Disruption of Cross-Feeding Inhibits Pathogen Growth in the Sputa of Patients with Cystic Fibrosis

Abstract

A critical limitation in the management of chronic polymicrobial infections is the lack of correlation between antibiotic susceptibility testing (AST) and patient responses to therapy. Underlying this disconnect is our inability to accurately recapitulate the in vivo environment and complex polymicrobial communities in vitro. However, emerging evidence suggests that, if modeled and tested accurately, interspecies relationships can be exploited by conventional antibiotics predicted to be ineffective by standard AST. As an example, under conditions where Pseudomonas aeruginosa relies on cocolonizing organisms for nutrients (i.e., cross-feeding), multidrug-resistant P. aeruginosa may be indirectly targeted by inhibiting the growth of its metabolic partners. While this has been shown in vitro using synthetic bacterial communities, the efficacy of a “weakest-link” approach to controlling host-associated polymicrobial infections has not yet been demonstrated. To test whether cross-feeding inhibition can be leveraged in clinically relevant contexts, we collected sputa from cystic fibrosis (CF) subjects and used enrichment culturing to isolate both P. aeruginosa and anaerobic bacteria from each sample. Predictably, both subpopulations showed various antibiotic susceptibilities when grown independently. However, when P. aeruginosa was cultured and treated under cooperative conditions in which it was dependent on anaerobic bacteria for nutrients, the growth of both the pathogen and the anaerobe was constrained despite their intrinsic antibiotic resistance profiles. These data demonstrate that the control of complex polymicrobial infections may be achieved by exploiting obligate or facultative interspecies relationships. Toward this end, in vitro susceptibility testing should evolve to more accurately reflect in vivo growth environments and microbial interactions found within them. IMPORTANCE Antibiotic efficacy achieved in vitro correlates poorly with clinical outcomes after treatment of chronic polymicrobial diseases; if a pathogen demonstrates susceptibility to a given antibiotic in the lab, that compound is often ineffective when administered clinically. Conversely, if a pathogen is resistant in vitro, patient treatment with that same compound can elicit a positive response. This discordance suggests that the in vivo growth environment impacts pathogen antibiotic susceptibility. Indeed, here we demonstrate that interspecies relationships among microbiotas in the sputa of cystic fibrosis patients can be targeted to indirectly inhibit the growth of Pseudomonas aeruginosa. The therapeutic implication is that control of chronic lung infections may be achieved by exploiting obligate or facultative relationships among airway bacterial community members. This strategy is particularly relevant for pathogens harboring intrinsic multidrug resistance and is broadly applicable to chronic polymicrobial airway, wound, and intra-abdominal infections.

From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment

“…Moreover, a range of microbial interactions can either limit or promote P. aeruginosa persistence and, thus, adaptation within CF lung infections [156–158, 160–162]. In line with this, the presence of Staphylococcus aureus has been shown to promote P.…”

“…Besides pathogens, the role of the normal lung microbiota is increasingly considered since commensal anaerobes have been shown to impact the antibiotic resistance and virulence of P. aeruginosa [161, 162]. Thus, the presence of these micro-organisms may influence establishment and adaptation of P.…”

Weakest-Link Dynamics Predict Apparent Antibiotic Interactions in a Model Cross-Feeding Community

“…Weakest-link dynamics are just one of a growing list of ways that microbial interactions have been shown to alter the impact of antibiotics ( 55 – 57 ). Intriguing recent work suggests that drug effects in patients may be more accurately predicted by simply testing resistance profiles of mixed communities rather than monocultures ( 58 ).…”

Nasopharyngeal microbial communities of patients infected with SARS-COV-2 that developed COVID-19

“…are keystone species in microbiomes during airway disease progression, especially in diseases associated with mucus accumulation such as cystic fibrosis [30][31][32]. These anaerobes are efficient at degrading mucin molecules on the airway mucosa, releasing byproducts that enable the colonization and growth of pathogenic bacteria that are poor at degrading mucus for growth [33]. In COVID patients, Prevotella sp.…”