2.  The respiratory system is a system of organs functioning in
respiration and in humans consisting esp. of the nose, nasal
passages, pharynx, larynx, trachea, bronchi, and lungs
 The respiratory tract is the site of an exceptionally large range of
disorders for three main reasons:
 It is exposed to the environment and therefore may be affected
by inhaled organisms, dusts, or gases
 It possesses a large network of capillaries through which the
entire output of the heart has to pass, which means that diseases
that affect the small blood vessels are likely to affect the lungs
 It may be the site of “sensitivity” or allergy that may profoundly
affect the functioning of the entire body systems.
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3.  The upper respiratory tract as defined, is the anatomic
area extending from the anterior nasal passages to the
larynx.
 Upper respiratory tract infection (URTI) has been
recognized as one of the most common medical
problems in the daily lives of people worldwide.
 URTIs can be characterized by a group of disorders
which include common cold, pharyngitis, tonsillitis,
epiglottitis, sinusitis, bronchitis, rhinitis, and
nasopharyngitis, which significantly occurs in upper
respiratory tract.
3

4.  The lower respiratory tract therefore comprises of the
anatomical region extending from the trachea to the
lungs.
 Due to its location and the activities of the lungs in
oxygenation, the Lower respiratory tract, by all
standards, is a sterile part of the body, hence lower
respiratory tract infections are minimal.
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5. 5

6. URTIs have been characterized as acute febrile
illnesses presenting
with cough, coryza, sore throat, and hoarseness,
which forms the prime reason to get affected by
URTI.
However, it has been suggested that the vast
majority of URTIs cases have been benign, and
thus, the exact aetiology of URTIs has not been
understood completely.
The infection show various symptoms like
coughing, sore throat, sneezing, difficulty in
breathing, runny nose, muscle pain, and weakness.
6

7.  Upper respiratory tract infections are the most common
types of infectious diseases among adults. It is estimated
that each adult experiences two(2) to four(4) respiratory
infections annually.
 Lower RTIs are the less common but the most common
cause of deaths in developing countries.
 As of 2010, LRTIs caused about 2.8 million deaths
which is a slight fall when compared with the 3.4 million
in 1990.
 The morbidity of these infections is estimated to be about
75 million physician visits per year in developed
countries.
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8. Common cold
 The term common cold can be referred to as one of
the upper respiratory infection whose first infectious site is
the nose, which further radiates to throat and sinuses.
 It is caused by approximately 200 viruses, with a
developing time of symptoms of 7-10 days.
 It occurs frequently, especially in young during the dry
harmattan period.
Symptoms include:
1. Nasal discharge
2. Nasal obstruction
3. Sneezing
4. Cough
5. Fever may be present
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9. Pharyngitis
Pharyngitis, the inflammation of pharynx or throat at back
side, can be divided into two types, i.e., acute and
chronic.
In addition, the pharyngitis can be classified into viral
pharyngitis and bacterial pharyngitis according to their
cause.
It has been known to occur at an age of 4-8 years.
Factors like cold, allergies, toxic fumes, accumulation of
chemicals, and flu have been suggested to result in
pharyngitis.
9

10. Pneumonia
 Acute pneumonia has its onset either prior to or i
mmediately after admission to hospital. It is one of the
most common infectious causes of death worldwide.
 Patients with acute pneumonia usually have a
cough, chest signs and fever.
 The cough may or may not be productive of purulent
sputum. Chest signs are variable and prone to
subjective interpretation.
10

11. Others include:
 Acute sinusitis
 Laryngitis
 Tonsillitis
 Epiglottitis
 Rhinitis
 Nasopharyngitis
 Bronchitis
1. Tracheobronchitis
2. Acute bronchitis
3. Chronic bronchitis
11

12. Features of pneumonia caused by
different organisms
12

13. PULMONARY TUBERCULOSIS
Pulmonary tuberculosis is common throughout the
developing world.
Primary infection follows airborne transmission from
an individual with pulmonary tuberculosis.
Clinical Features Of Pulmonary Tuberculosis
 Fever
 Night sweats
 Weight loss
 Haemoptysis
13

14. Clinical Features Of Pulmonary Tuberculosis
 Fever
 Night sweats
 Weight loss
 Haemoptysis
Diagnosis of Sputum for Tuberculosis
Sputum should be subjected to acid fast stain (either by
Ziehl–Neelsen or auramine–phenol with the use of the
fluorescent microscope).
14

15.  Organisms that infects the Respiratory tract
15
BACTERIA FUNGI VIRUSES
Streptococcus pneumoniae Aspergillus niger Rhinoviruses
Staphylococcus aureus Corona viruses
Corynebacterium diphtheriae Adenoviruses
Streptococcus pyogenes Influenza virus
Mycobacterium tuberculosis Respiratory syncytial
virus
Pseudomonas aeruginosa Parainfluenza viruses
Haemophilus influenzae Epstein–Barr virus
Arcanobacterium haemolyticum
Klebsiella pneumoniae

16. 16

17. 17

18. The features of different respiratory tract infections
largely depend on the structures where inflammation is
localised and the extent to which function is altered.
So,
infection of the nasopharynx will result in a nasal
discharge, bronchitis in cough and sputum
production, and
pneumonia in cough and sputum, but also in increased
respiratory rate and chest radiograph changes.
Most upper respiratory tract infections are caused by
viruses and are self-limiting
18

19. SAMPLES COLLECTED
 Throat swab
 Saliva
 Sputum
 Pleural aspirates
 Bronchial aspirates
 Nasal swab
 Pernasal swab
19

20.  COLLECTION OF RESPIRATORY TRACT
SPECIMENS
Specimens should be collected before the
commencement of antibiotic therapy by an
experienced physician, nurse or laboratory
scientist.
20

21.  RECEPTION
The sample is forwarded from the clinicians in the wards to the
laboratory via a transport medium or in a ice- frozen flask
It is received at the reception and adequately recorded into the
various registers and sample jackets.
It is then taken into the laboratory for the laboratory diagnosis
proper.
21

22.  The diagnosis for each samples includes:
22
SITE OF
CCOLLECTIO
N
TYPE OF
SAMPLE
INCRIMINATING
PATHOGENS
DIAGNOSIS
1. Anterior nares Nasal Swab 1. Streptococcus pneumoniae
2. Haemophilus influenzae
4. Staphylococcus aureus
5. Gram negative bacilli
• Microscopy
• Gram stain
• Culture
• Biochemical
tests
2. Pharynx and
Larynx
Throat swab
Pernasal swab
Sputum
1. Streptococcus pneumoniae
2. Staphylococcus aureus
3. Gram negative bacilli
• Microscopy
• Gram stain
• Culture
• Biochemical
tests
3. Trachea,
bronchi and
lungs
•Tracheal
aspirates
•Pleural
aspirates
•Blood
1. Same as larynx
2. Neisseria gonorrhea

23. PATHOGENS AVAILABLE ASSAYS
Legionella species Culture of respiratory secretions and tissues on buffered
charcoal yeast extracts(BCYE)
Serology
PCR
Chlamydia species Serology
Culture
PCR
Mycoplasma pneumoniae Serology
Culture
VIRUSES
Herpse Simplex virus Virus isolation and PCR
Varicella-zoster virus Virus isolation
Direct Fluorescent Antibody test
FUNGI
Cryptococcus species Gomori methanamine stain
Calcoflour white
Periodic Acid Schiff
Candida species Gram stain
Gomori methanamine stain
Calcoflour white
23

24.  Gram reaction (direct gram)
 Culture on MacConkey and Chocolate agars
 Microscopical examination of wet preparation
 Biochemical tests
 Susceptibility testing
24
Gram Positive Cocci Gram Negative cocci Gram Negative
Bacilli
Catalase Catalase Oxidase
Coagulase Coagulase Motility
Optochin Indole
Bacitracin Citrate
Urease

25. NONE SPECIFIC TESTS
 Nucleic Acid Amplification Test (NAAT)
NAATs for the detection of upper and lower respiratory tract
infections offer several advantages over the traditional
detection methods, never the less it has some disadvantages in
cost, carryover contamination.
These NAATs include:
PCR
ELISA
25

26. DIAGNOSIS OF SPUTUM FOR TUBERCULOSIS
Sample collection
Three consecutive early morning specimens should be
stained in this way. Sputum specimens should be
treated as a potential infection hazard, with proper
warning given to ward, pottering and laboratory staff.
26

27. Diagnosis of Sputum for Tuberculosis
1. Sputum should be subjected to acid fast stain (either
by Ziehl–Neelsen or auramine–phenol with the use of the
fluorescent microscope).
2. Culture
3. Susceptibility Testing
The results of acid-fast stain can be provided the same
day, but culture, identification and susceptibility results
take several weeks because of the slow growth rate of
mycobacterium.
27

28.  The radiographic appearance of the neck and lungs in
tuberculosis

 A. X-ray of the neck B. X-ray of the lungs
28

29.  NUCLEIC ACID AMPLIFICATION TEST (NAAT)
NAATs for the detection of upper and lower respiratory tract
infections offer several advantages over the traditional
detection methods, never the less it has some disadvantages in
cost, carryover contamination.
These NAATs include:
PCR
ELISA
29

30.  Serology
 Chlamydia species Neisseria meningitidis
 Sources: Laboratory images http://www.krackeler.com/graphics/0010/jpg/3506.jpg
IMAGES OF SEROLOGICAL KITS
30

31.  Agius G., Dindinaud G., Biggar J., Peyre R., Vaillant V., Poupet J.Y.,
Cisse M.F., and Castets M. (1990). An epidemic of respiratory syncytial
virus in elderly people: clinical and serological findings. Journal of
Medical Virology. 30: 117–127.
 Bartlett J. G., Dowell S.F., Mandell L.A., and Fine M.J. (2000). Practice
guidelines for the management of community acquired pneumonia in
adults. Clinical Infectious Diseases. 31:347–382.
 Hindiyeh M.A., Hillyard D.Y., and Carroll K.C. (2001). Evaluation of the
Prodesse Hexaplex multiplex PCR assay for direct detection of seven
respiratory viruses in clinical specimens. American Journal of Clinical
Pathology. 116:218–224.
 Karen C. C (2002). Laboratory Diagnosis of Lower Respiratory Tract
Infections: Controversy and Conundrums. Journal Of Clinical
Microbiology. 40(9): 3115–3120
 Laboratory Diagnosis of Lower Respiratory Tract Infections, Cumitech,
7A, Sep. 1987.
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32.  Lozano R., Naghavi M., Foreman K., and Bolliger I. (2012). Global and regional
mortality from 235 causes of death for 20 age groups in 1990 and 2010; a
systematic analysis for the global burden of disease study. The Lancet Journal.
380: 2095-2128.
 Mortality and burden of diseases estimates for WHO member states in 2002.
World Health Organisation.
 Murdoch D. R., Laing R.T., Mills G.D., Karalus N.C., Town G.I., and
Reller L.B. (2001). Evaluation of a rapid immunochromatographic test for
detection of Streptococcus pneumoniae antigen in urine samples from adults with
community-acquired pneumonia. Journal of Clinical Microbiology. 39:3495–
3498.
 Reimer L.G., Carroll K.C. (2008). Role of the Microbiology Laboratory in the
Diagnosis of Lower Respiratory Tract Infections. Clinical Infectious Diseases.
26:743-748.
 The American Journal of Medicine, Continuing Education Series, New Challenges
in Respiratory Tract Infections and Causative Pathogens, Nov. 1997.
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33.  THANK YOU FOR LISTENING
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