Convergent evolution of antibiotic resistance mechanisms between synthetic pyrrolobenzodiazepines (PBDs) and the naturally occurring albicidin in multidrug resistant Klebsiella pneumoniae

TY - JOUR

T1 - Convergent evolution of antibiotic resistance mechanisms between synthetic pyrrolobenzodiazepines (PBDs) and the naturally occurring albicidin in multidrug resistant Klebsiella pneumoniae

AU - Surani, Yasmin

AU - Hasan, Md. Mahbub

AU - Andriollo, Paolo

AU - Nahar, Kazi

AU - Steiner, Roberto

AU - Wand, Matthew E.

AU - Picconi, Pietro

AU - Di Palma, Michele

AU - Rahman, Miraz

AU - Hind, Charlotte K.

AU - Sutton, John

PY - 2025/4/9

Y1 - 2025/4/9

N2 - Klebsiella pneumoniae is designated as one of six priority ESKAPE pathogens by the World Health Organisation (WHO). It is the causative agent of a number of serious infections, including pneumonia, and worryingly strains are known to have resistance to the four major antibiotic classes. Pyrrolobenzodiazepines (PBDs) with a C8-linked aliphatic heterocycle have been developed as a new class of potent antibacterial compounds. They are active against multidrug resistant (MDR) Gram-negative pathogens, including K. pneumoniae. When K. pneumoniae isolates were exposed to PBDs, they acquired resistance, with an increase in minimum inhibitory concentration (MIC) from 1-4 µg/mL to >32 µg/mL. Resistant strains showed mutations in genes associated with resistance to albicidin, a natural antimicrobial produced by Xanthomonas albilineans, specifically tsx and merR-family regulator albA. Heterologous expression of AlbA in Escherichia coli, and introduction of a proposed resistance-mediating single-nucleotide modification (AlbA L120Q) into the genome of a sensitive K. pneumoniae strain confers both PBD and albicidin resistance. This is further supported by proteomic analysis of the recombineered K. pneumoniae strain (NCTC 7427 AlbA L120Q) together with two strains that have acquired PBD resistance (NCTC 13438 AlbA L120Q and NCTC 13368 AlbA H50N), which all show significantly elevated levels of the AlbA protein compared to isogenic wild-type strains. Crystallographic studies with the purified antibiotic binding domain of K. oxytoca AlbA (termed AlbAS) show binding of KMR-14-14 to the same groove which has been previously shown to bind albicidin, but with a stoichiometry of two PBD bound to each molecule of AlbAS protein. Given the parallels between these two structurally unrelated compound classes, these mechanisms may offer resistance to further antibiotics in K. pneumoniae and should be considered in future antibiotic discovery.

AB - Klebsiella pneumoniae is designated as one of six priority ESKAPE pathogens by the World Health Organisation (WHO). It is the causative agent of a number of serious infections, including pneumonia, and worryingly strains are known to have resistance to the four major antibiotic classes. Pyrrolobenzodiazepines (PBDs) with a C8-linked aliphatic heterocycle have been developed as a new class of potent antibacterial compounds. They are active against multidrug resistant (MDR) Gram-negative pathogens, including K. pneumoniae. When K. pneumoniae isolates were exposed to PBDs, they acquired resistance, with an increase in minimum inhibitory concentration (MIC) from 1-4 µg/mL to >32 µg/mL. Resistant strains showed mutations in genes associated with resistance to albicidin, a natural antimicrobial produced by Xanthomonas albilineans, specifically tsx and merR-family regulator albA. Heterologous expression of AlbA in Escherichia coli, and introduction of a proposed resistance-mediating single-nucleotide modification (AlbA L120Q) into the genome of a sensitive K. pneumoniae strain confers both PBD and albicidin resistance. This is further supported by proteomic analysis of the recombineered K. pneumoniae strain (NCTC 7427 AlbA L120Q) together with two strains that have acquired PBD resistance (NCTC 13438 AlbA L120Q and NCTC 13368 AlbA H50N), which all show significantly elevated levels of the AlbA protein compared to isogenic wild-type strains. Crystallographic studies with the purified antibiotic binding domain of K. oxytoca AlbA (termed AlbAS) show binding of KMR-14-14 to the same groove which has been previously shown to bind albicidin, but with a stoichiometry of two PBD bound to each molecule of AlbAS protein. Given the parallels between these two structurally unrelated compound classes, these mechanisms may offer resistance to further antibiotics in K. pneumoniae and should be considered in future antibiotic discovery.

M3 - Article

SN - 2731-8745

JO - npj Antimicrobials and Resistance

JF - npj Antimicrobials and Resistance

ER -