Antimicrobial resistance (AMR) is an urgent global threat with major economic and public health consequences. Infections caused by Klebsiella pneumoniae, including urinary tract infections (UTIs) and septicaemia, are leading contributors to AMR-related deaths. A comprehensive understanding of resistance mechanisms – which are primarily mediated by changes in the proteome, is needed to identify relevant targets for diagnostics and treatments to combat the threats of AMR.
The bacterial proteome is highly dynamic and will change in response to its external environment. During an infection, the external environment of the infection site can impose stress on the bacteria due to changes in nutrient availably, pH, salt concentrations, or the presence of an antibiotic. These environmental factors can ultimately lead to changes in proteoform abundance, metabolic state, growth rate, or signalling and stress responses, and therefore change the bacterial phenotype. For example, it has been demonstrated that bacterial isolates cultured in physiologically relevant media (i.e., representative of in vivo conditions of an infection site) changes the minimum inhibitory concentration and antibiotic susceptibility of isolates compared to the isolates cultured in standard growth media.
Using shotgun-based proteomics, we compare the changes in the proteome of K. pneumoniae when cultured in infection mimicking mediums: artificial urine media (AUM) and brain heart infusion (BHI) supplemented with serum to mimic the environment of UTIs and septicaemia, respectively, and standard bacterial growth media, Luria-Bertani (LB) broth. We identified 271 unique proteins in K. pneumoniae grown in BHI supplemented with serum including those involved in iron acquisition – an essential nutrient for bacterial survival and virulence, tetrapyrrole synthesis and metabolic pathways, and cobalamin biosynthetic processes. In K. pneumoniae grown in AUM, 367 proteins were uniquely identified including those involved in amino acid catabolism such as lysine, valine, leucine and isoleucine degradation, and tyrosine metabolism.
Assessing changes in the proteome of K. pneumoniae cultured in media mimicking the environment of infection sites acts as an affordable proxy to provide insights into infection site-specific bacterial responses to reveal potentially clinically relevant proteome changes, resistance mechanisms, and potential therapeutic targets that standard bacterial growth media may not capture.