (PAS)
•Direct immunofluorescence
4/21/2023 Tsegaye A(assistant Professor) 65
Cont’d…
Immunologic Methods
• Antibody
• Antigen
Molecular Methods
• Direct detection (nucleic acid amplification)
• Identification
• Strain typing
Biochemical Methods
• Metabolites
• Cell wall components
• Enzymes
4/21/2023 Tsegaye A(assistant Professor) 66
Prevention & Control of
Infectious Disease
4/21/2023 Tsegaye A(assistant Professor) 67
Infectious Process
68
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
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
The stages in the natural history of
disease
71
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
Components of Infectious Disease
Process
 Infectious diseases result from the interaction of
 Infectious agent
 Susceptible host
 Environment
73
The epidemiologic triad or triangle is the traditional
model of infectious disease causation
74
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.
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
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
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
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
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
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
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
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
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
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
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.
86
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.
87
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
88
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.
89
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
90

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Laboratory Diagnosis of infections.pptx

  • 1. Lab Diagnosis of Infectious Diseases Tsegaye A. (assistant Professor of Microbiology) 4/21/2023 Tsegaye A(assistant Professor) 1
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 2
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 3
  • 4. Specimen collection, transportation, detection & identification of microorganism 4/21/2023 Tsegaye A(assistant Professor) 4
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 5
  • 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 4/21/2023 Tsegaye A(assistant Professor) 6
  • 7. Commensals • Blood does not have a normal microbial flora. • Common skin contaminants include  CoNS  V. streptococci  Micrococci, &  Corynebacterium species 4/21/2023 Tsegaye A(assistant Professor) 7
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 8
  • 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 4/21/2023 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. 4/21/2023 Tsegaye A (assistant Professor) 10
  • 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 4/21/2023 Tsegaye A(assistant Professor) 11
  • 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 4/21/2023 Tsegaye A(assistant Professor) 12
  • 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 4/21/2023 Tsegaye A(assistant Professor) 13
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 14
  • 15. Possible pathogen in throat & mouth specimens Gram positive • S. pyogenes • C. diphtheriae • C. ulcerans  Gram negative • Vincent’s organisms (Borrelia vincenti) 4/21/2023 Tsegaye A(assistant Professor) 15
  • 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 4/21/2023 Tsegaye A(assistant Professor) 16
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 17
  • 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 4/21/2023 Tsegaye A(assistant Professor) 18
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 19
  • 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 4/21/2023 Tsegaye A(assistant Professor) 20
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 21
  • 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 4/21/2023 Tsegaye A(assistant Professor) 22
  • 23. Commensals Gram positive • Staphylococci • Micrococci • V. streptococci • Enterococci • Diphtheroids • Propionibacterium acnes  Gram negative • E. coli • Coliforms 4/21/2023 Tsegaye A(assistant Professor) 23
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 24
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 25
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 26
  • 27. Possible pathogen Gram positive • S. saprophyticus • E. faecalis • Enterobacter aerogenes  Gram negative • E. coli • Proteus species • P. aeruginosa • Klebsiella Species • S. marcescens 4/21/2023 Tsegaye A(assistant Professor) 27
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 28
  • 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 4/21/2023 Tsegaye A(assistant Professor) 29
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 30
  • 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 4/21/2023 Tsegaye A(assistant Professor) 31
  • 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. 4/21/2023 32 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” 4/21/2023 Tsegaye A(assistant Professor) 33
  • 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 4/21/2023 Tsegaye A(assistant Professor) 34
  • 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 4/21/2023 Tsegaye A(assistant Professor) 35
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 36
  • 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). 4/21/2023 Tsegaye A(assistant Professor) 37
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 38
  • 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). 4/21/2023 Tsegaye A(assistant Professor) 39
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 40
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 41
  • 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 4/21/2023 Tsegaye A(assistant Professor) 42
  • 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 4/21/2023 Tsegaye A(assistant Professor) 43
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 44
  • 45. GP vs GN 4/21/2023 Tsegaye A(assistant Professor) 45
  • 46. GP vs GN  Gram positive  Staphylococcus  Streptococcus  Clostridium  Bacillus  Corynebacterium  Gram negatives  Neisseria spp  Shigella  Haemophilus spp  Vibrio  Salmonella  Klebsiella 4/21/2023 Tsegaye A(assistant Professor) 46
  • 47. GP vs GN 4/21/2023 Tsegaye A(assistant Professor) 47
  • 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 4/21/2023 Tsegaye A(assistant Professor) 48
  • 49. AFB Positive 4/21/2023 Tsegaye A(assistant Professor) 49
  • 50. C)Special Stains a) Capsule Staining Method b) Spore Staining Method c) Flagella Staining 4/21/2023 Tsegaye A(assistant Professor) 50
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 51
  • 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 4/21/2023 Tsegaye A(assistant Professor) 52
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 53
  • 54. Cont’d… • Lowenstein-Jensen medium: selective for mycobacteria • Middlebrook agar: selective for mycobacteria 4/21/2023 Tsegaye A(assistant Professor) 54
  • 55. Transport media Amies transport media • Is used for transportation of gonococci. Cary Blair transport media • Is used for preserving & transporting enteric pathogens. 4/21/2023 Tsegaye A(assistant Professor) 55
  • 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 4/21/2023 Tsegaye A(assistant Professor) 56
  • 57. Enrichment media • This term is usually applied to fluid selective media • E.g. Tryptosoya broth & Selenite F broth 4/21/2023 Tsegaye A(assistant Professor) 57
  • 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 4/21/2023 Tsegaye A(assistant Professor) 58
  • 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. 4/21/2023 Tsegaye A(assistant Professor) 59
  • 60. Serodiagnosis • A high or rising titter of specific IgG antibodies or • The presence of specific IgM antibodies may suggest or confirm a diagnosis. 4/21/2023 Tsegaye A(assistant Professor) 60
  • 61. Antimicrobial Susceptibility • Microorganisms, particularly bacteria, are tested in vitro to determine whether they are susceptible to antimicrobial agents. 4/21/2023 Tsegaye A(assistant Professor) 61
  • 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 4/21/2023 Tsegaye A(assistant Professor) 62
  • 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 4/21/2023 Tsegaye A(assistant Professor) 63
  • 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 4/21/2023 Tsegaye A(assistant Professor) 64
  • 65. Cont’d… • Histopathologic Methods • Routine stains (H & E) • Spécial Stains: •Gomori Methanamine silver (GMS) •Periodic acid–Schiff (PAS) •Direct immunofluorescence 4/21/2023 Tsegaye A(assistant Professor) 65
  • 66. Cont’d… Immunologic Methods • Antibody • Antigen Molecular Methods • Direct detection (nucleic acid amplification) • Identification • Strain typing Biochemical Methods • Metabolites • Cell wall components • Enzymes 4/21/2023 Tsegaye A(assistant Professor) 66
  • 67. Prevention & Control of Infectious Disease 4/21/2023 Tsegaye A(assistant Professor) 67
  • 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
  • 71. The stages in the natural history of disease 71
  • 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. 86
  • 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. 87
  • 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 88
  • 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. 89
  • 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 90

Editor's Notes

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