1. Respiratory tract infections
Upper respiratory tract infections
Lower respiratory tract infections

2. At the end of this lesson
You should be able to list :
the microorganisms responsible from
-upper and lower respiratory tract infections
The laboratory tests used in the diagnosis

3. Upper respiratory tract infections
THE COMMON COLD
Rhinoviruses and
Coronaviruses together cause more than 50% of colds

4. Upper respiratory tract infections
PHARYNGITIS AND TONSILLITIS:
About 70% of acute sore throats are caused by viruses
Bacterial infections:
S. pyogenes (group A β-hemolytic) the commonest and most important to diagnose because it can lead to complications , but can be readily treated with penicillin

5. Beta-hemolytic colonies
S.pyogenes:-small
A grubu great zone of hemolysis
S. Agalatiae:-büyük koloni
B grubu -küçük zon 5

6. Bacteria responsible for pharyngitis
Strep. pyogenes (group A β-hemolytic)
Corynebacterium diphtheriae
Haemophilus influenzae (type B), which occasionally causes severe epiglottitis with obstruction of the airways, especially in young children
Borrelia vincentii together with certain fusiform bacilli, which can cause throat or gingival ulcers
Neisseria gonorrhoeae

7. Complications of S. pyogenes
Quinsy ( Peritonsillar abscess)
scarlet fever,
rheumatic fever,
rheumatic heart disease and glomerulonephritis

8. It is especially important to diagnose Strep
It is especially important to diagnose Strep. pyogenes infection by culture because of the possible complications
It remains susceptible to penicillin.
Resistance to erythromycin and tetracycline, however, is increasing.
Although during the winter months up to 16% of schoolchildren carry group A streptococci in the throat without symptoms, treatment is recommended.

9. A groubstreptococci
Rapid antigen test
Culture

10. Sample:Throat
Two swabs
Convinient transport medium

11. Rapid antigen test
Group specific carbohydrate antigen detection

12. Aglutinasyon negatif

13. Aglutinasyon pozitif

14. Rapid antigen test Duyarlılık(sensitivite):58-96%
Özgüllük (spesifisite):63-100%

15. Throat culture Gold standart (Culture) Antigen test(rapid)+
Antigen test(rapid)
Therefore applied together

16. Serologic tests
Streptococcal antibodies:
Poststreptococsic diseases

17. Antistreptolizin O (ASO)
In 3-6 weeks the maximum titre

18. Anti-DNaz B
In 6- 8 weeks maximum

19. In Rheumatic fever in only 80-85% ASO titre is high
anti-Dnase B should be tested

21. OTITIS AND SINUSITIS
Otitis and sinusitis can be caused by many viruses and a range of secondary bacterial invaders
Common causes of acute otitis media are viruses, Strep. pneumoniae and H. influenzae
This condition is extremely common in infants and small children, partly because the eustachian (auditory) tube is open more widely at this age.

22. Otitis externa Staph. aureus, Candida albicans and
Gram-negative opportunists

23. Acute sinusitis
The etiology and pathogenesis of acute sinusitis are similar to those of otitis media.
It may be possible to identify the causative bacteria by microscopy and culture of pus aspirated from the sinus, but sinus puncture is not often carried out.
In addition, as is the case for otitis media, the patient can be treated empirically with ampicillin or amoxicillin, or with the newer oral cephalosporins (e.g. cefixime) to deal with beta-lactamase-producing organisms.

24. ACUTE EPIGLOTTITIS
generally due to H. influenzae capsular type B infection
Acute epiglottitis is most often seen in young children.
Acute epiglottitis is an emergency and necessitates intubation and treatment with antibiotics
The H. influenzae type B (Hib) vaccine greatly reduces the frequency of this and other infections due to H. influenzae type B.

25. ORAL CAVITY
Saliva flushes the mouth and contains a variety of antibacterial substances
Changes in the oral flora produced by broad spectrum antibiotics and impaired immunity predispose to thrush
In the USA and Western Europe, 80-90% of people are colonized by Streptococcus mutans, which causes dental caries
Actinomyces viscosus, Actinobacillus and Bacteroides spp. are commonly involved in periodontal disease

26. Lower respiratory tract infections
Although the respiratory tract is continuous from the nose to the alveoli,
It is convenient to distinguish between infections of the upper and lower respiratory tract,
even though the same microorganisms might be implicated in infections of both.
These infections tend to be:
more severe than infections of the upper respiratory tract, and
the choice of appropriate antimicrobial therapy is important and
may be life saving.

27. LARYNGITIS AND TRACHEITIS
Parainfluenza viruses
RSV, influenza virus or an adenovirus.
Diphtheria
-hoarseness and a burning retrosternal pain.
-The larynx and trachea have non-expandable rings of cartilage in the wall, and are easily obstructed in children because of their narrowness. Swelling of the mucous membrane may lead to a dry cough and inspiratory stridor ('crowing') known as croup. Difficulty with respiration may lead to hospital admission.
Bacteria such as group A streptococci, Haemophilus influenzae and Staphylococcus aureus are less common causes of laryngitis and tracheitis.

28. DIPHTHERIA
caused by toxin-producing strains of Corynebacterium diphtheriae and can cause life-threatening respiratory obstruction
now rare in resource-rich countries due to widespread immunization with toxoid

29. DIPHTHERIA
They can colonize the pharynx (especially the tonsillar regions), the larynx, the nose and occasionally the genital tract.
The toxin destroys epithelial cells and polymorphs, and an ulcer forms, which is covered with a necrotic exudate forming a 'false membrane'. This soon becomes dark and malodorous, and bleeding occurs on attempting to remove it.
Nasopharyngeal diphtheria is the most severe form of the disease. When the larynx is involved, it can result in life-threatening respiratory obstruction.
Anterior nasal diphtheria is a mild form of the disease if it occurs on its own, because the toxin is less well absorbed from this site, and a nasal discharge may be the main symptom. The patient will, however, be highly infectious.

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31. DIPHTHERIA
Diphtheria toxin can cause fatal heart failure and a polyneuritis
Diphtheria is managed by immediate treatment with antitoxin and antibiotic
Diphtheria is a life-threatening disease, and clinical diagnosis is a matter of urgency. As soon as the diagnosis is suspected clinically, the patient is isolated to reduce the risk of the toxigenic strain spreading to other susceptible individuals, and treatment is begun with antitoxin.

32. DIPHTHERIA
The antitoxin is produced in horses, and tests for hypersensitivity to horse serum should be carried out. Penicillin or erythromycin is given as an adjunct. Laryngeal diphtheria may require a tracheotomy to assist with respiration
The diagnosis is confirmed in the laboratory by isolation and identification of the organism
and demonstrating toxin production by a gel-diffusion precipitin reaction (Elek test).

33. Diphtheria toxin
The genes encoding toxin production are carried by a temperate bacteriophage which, during the lysogenic phase, is integrated into the bacterial chromosome. The toxin is synthesized as a single polypeptide consisting of: fragment B (binding) at the carboxy terminal end, which attaches the toxin to the host cells (or to any eukaryotic cell)
fragment A (active) at the amino terminal end, which is the toxic fragment.

34. WHOOPING COUGH Bordetella pertussis
Pertussis is a severe disease of childhood.
Bordetella pertussis is confined to humans and is spread from person to person by air-borne droplets.
B. pertussis infection is associated with the production of a variety of toxic factors

35. WHOOPING COUGH
B. pertussis infection is characterized by paroxysms of coughs followed by a 'whoop’
Whooping cough is managed with supportive care and erythromycin
Whooping cough can be prevented by active immunization

36. ACUTE BRONCHITIS rhinoviruses coronaviruses, influenza virus,
Adenoviruses
Mycoplasma pneumoniae.
Secondary bacterial infection with Streptococcus pneumoniae and Haemophilus influenzae may also play a role in pathogenesis

37. BRONCHIOLITIS
Some 75% of bronchiolitis infections are caused by respiratory syncytial virus
Bronchiolitis is a disease restricted to childhood, and usually to children under 2 years of age.
As many as 75% of these infections are caused by respiratory syncytial virus (RSV) and most of the remaining 25% are also of viral etiology, although Mycoplasma pneumoniae is implicated occasionally.

38. RESPIRATORY SYNCYTIAL VIRUS INFECTION
RSV is the most important cause of bronchiolitis and pneumonia in infants
RSV infection can be particularly severe in young infants

39. RESPIRATORY SYNCYTIAL VIRUS INFECTION
In most children, treatment is supportive, involving hydration, bronchodilators and, if needing admission to hospital, oxygen.
The antiviral agent ribavirin, given as an aerosol, has been used successfully in a number of clinical settings, including children with severe infection and immunosuppressed individuals at risk of severe disease.
A monoclonal antibody, palivizumab, can be used as prophylaxis to prevent RSV infection in under-2-year-old infants at risk of severe disease such as those with chronic lung disease, congenital heart disease or those born at <32 weeks of age.
At present, there is no vaccine available.

40. HANTAVIRUS CARDIOPULMONARY SYNDROME (HCPS)
The reservoir host for Sin Nombre virus (SNV), a New World hantavirus, is the deer mouse found commonly in North America. In 1993, individuals were infected in south-west USA and developed severe cardiopulmonary disease. HCPS followed flu-like symptoms as viral invasion of the pulmonary capillary endothelium led to fluid pouring into the lungs due to increased vascular permeability, and at least 26 deaths were reported secondary to pulmonary edema, hypotension and cardiogenic shock. The route of transmission is by inhaling SNV-infected rodent feces, saliva or urine. The Old World hantaviruses cause hemorrhagic fever with renal syndrome. The pathogenesis of both diseases is thought to involve aberrant immune responses by SNV-infected endothelial cells that are also involved in regulating vascular permeability. By 2005, around 380 individuals with HCPS had been reported in the USA, with a 38% mortality rate.

41. PNEUMONIA
Pneumonia has long been known as 'the old man's friend' as it is the most common cause of infection-related death in the USA and Europe. It is caused by a wide range of microorganisms giving rise to indistinguishable symptoms. The challenge lies not in the clinical diagnosis of pneumonia - except perhaps in children, in whom it may be more difficult to diagnose - but in the laboratory identification of the microbial cause.
Microorganisms reach the lungs by inhalation, aspiration or via the blood

42. Four types of pneumonia.
(A) Pneumococcal lobar pneumonia, showing consolidated alveoli filled with neutrophils and fibrin.
(B) Mycoplasma bronchopneumonia, with patchy consolidation in several areas of both lungs.
(C) Interstitial pneumonia due to influenza virus.
(D) Lung abscess, showing an abscess cavity in the lower lobe of the right lung.

43. Causes of pneumonia related to age
Children
Mainly viral (e.g. respiratory syncytial virus, parainfluenza) or bacterial secondary to viral respiratory infection (e.g. after measles)
Neonates may develop interstitial pneumonitis caused by Chlamydia trachomatis acquired from the mother at birth

44. Causes of pneumonia related to age
Adults
Bacterial causes more common than viral
Etiology varies with age, underlying disease, occupational and geographic risk factors

45. BACTERIAL PNEUMONIA
Streptococcus pneumoniae is the classic bacterial cause of acute community-acquired pneumonia
In the past, 50-90% of pneumonias were caused by Streptococcus pneumoniae (the 'pneumococcus'), but the relative importance of this pathogen has decreased and it now causes only 25-60% of cases Haemophilus influenzae is estimated to be the cause of 5-15% of cases, but the true incidence is difficult to determine because this organism frequently colonizes the upper respiratory tract of bronchitic patients

46. BACTERIAL PNEUMONIA Streptococcus pneumoniae Legionella pneumophila
Mycoplasma and Chlamydia
Haemophilus influenzae
Moraxella catarrhalis
Staphylococcus aureus

47. BACTERIAL PNEUMONIA
Patients with pneumonia usually present feeling unwell and with a fever
Pneumonia is the most common cause of death from infection in the elderly
Sputum samples are best collected in the morning and before breakfast
It is important that the specimen submitted for examination is truly sputum and not simply saliva.

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49. The usual laboratory procedures on sputum
Gram stain and culture
a host response in the form of abundant polymorphs and the putative pathogen, e.g. Gram-positive diplococci characteristic of Streptococcus pneumoniae .
The presence of organisms in the absence of polymorphs is suggestive of contamination of the specimen rather than infection, but it is important to remember that immunocompromised patients may not be able to mount a polymorph leukocyte response. Also, remember that the causative agents of atypical pneumonia, with the exception of Legionella pneumophila , will not be seen in Gram-stained smears.

50. Standard culture techniques
will allow the growth of the bacterial pathogens such as Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae and Klebsiella pneumoniae and other non-fastidious Gram-negative rods.
Special media or conditions are required for the causative agents of atypical pneumonia, including Legionella
Rapid non-cultural techniques have been applied successfully to the diagnosis of pneumococcal pneumonia. Detection of pneumococcal antigen by agglutination of antibody-coated latex particles can be used with both sputum and urine specimens, as antigen is excreted in the urine. Use of this technique means the result is available within 1 h of receipt of the specimen, but antibiotic susceptibility tests cannot be performed unless the organisms are isolated.

51. Microbiologic diagnosis of atypical pneumonia is usually confirmed by serology or PCR:
Mycoplasma pneumoniae:ELISA:IgM
Legionella pneumophila: Urinary antigen test
Chlamydophila pneumoniae Chlamydophila psittaci :Microimmunofluorescence or ELISA using species-specific antigens
Coxiella burnetii:ELISA IgM

52. Pneumonia is treated with appropriate antimicrobial therapy
Prevention of pneumonia involves measures to minimize exposure, and pneumococcal immunization post-splenectomy and for those with sickle cell disease

53. Viral pneumonia Influenza A or B Parainfluenza (types 1-4) Measles
Respiratory syncytial virus
Adenovirus
Varicella-zoster virus

54. PARAINFLUENZA VIRUS INFECTION
There are four types of parainfluenza viruses with differing clinical effects
Adenoviruses cause about 5% of acute respiratory tract illness overall
NEW viruses:
HUMAN METAPNEUMOVIRUS
HUMAN BOCAVIRUS

55. CYTOMEGALOVIRUS INFECTION
CMV infection can cause an interstitial pneumonitis in immunocompromised patients

56. INFLUENZA VIRUS INFECTION
Influenza viruses are classic respiratory viruses and cause endemic, epidemic and pandemic influenza
There are three types of influenza virus: A, B and C

57. SEVERE ACUTE RESPIRATORY SYNDROME-ASSOCIATED CORONAVIRUS INFECTION
SARS

58. Middle East respiratory syndrome coronavirus (MERS-CoV)!
New virus strain (September 2012): severe acute respiratory illness occurring in the Arabian Peninsula, some of whom were transferred for care to hospitals in Europe.
This coronavirus differs from the previously identified coronaviruses such as the SARS coronavirus (SARS-CoV), which caused the 2003 SARS outbreaks.
There is still much to be investigated, but it is considered likely that this virus originated from an animal source.

59. Respiratory infection
Viral detection:
Antigen detection(RSV/Influenza/Adenovirus)
Multiplex PCR

60. CYSTIC FIBROSIS
Individuals with cystic fibrosis are predisposed to develop lower respiratory tract infections
The disease is characterized by pancreatic insufficiency, abnormal sweat electrolyte concentrations and production of very viscid bronchial secretions
P. aeruginosa colonizes the lungs of almost all year-olds with cystic fibrosis

61. LUNG ABSCESS
Lung abscesses usually contain a mixture of bacteria including anaerobes (Bacteroides and Fusobacterium )
Treatment of lung abscess should include an anti-anaerobic drug and last 2-4 months
Pleural effusion and empyema :Aspiration of pleural fluid provides material for microbiologic examination, and Staph. aureus, Gram-negative rods and anaerobes are commonly involved.

62. FUNGAL INFECTIONS
most commonly seen in patients with defective immunity
Aspergillus fumigatus
Pneumocystis jiroveci (formerly P. carinii)

63. PARASITIC INFECTIONS
A variety of parasites localize to the lung or involve the lung at some stage in their development :
Nematodes such as Ascaris and the hookworms
Schistosome larvae
Echinococcus granulosus
Paragonimus westermani