Can proteomics elucidate mechanisms of antimicrobial resistance in that whole genome sequencing is unable to identify? An analysis of protein expression within the 2016 WHO reference strains.

OBJECTIVES

Antimicrobial resistance (AMR) in is of increasing concern. This study established a quantitative, scalable proteomics method to examine the WHO panel of isolates with completed closed genomic sequences and well-defined phenotypical and genotypical AMR patterns, to gain a greater understanding of AMR in .

METHODS

14 WHO reference strains were propagated, pooled stable isotope labelled lysates were used as an internal standard (IS). Protein lysates were mixed with IS, digested with trypsin and fractionated before analysis by nano-LC/MS/MS, in triplicate. The susceptible strain WHO F was used as reference to which the proteomic profiles of other strains were compared. Hierarchical clustering and permutation adjusted t-tests were performed to find proteins with significant fold changes.

RESULTS

Standardised, reproducible protein expression profiles in reference strains were produced. Strains that have previously been shown to be highly similar using genomics, displayed different proteomic profiles. Several proteins from efflux pumps to stress responses, such as oxidative stress, toxin/antitoxin systems, were found to be altered in AMR strains. LtgE was upregulated in strains which displayed chromosomally mediated resistance to penicillin. MacB (the ATP hydrolysis part of macrolide efflux pump MacA-B), was ~twofold upregulated in WHO V (MIC of azithromycin >256 mg/L) and maybe associated with azithromycin resistance.

CONCLUSIONS

A robust method was developed to study protein expression in . The proteome profiles could differentiate genetically similar stains. This study identified complex mechanisms in which may be associated with AMR.