INFECTIOUS DISEASES
PNEUMONIA
Clinical manifestations
• “Typical”: acute onset of fever, cough w/ purulent sputum, dyspnea, consolidation on CXR
• “Atypical” (originally described as cx 
): insidious onset of dry cough, extrapulm sx (N/V, diarrhea, headache, myalgias, sore throat), patchy interstitial pattern on CXR
• S/s & imaging do not reliably distinguish between “typical” (S. pneumo, H. flu) and “atypical” (Mycoplasma, Chlamydia, Legionella, viral); ↑ aminotransferases & ↓ Na w/ Legionella
Diagnostic studies
• Sputum Gram stain: utility debated. Good sample (ie, sputum not spit) has <10 squamous cells/lpf. Purulent sample has >25 PMNs/lpf.
• Sputum bacterial culture: transport to lab w/in 1–2 h of collection
• Blood cultures (before antibiotics!): 
in ~10% of inPts, depending on pathogen
• CXR (PA & lateral; see Radiology inserts) → tap effusions if >5 cm or severe PNA
• Other: SaO2 or PaO2, arterial pH (if severe), CBC w/ diff, Chem-20; HIV test (if unknown)
• Other micro based on clinical suspicion (paired serologies available for most atypicals):
Mycoplasma: PCR of throat or sputum/BAL before first dose abx
Legionella urinary Ag (detects L. pneumophila L1 serotype, 60–70% of clinical disease)
S. pneumoniae urinary Ag (Se 50–80%, Sp >90%)
MTb: induced sputum for AFB stain and mycobacterial cx (empiric respiratory isolation while pending); avoid quinolones if suspect TB; request rapid DNA probe if stain
Induced sputum for PCP if HIV or known ↓ cell-mediated immunity
• Viral testing (DFA or PCR) on nasopharyngeal swab or sputum; rarely viral cx
• Bronchoscopy: consider if immunosupp., critically ill, failing to respond, or chronic pneumonia. Also if suspected TB or PCP, but inadequate or sputum cx. Some pathogens need specific cx (eg,Legionella on BCYE); collaborate with lab.
• Reasons for failure to improve on initial Rx:
Insufficient time: may take ≥72 h to see clinical improvement
Insufficient drug levels: eg, vanco trough <15–20 µg/mL (needed for lung penetration)
Resistant organisms (or superinfxn): eg, MRSA, Pseudomonas; consider bronchoscopy
Wrong dx: fungal/viral, chemical pneumonitis, PE, CHF, ARDS, DAH, ILD; consider CT
Parapneumonic effusion/empyema/abscess: esp. seen w/ strep; if CXR , consider CT (dx tap ± chest tube if effusion present, esp. if loculated)
Metastatic infection (eg, endocarditis, meningitis, arthritis)
Prognosis
• Pneumonia and influenza are the 8th leading cause of death in the U.S.
• For low-risk Pts, can discharge immediately after switching to PO abx (CID 2007;44:S27)
• CXR resolves in most by 6 wk; consider f/u to r/o underlying malignancy (esp. if age >50 y or smoker, Archives 2011;171:1192) or other dx
• Severe CAP (generally requiring ICU) defined as: septic shock, resp failure, or ≥3 of: RR ≥30, PaO2/FiO2 ≤250, <36°C, HoTN, DMS, multilobar, WBC <4k, plt <100, BUN ≥19.9, metabolic acidosis, ↑ lactate (ATS/IDSA criteria, CID 2007;44:S27)
• SMART-COP risk score: SBP <90 (2 points), Multilobar infiltrates, Alb <3.5 g/dL, RR ≥30, Tachycardia (HR >125), Confusion, O2 sat <90% (2 points), arterial pH <7.35 (2 points) score ≥3 points has Se ~60–90% & Sp 45–75% for need for ICU care (CID 2008;47:375)
Prevention
• Pneumococcal vaccine (PPSV23): all persons >65 y of age. If high-risk comorbidity, give at younger age and consider additional vaccination with PCV13.
• VAP precautions: HOB >30°, chlorhexidine rinse; aspiration precautions in high-risk Pts
• Tdap booster: 1 time dose in adults with uncertain vaccination history (MMWR 2012; 61:468)
VIRAL RESPIRATORY INFECTIONS
URI, bronchitis, bronchiolitis, pneumonia (Lancet 2011;377:1264)
Microbiology & epidemiology
• Typical pathogens: short, mild = rhinovirus, coronavirus; longer, more severe or complicated = influenza, parainfluenza, respiratory syncytial virus (RSV), adenovirus, metapneumovirus. Can be esp. severe in immunosupp.
• Seasonal flu: 365,000 hosp, 51,000 deaths per y in U.S.; most >65 y (NEJM 2008;359:2579)
• Pandemic 2009 H1N1 (swine): more severe in younger and obese Pts (JAMA 2009;302:1896)
• Sporadic 2011 H3N2: adults exposed to swine (also human-to-human) (MMWR 2011;60:1615)
• H5N1 influenza (avian): ongoing small outbreaks globally.
• For weekly influenza updates: http://www.cdc.gov/flu/weekly
Diagnosis
• Primarily clinical: cough, fever, myalgias, arthralgias, rhinorrhea, pharyngitis (in contrast, viral bronchitis p/w cough ± low-grade temp; usually benign & self-limited)
• Respiratory viral panel on nasal washing or sputum/BAL
• Rapid influenza test on nasal swab: Se ~50–70% (? lower for pandemic flu), Sp >95%
• DFA (Se ∼85%), RT-PCR (gold standard) avail. for influenza (PCR distinguishes type)
Treatment (NEJM 2008;359:2579)
• Seasonal influenza: treat with neuraminidase inhib. (oseltamivir, zanamivir), which are effective vs. A & B, but resistance emerging. M2 inhib. (amantadine, rimantadine) not recommended due to widespread resistance (MMWR 2011;60:1).
• Pandemic H1N1: nearly 100% sens. to oseltamivir. H5N1: Uncertain resistance pattern.
H7N9: newly emerging in Asia (NEJM 2013;368:1888)
• Oseltamivir dosed 75 mg PO bid × 5 d. Must start w/in 48h of sx for low-risk; for critically ill or immunosupp., start ASAP even if >48 h.
• Consider inhaled ribavirin for RSV in immunosupp. (eg, BMT, lung tx); limited adult data
Prevention
• Inactivated influenza vaccine: incl. H1N1. Rec for all >6 mo of age and esp. if pregnant, >50 y, immunosupp., or HCW (MMWR 2012;61:613)
• Isolation, droplet precautions for inPts strongly recommended
• Prophylaxis for high-risk contacts of confirmed influenza: oseltamivir 75 mg PO daily × 10 d