Phenotyping and molecular characterization of bacteriocin-producing Escherichia coli isolated from the gastrointestinal tract of poultry

Ramzi Guerbaa^1,2, Laila Ben Said², Séverine Zirah³, Karim Ben Slama¹, Ismail Fliss²

1 Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisia
2 Institute of Nutrition and Functional Foods, Université Laval, Quebec, Quebec, Canada
3 Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France

Context and Problematics:

Antibiotic resistance is a major healthcare concern that threatens both animal and human health. The use of antimicrobial peptides is a promising alternative to antibiotics and can contribute to reduce the pressure of selection and thus reducing the spread of drug resistant bacteria.

Objectives: 

The aim of this work is to characterize E. coli strains isolated from avian caecal content of broiler chicken, in terms of antibiotic resistance, virulence profile and capacity to produce bacteriocins. Correlation between virulence and production of bacteriocins will also be studied.

Methodology:

A total of 388 lactose positive isolates were recovered from Forty-nine composite samples were collected from avian caecal content and identified by biochemical and molecular methods. Upon identification, isolates were screened by direct antagonism against a collection of 10 Beta-lactam resistant enterobacteria. Active isolates were further screened for antimicrobial activity from their supernatant against a two Type strains (E. coli ATCC 25922 and Salmonella enterica Newport ATCC 6269) and two E. coli isolates remarkably sensitive to tested supernatants. A subset of strains, selected based on their antimicrobial activity, were phenotypically characterized for susceptibility to antibiotics. Whole genome of these strains was extracted and sequenced. 

Results and discussion:

Among 388 isolates, 66 were shown to be active by direct antagonism. Screening from the supernatants led to the selection of 21 active strains and 18 non active strains. Antimicrobial susceptibility testing showed an overall high level of resistance to Quinolones (85 %), Tetracyclines (64 %) and Betalactams (94 %). One strain showed resistance to colistin. Genome screening using the resistance genes identifier (RGI) revealed the presence of TEM Betalactamase (26/39) CTX-M Betalactamase (7/39), AmpC Betalactamase (11/39), tetracycline efflux  pump tet(A) (1/39), Quinolone-like protein QnrS (3/39), gyrA and parC mutations (22/39 and 15/39 respectively with co-occurrence in 10/39) , type 3 Amino-acetyltransferase (2/39) and Aminoglycoside nucelotidyltransferase genes aadA2 et aadA5 (8/39), sulfonamide resistance genes sul (17/39), trimethoprim resistance genes dfr (15/39) and colistin resistance gene mcr-1 (1/39) with an identity percentage ≥95%. No carbapenemase resistance gene were detected. Virulence factors were analysed using the tool VFDB. Relevant APEC (Avian Pathogenic E. coli) virulence factors were detected as following: fimA (31/39), iroN (16/39), fyuA (11/39), irp2 (11/39) and papC (5/39). Screening for Secondary metabolites gene clusters using ANTISMASH showed presence of biosynthesis gene clusters of the following: Microcin J25 (5/39), Colicin V (15/39), Microcin C7 (2/39), siderophore metabolites (7/39), non-ribosomal peptides (35/39), thiopeptide (29/39), arylpolyene (5/39).

Conclusion:

These results that will be obtained may lead to better understanding of the involvement of the bacteriocin of E. coli in its pathogenicity and persistence in the avian caecal niche.