Genomic characterization of multidrug-resistant Salmonella Heidelberg E2 strain isolated from chicken carcass in southern Brazil

• Published in: International journal of food microbiology 2022-10, Vol.379, p.109863-109863, Article 109863
• Main Authors: Núncio, Adriana Souto Pereira, Webber, Bruna, Pottker, Emanuele Serro, Cardoso, Brenda, Esposito, Fernanda, Fontana, Herrison, Lincopan, Nilton, Girardello, Raquel, Pilotto, Fernando, dos Santos, Luciana Ruschel, Rodrigues, Laura Beatriz
• Format: Article
• Language: English
• Subjects: Antimicrobial resistance; Food safety; Poultry; Salmonella enterica; Virulence factors
• ISSN: 0168-1605; 1879-3460
• DOI: 10.1016/j.ijfoodmicro.2022.109863

Salmonella Heidelberg is a clinically-important serovar linked to food-borne illness, and commonly isolated from poultry products. Since 1962, Salmonella Heidelberg has been widely reported from poultry production systems in several countries, including Brazil. The emergence of multidrug-resistant (MDR) Salmonella Heidelberg strains in food animals underscores a significant food safety hazard. In our study, we performed antimicrobial susceptibility testing (AST) and Whole-genome sequencing (WGS) to identify the antimicrobial resistance (AMR) genes, pathogenicity mechanisms and virulence factors (VF) in Salmonella Heidelberg E2 strain recovered from a chicken carcass in Southern Brazil. Salmonella Heidelberg strain belonged to ST15 and showed to be susceptible to colistin (MIC ≤2 μg/mL) and multidrug-resistant to amoxicillin-clavulanic acid, gentamicin, ampicillin, cefaclor, cefazolin, ceftiofur, nalidixic acid, azithromycin, erythromycin, doxycycline, tetracycline and sulfonamide. We identified AMR genes mediating resistance to aminoglycosides (aac(6′)-Iaa, aac(3)-VIa, aph(3′)-Ia, aadA, 16S rrsD), β-lactams (blaCTX-M-2), quinolones (parC), macrolides (acrB), tetracyclines (tet(A)), fosfomycin (fosA7) and sulfonamide (sul1). Interestingly, the mutation in parC T255S has never been reported among Salmonella Heidelberg strains. To our knowledge, this is the first report of a Salmonella enterica strain harbouring 16S rrsD 471G > A, acrB F28L and acrB L40P chromosomal point mutations. Three plasmid replicon types, ST2-IncHI2, ST2-IncHI2A and IncX1 were identified. Nine Salmonella Pathogenicity Islands and 98 virulence genes encoding virulence factors were identified associated with cell adhesion, invasion, intracellular survival and resistance to antimicrobial peptides. Although Salmonella Heidelberg E2 strain likely originated from poultry, cross-contamination during meat processing cannot be excluded. This study adds to our understanding of Salmonella Heidelberg transmission along the food-chain and informs ongoing regulatory discussions on Salmonella Heidelberg in poultry. •S. Heidelberg E2 strain was MDR and susceptible to colistin (MIC ≤2 μg/mL).•WGS data revealed 14 AMR genes such as aadA, blaCTX-M-2, tet(A), fosA7 and sul1.•First report of a Salmonella enterica strain harbouring 16S rrsD 471G > A mutation.•Novel point mutations detected in the parC (T255S) and acrB (F28L and L40P) genes.•The genome of S. Heidelberg E2 strain carried 9 SPIs and 98 virulen