Molecular and phenotypic characteristics of isolated Escherichia coli from the skin, gills, and intestine of rainbow trout in retail stores of Kerman, Iran.

Background: Escherichia coli is not naturally present in fish microbiota but can be acquired from sewage-contaminated aquatic environments.

Aims: This study was performed to isolate and characterize the E. coli strains in rainbow trout fish marketed for human consumption.

Methods: A total number of 166 fish were randomly collected from different retail settings in Kerman, Iran. The fish samples were analyzed to detect E. coli isolates. Antimicrobial resistance genes, Shiga toxin virulence subtypes and phylogenetic sequences were screened by PCR.

Results: Prevalence of E. coli isolates on the skin, in the gills and intestine were 76.5% (127/166), 6.6% (11/166), and 3% (5/166), respectively. The most prevalent antimicrobial resistance phenotypes were observed against florfenicol (86.61%), erythromycin (83.46%), flumequine (82.67%), and oxytetracycline (81.88%); and 98.42% of the isolates were multi-drug resistant. The most frequent resistance gene was bla _TEM (14.17%), followed by qnrA (10.23%), tetB (9.44%), sul2 (8.66%), bla _SHV (7.87%), sul1 (7.87%), dhfr1 (3.93%), bla _{CTX -M} (3.14%), dhfrV (1.57%), bla _OXA (0.78%). Totally, 8.66% of isolates were categorized into three pathotypes including STEC, EPEC and EHEC. The stx subtypes including stx1a, stx1c, stx1d, stx2c, stx2d, stx2e and stx2f were identified in stx-positive strains. The E. coli isolates were classified into five phylogenetic groups including A (23.62%), B2 (3.93%), D (2.36%), F (9.44%) and cryptic clade I (11.81%).

Conclusion: The study revealed that the skin of retail rainbow trout marketed in Kerman may be one of the potential passive carriers of multi-drug resistant and virulent E. coli strains.