Macrolide resistance rates in clinical isolates of S. pneumoniae vary greatly among countries. The rate in our collection of isolates from Arizona patients, 23.6%, is consistent with other studies targeting S. pneumoniae in North America [15, 38].
The temporal trend in mef(E) and erm(B) prevalence that we observed in our collection, the rise in proportion dual gene-positive inversely to the proportion mef(E)-positive, is similar to those of other non-invasive isolate studies . Recent studies of invasive isolates have shown low rates of dual gene carriage and multidrug resistance [11, 14, 40]. Likewise, only one of the invasive isolates we tested was dual-gene positive. These significant differences between invasive and non-invasive isolate gene carriage and susceptibility profiles may arise because macrolide-induced selection pressures on invasive S. pneumoniae may be different from those on non-invasive S. pneumoniae, due to the pharmacodynamics of macrolide antibiotics.
Over half of our macrolide resistant S. pneumoniae isolates are positive for both erm(B) and mef(E). All these dual-positive strains belong to CC271, have almost identical multidrug resistance profiles, and are likely carrying Tn2010. Clonal lineages of multidrug-resistant S. pneumoniae belonging to CC271 are now distributed worldwide and make up a significant portion of the macrolide resistant S. pneumoniae isolates in many regions [7, 10, 14, 41, 42]. The emergence of these clones is at least partly a response to introduction of PCV7, in which lineages of the successful multidrug resistant Taiwan19F-14 ST236 clone acquired erm(B) and switched serotypes in response to the selective pressures of an immunized population [6, 43]. One cosmopolitan lineage recombined into ST320 and serotype 19A [35, 36]. This clone has afflicted Arizona children since the PCV7 release in 2000; of the 73 dual-positive isolates in our collection, 47 are ST320, 38 of which are from children of vaccine age. Most of these are from ear and respiratory specimens, an observation consistent with that of the global PROTEKT studies [6, 15]. These data display the opportunistic dominance of a few S. pneumoniae clones in the post-PCV7 era. The pervasiveness of the multidrug resistant phenotype poses a serious public health concern for increased treatment failure and selection of these clones with the usage of any one of several antibiotics.
Genotyping our collection revealed high strain diversity within the mef(E)-positive population. The variety of antibiotic susceptibility profiles and mobile genetic elements carrying mef(E) reflect the sequence type and serotype diversity found in this population. These data indicate that mef(E)-carrying S. pneumoniae are the ancestral macrolide-resistant strains in the U.S. Serotype replacement and a possible serotype switching event are evident in this population; NVTs outnumber VTs in later time periods, and ST156, the identifier of the Spain9V-3 clone, typed as NVT 6A. One notable observation of the mef(E)-positive population is that the latest ST236 seen is 2005-2006, more evidence that this clone acquired the erm(B) gene, and its lineages now comprise the dual mef(E)/erm(B)-positive population.
Genotype analyses of the small erm(B)-positive population illustrate serotype replacement. ST315, VT 6B is not seen after 2000, while ST63, NVT 15A became dominant . These findings could be the result of loss in ST315 or acquisition in ST63 of erm(B) and consequent sampling bias, however neither strain carries erm(B) in a Tn917-family transposon leaving the mobility of the erm(B) element in these strains unknown.
The dramatic increase in erm(B)-carrying S. pneumoniae isolates is important in regions where mef-carrying isolates have historically predominated. Treatment with macrolides is an option for patients suffering localized infections caused by mef-carrying S. pneumoniae, as drug concentrations in tissues can supercede these bacteria's macrolide MICs [44, 45]. However, macrolide MICs for erm(B)-carrying strains are significantly higher than those of mef-carrying isolates , increasing the need for alternative antibiotics where erm(B) predominates. It remains to be seen whether the U.S. will see an increase in clinical failure in macrolide-treated cases parallel to the increase in erm(B)-carrying S. pneumoniae.