Optimal Sampling Sites and Methods for Detection of Pathogens Possibly Causing Community-Acquired Lower Respiratory Tract Infections

Acute respiratory tract infections (RTIs), both upper (URTIs) and lower respiratory tract infections (LRTIs), are the most common reason for consultation with a general practitioner. RTIs result in about 180 million antibiotic prescriptions per year in the EU-27 member states (ESAC website, 2008; www.esac.ua.ac.be), and 6.4 million antibiotic prescriptions were prescribed for acute bronchitis and cough in 2003 in adults between 16 and 64 years old in the United States (65). The number of pathogens involved in LRTI, with various susceptibilities to antimicrobials, is large constituting an enormous challenge for diagnostic microbiology. In general, in only 50% of cases is an etiologic agent detected. Documented infection is uncommon in community-managed infection and is usually only defined in 25 to 50% of hospital-managed infections. The upper end of the respiratory tract, the rhinopharynx, is widely open to the introduction of airborne microorganisms. It is, however, also a very efficient barrier for invading bacteria. The barrier function of the rhinopharynx results from the local lymphoid tissue producing phagocytic cells and secretory immunoglobulin (Ig) and from the rich commensal flora of aerobic and anaerobic microbes establishing an interfering colonization resistance. The number of these organisms varies from 2.6 × 104 to 4 × 108 CFU of cultivable bacteria per cm2 (95). Aerobes tend to decrease and anaerobes tend to increase with age (98). Colonization starts during the first year of life and is composed not only of commensal organisms but also of potential pathogens: group A β-hemolytic streptococci, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. These are present permanently or intermittently, with rates varying with age (decreasing in adults), exposure to other children, geographic location, socioeconomic status, and vaccination status (39). In most cases, these organisms cause disease in only a small percentage of persons colonized. Viruses do not normally colonize the rhinopharynx. However, most bacterial respiratory infections start with or are accompanied by their proliferation in the nasopharynx. Thus, the URT with its commensal flora acts both as a defense mechanism and as a primary site for LRTI, which creates tremendous diagnostic challenges. Any bacteriological examination of nonsterile respiratory specimens must indeed distinguish between organisms infecting the LRT and organisms colonizing the rhinopharynx. Normally sterile samples therefore are considered the “gold standard. ” Different specimens commonly collected to detect pathogens causing LRTI have been compared, but the results were not consistent (12, 43, 49, 58, 103) (Table ​(Table1;1; and see Table S1 in the supplemental material). This minireview presents an overview of the optimal detection of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, and respiratory viruses from specimens in patients with community-associated (CA)-LRTI (Table ​(Table22). TABLE 1. Comparison of specimens and sampling methods for the detection of different respiratory pathogensa TABLE 2. Diagnostic approach for the most common specific agents in LRTIsa