Critical role of growth medium for detecting drug interactions in Gram-negative bacteria that model in vivo responses

Abstract

The rise in infections caused by multidrug-resistant (MDR) bacteria has necessitated a variety of clinical approaches, including the use of antibiotic combinations. Antibiotic susceptibility is affected in part by the growth state of bacteria within various tissues. Here we tested the hypothesis that drug-drug interactions vary in different media, and hence, using a medium that reflects tissue environments will better predict in vivo outcomes. We systematically studied pair-wise antibiotic interactions in three different media (CAMHB, a urine mimetic, and a lung mimetic) using three Gram-negative ESKAPE pathogens, Acinetobacter baumannii (Ab), Klebsiella pneumoniae (Kp), and Pseudomonas aeruginosa (Pa). There were pronounced differences in responses to antibiotic combinations between the three bacterial species grown in the same medium. However, within species, Pa responded to drug combinations similarly when grown in all three different media, whereas Ab responded similarly when grown in CAMHB and a lung mimetic medium. By contrast, drug interactions in Kp were poorly correlated across three different media. To assess whether distinct media were predictive of antibiotic interactions in Kp in the lungs of mice, we developed a treatment strategy and tested three antibiotic combination pairs. Measurements obtained in vitro from lung mimetic medium, but not rich medium, predicted in vivo outcomes. This work demonstrates that antibiotic interactions are highly variable when comparing across three gram-negative pathogens and highlights the importance of growth medium by showing a superior correlation between in vitro interactions in a growth medium that resembles the tissue environment and in vivo outcomes.

Discovery of Broad‐Spectrum Repurposed Drug Combinations Against Carbapenem‐Resistant Enterobacteriaceae (CRE) Through Artificial Intelligence (AI)‐Driven Platform

“…To examine BLM/MEM combination in a more clinically relevant setting, the checkerboard assays were repeated against the 9 CRE strains in M9 broth supplemented with 0.4% glucose, which has been reported to mimic the lung environment. [54] We found that BLM/MEM retains its antibacterial activity and strong synergistic interactions against all tested pathogens in M9 media (Figure S7, Supporting Information).…”

Preserving the efficacy of antibiotics to tackle antibiotic resistance

“…Additionally, synergistic or antagonistic interactions between different antibiotics depend on the composition of the environment. Understanding these interactions in vivo can inform the selection of combination therapies for difficult‐to‐treat infections (Davis et al., 2024).…”

Wiring between close nodes in biological networks evolves more quickly than between distant nodes

“…Only a few studies have explored interspecific variation of DDI scores (Spitzer et al 2011; Robbins et al 2015; Brochado et al 2018; Davis et al 2022), but they have demonstrated that DC experiments (used to obtain DDI scores) could be scalable in the number of species and strains. A high throughput study of DDIs in gram-negative bacteria has shown that synergies are more conserved across species than antagonisms and additive combinations (Brochado et al 2018).…”