Antimicrobial resistance mechanisms in the presence of sub-inhibitory antibiotics and the microbiome

Hughes, Naomi 2025. Antimicrobial resistance mechanisms in the presence of sub-inhibitory antibiotics and the microbiome. PhD Thesis, Cardiff University. Item availability restricted.

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Abstract

People with cystic fibrosis (pwCF) suffer lifelong lung infections which are often driven by polymicrobial communities. Conventional antimicrobial susceptibility testing (AST) poorly predicts clinical outcomes in pwCF, a consequence thought to be driven by the complex interactions among CF lung pathogens, the formation of biofilms in thick mucus secretions and the effects of additional host factors. This work investigated dual-species interactions between prevalent, recently emerged and increasingly important CF pathogens found in adults. This included Pseudomonas aeruginosa and other recognised CF pathogens (Achromobacter xylosoxidans, Burkholderia multivorans, Staphylococcus aureus, and Stenotrophomonas maltophilia), focusing on virulence traits and antimicrobial susceptibility. First, motility, protease secretion, and susceptibility of single and dual species were assessed. There was little significant alteration in motility for most comparisons. Protease secretion was notably suppressed in P. aeruginosa when co-cultured with B. multivorans. Protease secretion was also dependent on media type and inoculation density. The antimicrobial agents of focus were ciprofloxacin, meropenem, tobramycin, and trimethoprim-sulfamethoxazole. Dual-species cultures showed reduced antibiotic susceptibility compared to P. aeruginosa alone, with species- and agent-specific variations. Growth medium influenced efficacy—synthetic cystic fibrosis medium 2 (SCFM2) hindered antibiotic action compared to conventional Mueller-Hinton broth. The suppressed protease secretion identified in P. aeruginosa and B. multivorans co-cultures prompted a transcriptomic analysis. Gene expression in dual-cultures of P. aeruginosa and B. multivorans, and of P. aeruginosa and S. aureus was compared to single-species cultures. Gene expression in P. aeruginosa was altered by both B. multivorans and S. aureus, while secondary pathogens remained unaffected. The effects of antimicrobials and pathogen interactions were also studied in a biofilm context. Biofilm assays revealed that antimicrobial tolerance in dual and single-species varied by species combination and drug used when grown in biofilms with long-term antimicrobial exposure. Sub-inhibitory antibiotic exposure altered species viability ratios and, impacted metabolic activity and biomass although these did not consistently correlate with viability. However, the time spent (4–12 days) in a biofilm, regardless of meropenem exposure significantly impacted susceptibility of biofilm-derived isolates. Interspecies competition of long-term biofilm derivatives changed according to exposure with meropenem sub-MIC. These findings underscore the limitations found previously with conventional AST in polymicrobial CF infections and highlight the need for standardized, context-aware testing methods. These ideas are presented and discussed in consideration of the current challenges facing polymicrobial infection modelling and the potential for the future development of a predictive AST approaches tailored to pwCF. Key words: Antimicrobial susceptibility testing; cystic fibrosis; lung infection; polymicrobial biofilms; sub-inhibitory antimicrobial concentrations; Achromobacter xylosoxidans; Burkholderia multivorans; Pseudomonas aeruginosa; Staphylococcus aureus; Stenotrophomonas maltophilia.

Item Type:	Thesis (PhD)
Date Type:	Completion
Status:	Unpublished
Schools:	Schools > Biosciences
Subjects:	Q Science > Q Science (General)
Date of First Compliant Deposit:	5 May 2026
Last Modified:	06 May 2026 09:13
URI:	https://orca.cardiff.ac.uk/id/eprint/186764

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