Professor Pangloss and the Pangenome: Does Staphylococcus aureus Have the Best of All Possible Worlds?

In Voltaire’s 1759 novel Candide, the eponymous hero is indoctrinated by his tutor, Professor Pangloss, to believe that “everything is for the best in the best of all possible worlds.” In this issue of the Journal, Long and colleagues (pp. 1127–1137) present a meticulous and detailed analysis of whole genome sequencing data of 1,382 isolates of Staphylococcus aureus from 246 children with cystic fibrosis (CF), attending five U.S. care centers (1). The authors suggest that S. aureus, through access to an open pangenome (the collective genetic content of all isolates), develops persistent genotypes, well adapted to the CF lung. For S. aureus, this may indeed be “the best of all possible worlds.” The authors offer us some intriguing insights into how S. aureus achieves this and the implications this may have for the patient with CF.

In the first account of CF, Dorothy Andersen described “. . . plugging of the lumens of most if not all of the bronchi with tenacious, greenish-gray mucopurulent material . . .” (2). We now know that these appearances result from dysfunction of the CF transmembrane conductance regulator, leading to viscid respiratory secretions, failure of the mucociliary escalator, bacterial infection, and bronchiectasis (3). In a subsequent article (4), Andersen described the microbiology of CF as, “Cultures taken early in the course of the disease grow S. aureus hemolyticus in nearly every case. . . .” Contemporary registry data support the high prevalence of S. aureus early in life, but suggest that the organism is present in over half of individuals with CF well into the fourth decade (5). Long and colleagues describe some of the secrets behind the organism’s remarkable longevity in the CF airway.

Almost half of the 246 children studied were infected with multiple, coexisting S. aureus lineages, often with different antibiotic susceptibility profiles. The authors show that these infections were more often concurrent than they were sequential. Multiple lineages of S. aureus do not primarily arise from hypermutation of resident organisms in the CF airway—mutation rates in this study were comparable to other patient groups. Mutations in the agrA and rsbU transcriptional regulators, well recognized as important mediators of the acute–chronic transition in S. aureus, were common in S. aureus isolates in this study and were confirmed to modulate virulence through altered protease production and hemolysis.

But the ability to interrogate relationships between pathogen genotype and patient history in this large cohort adds interesting new detail to the picture of how persistent infection is established. Mutations in thyA, which confer resistance to trimethoprim-sulfamethoxazole, were associated with the patient being treated with this specific antimicrobial. In addition to trimethoprim-sulfamethoxazole resistance, thyA mutation has been associated with a switch to the small colony variant phenotype, which results in generally increased antibiotic tolerance and in vivo persistence (6). In contrast, rpoB, mutations in which confer resistance to rifamycin, had the strongest signature of natural selection in the study, despite the fact that only a minority of patients with de novo mutations in this gene were exposed to this drug. Mutations in rpoB have previously been associated with S. aureus persistence through increased tolerance of mammalian antimicrobial peptides (7). Thus, antibiotic-mediated selection for resistance may also confer a general survival advantage in the CF airway (thyA), and, conversely, selection for increased survival in the CF airway may have the byproduct of resistance to an antibiotic (rpoB) that the organism has not yet encountered.

The data presented by Long and colleagues raise an important question about microbial ecology: How spatially structured are the diverse S. aureus populations within the lungs of people with CF? There is good evidence for spatial structuring of microbial populations across the CF lungs (8), and the degree of intermixing (or not) of S. aureus subpopulations will be key in understanding the selection of persisting strains. Do different strains of S. aureus coexist side by side or do they rarely meet? This may also resolve some open questions about how S. aureus lives in CF lungs: are some or all populations intracellular (9), associated with the bronchiolar tissue surface (10), or living within mucus in the bronchial lumen (11)?

This study not only provides insights into the lifestyle of S. aureus but also suggests practical conclusions for infection prevention and control. Using granular molecular epidemiology, Long and colleagues provide detailed information on 11 paired cases in which “strain sharing” between individuals with CF is likely (isolates were separated by ≤36 variants). Strain sharing may be explained by sibling pairs (5 pairs). However, for several pairs attending different CF centers, acquisition of the organism appeared after contact with a single care provider who moved from one CF center to another. Around one-third of the U.S. population will carry S. aureus in the nasopharynx (12). These data underscore the need for scrupulous adherence to infection prevention and control guidelines (13).

The data on antimicrobial resistance are important for clinical practice. In the United Kingdom, but not in the United States (14), it is standard practice to use prophylactic antistaphylococcal antibiotics in young infants with CF from diagnosis (15). As noted above, children in this study could be infected simultaneously with multiple, different S. aureus lineages. One individual might harbor both methicillin-resistant S. aureus (MRSA) and sensitive strains. Indeed, lineages could change from methicillin-resistant to methicillin-sensitive over time. This suggests that culture and sensitivity techniques, currently used in CF centers, may not be sufficiently comprehensive for optimal treatment of MRSA. The authors propose that routine laboratory tests might be developed to characterize coexisting S. aureus lineages better, using either culture or whole genome sequencing. Furthermore, long-term surveillance may be necessary before successful eradication of MRSA can be claimed. The STaph Aureus Resistance - Treat Or Observe (STAR-too) trial of MRSA eradication (16) reported 82% eradication at 28 days, dropping to 54% at 84 days.

Finally, the authors suggest that new antimicrobial agents might be designed to reduce the virulence of the organism without exerting selective pressure for resistance, and such agents have been proposed as useful “antibiotic adjuvants” (17). Voltaire’s novel Candide contains an incident (based on historical fact) in which a British Admiral is shot by firing squad “to encourage the others.” Candide is a satire—it is plainly ridiculous to expect survivors to be encouraged by the execution of one of their number—or is it? In the field of antimicrobial resistance, the execution of bacteria, with an antimicrobial, exerts selective pressure and “encourages” bacterial resistance. Long and colleagues have described an organism exquisitely adapted for long-term survival in the CF airway. New approaches are needed to combat S. aureus infection as it enjoys “the best of all possible worlds.”