Antibiotics and phages drive region-specific diversity of OmpK36 in Klebsiella pneumoniae
Résumé
The Enterobacterales outer membrane is impermeable to many antibiotics, but they can enter the cell via channel proteins, called porins. In Klebsiella pneumoniae, the porin OmpK36 is a major determinant of antibiotic resistance. Insertion of amino acids into the L3 constriction loop is frequently reported, leading to decreased channel size and reduced antibiotic susceptibility. While the involvement of the L3 loop in resistance is well-established, studies focused on a limited number of sequences, without considering any role for diversity outside L3. To fill this gap, we carried out a large-scale genomic comparison combined with experimental analysis. We analyzed 16,086 K. pneumoniae genomes to decipher the diversity of OmpK36 at the species level. We identified 385 protein variants classified into 7 main backbones, some associated with high-risk clones and, consequently, with major resistance classes. Comparison of predicted three-dimensional structures indicates variation in pore size depending on backbones. We constructed mutants carrying the main variants and compared their fitness and susceptibility to antibiotics and phages. Despite OmpK36 diversity and predicted pore radius differences, variations beyond the constriction loop do not seem to significantly impact antibiotic susceptibility and fitness. However, this diversity may have been partly shaped by phages targeting OmpK36, as evidenced by varying susceptibility to a T4-like phage depending on the backbones and the rapid acquisition of mutations in ompK36 among initially susceptible mutants following phage exposure. These findings suggest that while antibiotic pressure selects for L3 loop variations, phage predation may be a key driver of broader OmpK36 diversity.
| Origine | Fichiers éditeurs autorisés sur une archive ouverte |
|---|---|
| Licence |