Lower respiratory infections Bacteriological Diagnosis

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Lower Respiratory Tract Infections

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Lower respiratory infections Bacteriological Diagnosis

  1. 1. LOWER RESPIRATORY BACTERIAL INFECTIONS AETIOLOGY, DIAGNOSIS Dr.T.V.Rao MDDR.T.V.RAO MD 1
  2. 2. RESPIRATORY SYSTEM ENVIRONMENT IS DIVERSE• Upper respiratory system • Nose, pharynx, associated structures • Purpose: to take in, warm and moisten air • Most common site of infections• Lower respiratory system • Larynx, trachea, bronchi, alveoli • Purpose: ventilation, gas exchange DR.T.V.RAO MD 2
  3. 3. ANATOMY OF THE RESPIRATORY SYSTEM (AND SITES OF INFECTION)DR.T.V.RAO MD 3
  4. 4. CLINICAL PRESENTATION: LOWER RESPIRATORY TRACT INFECTION• Acute Infection: • Fever, chills • Back pain, myalgias, arthralgias • Headache, malaise, chills • Nausea, vomiting• Chest Infection: • Cough • Chest pain • Rales, wheezing, noisy chest• Characteristic changes on chest x-rays• Increasing respiratory distress, may require mechanical ventilation DR.T.V.RAO MD 4
  5. 5. LOWER RESPIRATORY TRACT INFECTIONS EPIDEMIOLOGY• Pneumonia is the sixth leading cause of death in US• Increasing numbers of patients at risk • Aging population • Increase in patients with immunocompromising conditions
  6. 6. DIAGNOSIS DEPENDS ON CLINICAL PRESENTATION AND AGE TOO• Most of these cases diagnosis depends on clinical presentation and minimum laboratory and radiologic investigations may be needed most of these cases recovered smoothly with appropriate management unless an underlying lung pathological or systemic disease may worsen the condition or continue with chronicity appropriate follow-up of these patients in OPC is appreciated especially after discharge from hospitalDR.T.V.RAO MD 6
  7. 7. LOWER RESPIRATORY TRACT • Infections of the lower respiratory tract are the leading cause of cause of mortality world wide. Streptococcus pneumoniae is the leading bacterial agent of community acquired pneumonia along with Haemophilus influenza and Moraxella catarrhalisDR.T.V.RAO MD 7
  8. 8. PNEUMOCOCCUS A SIGNIFICANT PATHOGEN Pneumococcus is the most common bacterial pathogen causing febrile pneumonia in children and adults The clinical syndrome is characteristic and distinctive : acute onset of high, spiking fever, with chills, cough, and sputum productionDR.T.V.RAO MD 8
  9. 9. CATEGORIES OF LOWER RESPIRATORY TRACT INFECTIONS• Acute bronchitis• Community acquired pneumonia• Hospital acquired pneumonia• Pneumonia in the immunocompromised hostDR.T.V.RAO MD 9
  10. 10. COMMUNITY ACQUIRED PNEUMONIA ETIOLOGIC AGENTSPathogen Frequency (%)Streptococcus pneumoniae 66Haemophilus influenza 1-12M catarrhalis 10Legionella species 2-15Mycoplasma pneumoniae 2-14Klebsiella species 3-14Enteric gram negative bacilli 6-9Staphylococcus aureus 3-14Chlamydia species 5-15Influenza viruses 5-12Other viruses <1-12Unknown 23-49 DR.T.V.RAO MD 10 Carroll KC. 2002. J Clin Microbiol 40:3115-3120. Sharp SE, et.al. Cumitech 2003
  11. 11. SPECIMEN COLLECTION:The patient should be standing, If possible or sitting upright inbed.He or she should take deep breath to full the lungs, and emptythen in one breath, coughing as hard and as deeply aspossible.Sputum brought up should be spit into screw cappedcontainer.Visually inspect the specimen.Tighten the cap of the container and send immediately to lab. DR.T.V.RAO MD 11
  12. 12. SPUTUM COLLECTION• Sputum of less than 2ml should not be processed unless obviously purulent• Only 1 sputum per 24hr .submitted• Some scoring system should be used to reject specimen that re oral contamination.DR.T.V.RAO MD 12
  13. 13. TRANSPORTATION OF SPUTUM• Transportation in <2 hr is recommended with refrigeration if delays anticipated.• Handle all samples using universal precautions.• Perform Gram stain and plant specimen as soon as possibleDR.T.V.RAO MD 13
  14. 14. INDUCED SPUTUM Patients who are unable to produce sputum may be assisted by respiratory therapy technician. Aerosol induced specimen are collected by allowing the patient to breath aerosolized droplets of a solution of 15% sodium chloride and 10% glycerin for approximately 10 minute obtaining such specimen may avoid the need for a more invasive procedures ,such as bronchoscopy or needle aspiration, in many cases.DR.T.V.RAO MD 14
  15. 15. BRONCHOALVEOLAR LAVAGE (BAL) SPECIMEN ACCEPTABILITY• Microscopic examination of Gram-stained smear • Acceptable • <1% of cells present are squamous epithelial cells • Unacceptable • >1% of cells present are squamous epithelial cellsThorpeMD et. al. 1987. Bronchoalveolar lavage for diagnosing acute bacterial JEDR.T.V.RAO 15pneumonia. J. Infect. Dis. 155:855-861
  16. 16. METHODS OF COLLECTION IS IMPORTANT..• Sputum collected under supervision of nurse or resident • Samples were processed immediately • Screened for epithelial cells • Screened for predominant morphotype (> 75% of the organisms seen) • Sputum planted to blood agar, chocolate agar and MacConkey agar• Strictly defined clinical and diagnostic parameters DR.T.V.RAO MD 16
  17. 17. MICROSCOPIC EXAMINATION• Prepare a gram stain smear for all lower respiratory tract specimens to determine the presence of oropharyngeal contamination (indicated by squamous epithelial cells) and lower respiratory tract secretions (indicated by WBCs) as well as to identity the most likely pathogens (Indicated by the predominant organisms associated with WBCs).DR.T.V.RAO MD 17
  18. 18. SPUTUM GRAM STAINGood quality specimens• Quantify number and types of inflammatory cells• Note presence of bronchial epithelial cells• Concentrate on areas with WBCs when looking for organisms• Determine if there is a predominant organism (> 10 per oil immersion field) • Semiquantitate and report organism with descriptive • If no predominant organism is present, report ―mixed gram positive and gram negative flora‖ DR.T.V.RAO MD 18
  19. 19. SPUTUM GRAM STAIN IS HELPFUL - YES Proponents Antagonists• Demonstration of • Poor specimen collection predominant • Intralaboratory variability morphotype on Gram (Gram stain interpretation) stain guides therapy • Low sensitivity and specificity• Accuracy is good when • Empiric treatment strict criteria are used guidelines• Cheap, so why not? • Do much dependence ???DR.T.V.RAO MD 19
  20. 20. STUDIES PROVE ...• Overall sensitivity and specificity for pneumococcal pneumonia: 57% and 97%• Overall sensitivity and specificity for H. influenza pneumonia: 82 % and 99%• Gram stain gave presumptive diagnosis in 80% of patients who had a good specimen submitted• > 95% of patients in whom a predominant morphotype was seen on Gram stain received monotherapy DR.T.V.RAO MD 20
  21. 21. REPORT GRAM STAINING WITH CAUTION• Be as descriptive as possible • Moderate neutrophils • Moderate Gram positive diplococcic suggestive of Streptococcus pneumoniae • Few bacteria suggestive of oral flora• Keep report short—avoid line listing of all morphotypes present DR.T.V.RAO MD 21
  22. 22. SQUAMOUS EPITHELIAL CELLS• If no squamous epithelial cell are found, report ― No epithelial cells seen‖• If only a few epithelial cells are found report ― Few epithelial cells seen‖• If abundant epithelial cells seen, indicating oropharyngeal contamination, such specimens are graded as unsatisfactory sample.•DR.T.V.RAO MD 22
  23. 23. REPORTING THE PRESENCE OF LEUCOCYTES:• If no WBC are found report ―No WBCs seen‖• If WBCs are present in any amount state as few, moderate or numerous WBCs seen.DR.T.V.RAO MD 23
  24. 24. INTERPRETATION OF GRAM STAIN:• None Few Moderate NumerousSquamous epithelial cells/ LPF* 0 1-9 10-24 >25• Neutrophils/LPF* 0 1-9 10-24 >25•DR.T.V.RAO MD 24
  25. 25. GRAM STAINING – REPORTING MICROBIAL OBSERVATIONS• Type / Number of organisms / HPF**• Gram-positive cocci• Gram-negative cocci• Gram-negative rods• Gram-positive rods• PF*: (low power field) x 10 (examine 10-20 fields)• HPF**: (high power field) oil immersionDR.T.V.RAO MD 25
  26. 26. PROCESSING SPECIMENS FOR CULTURE• Process specimens in biological safety cabinet, as aerosol can result in laboratory-squired respiratory infections.• Process all specimens as rapidly as possible, especially specimen from emergency department, and inpatients. Select the most purulent or most blood- tinged portion of the specimen. Significant growth above the cutoff should be reported; however if more than one pathogen is isolated than it is suggestive of oropharyngeal contamination and clinical correlation should be done before reporting the samples.DR.T.V.RAO MD 26
  27. 27. CHOOSING CULTURE MEDIA: • Sheep Blood Agar • MacConkey agar • Chocolate agarDR.T.V.RAO MD 27
  28. 28. ROUTINE CULTURE• Most of the commonly sought etiologic agents of lower respiratory tract infection will isolated on routinely used media : 5% sheep blood agar ,MacConkey agar for isolation and differentiation of gram-negative bacilli ,and chocolate agar for Neisseria spp and Haemophilus .DR.T.V.RAO MD 28
  29. 29. CONTAMINATION WITH ORAL FLORA INTERFERES RESULTS• Because of contaminating oral flora ,sputum specimens, specimens obtained by bronchial washing, and lavage tracheostomy, or endotracheal tube aspirates are not inoculated to enriched broth or incubated anaerobically. Only specimens obtained by percutaneous aspiration (including trans tracheal aspiration )and by protected bronchial brush are suitable for anaerobic culture: he latter must be done quantitatively for proper interpretation. DR.T.V.RAO MD 29
  30. 30. CULTURING SPECIMENS FROM CYSTIC FIBROSIS• Sputum specimens from patients known to have cystic fibrosis should be inoculated to selective agar ,such as manitol salt agar for recovery of S .aureus and selective horse blood-bacitracin ,incubated anaerobically and aerobically ,for recovery of H,influenzae that may be obscured by the mucoid P,aeroginosa on routine media.DR.T.V.RAO MD 30
  31. 31. SPUTUM AND ENDOTRACHEAL SUCTION CULTURE EVALUATION • Identify and perform susceptibility testing on 2-3 potential pathogens seen as predominant on Gram stain • Alpha strep—rule out S. pneumoniae • Yeast—rule out Cryptococcus neoformans only • S. aureus, Gram negative bacilli • < normal flora, quantify and limit ID; no susceptibility • Add comment that organism not predominant on stain • ID mould, Mycobacteria or Nocardia spp. Modified from Sharp SE, et. Al. 2003. Cumitech 7B. ASM Press.DR.T.V.RAO MD 31
  32. 32. INTERPRETATION OF QUANTITATIVE PSB/BAL• Dilution Method • Quantify each morphotype present and express as CFU/ml• Calibrated Loop Method • Quantify each morphotype present and express as log 10 colony count ranges• Thresholds for significance • PSB > 103 CFU/ml • BAL > 104 CFU/mlBaselski and Wunderink. 1994. Clin Micro Rev 7:547 DR.T.V.RAO MD 32
  33. 33. EXAMINE FOR AND ALWAYS REPORT.• Streptococcus pyogenes• Group B streptococci in pediatric population• Francisella tularensis• Bordetella spp., especially Bordetella bronchiseptica• Yersinia pestis• Nocardia spp.• Bacillus anthracis• Cryptococcus neoformans• Molds, not considered saprophytic contaminants• Neisseria gonorrhoeaeDR.T.V.RAO MD 33
  34. 34. ALWAYS REPORT, BUT DO NOT MAKE AN EFFORT TO FIND LOW NUMBERS, UNLESS THEY ARE SEEN IN THE SMEAR.• Streptococcus pneumoniae• Haemophilus influenza report beta-lactamase•DR.T.V.RAO MD 34
  35. 35. REPORT IF PRESENT IN SIGNIFICANT AMOUNTS, EVEN IF NOT PREDOMINANT• 1 Moraxella catarrhalis• 2 Neisseria meningitides• Report the following for nosocomial infections:• 3. Pseudomonas aeruginosa• 4. Stenotrophomonas maltophilia• 5. Acinotobacter spp.• 6. Burkholderia spp.DR.T.V.RAO MD 35
  36. 36. REPORT IF PRESENT IN SIGNIFICANT AMOUNT AND IF IT IS THE PREDOMINANT ORGANISM IN THE CULTURE, PARTICULARLY IF SUGGESTS INFECTION WITH MORPHOLOGY CONSISTENT WITH ISOLATE.• Staphylococcus aureus• Beta-hemolytic streptococcus B (adults), C, or G• Single morphotype of gram-negative rod (especially Klebsiella pneumoniae)• Fastidious gram-negative rods; usually report beta- lactamase• Corynebacterium spp. if urea positive or from ICU• Rhodococcus equi in immunocompromised patientsDR.T.V.RAO MD 36
  37. 37. ATS GUIDELINES DIAGNOSTIC TESTS FOR CAP• Empiric therapy for outpatients • Macrolide or tetracycline• Hospitalized patients with CAP • 2 sets of pre-treatment blood cultures • Pleural fluid Gram stain/culture when appropriate • Studies for Legionella, Mtb, fungi in select patients • Sputum Gram stain/culture only if resistant or unusual pathogen is suspected • Avoid extensive testing ATS. 2001. Am J Respir Crit Care Med 163: 1730-1754. DR.T.V.RAO MD 37
  38. 38. CRITERIA FOR REJECTING SAMPLESMismatch of information on the label and the requestInappropriate transport temperatureExcessive delay in transportationInappropriate transport medium • specimen received in a fixative • dry specimen • sample with questionable relevanceInsufficient quantityLeakageDR.T.V.RAO MD 38
  39. 39. IMMUNOCOMPROMISED PATIENTS SUGGESTED BAL PROTOCOL• Aerobic Gram stain quantitative bacterial culture• Fungal stain and culture• Mycobacterial stain and culture• Viral culture/Respiratory DFA• Pneumocystis DFA• Legionella cultureDR.T.V.RAO MD 39
  40. 40. MANY OTHER CAUSES OF PNEUMONIA WITH ACUTE RESPIRATORY DISEASE & FEVER S.Pneumoniae Legionella TBPlague Tularemia RICIN toxin SARS Staphylococcal Enterotoxin B
  41. 41. SUMMARY• Respiratory system can host a variety of microbes• Normal flora in ―restricted areas‖• Susceptibility depends on age, immune system• Some organisms are adept at evading immune system• Damage generally due to cytotoxicity and inflammation• Vaccines are available for some organisms DR.T.V.RAO MD 41
  42. 42. CHILDHOOD IMMUNIZATIONS CAN REDUCERESPIRATORY INFECTIONS – FOLLOW THE SCHEDULES Birth 1m 2m 3m 4m 6m 12m 15m 18m 4-6y 11-12y HBV1 HBV3 HBV2 DTP DTP DTP DTP Hib Hib Hib Hib Polio Polio Polio MMR MMR or MMR Varicella Varicella
  43. 43. DO REMEMBER • The culture of lower respiratory specimens may result in more unnecessary microbiologic effort than any other type of specimen.‖ Raymond C BartlettDR.T.V.RAO MD 43
  44. 44. • Programme created by Dr.T.V.Rao MD for Medical and Health Workers in the Developing World • Email • doctortvrao@gmail.comDR.T.V.RAO MD 44

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