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

Abstract

Introduction: Commensal 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.

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 of S. Infantis and E. coli from broiler sources.

Results: The 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.

Conclusion: This 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.

Keywords: Escherichia coli; Salmonella Infantis; antibiotic resistance; core genome; plasmid; resistome.

FIGURE 1

Diversity of commensal (caecal and faecal) and extraintestinal (bone marrow) E. coli strains from broilers according to the sample source. A Minimum Spanning Tree of 90 commensal and clinical E. coli strains was generated based on the polymorphism of seven housekeeping genes. Strains are separated by grey lines in nodes with multiple strains. Allelic patterns with missing values represented a category of its own and were designated as novel clones highlighted with red dotted circles. Distance lines change from black to dotted grey as the phylogenetic distance between the strains increases. Maximum distance in cluster was set to 2, making it therefore possible to group STs into clonal complexes (CCs). The thickness of the distance line is inversely proportional to the distance value.

FIGURE 2

Core genome diversity and phylogroups of commensal (caecal and faecal) and extraintestinal (bone marrow) strains of E. coli from broilers. The Neighbour Joining Tree showing the genomic diversity of 90 E. coli strains was calculated based on the polymorphism of 2398 target genes of the core genome. Core genes were identified by blasting all genome sequences against the reference strain E. coli K-12 MG1655 (GenBank accession no. NC_000913). By distance calculation, gene columns with missing values were removed. Only the large STs of E. coli with at least four isolates are indicated. Black and white dots indicate extraintestinal and commensal (caecal and faecal) strains, respectively, representing larger STs. C1-3 describes Clusters 1–3.

FIGURE 3

Relation between the genomic diversity and pulsotype in broiler and human strains of S. Infantis. Minimum Spanning Tree showing the core genome diversity of S. Infantis strains was generated based on the polymorphism of 3647 target genes of the core genome. By distance calculation, gene columns with missing values were removed. Distances are shown by the line style, distance numbers are also indicated. Distance lines change from black to dotted grey as the phylogenetic distance between the strains increases. Logarithmic scale was used for distance line length calculation. Strains are separated by grey lines in nodes with multiple strains. Besides the 56 S. Infantis strains studied here, the whole-genome sequences of S. Infantis strains SI69/94 (GenBank accession no. JRXB00000000) and SI54/04 (GenBank accession no. JRXC00000000) were also included, and blasted against the reference strain S. Infantis 1326/28 (GenBank accession no. LN649235). Both of these S. Infantis strains (framed by thick black line) were included as a Hungarian references for the ancient, pansensitive strains of the late 1990s (SI69/94) and for strains representing the emergent endemic MDR clone B2 (SI54/04) (Olasz et al., 2015).

FIGURE 4

Diversity and distribution (%) of plasmid replicon types of E. coli and S. Infantis strains from different host sources.

FIGURE 5

Mobile resistome tree of S. Infantis isolated from broilers and humans and of E. coli from broilers. E. coli strains are coloured in light green, while light blue represents S. Infantis strains. Abbreviations for the source of isolation are: F, faeces; BM, bone marrow; C, caecum; B, broiler; and H, human. The identified E. coli clusters are framed by red lines.

FIGURE 6

Antibiotic resistance genes as potentially exchangeable between cohabitant strains of E. coli and S. Infantis from caecal samples of broilers. S. Infantis strains are coloured in blue, while green represents E. coli strains. Abbreviations for antibiotic resistances are: AG, aminoglycosides; SU, sulfonamides; TE, tetracyclines; BL, beta-lactams; FQ, fluoroquinolones; PH, phenicols; and TP, trimethoprim.