Role of Conjugative Elements in the Evolution of the Multidrug-Resistant Pandemic Clone Streptococcus pneumoniaeSpain23F ST81

Streptococcus pneumoniae is a human commensal and pathogen able to cause a variety of diseases that annually result in over a million deaths worldwide. The S. pneumoniae^Spain23F sequence type 81 lineage was among the first recognized pandemic clones and was responsible for almost 40% of penicillin-resistant pneumococcal infections in the United States in the late 1990s. Analysis of the chromosome sequence of a representative strain, and comparison with other available genomes, indicates roles for integrative and conjugative elements in the evolution of pneumococci and, more particularly, the emergence of the multidrug-resistant Spain 23F ST81 lineage. A number of recently acquired loci within the chromosome appear to encode proteins involved in the production of, or immunity to, antimicrobial compounds, which may contribute to the proficiency of this strain at nasopharyngeal colonization. However, further sequencing of other pandemic clones will be required to establish whether there are any general attributes shared by these strains that are responsible for their international success.Streptococcus pneumoniae (the pneumococcus) is a human commensal and pathogen that represents a major cause of otitis media, pneumonia, and meningitis (8). Worldwide, pneumococcal disease is thought to be responsible for over a million fatalities annually, including more than 800,000 deaths in children under 5 years of age living in developing countries (64). While the introduction of the heptavalent polysaccharide conjugate vaccine (PCV7) has dramatically reduced the incidence of pneumococcal disease in some areas (37), limited serotype coverage, strain replacement, and capsule switching have resulted in a smaller, and decreasing, impact in other communities (66).S. pneumoniae is a naturally competent, genetically diverse species, with less than half of the pan-genome conserved between all strains thus far studied (33). The pneumococcal population is normally confined to the human nasopharynx, with rates of asymptomatic carriage varying with demographics, region, and season: surveys of colonization in healthy children generally estimate between 20 and 97% of younger individuals carry pneumococci (9, 32), with levels falling with age. Epidemiological data and animal models of infection indicate that strains exhibit differing propensities for causing invasive disease (13, 29, 63). The invasive disease potential odds ratio, which takes into account the relative frequencies of invasive disease and asymptomatic carriage observed in the human population, varies 80-fold between serotypes (13). However, the functional genetic variation to which this differing ability to cause disease is attributable remains largely unknown. Genome sequencing efforts have mainly focused on clinical pneumococcal isolates; the complete genomes of two highly invasive strains, TIGR4 (70) and D39 (38) (and the laboratory-adapted D39 derivative R6) (34), have been published, along with draft sequences for serotype 19F strain G54 (26) and eight clinical isolates from a hospital in Pittsburgh (65). However, in order to understand the bacterial population structure, and the reasons underlying the variation in pathogenicity, genomic studies of strains that only rarely invade past the mucosal surfaces are required.S. pneumoniae^Spain23F sequence type 81 (ST81) was one of the first pandemic penicillin-resistant clones identified (47). Initially characterized among isolates from Spain in the 1980s, it spread globally, and by the late 1990s it was estimated to constitute almost 40% of penicillin-resistant disease isolates in the United States (21). The clone is also resistant to chloramphenicol and tetracycline and is one of those most frequently associated with the emergence of fluoroquinolone and macrolide resistance (58, 60). This lack of susceptibility to the major classes of antimicrobial chemotherapies used to treat pneumococcal infections has undoubtedly aided the spread of the strain and lead to the inclusion of the 23F serotype in PCV7. This has resulted in a reduction in the prevalence of the S. pneumoniae^Spain23F ST81 clone in some regions (35). However, the lineage has undergone capsule switching to alternative capsule types on at least three occasions (from serotype 23F to 14 (36), 19A (20), and 19F (19), suggesting it is liable to eventually evade the vaccine. Despite its high carriage prevalence (22), it has a low propensity for causing invasive disease (67) (odds ratio of 0.4 [13]), suggesting its intercontinental distribution has been facilitated by adaptations to colonization of, and survival within, the human nasopharynx. Here we report our analysis of the complete genome of S. pneumoniae ATCC 700669, a member of the serotype 23F ST81 lineage that was isolated in a hospital in Barcelona in 1984 (18).