Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli

Szmolka A, Wami H, Dobrindt U

Abstract

Introduction:Commensal and pathogenic strains of multidrug-resistant (MDR)Escherichia coliand non-typhoid strains ofSalmonellarepresent a growing foodborne threat from foods of poultry origin. MDR strains ofSalmonellaInfantis andE. coliare frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants. Objectives:In order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes ofS. Infantis andE. colifrom broiler sources. Results:The core genome MLST analysis of 56S. Infantis and 90E. colicontemporary strains revealed a high genomic heterogeneity of broilerE. coli.It also allowed the first insight into the genomic diversity of the MDR clone B2 ofS. Infantis, which is endemic in Hungary. We also identified new MDR lineages forS. Infantis (ST7081 and ST7082) and forE. coli(ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes ofE. coliandS. Infantis. The mobile resistance genestet(A),aadA1, andsul1were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 ofS. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains ofE. coliandS. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes betweenS. Infantis andE. coliin broilers. Conclusion:This is the first comparative genomic analysis of contemporary broiler strains ofS. Infantis andE. coli. The diversity of mobile resistomes suggests that commensalE. colicould be potential reservoirs of resistance forS. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction betweenE. coliandS. Infantis.