Tell me if you prefer bovine or poultry sectors and I’ll tell you who you are: Characterization of Salmonella enterica subsp. enterica serovar Mbandaka in France

Abstract

IntroductionIn north-western France, Salmonella enterica susp. enterica serovar Mbandaka (S. Mbandaka) is most frequently isolated from bovine and dairy samples. While this serovar most often results in asymptomatic carriage, for a number of years it has caused episodes of abortions, which have serious economic consequences for the sector. Interestingly, this serovar is also isolated from Gallus gallus in the same geographic zone. Despite its prevalence in bovines in north-western France, S. Mbandaka has not been broadly studied at the genomic level, and its prevalence and host adaptation are still not fully understood.MethodsIn this study, we analyzed the genomic diversity of 304 strains of S. Mbandaka isolated from the bovine and poultry sectors in this area over a period of 5 years. A phylogenetic analysis was carried out and two approaches were followed to identify conserved genes and mutations related to host associations. The first approach targeted the genes compiled in the MEGARESv2, Resfinder, VFDB and SPI databases. Plasmid and phage contents were also investigated. The second approach refers to an in-house algorithm developed for this study that computes sensitivity, specificity, and accuracy of accessory genes and core variants according to predefined genomes groups.Results and discussionAll the analyzed strains belong to the multi-locus sequence type profile ST413, and the phylogenomic analysis revealed main clustering by host (bovine and poultry), emphasizing the circulation of 12 different major clones, of which seven circulate in poultry and five in the bovine sector in France and a likely food production chain adaptation of these clones. All strains present resistance determinants including heavy metals and biocides that could explain the ability of this serovar to survive and persist in the environment, within herds, and in food processing plants. To explore the wild animal contribution to the spread of this serovar in north-western France, we retrieved S. Mbandaka genomes isolated from wild birds from EnteroBase and included them in the phylogenomic analysis together with our collection. Lastly, screening of accessory genes and major variants allowed us to identify conserved specific mutations characteristic of each major cluster. These mutations could be used to design useful probes for food safety surveillance.

Genomic Features and Phylogenetic Analysis of Antimicrobial-Resistant Salmonella Mbandaka ST413 Strains

“…Mbandaka ST413 and evolutionary insight into the dynamics of this serovar with sequences from different regions of the world. This sequence type has been implicated in foodborne outbreaks in the EU/EEA, Israel, and the UK [ 7 , 41 ] and identified in cases of salmonellosis in Brazil [ 42 ]. The recent identification of S .…”

“…Additionally, for virulence factors, this study showed that S. Mbandaka ST413 strains carry plasmid-borne or chromosomal genes conferring resistance to several antimicrobials commonly used in both the poultry industry and human medicine, such as aminoglycosides ( aac(6′) -Iaa ), sulfonamide ( sul2 ), streptomycin ( aph(6)-Id ), tetracycline ( tetA and tetB ), and trimethoprim ( dfrA14 ) [ 41 ]. The presence of the aac(6′)-laa gene is in line with the wide distribution of aminoglycoside resistance genes among Salmonella strains of different serovars [ 52 , 53 ].…”

For Someone, You Are the Whole World: Host-Specificity of Salmonella enterica

“…Fenske et al showed that the clustering of various Salmonella genomes corresponds to geographical origin rather than host specificity [ 28 ]. Even within a single serovar, Mbandaka genetic lineages infecting poultry and bovine hosts were scattered along the core SNP-based phylogeny [ 43 ]. No evidence of genomic differentiation between strains of Salmonella enterica serovar Typhimurium DT160 reflecting the shape of a phylogenetic tree was reported either [ 44 ].…”

“…The analysis of S . Mbandaka ST143 strains, which was focused on identifying the origin of the isolates for the sake of better epidemiological surveillance, revealed no universal pattern of specialization to bovine or avian hosts, but showed a variety of clonal populations forming distinct clades [ 43 ]. Groups of strains classified according to attributed hosts differed primarily in the composition of prophages; however, specific alleles in secretion systems were found as well [ 43 ].…”

Genomic insights of Salmonella isolated from dry fermented sausage production chains in Spain and France

“…Spanish and French raw reads were quality checked and filtered as described by De Sousa Violante et al 69 and with an in-house pipeline. In brief, Trimmomatic v0.40 70 was used for the trimming step, FastQC v0.11.5 to check the read quality and ConFindr v0.8.1 to identify intra-and cross-species contamination 71 .…”