Experimental Evolution In Vivo To Identify Selective Pressures during Pneumococcal Colonization

Abstract

Experimental evolution is a powerful technique to understand how populations evolve from selective pressures imparted by the surrounding environment. With the advancement of whole-population genomic sequencing, it is possible to identify and track multiple contending genotypes associated with adaptations to specific selective pressures. This approach has been used repeatedly with model species in vitro, but only rarely in vivo. Herein we report results of replicate experimentally evolved populations of Streptococcus pneumoniae propagated by repeated murine nasal colonization with the aim of identifying gene products under strong selection as well as the population genetic dynamics of infection cycles. Frameshift mutations in one gene, dltB, responsible for incorporation of d-alanine into teichoic acids on the bacterial surface, evolved repeatedly and swept to high frequency. Targeted deletions of dltB produced a fitness advantage during initial nasal colonization coupled with a corresponding fitness disadvantage in the lungs during pulmonary infection. The underlying mechanism behind the fitness trade-off between these two niches was found to be enhanced adherence to respiratory cells balanced by increased sensitivity to host-derived antimicrobial peptides, a finding recapitulated in the murine model. Additional mutations that are predicted to affect trace metal transport, central metabolism, and regulation of biofilm production and competence were also selected. These data indicate that experimental evolution can be applied to murine models of pathogenesis to gain insight into organism-specific tissue tropisms. IMPORTANCE Evolution is a powerful force that can be experimentally harnessed to gain insight into how populations evolve in response to selective pressures. Herein we tested the applicability of experimental evolutionary approaches to gain insight into how the major human pathogen Streptococcus pneumoniae responds to repeated colonization events using a murine model. These studies revealed the population dynamics of repeated colonization events and demonstrated that in vivo experimental evolution resulted in highly reproducible trajectories that reflect the environmental niche encountered during nasal colonization. Mutations impacting the surface charge of the bacteria were repeatedly selected during colonization and provided a fitness benefit in this niche that was counterbalanced by a corresponding fitness defect during lung infection. These data indicate that experimental evolution can be applied to models of pathogenesis to gain insight into organism-specific tissue tropisms.

An in vivo atlas of host–pathogen transcriptomes during Streptococcus pneumoniae colonization and disease

“…Mutants lacking the dltB gene (SP_2175) were shown by Cooper et al ( 43 ) to be selected for during in vivo experimental evolution during colonization, probably because the authors removed the transmission bottleneck by performing multiple experimental passages. Cooper et al hypothesized that the dlt locus was maintained across the pneumococcal population because it is required for transmission to new hosts despite increased adhesion and colonization when the locus was deleted.…”

Identification of colonisation and virulence determinants of Streptococcus pneumoniae via experimental evolution in mouse infection models

“…Experimental evolution is a powerful tool for identification of genetic elements under selection within different environments 4 . Cooper and colleagues recently showed the value of this approach for Streptococcus pneumoniae in mouse models, using a nasopharyngeal colonisation model similar to that described here, but using a 19F pneumococcal strain (BHN97x) 29 . There are some interesting commonalities in the findings of the two studies.…”

Competitive exclusion strengthens selection for transmissibility and increases the benefit of recombination for within-host adaptation

“…Relaxing selection for transmission, however, selects for within-host fitness without consideration for transmissibility. Serial passage experiments in mice, for example, have resulted in the inactivation of genes that promote transmission at the expense of within-host fitness, such as dltB in S. pneumoniae [30], or selected for accelerated growth in Plasmodium chabaudi [31, 32]. Analogous dlt inactivation and evolution of more virulent Plasmodium knowlesi parasites have also been observed during human infections, suggesting that within-host adaptation has important consequences for disease severity and warranting further study of how transmission affects the rate of such adaptation [11, 33].…”

“…The balance between transmissibility and within-host fitness parallels an invasion-persistence trade-off in other organisms—some genotypes may more readily disperse and colonize new hosts/territories, but are less persistent and thus fare poorly when present in the same environment as less dispersable but more competitive genotypes. This trade-off is evident in several S. pneumoniae genes, such as toxin pneumolysin [40, 41], capsule serotype (for example, serotype 4 compared to 23F) [40, 42], and the aforementioned dltB [30, 43], which promote transmissibility at the expense of within-host fitness. Whether these genes are favored by selection and maintained depends on the relative importance of transmissibility and within-host fitness, as shown by the loss of dltB in serial passage where transmission is more certain.…”