Not Quite the Bully in the Schoolyard: Staphylococcus aureus Can Survive and Coexist with Pseudomonas aeruginosa in the Cystic Fibrosis Lung.

Microorganisms often dwell and interact in complex environmental communities. These interactions may benefit multiple parties (e.g., protection in biofilms) or just one member (e.g., metabolite exchange). However, interspecies interactions can be antagonistic interactions in which one organism inhibits or kills its neighbor, especially involving nutrient and niche competition. In either case, polymicrobial interactions can alter the behavior, physiology, and persistence of microbes impacting human infections (1). Scientists have gained a greater appreciation for the constituents and causes of human polymicrobial infections, including respiratory tract infections (1). In addition to identifying the microbiota, studies have begun to define the interactions between microbes in these infections. The cystic fibrosis (CF) lung environment represents an ideal location for diverse microbes to interact.

Although diverse bacterial species colonize the airways of individuals with CF, Pseudomonas aeruginosa and Staphylococcus aureus are two key pathogens in terms of prevalence, sputum abundance, and associations with lung disease (2–4). P. aeruginosa has long been considered the dominant CF pathogen on the basis of circumstantial evidence. First, the U.S. CF Foundation Patient Registry reports an inverse relationship between the prevalence of both species; specifically, S. aureus declines during late teenage years, whereas P. aeruginosa increases (2) (Figure 1). Given the relatively high S. aureus prevalence in children and young adults (60–80%), P. aeruginosa is often believed to actively supplant S. aureus in secretions (5, 6). Second, P. aeruginosa outcompetes and suppresses S. aureus growth during in vitro coculture by producing antistaphylococcal compounds (7), which are induced by S. aureus (8) and are detected in CF sputum (9, 10). P. aeruginosa benefits from iron released after S. aureus lysis (11), potentially explaining why it targets S. aureus.

Figure 1.

Data from the U.S. Cystic Fibrosis Foundation Patient Registry showing the prevalence of individuals with cystic fibrosis who had positive culture results for a bacterial species according to age group during 2018. The age cohort is presented on the x-axis, and the percentages of positive culture results are displayed on the y-axis for the following organisms: Pseudomonas aeruginosa, Staphylococcus aureus (methicillin-susceptible), MRSA, Haemophilus influenzae, Achromobacter species, Burkholderia cepacia complex, and Stenotrophomonas maltophilia. Although coinfections are not displayed, individuals may have been colonized with multiple organisms. Reprinted by permission from Reference 2. MRSA = methicillin-resistant S. aureus.

Based on this evidence, an assumption is that P. aeruginosa suppresses S. aureus in the CF lung, shifting prevalence with age. However, the Patient Registry figure depicts cross-sectional rather than longitudinal data of individuals and lacks quantitative culture results to measure changes in bacterial abundance (Figure 1). Rather than succumbing to P. aeruginosa antagonism, S. aureus may simply disappear with age, either in response to host physiological changes or with treatment, allowing other pathogens to occupy the space. S. aureus prevalence and coinfection rates with P. aeruginosa have risen over the last decade (2), which also challenges the assumed in vivo dominance of P. aeruginosa over S. aureus. Finally, in vitro coculture models involve cells in a metabolically active state and in physical contact or immediate proximity to each other, both of which may not exist in vivo.

In this issue of the Journal, Fischer and colleagues (pp. 328–338) thoughtfully scrutinize the dynamic relationship between P. aeruginosa and S. aureus. The authors examined retrospective, longitudinal, and quantitative culture data from people with CF who regularly expectorated sputum (12). This large collection of culture data provided a unique resource to assess the presence and densities of these pathogens over an extended timeframe. Among patients with CF who provided ≥10 sputum or BAL quantitative cultures over 13 years, a majority of patients had cultures positive for each organism, high rates of simultaneous coinfection, and high bacterial densities of each (median log10 colony-forming units/ml of 6.52 for P. aeruginosa and 6.42 for S. aureus). This permitted longitudinal analyses of changes in culture abundance after acquisition of the competing species or during simultaneous coinfection. Contrary to the longstanding assumptions of P. aeruginosa dominance, the authors found that S. aureus had stable, long-term coexistence with P. aeruginosa in CF samples. Regardless of whether S. aureus preceded the introduction of P. aeruginosa or whether both organisms were cocultured early in the study, S. aureus bacterial densities did not decline with time in the presence of P. aeruginosa. Interestingly, coinfections actually increased rather than decreasing over time, and replacement of S. aureus by P. aeruginosa rarely occurred. In comparison, Haemophilus influenzae, another early CF pathogen, did not compete well against either organism. S. aureus is typically categorized according to methicillin susceptibility (methicillin-susceptible S. aureus [MSSA] and methicillin-resistant S. aureus [MRSA]). National surveillance has shown an increase in MRSA culture positivity in U.S. patients with CF from 2000 to 2010 (2). This increase was even more pronounced at the authors’ center, raising doubts whether persistence was related to changes in S. aureus susceptibility rather than resilience to P. aeruginosa antagonism. To address this question, the authors repeated their analyses for MSSA and MRSA individually and found both subtypes had similar durations of infection and maintained high culture abundances when coinfecting with P. aeruginosa, although MRSA sputum densities were generally higher and persisted longer than MSSA.

Because these findings are provocative, a number of questions emerge. How generalizable are these single site findings to the broader CF population and other centers? The authors analyzed quantitative culture results from subjects who expectorated. These subjects represented ∼40% of the clinic population, were relatively older, had worse lung disease, and had higher P. aeruginosa culture rates than the other patients with CF in the center. The interactions between P. aeruginosa and S. aureus may differ in younger, healthier patients with newly acquired bacteria. For example, persistent (late) CF P. aeruginosa isolates lose their competitive advantage in vitro over S. aureus compared with recently acquired (early) P. aeruginosa isolates (13, 14). In addition, the relatively high MRSA rates at this center raise doubts about whether treatment and antibiotic susceptibility alter outcomes between P. aeruginosa and S. aureus. A prospective, multicenter study encompassing a larger, younger, and healthier patient population with lower MRSA prevalence and including a longitudinal linkage between microbiology and antibiotic usage would alleviate these limitations.

Regardless of limitations, these results suggest that S. aureus is more resilient than previously believed, but how does S. aureus coexist with P. aeruginosa in vivo, given P. aeruginosa’s in vitro dominance? These two species may be compartmentalized within the airways and only mix on expectoration. The concept of microbial compartmentalization in the CF airway has previously been demonstrated (15). Alternatively, S. aureus may adapt to the presence of P. aeruginosa, facilitating its in vivo coexistence. For example, P. aeruginosa and certain antibiotics select for S. aureus small colony variants in vitro that are tolerant to P. aeruginosa antagonism (9). The detection of small colony variants was not evaluated in this report.

Importantly, what does this information mean for the health and care of people with CF? Patients with CF coinfected with P. aeruginosa and S. aureus reportedly have worse respiratory outcomes than those with single infections (16). Characteristics associated with persistence, pathogenesis, and response to therapy of each species were affected by interactions between these bacteria in vitro (7). Fischer and colleagues (12) conclude that P. aeruginosa and S. aureus can coinfect for much longer than previously anticipated. These results suggest that concurrent treatments directed at both organisms may improve CF clinical outcomes.