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

Abstract

During the last decade, Salmonella enterica subspecies enterica serovar Infantis (S. Infantis) has become more prevalent across Europe with an increased capability to persist in broiler farms. In this study, we aimed to identify potential genetic causes for the increased emergence and longer persistence of S. Infantis in German poultry farms by high-throughput-sequencing. Broiler derived S. Infantis strains from two decades, the 1990s (n = 12) and the 2010s (n = 18), were examined phenotypically and genotypically to detect potential differences responsible for increased prevalence and persistence. S. Infantis organisms were characterized by serotyping and determining antimicrobial susceptibility using the microdilution method. Genotypic characteristics were analyzed by whole genome sequencing (WGS) to detect antimicrobial resistance and virulence genes as well as plasmids. To detect possible clonal relatedness within S. Infantis organisms, 17 accessible genomes from previous studies about emergent S. Infantis were downloaded and analyzed using complete genome sequence of SI119944 from Israel as reference. In contrast to the broiler derived antibioticsensitive S. Infantis strains from the 1990s, the majority of strains from the 2010s (15 out of 18) revealed a multidrug-resistance (MDR) phenotype that encodes for at least three antimicrobials families: aminoglycosides [ant(3")-Ia], sulfonamides (sul1), and tetracyclines [tet(A)]. Moreover, these MDR strains carry a virulence gene pattern missing in strains from the 1990s. It includes genes encoding for fimbriae clusters, the yersiniabactin siderophore, mercury and disinfectants resistance and toxin/antitoxin complexes. In depth genomic analysis confirmed that the 15 MDR strains from the 2010s carry a pESI-like megaplasmid with resistance and virulence gene patterns detected in the emerged S. Infantis strain SI119944 from Israel and clones inside and outside Europe. Genotyping analysis revealed two sequence types (STs) among the resistant strains from the 2010s, ST2283 (n = 13) and ST32 (n = 2). The sensitive strains from the 1990s, belong to sequence type ST32 (n = 10) and ST1032 (n = 2). Therefore,

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

“…In contrast to the heterogeneity of E. coli described above, strains of S. Infantis have shown a very homogenous clonal structure by almost all being assigned to ST32, which is considered the predominant ST of this serovar worldwide. However, it appears that S. Infantis is genetically "open" for a clonal diversification, as indicated by the emergence of MDR STs such as the ST2283, which has recently spread in the broiler population in Germany (García-Soto et al, 2020). Our data also contribute to the global clonal diversity of S. Infantis through the identification of two new MDR STs ST7081 and ST7082 for a human and a broiler strain, respectively.…”

Antimicrobial Resistance and in silico Virulence Profiling of Aliarcobacter butzleri Strains From German Water Poultry

“…The raw reads together with the raw data of the 45 A. butzleri isolates sequenced herein were de novo assembled. For the analyses, we used the WGSBAC pipeline ( https://gitlab.com/FLI_Bioinfo/WGSBAC ) as described previously (Garcia-Soto et al, 2020 ; Wareth et al, 2020 ). WGSBAC assembled the raw data using shovill version 1.0.4 ( https://github.com/tseemann/shovill ) after adapter trimming with Trimmomatic (Bolger et al, 2014 ).…”

Molecular Identification of Five Multidrug-resistant Salmonella Enterica Serovars Isolated from Egyptian Poultry Farms

“…The puri ed PCR fragments were sequenced by Macrogen Company, South Korea applying automated Sanger Sequencing method. The obtained sequences for 16S rRNA gene were surveyed using Standard Nucleotide BLAST tool and registered at NCBI database under accession numbers [1], MW311328.1, MW310702.1, MN822653.1 and MN820824.1 for Salmonella enterica subsp. enterica serovar Enteritidis strains EG.SmE2, EG.SmE1 and Salmonella enterica subsp.…”