Antimicrobial Activity of a Polymyxin A-like Compound and Characterisation of the Cognate Biosynthetic Gene Cluster Within the Genome of the Producing Paenibacillus polymyxa

Background: Here, we report the isolation and identification of a Paenibacillus polymyxa strain from the citizen science project, Swab and Send. P. polymyxa is well known for its production of polymyxin E (colistin), and polymyxin B. Polymyxins are ranked in the highest-priority critically important antimicrobial classification by the WHO and are of particular importance for treating Gram-negative multi-drug-resistant pathogens. Due to their clinical use, most of the literature focusses on these polymyxin variants, and there is sparse genetic research on other polymyxin variants. Methods: The Paenibacillus polymyxa 1G strain was isolated and tested for antimicrobial activity using a combination of on-agar and liquid-based inhibition assays to detect antimicrobial activity against Escherichia coli. The isolate was also tested for activity in liquid media against a panel of isolates showing various resistances to test if our strain could overcome current clinically important resistance mechanisms. Our isolate was whole-genome-sequenced, and bioinformatics was carried out on the resulting sequence to analyse the relevant biosynthetic gene cluster. The cell-free supernatant from the P. polymyxa 1G isolate was also analysed using mass spectrometry to confirm the production of the polymyxin. Results: P. polymyxa 1G was active on agar and resulted in antimicrobial activity, with a 99% reduction in area under the curve when tested in liquid media against E. coli. P. polymyxa 1G did not inhibit the growth of E. coli containing mcr-1 or mcr-4 colistin-resistance genes. Using whole genome sequencing, we are able to describe the biosynthetic gene cluster of the putative polymyxin A, compare the pmxA, pmxB, and pmxE genes to five other polymyxin genes that encode known polymyxin variants, and provide mass spectrometry data that supports the production of polymyxin A1 (1157 m/z) and A2 (1143 m/z). Conclusions: Here, we report the isolation and identification of a P. polymyxa strain producing a polymyxin A-like compound that was discovered through the citizen science project, Swab and Send. We add to the genetic and mass spectrometry data for polymyxin A, and demonstrate that this putative polymyxin A, produced naturally by our strain, is unable to overcome the current clinically relevant resistance mechanisms to colistin.