2 Concepts: Normal Respiratory Flora Exists in symbiotic relationship with hostNormal flora also produces bacteriocins, which are toxic to other bacteriaKeeps host system primed for invasion by pathogenic microbes.
3 Concepts: Normal Respiratory Flora In absence of disease, presence of normal flora is called “colonization”Colonizers prevent proliferation and invasion by pathogenic bacteria through competition for nutrients and receptor sites
4 Concepts: Normal Respiratory Flora Patients receiving broad-spectrum antibiotics, hospitalized, or with chronic illnesses may have altered normal floraMicrobiologists must be able to determine whether the organism is a colonizer or a disease causer
5 Concepts: Immune Status of Host Age as a risk factorinfants and elderly more susceptibleImmunocompromisedOpportunistic infectionsReduced clearance of secretionsImmature anatomical development (e.g., eustachian tube)Reduced function of respiratory cilia after viral infectionObstruction by foreign body(e.g., aspirated foods)Disease that alters RT anatomy (tumors)Alterations in viscosity of mucus (e.g., cystic fibrosis)Infection-induced airway obstruction(e.g., epiglottitis)
6 Concepts Seasonal and Community Trends in Infections Fall/winter: viralYear round: mycoplasmaEmpiric Antimicrobial TherapyTreating patient prior to getting culture results
7 Concepts Always consider the following: Source of specimen Patient’s ageImmunologic status of hostClinical setting of the patient
8 Specimen Collection, Transport and Handling Specimen TypesSputum- specimen resulting from a deep cough, often contaminated with oropharyngeal floraBronchial washing/brushing- collected through bronchoscope, minimizes contamination with upper respiratory floraNeedle or open biopsy of lung- minimizes contamination with upper respiratory floraThroat swab- swab areas with pus or that are red and swollen, avoid tongue, cheeks and roof of mouthNasopharyngeal swab- using a calgiswab, insert through nostril into nasopharynx hold for several seconds before withdrawal
9 Specimen Collection, Transport and Handling Place specimens in a sterile container with a tight fitting lid, get to lab asapRefrigerate specimens for up to 24 hours if a delay in processing occursSpecimens submitted for anaerobic analysis should be processed asap
13 Function of RT Perform respiration: exchange of CO2 and O2 Deliver air from outside body to the alveoli where gas exchange occursComponents within RT defend against invaders
14 Barriers to Infection Nasal hairs Filters air Cilliary cells Clears particulates and secretes antimicrobial substancesCoughingExpels particulate matterNormal floraPrevents colonizationPhagocytes/Inflammatory cellsIngest organismsTracheobronchial tree secretes immunoglobulins
15 URT Infections: Pharyngitis Most common bacterial causeS. pyogenes (Group A)VirusesOccurs in winter and early springUnusual pathogensN. gonorrhoeaeC. diphtheriae
16 URT Infections: Pharyngitis Specimen CollectionCollect two swabsTarget tonsillar exudateLaboratory diagnosisRapid strep screeningCulture with A disk or PYR positiveGram stain from throats NOT helpful
17 URT Infections: Sinusitis CausesBacterial pathogensS. pneumoniae and H. influenzaeLess common isolates: S. pyogenes, M. catarrhalis, S. aureusViruses: most frequent causeRespiratory allergiesObstructionOccurs in winter and springSymptomsPurulent nasal dischargePain in face, headache
18 URT Infections: Sinusitis Laboratory diagnosisNasal secretions, sputums are not reliable culture sourcesBest culture material is from sinus puncture and aspiratesGram stain, culture media (aerobic and anaerobic)X-rays and CT scans are reliable indicators of infection
19 URT Infections: Sinusitis Treatment – since specimens are difficult to obtain, most sinus infections are treated with antibiotics known to be effective against the most common pathogens (empiric treatment)ComplicationsSpread of infection to adjacent sitesAnaerobic infection
20 URT Infections: Otitis media Middle ear infectionSeen mostly in pre-school age children due to crowded conditions in day care and immature eustachian tubeCausesBacterial pathogensS. pneumoniae and H. influenzaeLess common isolates: S. pyogenes, M. catarrhalis, S. aureus
21 URT Infections: Otitis media Laboratory diagnosisSpecimens not normally culturedIf ordered a gram stain, and aerobic plates inoculated
22 URT Infections: Otitis Media Treatment – usually empiricHigh- dose amoxicillinComplicationsDamage to ear drum and possible hearing lossInfection spread to adjacent area
23 URT Infections: Epiglottitis Infection causes the epiglottis to swell which is a serious condition due to potential airway obstructionVery painful swallowingSeen in preschool-age children
24 URT Infections: Epiglottitis CausesBacterial pathogenH. influenzae type BLaboratory diagnosisDirect smear and culture with swabTreatment: vaccine
25 URT Infections: Pertussis Respiratory illness with severe “whooping” coughMostly seen in infants and young childrenHighly transmissibleCausesBacterial pathogensBordetella pertussisBordetella parapertussisComplications: pneumonia, seizures
26 URT Infections: Pertussis Laboratory diagnosisNasopharyngeal swabs( calcium alginate) for FA direct staining and cultureBordet-Gengou/Regen Lowe selective mediaTreatment: vaccine
27 LRT Infections Bypass the mechanical and nonspecific barriers of URT Acquired by:Inhalation of aerosolsAspiration of oral or gastric contentsSpread of infection
29 LRT Infections: Bronchitis & Bronchiolitis Peaks in winter monthsCough and fever; cough is productive later in illnessX-rays do NOT show radiographic findingsLaboratory diagnosisGram stainCulture
30 LRT: Pneumonia Causes Bacterial Viral Chemical irritants Categories Community-acquiredNosocomialAspirationChronic
31 LRT Infections: Community-Acquired Pneumonia ChildrenMost common pathogensUsually due to viral pathogens that cause RTI in winter monthsRSV, Parainfluenza virusAdenovirus, Mycoplasma pneumoniaeLess commonS. pneumoniae, H. influenzae,Grp B. Strep (neonates)
32 LRT Infections: Community-Acquired Pneumonia AdultsMost common pathogensUsually due to bacterial infectionS. pneumoniaeM. pneumoniae (“walking” pneumonia)Less common pathogensH. influenzaeGram negative rodsS. aureusLegionella sp.
35 LRT Infections: Nosocomial pneumoniae Onset occurs 48 hours or longer after hospital admissionResult of compromise of barriers and colonization with pathogensSub-categoryVAP- ventilator-associated pneumoniaCommon pathogensG N Rods (60%) – Klebsiella, Enterobacter, Escherichia, Serratia, and Pseudomonas sp.G P Organisms (16%)Anaerobes, Legionella sp.
36 LRT Infections: Aspiration Pneumonia Aspiration of oropharyngeal or gastric contents into LRTAffects both adults and childrenCommon pathogens – mixed anaerobes and aerobes
38 LRT Infections: Empyema Localized extension of a lung infection between lung and chest wallCommon pathogensS. aureusS. pneumoniaeS. pyogenesG N Rods
39 Influenza A & B Seen in winter months Symptoms include fever, fatigue and myalgiasTwo types of virusA: Involved in annual outbreaks or epidemicsB: Outbreaks every 2-4 yearsSubtypes undergo antigenic driftAmino acid substitution allows virus to evade host immunityDrifts cause outbreaks
40 Influenza Testing: Why is it done? Identification of influenza strainsIdentification of outbreaksClinical decision making
41 Influenza: How is Testing Done? Laboratory DiagnosisDetection of virus in throat swabs, nasal washes, sputum, and BAL’sViral cultureImmunofluorescence, PCR, EIARapid testsTreatmentAnnual vaccineUses surveillance data to identify dominant strains
42 Emerging Viral RT Infections Avian Influenza- H5N1“Bird flu”Acquired from birdsSevere Acute Respiratory Syndrome- SARSPneumonia outbreak caused by Coronavirus in ChinaRapidly spread via respiratory secretions or droplets
44 Respiratory Tract Infections in the Immunocompromised Occurs due to impairment of host defense mechanismsChemotherapeutic protocals for malignancyOrgan & bone marrow transplantsAutoimmune & congenital immune disordersHIV/ AIDS
45 Respiratory Tract Infections in the Immunocompromised Pulmonary infection most common presenting factorCommon pathogensS. aureusS. pneumoniaeH. influenzaeMycobacterium spp.FungusCMV
46 Normal Flora Upper Respiratory Tract Coagulase negative Staphylococcus speciesStreptococcus species viridans groupNeisseria species, other than N. gonorrhoeae or N. meningitidisEnterococcus and Non-EnterococcusDiptheroidsYeast, in rare amountsEnteric gram negative rods, in rare amountsHaemophilus species, in rare amountsStaphylococcus aureus, in rare amountsAnaerobic organismsLower Respiratory TractNormally sterile
47 ReferencesAppold, K. (2010, February). A Mid-Winter Check-Up on H1N1. Advance/Laboratory.Mahon, C. R., Lehman, D. C., & Manuselis, G. (2011). Textbook of Diagnostic Microbiology (4th ed.). Maryland Heights, MO: Saunders.Penno, K. (2007, October). The Flu and You. ADVANCE for Medical Laboratory Professionals.
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