Convergent evolution of antibiotic resistance mechanisms between pyrrolobenzodiazepines and albicidin in multidrug resistant Klebsiella pneumoniae

Introduction

Antibiotics are heavily relied upon in the clinic, both to treat and prevent bacterial infection¹. Exposure to antibiotics presents a survival challenge to the bacteria, which may result in the emergence of resistant populations through genomic mutations followed by either vertical or horizontal transmission². Multidrug-resistant (MDR) bacterial populations are on the rise, and pose a real threat to public health, both economically and with regards to the loss of human life¹.

Species of particular concern have been termed the ESKAPE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species³. Of these, the last four are Gram-negative bacteria, which present a greater challenge due to the need to penetrate their two cell membranes with very different properties while avoiding drug efflux^4,5.

K. pneumoniae inhabits the gastrointestinal tract, but it is also an opportunistic hospital-associated pathogen. One-third of all Gram-negative infections are attributed to it, including pneumonia, urinary tract infections, wound colonisation, and, more seriously: endocarditis, and septicaemia. K. pneumoniae strains have exhibited resistance to the four major antibiotic classes: third generation cephalosporins, aminoglycosides, fluoroquinolones, and even carbapenems, which were a last resort against extended-spectrum β-lactamase (ESBL) producers².

Pyrrolobenzodiazepines (PBDs) are sequence-selective DNA minor groove binding agents with antitumour⁶ and antibacterial⁷ activities. While their antitumour activities have been shown to be due to covalent DNA binding and transcription factor inhibition⁸, their antibacterial activities are thought to be due to a combination of DNA binding and the inhibition of DNA gyrase⁹. The core PBD scaffold has been described in Streptomyces species¹⁰, naturally-occurring PBDs have also been identified in Klebsiella spp¹¹, and synthetic derivatives have demonstrated activity against Gram-negative bacteria including K. pneumoniae⁹. These compounds represent a potential new scaffold for antibiotic development. The antibacterial PBDs have been designed to simultaneously minimise eukaryotic toxicity whilst incorporating chemical features thought to facilitate Gram-negative entry ^9,12.

Resistance to PBDs in K. pneumoniae has been observed through sequence changes in a number of genes, including those encoding Tsx and MerR-family regulator AlbA⁹. Tsx is an outer membrane nucleoside transporter¹³, and AlbA is...