The potential of microcins as new therapies. A phenotypical and genomic study of their efficiency regarding Enterobacteriaceae and their resistance mechanisms

Sofiane Telhig^1,2,3, Phuong Nguyen-Phuong⁴, Laila Ben Said¹, Sylvie Rebuffat³, Carmen Torres⁵, Marc Ouellette⁴, Séverine Zirah³, Ismail Fliss^1,2

¹Food science department, Food and agriculture faculty, Laval University, Quebec, Quebec, Canada
²Institute of Nutrition and Functional Foods, Laval University, Quebec, Quebec, Canada
³Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
⁴Centre de recherche en Infectiologie et Axe des Maladies Infectieuses et Immunitaires du Centre de Recherche du CHU-Québec-Université Laval
⁵Department of Food and Agriculture, University of La Rioja, Logrono, Spain

Context: The emergence and spread of multi-resistant bacteria (MDRs) represents a major health risk. A notorious group of bacteria infamous for their capacity of evading and resisting antibiotics are Enterobacteriaceae. Microcins, antimicrobial peptides of enterobacteria produced ribosomally and targeting other Enterobacteriaceae, are a promising alternative to conventional antibiotics.

Objectives: The study of the potential of microcins to inhibit MDR Enterobacteriaceae strains, as well as define their spectra of activity; explore possible synergistic/antagonistic effects; elucidate and characterize the mechanisms of resistance, co-resistance and cross-resistance between  microcins and antibiotics.

Materials and Methods: The activity of four microcines: microcin J25 (a transcriptioninhibiting lasso peptide), microcin C (a translation-inhibiting nucleotide peptide), microcin B17 (a modified microcin with thiazol oxazol rings) and microcin E492 (a siderophore peptide) was examined against a collection of 54 natural isolates, including several MDRs and covering a variety of serotypes distributed over three species: E. coli, K. pneumoniae and S. enterica. The ability of the four microcins to inhibit the collection of isolates was assessed by minimal MIC and CMB measurements. Their potential synergistic/antagonistic effects were characterized by index FIC measures. The characterization of the phenotypes of resistance observed against the tested microcins was conducted by comparisons of the gene sequencesinvolved in the mechanisms of action said microcins, as well as a non-targeted study GWAS (Genome Wide Association Study).

Results and discussion: None of the strains tested were able to withstand all microcins at the concentrations tested (≤50 μ g/mL). Microcin C had the broadest inhibition spectrum, while microcin J25 had the most effective antimicrobial activities. Consortia microcins/antibiotics were the most beneficial. MFA analysis of microcin inhibition showed a single correlation between gentamicin resistance and MccJ25 resistance. In parallel, targeted and non-targeted genomic analyses did not detect a correlation between antibiotic resistance patterns, virulence genes and microcin resistance. Resistance to each microcin was correlated with the presence of mutations in genes involved either in the import of microcin or in metabolism or stress response.

Conclusions: Given the ability of the four microcins to inhibit varied Enterobacteriaceae species regardless of their antibiotic resistance gene and virulence genes arsenals. Our data highlights the potential of these microcins as new therapies. In addition, it is possible to overcome the narrow spectra of microcins by combining with each other or other antibiotics, since no antagonistic effects were recorded.