Evolutionary dynamics of the multidrug-resistant Salmonella Infantis harbouring the pESI megaplasmid across Europe

Abstract

Multidrug- resistant Salmonella enterica subsp. enterica serovar Infantis clone, harbouring the pESI megaplasmid, first described in Israel in 2014, is consistently reported in poultry and humans worldwide. This study aimed to investigate the genomic epi- demiology of S. Infantis collected by nine European Public Health Institutions from samples of different origins (human, food and animal sources) and understand the evolutionary dynamics of pESI-like in Europe. The resolved pESI-like sequences have also been compared with complete publicly available pESI-like sequences from other countries, in a One Health context. The circulation of a S. Infantis clone in Europe carrying the mosaic megaplasmid pESI-like has been associated with resistance to sulphonamides (sul), tetracycline (tet), streptomycin and spectinomycin (aadA1). In recent years, blaCTX- M- 1- positive pESI- like plasmids have been increasingly detected in the extended-spectrum beta-lactamase- producing S. Infantis clone. Using a com- bined short- and long-read sequencing approach, two main types of pESI variants have been identified, differing in the acces- sory gene content, including the blaCTX- M variant, indicating a certain stability of pESI variants detected in different geographical regions and sources over time (2011–2021). Moreover, the differences were related to the acquisition of resistance, virulence or fitness- enhancing genes that would potentially benefit the Salmonella host.