Assessment of Phenotype Relevant Amino Acid Residues in TEM-β-Lactamases by Mathematical Modelling and Experimental Approval

Single substitutions or combinations of them alter the hydrolytic activity towards specific beta-lactam-antibiotics and beta-lactamase inhibitors of TEM-beta-lactamases. The sequences and phenotypic classification of allelic TEM variants, as provided by the NCBI National Database of Antibiotic Resistant Organisms, does not attribute phenotypes to all variants. Some entries are doubtful as the data assessment differs strongly between the studies or no data on the methodology are provided at all. This complicates mathematical and bioinformatic predictions of phenotypes that rely on the database. The present work aimed to prove the role of specific substitutions on the resistance phenotype of TEM variants in, to our knowledge, the most extensive mutagenesis study. In parallel, the predictive power of extrapolation algorithms was assessed. Most well-known substitutions with direct impact on the phenotype could be reproduced, both mathematically and experimentally. Most discrepancies were found for supportive substitutions, where some resulted in antagonistic effects in contrast to previously described synergism. The mathematical modelling proved to predict the strongest phenotype-relevant substitutions accurately but showed difficulties in identifying less prevalent but still phenotype transforming ones. In general, mutations increasing cephalosporin resistance resulted in increased sensitivity to beta-lactamase inhibitors and vice versa. Combining substitutions related to cephalosporin and beta-lactamase inhibitor resistance in almost all cases increased BLI susceptibility, indicating the rarity of the combined phenotype.

Automated summary

This study demonstrates the significant impact of specific substitutions on the resistance phenotype of TEM variants, with mathematical modeling accurately predicting the strongest phenotype-relevant substitutions but facing difficulties in identifying less prevalent but still phenotype-transforming ones. In most cases, mutations increasing cephalosporin resistance resulted in increased sensitivity to beta-lactamase inhibitors and vice versa, indicating the rarity of the combined phenotype.