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

Abstract

IntroductionCommensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants.ObjectivesIn 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 of S. Infantis and E. coli from broiler sources.ResultsThe core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers.ConclusionThis is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. 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 between E. coli and S. Infantis.

Effect of aromatic oils on the expression of some virulence-associated and antimicrobial resistance genes of Escherichia coli isolated from broilers

“…The high prevalence of the int 1 gene agrees with Ibrahim et al [ 37 ] and is lower than Tran et al [ 38 ], at 22.2%. The results of qnr S in the current study are lower than the result reported as 31.8% by Szmolka et al [ 39 ].…”

Prevalence of efflux pump and heavy metal tolerance encoding genes among Salmonella enterica serovar Infantis strains from diverse sources in Brazil

“…It is interesting to note that previous studies also performed cgMLST to subtype S . Infantis isolated in European countries, and similarly reported the same high occurrence of MLST’s ST32 in contrast to a high diversity of cgSTs found by using cgMLST in related strains [ 21 , 37 , 38 ].…”

“…While cgMLST has still been less employed in the study of S . Infantis strains [ 21 , 37 , 38 ], MLST has been largely employed over the years and shows a high global predominance of the sequence type ST32 for strains of this serovar [ 6 , 16 , 21 , 22 ]. Previously, the dominance of ST32 has also been determined by MLST in the 80 Brazilian S .…”

Genomic Analysis of Escherichia coli Longitudinally Isolated from Broiler Breeder Flocks after the Application of an Autogenous Vaccine

“…ST162 and ST23 formed separate clusters and were detected only on Farm A. Both STs included a variety of phylogenetic groups of which most are considered commensal, although they have previously been isolated from both diseased and healthy poultry [32][33][34]. Vaccination on Farm A significantly influenced the selection of strains in the consecutive flocks, but also showed to be non-protective against the heterologous strains.…”