Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid

Abstract

Salmonella Infantis is one of the five serovars most frequently causing human salmonellosis in Europe, mainly associated with poultry. A clone harbouring a conjugative plasmid of emerging S . Infantis (pESI)-like megaplasmid, carrying multidrug resistant (MDR) and extended-spectrum beta-lactamases (ESBL) genes, has spread in the Italian broiler chicken industry also causing human illness. This work is aimed at elucidating the molecular epidemiology of S . Infantis and pESI-like in Europe using whole-genome sequencing and bioinformatics analysis, and to investigate the genetic relatedness of S . Infantis clones and pESI-like from animals, meat, feed and humans provided by institutions of nine European countries. Two genotyping approaches were used: chromosome or plasmid SNP-based analysis and the minimum spanning tree (MST) algorithm based on core-genome multilocus sequence typing (cgMLST). The European S . Infantis population appeared heterogeneous, with different genetic clusters defined at core-genome level. However, pESI-like variants present in 64.1 % of the isolates were more genetically homogeneous and capable of infecting different clonal lineages in most of the countries. Two different pESI-like with ESBL genes ( n =82) were observed: bla CTX-M-1 -positive in European isolates and bla CTX-M-65 -positive in American isolates (study outgroup). Both variants had toxin-antitoxin systems, resistance genes towards tetracyclines, trimethoprim, sulphonamides and aminoglycosides, heavy metals ( mer A) and disinfectants ( qac EΔ). Worryingly, 66 % of the total isolates studied presented different gyr A chromosomal point mutations associated with (fluoro)quinolone resistance (MIC range 0.125–0.5 mg/L), while 18 % displayed transferable macrolide resistance mediated by mph , mef and erm (B) genes. Proper intervention strategies are needed to prevent further dissemination/transmission of MDR S . Infantis and pESI-like along the food chain in Europe.

Emergence of Multidrug-Resistant Salmonella enterica Subspecies enterica Serovar Infantis of Multilocus Sequence Type 2283 in German Broiler Farms

“…We also detected two non-resistant ST1032 clones from the 1990s. This variant of ST32 had been described before in a non-resistant isolate from food (Alba et al, 2020). In this study, bioinformatics analysis revealed a correlation between the resistance gene pattern named as ESIr [ant(3")-la, sul1, tet(A)] and the phenotypic resistance profile to aminoglycosides, sulfonamides, and TETs.…”

“…Finally, we were interested if the plasmid evolves independently or if there has occurred a co-evolution together with the chromosomes. Therefore, we studied the plasmid-based SNP phylogeny as previously performed (Alba et al, 2020) for the 15 S. Infantis strains harboring the pESI-like plasmid (Supplementary Figure S2). In general the plasmid phylogeny seems to be similar to the chromosomal phylogeny.…”

Genetic Profiles and Antimicrobial Resistance Patterns of Salmonella Infantis Strains Isolated in Italy in the Food Chain of Broiler Meat Production

“…However, it should be further underlined that in the previous investigations on Italian S . Infantis strains the ECDC nomenclature has not been used for the PFGE analysis [ 4 , 12 ]. Finally, there was no correlation neither between the PFGE profiles and resistance patterns nor between matrices and pulsotypes.…”

“…Infantis isolates has been reported in humans (39.4%) from food and animal sources and data obtained from cross-sectional studies in broilers at slaughter revealed that S . Infantis accounted for 75% and 90% of all isolates detected, respectively in 2014 and 2016 [ 4 , 5 ]. The surveillance and monitoring of S .…”

Detection of Antimicrobial Resistant Salmonella enterica Strains in Larval and Adult Forms of Lesser Mealworm (Alphitobius diaperinus) From Industrial Poultry Farms

“…The S. Infantis drug resistance has been associated with the unique pESI megaplasmid which was initially described in Israeli isolates in 2007 (42), and along withwith some pESIlike variants, has since been described in other territories across the world (43)(44)(45). This mobile genetic structure can be transferred to other commensal or pathogenic bacteria within the host intestinal environments (19).…”