Genomic Characterization of Salmonella Minnesota Clonal Lineages Associated with Poultry Production in Brazil

SIMPLE SUMMARY: Salmonella is a leading cause of foodborne illnesses and a global public health concern. Salmonella enterica serotype Minnesota has been increasingly isolated from Brazilian poultry farms. The present study investigated the phylogenetic relationships, evolution and genetic characteristics of S. Minnesota isolates from Brazilian poultry farms. The results demonstrated two main S. Minnesota lineages in the poultry production chain from Brazil, both presenting genes for antibiotic resistance and virulence. The present study also provides insights into the temporal evolution, population structure, and genetic characteristics of the two S. Minnesota lineages disseminated in Brazilian poultry farms. ABSTRACT: Salmonella serotype Minnesota has been increasingly detected in Brazilian poultry farms and food products (chicken meat, eggs) in recent years. In addition, S. Minnesota isolates from poultry are generally resistant to several antibiotics and persistent in farm environments. The present study aimed to assess phylogenomic diversity of S. Minnesota isolates from the poultry production chain in Brazil. In total, 107 worldwide S. Minnesota whole genomes (including 12 from Brazil) were analyzed using a comparative approach. Phylogenetic analysis demonstrated two clades more related to poultry production in Brazil: S. Minnesota poultry lineages I and II (SM-PLI and SM-PLII). Phylodynamic analysis demonstrated that SM-PLI had a common ancestor in 1915, while SM–PLII originated circa 1971. SM-PLII encompassed a higher number of isolates and presented a recent increase in effective population size (mainly from 2009 to 2012). Plasmids IncA/C2 and ColRNA, antimicrobial resistance genes (aph(3′)-Ia, blaCMY-2, qnrB19, sul2, and tet(A)) and mainly a virulence genetic cluster (including the yersiniabactin operon) were detected in isolates from SM-PLI and/or SM-PLII. This study demonstrates the dissemination of two distinct S. Minnesota lineages with high resistance to antibiotics and important virulence genetic clusters in Brazilian poultry farms.