The document provides guidelines for collecting and transporting respiratory tract specimen for various infections, including proper labeling and storage. It describes common respiratory tract infections like pneumonia, their causes, symptoms, and treatment options. Pneumonia is classified as lobar, bronchopneumonia, or interstitial based on anatomical location and involvement; and as typical, atypical, community-acquired, or hospital-acquired based on etiology.

1. Respiratory Tract Infections Professor Mark Pallen Dr Kamran Afzal Classified Microbiologist

2. Throat/Nasal Swab specimens Taken under direct visualization with good lighting Areas of exudation, membrane formation or inflammation are choice sites, otherwise rub the tonsillar crypts For Bordetella pertussis , collect nasopharyngeal or per nasal swab Inform lab in advance to prepare fresh culture media for this organism

3. For viral agents, instruct patient to gargle with nutrient broth For M. leprae , nasal swab or nasal washing is used TRANSPORTATION Streptococcal pharyngitis or Diphtheria Stuart tpt medium, silica gel Whooping cough Bordetella tpt medium Viral infection VTM, but if delay, keep at -70 0 C

4. Collection of Sputum specimens Specimen obtained before start of antibiotic therapy If started, inform lab about antibiotics Instruct patient appropriately Proper labeling Patient’s name, test type, date, clinical info Preferably collect in working hours Collect specimen as early as possible in acute phase, these agents tend to disappear rapidly after the onset of symptoms All specimens for viral culture to be frozen and stored at -70 o C

5. Give the patient a dry, wide mouthed, leak proof container Collect sufficient quantity, sterile container Early morning specimen is preferred Patient should cough deeply to produce a sputum specimen For MTB culture, collect 3 x fresh, early morning specimens, keep in a refrigerator to be pooled or processed individually In un-cooperative patients, MTB may be recovered from gastric aspiration in the ward

6. Respiratory tract defences Ventilatory flow Cough Mucociliary clearance mechanisms Mucosal immune system

7. Predisposing factors for RTIs Low immunity Environmental pollution Smoking Bad nutrition Tumors Alcohol Decreased cough reflex Injury to cilia Decreased function of alveolar macrophages Edema or congestion Retention of secretions

8. Upper respiratory tract infections (URTIs)

9. 1. Cold and Flu Causative organisms Rhino, corona, adeno and parainfluenza viruses A novel respiratory pathogen (hMPV) Causes respiratory illness in elderly, young children and immunocompromised patients Symptoms Coryzal symptoms, rhinitis, pharyngitis, laryngitis Management Symptomatic and consists of rest, adequate hydration, simple analgesics and antipyretics Antibacterials are not effective and cause adverse consequences of its overuse in treatment of viral infections

10. 2. Influenza Causative organisms Influenza viruses (A, B and C) Symptoms Severe malaise and myalgia complicated by life-threatening secondary bacterial infections as staphylococcal pneumonia Management Neuraminidase inhibitors (Zanamivir and oseltamivir)

11. 3. Sore throat (pharyngitis) Causative organism Streptococcus pyogenes Symptoms Ranging from fever and symptoms of common cold to inflammation of pharynx with whitish exudate on the tonsils plus enlarged tender cervical lymph nodes Diagnosis Is a must to differentiate between viral or streptococcal infections by taking a throat swab for culture Treatment Wait for results of culture before starting antibiotics Penicillins, cephalosporins and macrolides

12. 3. Laryngitis Most commonly upper respiratory viruses Diphtheria C. diphtheriae produces a cytotoxic exotoxin causing tissue necrosis at site of infection with associated acute inflammation Membrane may narrow airway and/or slough off (asphyxiation)

13. 4. Acute epiglottitis H. influenzae type B Another cause of acute severe airway compromise in childhood

14. 5. Otitis media Causative organisms Inflammation of middle ear seen most frequently in children under 3 years Streptococcus pneumoniae , H. influenzae, Strep. pyogenes Symptoms Ear pain, if the drum perforates, the pain is relieved and a purulent discharge follows Treatment It should be effective against the 3 main bacterial pathogens Co-amoxiclav or the newer cefixime having high activity against H. influenzae

15. 6. Acute sinusitis Causative organisms Caused by similar organisms as otitis media Viral upper respiratory tract infections Sometimes associated with dental disease Symptoms Facial pain and tenderness accompanied by headache and purulent nasal discharge Treatment As otitis media Addition of metronidazole (dental disease)

16. Lower respiratory tract infections (LRTIs)

17. 1. Acute bronchitis Acute bronchitis is usually infective Chronic bronchitis is a chronic inflammatory condition characterized by thickened, edematous bronchial mucosa with mucus gland hypertrophy and usually caused by smoking Symptoms Yellow or green sputum (pus cells), wheezing Treatment Airflow optimization Physiotherapy to aid expectoration, oxygen and bronchodilatation Antibiotic therapy First-line agents: Doxycycline, Amoxicillin Second-line agents: Co-amoxiclav, clarithromycin, cefixime Others: Moxifloxacin, a quinolone effective against gram +ve and -ve

18. 2. Bronchiolitis It is characterized by inflammatory changes in the small bronchi and bronchioles but not by consolidation It attacks infants in the 1 st year of life (airway narrowing) Causative organism Respiratory syncytial virus (RSV) Symptoms Fever, coryzal symptoms which progresses to wheezing, respiratory distress and hypoxia Diagnosis Viral culture of respiratory secretion or IF Treatment Supportive: oxygen, adequate hydration and vent. assistance Severe cases: Ribavirin

19. 3. Lung abscess Localized suppurative necrosis Organisms commonly cultured Staphylococci Streptococci Gram-negative Anaerobes Frequent mixed infections Pathogenesis Aspiration Pneumonia Septic emboli Tumors Bronchiectasis

20. 4. Bronchiectasis Dilatation of bronchi and bronchioles secondary to chronic inflammation Usually due to fibrous scarring following infection (pneumonia, tuberculosis, cystic fibrosis) Dilated airways accumulate purulent secretions Associated conditions Obstruction Cystic fibrosis Immotile cilia syndromes Necrotizing pneumonia

21. 5. Pulmonary tuberculosis M. tuberculosis/M.bovis main pathogens in man Others cause atypical infection especially in immunocompromised host Transmitted through inhalation of infected droplets T-cell response causes granulomatous inflammation, tissue necrosis and scarring - Hypersensitivity (type IV) Pathogenicity due to ability to avoid phagocytosis to stimulate a host T-cell response

22. Pathology Cavitary fibrocaseous lesions Bronchopneumonia Miliary TB Miliary Granuloma Fibrocaseous Mycobacterium

23. Primary and secondary TB Primary The site of infection shows non-specific inflammation with developing granulomas in nodes Secondary There are primed T cells which stimulate a localised granulomatous response

24. 6. Pneumonia Pneumonia is defined as inflammation of alveoli and interstitium of the lungs of infective origin and characterized by consolidation Alveoli are filled with a mixture of inflammatory exudates, bacteria and WBCs (opaque shadow on chest X-ray) It is classified as Community-acquired Hospital-acquired Opportunistic

25. Microbial Pathogens Causing Pneumonia Pneumocystis carinii S. pneumoniae H. Influenzae M. tuberculosis Enteric aerobic gram-negative bacilli Staph. aureus Pseudomonas aeruginosa Oral anaerobes Streptococcus pneumoniae Haemophilus influenzae Mycoplasma pneumoniae Chlamydia pneumoniae Legionella pneumophila Moraxella catarrhalis Staphylococcus aureus Nocardia spp. Mycobacterium tuberculosis Chlamydia psittacii Oral anaerobes Viruses Fungi Opportunistic Hospital-Acquired Community-Acquired

26. A. Community-acquired pneumonia Causative organisms Strep. pneumoniae causes both lobar and bronchopneumonia H. influenzae causes bronchopneumonia, also causes secondary bacterial pneumonia on primary viral pneumonia L. pneumophila is the cause of Legionnaire’s disease occurring sporadically and in outbreaks associated with contaminated air-conditioning or water systems, rapidly progressive with extensive consolidation and respiratory failure Chickenpox is complicated by primary varicella pneumonia

27. Symptoms Pneumococcal lobar pneumonia: Dry cough but later produce purulent or blood-stained, rust-colored sputum, dyspnea, fever, pleuritic chest pain Chest X-ray shows consolidation in one or two lobes

28. B. Hospital-acquired pneumonia Causative organisms Gram-negative bacilli, Staph aureus , pneumococcal pneumonia and Legionella infection Ventilator-associated pneumonia (VAP) is acquired in ICUs where broad spectrum antibiotics are frequently used and where there is resident flora with an antibiotic resistance pattern Symptoms Nosocomial pneumonia accounts for 10-15% of all hospital-acquired infections presenting with sepsis and respiratory failure Predisposing features: stroke, mechanical ventilation, chronic lung disease, recent surgery and broad spectrum antibiotic exposure

29. Aspiration pneumonia It can be seen in community or hospital Caused by inhalation of stomach contents contaminated by bacteria from the mouth (when the patient vomits while unconscious) Anaerobic bacteria are implicated often accompanied by aerobic organisms Gastric acid is very destructive to lung tissue causing severe tissue necrosis and infection with abscess Risk factors Alcohol, hypnotic drugs and GA Treatment Metronidazole plus amoxicillin or metronidazole plus cefotaxime if you suspect gram-negative infection

30. C. Opportunistic pneumonias Infections that affect immunosuppressed patients Associated disorders AIDS Cancer patients Transplant recipients Pneumocystis carinii Aspergillus Cytomegalovirus

31. Anatomical Classification LOBAR PNEUMONIA BRONCHOPNEUMONIA INTERSTITIAL

32. LOBAR PNEUMONIA Involvement of the entire lung lobe BRONCHOPNEUMONIA Patchy consolidation in 1 or several lobes, usually in dependent lower or posterior portions centered around bronchi and bronchioles INTERSTITIAL PNEUMONIA Inflammation of the interstitium, including the alveolar walls and connective tissue around the bronchovascular tree MILIARY PNEUMONIA Numerous discrete lesions due to hematogenous spread

33. A. Lobar Pneumonia Confluent consolidation involving a complete lung lobe Most often due to Streptococcus pneumoniae Can be seen with other organisms ( Klebsiella, Legionella )

34. Pathology Lung Congestion Red hepatisation Grey hepatisation Resolution A classical acute inflammatory response Exudation of fibrin-rich fluid Neutrophil infiltration Macrophage infiltration Resolution Immune system plays a part Antibodies lead to opsonisation, phagocytosis of bacteria

35. Pathogenesis Inhalation of air droplets Aspiration of infected secretions or objects Hematogenous spread

36. B. Bronchopneumonia The consolidation is patchy and not confined by lobar architecture Infection starts in airways and spreads to adjacent alveolar lung More varied microbiology Strep. pneumoniae, Haemophilus influenzae, Staphylococcus , anaerobes, coliforms Clinical context may help Staph/anaerobes/coliforms seen in aspiration

37. Viral pneumonia Gives a pattern of acute injury similar to adult respiratory distress syndrome (ARDS) Acute inflammatory infiltration less obvious Viral inclusions sometimes seen in epithelial cells

38. C. Atypical Pneumonia Atypical pneumonia is caused by atypical bacteria that do not stain with Gram stain or do not fit in any category like in virus or bacteria The inflammation is confined to interstitial spaces between alveoli Radiologically gives appearance of reticulo-nodular pattern Linear thread like opacities in lungs

39. Comparison Not prominent Prominent (myalgia, fatigue, N/V, diarrhea) Extra-pulmonary symptoms Purulent Scanty Sputum Productive cough Dry cough Cough Abrupt Gradual Onset S. pneumoniae , H. influenzae , K. pneumoniae , mixed aerobic and anaerobic oral flora M. pneumoniae , L. pneumophilia, C. pneumophilla, viruses, protozoa and fungi Etiology TYPICAL PNEUMONIA ATYPICAL PNEUMONIA

40. Investigations Microscopy is unreliable due to oropharyngeal contamination Gram stain ZN stain for AFB Sputum culture is the mainstay of diagnosis for pneumonia caused by pneumococci and H. influenzae Total and differential blood count Blood, urine, sputum -> Culture/sensitivity Serological investigations Antigen detection in sputum or urine by Fluorescent methods, Immunoelectrophoresis, Latex agglutination, ELISA

41. Fibreoptic bronchoscopy with bronchial washing/ brushing /biopsy -> Histopathology (more sensitive but more invasive) Molecular techniques Radiology -> CXR, MRI and CT scan Serology By serological methods using acute and convalescent sera Significantly raised titer or rising titer of antibodies give clues to diagnosis

42. Specific Serological Tests Legionella pneumophila Rapid microagglutination test Test for Legionella antigen in the urine Mycoplasma pneumoniae Complement fixation test IgM by latex agglutination or ELISA Cold agglutinin test

43. Chlamydia Microimmunofluorescence ELISA Coxiella burnetii Complement fixation test Serologic tests A four fold or greater rise in titer is confirmatory of an acute infection

44. Treatment Targeted treatment Pneumococcal pneumonia Benzyl penicillin or Amoxicillin Erythromycin (in penicillin-allergic patients) Combined β - lactam + macrolide when pneumonia is complicated by pneumococcal bacteremia H. influenzae Co-amoxiclav, parenteral cefuroxime, cefixime Clarithromycin and azithromycin

45. Morexella pneumonia Doesn’t possess cell wall so not susceptible to β -lactams Tetracyclins and quinolones Staphylococcal pneumonia Flucloxacillin + a second agent as rifampicin, fusidic acid or gentamycin Legionnaire’s disease Erythromycin or azithromycin

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