Respiratory tract infections Flashcards
Upper tract infections
Many isolates considered pathogenic are also considered to be colonizers depending upon culture predominating organisms. 60% of children carry S. pneumoniae by 2 y.o. The samples easily contaminated with NF. Nasal carriage cultures only for: MRSA
Immunocompromised screening for Aspergillus spp. or Mucor spp.
Lower tract infections
Infections are 6th leading cause of death in US, approximately 500,000 hospitalizations/year
40-60% of cases no pathogenic organism isolated
Common organisms causing lower respiratory tract infections (3)
- Mycoplasma pneumoniae - most common cause of community acquired pneumonia (CAP)
- Chlamydia pneumoniae, 2nd most common CAP
- Haemophilus influenzae 3rd, Legionella 4th
Clinical conditions associated with the respiratory tract (15)
- Candidiasis
- Cystic fibrosis
- Diptheria
- Epiglottitis
- Pharyngitis
- Laryngitis/bronchiolitis
- Lemierre’s disease
- Otitis externa
- Otitis media
- Chronic bronchitis
- Pneumonia - community and hospital acquired
- Empyema
- Lung abscess
- Sinusitis
- Nasopharyngeal screening
Mechanisms of transmission for respiratory tract infections (6)
- Person to person- airborne or contaminated secretions
- Environmental reservoirs
- Aspiration of endogenous flora
- Trauma
- Animal reservoirs
- Fomites
Epidemiology
Seasonal, travel, community information- epidemics, outbreaks or known exposures, eg. contacts of known TB cases
Structures of the upper respiratory tract (4)
- Nose
- Sinuses
- Throat
- Pharynx
Structures of the lower respiratory tract (3)
- Trachea
- Bronchial tree
- Lung parenchyma
Structures of the bronchial tree (3)
- Bronchus
- Bronchiole
- Alveolus
Other associated locations with the respiratory tract (2)
- Middle ear
- Eye
Colonization
Presence of an organism on epithelial cells of host without causing harm.
Infection
Process caused by growth of an organism which invades host tissues resulting in disease.
Normal respiratory flora species (8)
- S. pneumoniae
- S. aureus
- M. catarrhalis
- N. meningitidis
- Group B, C and G streptococci
- Order - Enterobacterales
- Acinetobacter, Stenotrophomonas
- Corynebacterium spp.
General considerations- lower respiratory tract
If less than normal flora, no identification needed, report as normal respiratory flora. If there are more than normal flora- full identification and sensitivity testing is required
Organisms to identify regardless of quantity (11)
- Group A streptococci
- Brucella
- Francisella tularensis
- Yersinia pestis
- Bacillus anthracis
- Pasteurella spp.
- P. aeruginosa
- Rhodococcus equi
- Actinomyctes, Norcardia spp. and Streptomyces
- Yeasts & molds not considered contaminants
- many others…Legionella, Mycobacteria, PCP, viruses
Specimens for candidiasis
swab of buccal mucosa, tongue or oropharynx
Specimens for cystic fibrosis
Young children- deep throat specimens
Specimens for diphtheria
nasopharyngeal swab
Specimens for epiglottitis
blood culture
Specimens for Pharyngitis
throat swab
Specimens for Lemierre’s disease
blood culture, starts as tonsillar abscess
Specimens for otitis externa
swab of inner ear canal
Specimens for otitis media
tympanocentesis fluid
Specimens for sinusitis
sinus aspirate
Nasopharyngeal screening samples
swab of nares
Diphtheria
Caused by C. diphtheriae. Acute, toxin-mediated disease (ADP-ribosylating toxin, interferes with protein synthesis, necrosis). Only strains infected with Beta phage produce the toxin and are pathogenic. Diphtheria is an upper respiratory infection with systemic toxin effects. Symptoms include sore throat, dysphagia, malaise, headache, fever, nausea.
What causes death in Diphtheria patients?
Obstruction of the airway by the pseudomembrane. There is a 10% mortality rate. Myocarditis -toxin adheres to myocardial, kidney and nerve tissue). CNS involvement is possible
Diphtheria diagnosis
Any throat or nasopharyngeal swabs for collection. Media - BAP, Cystine tellurite blood agar, Tinsdale agar (NOT FOR primary plating), or Loeffler agar. Incubate for 24 to 48 hours , aerobically NOT in 5% CO2. ID any beta hemolytic colonies on BAP, dark colonies on CTBA, dark zone around colony on Tinsdale agar. Pleomorphic GPR, Catalase+, Nonmotile, CAMP-neg, Urea-negative, halo on TINS = presumptive ID
Diphtheria treatment (3)
- First line – penicillin
- Second line – erythromycin
- Alternate - first generation cephalosporin or rifampin
Epiglottitis
Most commonly found in pre-school age children 2 to 4 y.o., experiencing acute respiratory distress. It is an infection of the epiglottis and surrounding soft tissues in upper airway. Intubation or endotracheal tube may be required due to swelling. S&S -fever, severe sore throat, difficulty swallowing, swollen red, edematous epiglottis, abrupt onset of fever, & drooling. There is a croup-like cough NOT found with epiglottitis, tonsillar or pharyngeal exudate absent.
Diagnosis of epiglottitis
Visualization of the epiglottis is important for diagnosis, need supportive care available due to risk of suffocation. The diagnosis can be made by epiglottis culture and blood culture
Organisms causing epiglottitis (5)
Haemophilus influenzae type B, non-typeable Haemophilus influenzae, S. aureus, S. pneumoniae, Group A strep
Treatment of epiglottitis
Hospitalization and IV treatment with beta-lactamase resistant antibiotics
Pertussis (Whooping cough) stages of infection
Caused by Bordetella pertussis. Other Bordetella species include B. parapertussis and B. bronchiseptica
Stages of infection:
1. Catarrhal stage: 1-3 week incubation period. Highly communicable
2. Paroxysmal stage: 1-4 weeks – severe repetitive cough resulting in whooping during this stage
3. Convalescent (recovery) weeks to months later – reduced frequency of coughing spells
Pertussis diagnosis
Isolated from the posterior nasopharynx. Use PCR, DFA. Media:
Regen-Lowe, Bordet-Gengou, BCYE
ID – “mercury drop” colonies, SBA(SBAP)-, Ox +
Pertussis treatment
Treat patient and contacts with erythromycin
Pharyngitis
Found in school age children, group A streptococci is found in 15 to 30% of patients, much less frequent in adults. Most commonly find viral cause of illness. Symptoms- pharyngeal exudate, fever, lymph adenopathy, NO cough
Streptococcus pyogenes
Includes group A streptococci; ß-hemolytic strep. Post-streptococcal sequelae: rheumatic fever & glomerulonephritis. Streptococci groups C & G and Arcanobacterium haemolyticum. Need to rule out infection with Neisseria gonorrhoeae or Corynebacterium diphtheriae. Treatment- penicillin, macrolides
Lemierre’s disease causative agents (4)
- Most common causative agent Fusobacterium necrophorum
- Bacteroides melanogenicus, Eikenella corrodens, non group A strep
Fusobacterium necrophorum
The most common causative agent of Lemierre’s disease. However, it is normal anaerobic flora, found in genital, GI, and upper respiratory tract.
Lemierre’s disease
Was commonly found in the pre-antibiotic era (1950s), but is still associated with a high mortality rate. Responsible for severe infection in children and young adults that begin as peritonsillar abscesses. The patient first has pharyngotonsillitis or associated with infectious mononucleosis. Proceeds to a localized infection that spreads to the neck and jugular vein septic thrombophlebitis. Progression to pleural effusion with empyema, metastatic abscesses (lung, liver, joints) resulting from bacteremia. Patient with pharyngitis and jaundice possible case.
Rhinitis
Inflammation of the mucous membranes in the nose. Main symptom is rhinorrhea - runny nose. When not allergy, usually caused by a virus. There is a 2-3 day incubation period. Symptoms: sneezing, nasal stuffiness, coryza, and scratchy throat. May be complicated by bacterial sinusitis or otitis media.
Laryngitis/bronchiolitis
Often has a viral cause. A cough is the most important symptom; fever may occur with influenza virus, adenovirus, or M. pneumoniae. It is important to distinguish from pneumonia. May cause cute exacerbations of chronic bronchitis. S. pneumoniae, S. aureus (including MRSA), GNR and respiratory virues
Otitis Externa
Inflammation of the outer ear and ear canal. Diagnose using a swab of the ear canal. Can be caused by scratches in the ear canal from placing objects in ear predispose to infection. Contaminants with normal flora are problematic. CoNS, diptheroids and SVA commonly isolated
Pathogens causing otitis externa (3)
Different than those causing otitis media
1. S. aureus, group A streptococci
2. Swimmer’s ear – P. aeruginosa, Vibrio alginolyticus
3. Chronic: anaerobes, Mycoplasma pneumoniae, viruses
Otitis media
Inflammation of the inner ear. Diagnosed by tympanocentesis - removal of fluid from behind ear drum, from inner ear. Viral infection such as RSV, rhinovirus, influenza and adenovirus predisposes to infection and may cause secondary bacterial infection. Most common in preschool-age children, still found in adults but much less common. Damage to the tympanic membrane leads to hearing loss. Since well-known, no culture collection is needed, just treatment
Pathogens causing otitis media (5)
S. pneumoniae, H. influenzae , S. pyogenes , Moraxella catarrhalis, S. aureus. Multiple treatments and chronic infections caused by: GNR, anaerobes
Sinusitis
Generally caused by a viral infection, leading to secondary bacterial infection ~2% of the time. Often patients receive antimicrobials. Common cold viruses - rhinovirus, parainfluenzae and influenza. May be caused by improper Neti pot usage. Usually self-limited in 1-3 weeks. Diagnosis by CT scan or MRI of sinuses. Patient complain of headache. Causative agents differ according to age
Organisms causing sinusitis in young adults (5)
Haemophilus influenzae, Streptococcus pneumoniae, Streptococcus pyogenes, Moraxella catarrhalis, C. acnes
Organisms causing sinusitis in children (3)
Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis
Organisms causing sinusitis in immunocompromised people
Fungal infection, especially if being treated with immunosuppressive therapy.
Nasopharyngeal screening
Swab for carriage of potential hospital acquired pathogen
MRSA, VRE, aminoglycoside resistant organisms
Prevent transmission to others in the institution. Mannitol Salt Agar(MSA) or MSA with oxacillin - what does SA look like? (48hr minimum for ID). CHROMagar - differential and selective, cefoxitin in agarID
CHROMagar nasopharyngeal screening
Moderate to large colonies that are “typical” SA morphology report MRSA, no further ID is required. 24hr minimum for ID
Small or slow growing colonies require confirmation for ID
Cystic fibrosis samples- lower respiratory tract
Young children - deep throat sample
Young adults - as pneumonia
Chronic bronchitis samples
Same as pneumonia
Pneumonia samples
Community and hospital acquired. Specimens - sputum, endotracheal aspirate, suction samples, lung aspirates, bronchial washings, bronchial alveolar lavage, protected brush specimens, lung biopsy
Empyema samples
Pleural fluid
Lung abscess samples
Lung aspirate or biopsy
Sputum samples
First morning specimen, this is the least invasive and least clinically relevant. Do not gargle prior to collection. A deep coughed specimen is expelled to a sterile container. May be contaminated by upper respiratory tract secretions. Screen the specimen by Gram stain. >10 squamous epithelial cells/lpf is cause for rejection
Aerosol-induced specimen
Specimen of choice for TB and PCP
Ultrasonic nebulizer, patient inhales 20 to 30ml of 3% NaCl
Tracheal aspirate or suction specimens (Luken’s trap)
Soft catheter passed into tracheobroncial tree
Frequent collection from children since they can not provide expectorated samples.
Specimen types- lower respiratory tract (10)
- Sputum (expectorated)
- Aerosol-induced specimen
- Tracheal aspirate or suction specimens
- Bronchoscopy - BAL, bronchial washing, transbronchial biopsy specimens
- Bronchial brush biopsy
- Transtracheal needle aspiration
- Transthoracic needle aspirate
- Open lung biopsy (OLB)
- Thoracentesis
- Blood culture
Bronchoscopy - BAL, bronchial washing, transbronchial biopsy specimens
endoscope into bronchial tree to visualize airway, sample is aspirated. Avoid blood contamination by collection before biopsy
Syringe attached to scope, injection of 20 to 30 mL sterile saline (5mL/child) then suction sample. Quantitative culture for BAL or washing samples can be requested.
BAL vs bronchial washing
BAL collected from distal bronchioles and alveoli from one or more lung segments (deeper sample). Larger sample received then washing, recovery of 75% of injected saline. Washing collected from major bronchi, at the branching of the left and right bronchi. Smaller sample received then from BAL
Bronchial brush biopsy
A small brush is encased in a double cannula and inserted into bronchial tree. The specimen is protected from contamination by normal upper respiratory tract flora. Place the brush in broth, vortex, & plate
suitable for anaerobic culture
Transtracheal needle aspiration
suitable for anaerobic culture
Transthoracic needle aspirate
lung fine needle aspiration
Aided by scan to locate lesion
Suitable for aerobic or anaerobic culture
Open lung biopsy (OLB)
Suitable for anaerobic culture
Surgical procedure
Thoracentesis
specimen for pleural empyema
What are blood cultures used to diagnose? (2)
- Diagnose pneumonia
- Diagnose Lemierre’s disease
Transport of respiratory tract samples
Transport immediately- especially sputum, BAL, bronchial brushings, endotracheal aspirates, suctioned samples. Store at 2 to 8 degrees C until they are processed. A delay of greater than 1-2 hours can decrease recovery of fastidious, pathogenic isolate. SPN, HFLU, NMEN. Invasive specimens are NEVER rejected
Transport of Chlamydia samples
For Chlamydia, 2 SP (sucrose phosphate) transport medium
Transport for viral samples
Viral transport medium (VTM)
with antimicrobials. Refrigerate, do not freeze at -20oC
Processing specimens of the lower respiratory tract
Direct smears - expectorated sputum only. Never reject suctioned samples, CF patients or cultures for AFB or Legionella.
Gram stain culture
accept: <10 epithelial cells/lpf
reject: >10 epithelial cells/lpf
excellent specimen: <10. Epithelial cells and >25 PMN/lpf
The presence of PMN is not required for a acceptable quality specimen.
Routine culture media
Routine: 5% SBA(SBAP), MAC or EMB, CAP
Special requests specimens (6)
- Legionella: BCYE agar
- Bordetella: Bordet Gengou
- Mycoplasma: Mycoplasma media
- Viral or chlamydia: cell culture
- Fungi: BHI agar, Sabouraud-dextrose, Mycosel
- Mycobacteria: Lowenstein-Jenson, Middlebrook 7H10
OLB specimens
OLB specimens should be inoculated to thioglycollate broth
Specimens from patients with cystic fibrosis
Patients with CF - Oxidative-fermentative polymixin B-bacitracin lactose (OFPBL) or PC (BC) media
Incubation conditions of routine culture
35 degrees C , 5% CO2. Incubate for 24 to 72 hours (CF patient samples- 96hr). Gram stain should be guide for culture- useful when immune cells present
Cystic fibrosis- plating
SBA(SBAP), CAP, MAC, MSA, SAB, CNA - read plates at 24, 48 and 72hr. B. cepacia selective media – PC(BC) or OFPBL - read plates to 96 hr
Identify which organisms for cystic fibrosis? (3)
- Any amount of - mold, S. aureus, P. aeruginosa, B. cepacia and all other non-fermenting GNR, rapidly growing Mycobacterium
- Predominating organism - Enterobacteriaceae, H. influenzae, S. pneumoniae
- Pseudomonas aeruginosa & Burkholderia cepacia
Bronchiolitis
A lower respiratory tract infection in the first 2 years of life. RSV is the primary cause, especially during winter epidemics. Parainfluenza and other viruses can also cause bronchiolitis. Symptoms-
wheezing and hyperaeration of lungs (air trapping due to obstruction). Resulting from mucous buildup in small air passages in lung
Pneumonia
Infection of lung parenchyma. Most often occurs in elderly patients – 4th leading cause of death. Symptoms- fever, cough, sputum, pleuritic pain. Long list of causative agents - usual respiratory
Diagnosis of pneumonia
Diagnosis is done by signs and symptoms or X-Ray. Causative agents can be viral or bacterial. Do a Gram stain on sputum
Sputum gram stain for pneumonia (3)
- PMN + predominant organism requires specific antimicrobials
- PMN without organisms requires erythromycin (Mycoplasma pneumoniae)
- Bloody and purulent - suggests TB
Legionella pneumophila
Legionnaires disease & Pontiac fever. Treatment – erythromycin
S. pneumoniae
vaccines available, 7 or 23 serotypes, PRSP
Chlamydia psittacine (psittacosis)
Found in pet birds (parrots, parakeets, macaws, and cockatiels). Poultry (turkeys and ducks) are most frequently involved in transmission to humans.
Coxiella burnetii (Q fever)
Cattle, sheep goats. Shed in milk, urine, feces
Community acquired lower respiratory tract organisms (6)
- S. pneumoniae
- L. pneumophila
- M. pneumoniae
- Oral anaerobes
- H. influenzae
- GNR
Hospital acquired lower respiratory tract organisms (3)
- Staphylococcus aureus
- Enterobacteriaceae
- other GNR
Viruses infecting the lower respiratory tract (7)
- influenza virus
- parainfluenza virus
- respiratory syncytial virus
- picornaviruses
- rhinoviruses
- coronavirus (e.g., SARS)
- Adenovirus
Fungal lower respiratory tract infections (7)
- Aspergillosis- allergic bronchopulmonary aspergillosis, fungus ball, invasive disease
- Cryptococcosis
- Histoplasmosis
- Coccidioidomycosis,
- Blastomycosis
- Paracoccidioidomycosis
- Pneumocystis jiroveci
Empyema samples
Pleural fluid - fluid between lung and chest wall collected by thoracentesis. The fluid is normally sterile. If grossly purulent, empyema is diagnosed. Other laboratory tests- normal: few cells and protein content < serum Abnormal: increased cell count and protein. Suitable for anaerobic culture. Make direct smear by cytospin method
Inoculate fungal or mycobacterial culture media, if requested. S. aureus, S. pyogenes, S. pneumoniae, Anaerobes
Anaerobic bacteria causing dental and oral infections (3)
- Bacteroides fragilis group, Prevotella oralis, Porphyromonas sp., Fusobacterium sp.
- Peptostreptococcus, Veillonella
- Actinomyces israelii (lumpy jaw)
Aerobic bacteria causing dental and oral infections (3)
- Streptococci and staphylococci
- Eikenella corrodens
- Aggregatibacter actinomycetocomitans
Fungi causing oral infections (2)
- Candida species
- Thrush
Viruses causing oral infections
HSV
Acute necrotizing ulcerative gingivitis
Vincent’s disease, also called trench mouth. Caused by large spirochete and fusiform bacilli- Fusobacterium, Treponema, Prevotella. Direct smears, not diagnosed by culture
Salivary gland infections (parotitis) caused by 3 types of organisms
- Staphylococcus aureus, alpha-streptococci viridians group, oral anaerobes
- Mycobacterium tuberculosis
- Viruses: mumps virus, influenza virus, enterovirus
Chlamydia trachomatis
Causes trachoma, inclusion conjunctivitis
Neisseria gonorrhoeae
Infects neonates during birth (acute)–ophthalmia neonatorum. Decreased occurrence since prophylactic drops applied to neonates’ eyes
Microorganisms found in adults with conjunctivitis (2)
- S. pneumoniae
- S. aureus & S. epidermidis - (CoNS need to ID here)
Microorganisms found in children with conjunctivitis (2)
- H. influenzae (esp. subspecies Aegyptus)
- S. pneumonia
Causes of eye infections (7)
- Chlamydia trachomatis
- Neisseria gonorrhoeae
- Adults- classic microorganisms
- Children- classic microorganisms
- C. diphtheriae & Moraxella lacunata (GNR)
- Fungi
- Viruses
Viruses causing eye infections (3)
- Adenovirus (20%) - types 4,3 &7A
- Enterovirus 70
- Coxsackie virus A24 (acute hemorrhagic conjunctivitis)
Causative agents of keratitis (7)
- Pseudomonas aeruginosa
- Staphylococcus aureus
- Streptococcus pneumoniae
- Moraxella sp.
- Herpes simplex virus & other viruses
- Acinetobacter sp.
- Fungal keratitis, associated with trauma
Other causes of keratitis (2)
- Extended wear contact lenses – Acanthamoeba & Naegleria.
- Ocular implants- Cutibacterium acnes may be significant
