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A SEMINAR PRESENTATION ON LABORATORY DIAGNOSIS OF
UPPER AND LOWER RESPIRATORY TRACT
INFECTIONSBY:
OGUNWOLA, OLUWATOSIN OPEYEMI
MARCH, 2016.
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INTRODUCTION 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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INTRODUCTION CONT’D 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.
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INTRODUCTION CONT’D 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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INTRODUCTION CONT’D
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INTRODUCTION CONT’D
URTIs have been characterized as acute febrile illnesses presentingwith 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.
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EPIDEMIOLOGY 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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PATHOGENESISCommon 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 discharge2. Nasal obstruction3. Sneezing4. Cough5. Fever may be present
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PATHOGENESIS CONT’DPharyngitisPharyngitis, 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.
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PATHOGENESIS CONT’DPneumonia
Acute pneumonia has its onset either prior to or immediately 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.
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PATHOGENESIS CONT’D
Others include: Acute sinusitis Laryngitis Tonsillitis Epiglottitis Rhinitis Nasopharyngitis Bronchitis
1. Tracheobronchitis2. Acute bronchitis3. Chronic bronchitis
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Features of pneumonia caused by different organisms
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PATHOGENESIS CONT’DPULMONARY 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
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PATHOGENESIS CONT’D
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).
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Organisms that infects the Respiratory tractBACTERIA FUNGI VIRUSESStreptococcus 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 virusArcanobacterium haemolyticumKlebsiella pneumoniae
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PHYSIO-ANATOMICAL DEFENCE MECHANISMS
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CLINICAL FEATURESThe features of different respiratory tract infectionslargely depend on the structures where inflammation
islocalised 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 byviruses and are self-limiting
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SAMPLES COLLECTED Throat swab Saliva Sputum Pleural aspirates Bronchial aspirates Nasal swab Pernasal swab
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LABORATORY DIAGNOSIS COLLECTION OF RESPIRATORY TRACT
SPECIMENSSpecimens should be collected before the commencement of antibiotic therapy by an experienced physician, nurse or laboratory scientist.
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LABORATORY DIAGNOSIS CONT’D
RECEPTIONThe 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.
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The diagnosis for each samples includes:SITE OF CCOLLECTION
TYPE OF SAMPLE
INCRIMINATING PATHOGENS
DIAGNOSIS
1. Anterior nares Nasal Swab 1. Streptococcus pneumoniae2. Haemophilus influenzae4. Staphylococcus aureus5. Gram negative bacilli
• Microscopy• Gram stain• Culture• Biochemical
tests
2. Pharynx and Larynx
Throat swabPernasal swabSputum
1. Streptococcus pneumoniae2. Staphylococcus aureus3. Gram negative bacilli
• Microscopy• Gram stain• Culture• Biochemical
tests
3. Trachea, bronchi and lungs
•Tracheal aspirates•Pleural aspirates•Blood
1. Same as larynx2. Neisseria gonorrhea
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PATHOGENS AVAILABLE ASSAYSLegionella species Culture of respiratory secretions and tissues on buffered
charcoal yeast extracts(BCYE)SerologyPCR
Chlamydia species SerologyCulturePCR
Mycoplasma pneumoniae SerologyCulture
VIRUSES
Herpse Simplex virus Virus isolation and PCR
Varicella-zoster virus Virus isolationDirect Fluorescent Antibody test
FUNGI
Cryptococcus species Gomori methanamine stainCalcoflour whitePeriodic Acid Schiff
Candida species Gram stainGomori methanamine stainCalcoflour whitePeriodic Acid Schiff
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TRADITIONAL METHODS OF LABORATORY DIAGNOSIS
Gram reaction (direct gram) Culture on MacConkey and Chocolate agars Microscopical examination of wet preparation Biochemical tests
Susceptibility testing
Gram Positive Cocci Gram Negative cocci Gram Negative Bacilli
Catalase Catalase OxidaseCoagulase Coagulase MotilityOptochin IndoleBacitracin Citrate
Urease
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LABORATORY DIAGNOSIS CONT’D
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:PCRELISA
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LABORATORY DIAGNOSIS CONT’DDIAGNOSIS OF SPUTUM FOR TUBERCULOSISSample 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.
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LABORATORY DIAGNOSIS CONT’DDiagnosis 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. Culture3. 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.
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DIAGNOSIS OF SPUTUM The radiographic appearance of the neck and lungs in
tuberculosis
A. X-ray of the neck B. X-ray of the lungs
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LABORATORY DIAGNOSIS CONT’D
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:PCRELISA
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LABORATORY DIAGNOSIS CONT’D
Serology
Chlamydia species Neisseria meningitidis Sources: Laboratory images http://www.krackeler.com/graphics/0010/jpg/3506.jpg
IMAGES OF SEROLOGICAL KITS
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REFERENCES 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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REFERENCES CONT’D 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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