Prevalence and Characterization of Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Enterobacterales from Tunisian Seafood

Aquaculture is a rapidly expanding sector in which it is important to monitor the occurrence of multi-drug resistant (MDR) bacteria. The presence of extended-spectrum beta-lactamase (ESBL-) or carbapenemase-producing Enterobacterales is a commonly used indicator of the resistance burden in a given sector. In this study, 641 pieces of farmed fish (sea bream and sea bass), as well as 1075 Mediterranean clams, were analyzed. All ESBL- and carbapenemase-producing Enterobacterales collected were whole-genome sequenced. The proportion of ESBL-producing Enterobacterales was 1.4% in fish and 1.6% in clams, carried by Escherichia coli (n = 23) and Klebsiella pneumoniae (n = 4). The ESBL phenotype was exclusively due to the presence of bla(CTX-M) genes, the most frequent one being bla(CTX-M-15). The bla(CTX-M-1) gene was also identified in six E. coli, among which four were carried by IncI1/pST3 plasmids, possibly betraying an animal origin. Carbapenemases were absent in fish but identified in two K. pneumoniae isolates from clams (bla(NDM-1) and bla(OXA-48)). Several sequence types (STs) identified were associated with human MDR clones such as E. coli ST131 and ST617, or K. pneumoniae ST307 and ST147. Our results might indicate that bacteria from hospital or farm effluents can reach the open sea and contaminate seafood and fish that are living or raised nearby. Therefore, monitoring the quality of water discharged to the sea and the presence of MDR bacteria in seafood is mandatory to ensure the quality of fishery products.

Automated summary

This study examined the presence of multi-drug resistant (MDR) bacteria in farmed fish and Mediterranean clams. The results suggest that bacteria from hospital or farm effluents can contaminate nearby seafood and fish, highlighting the importance of monitoring water quality and MDR bacteria in seafood.