Characterization and whole genome sequencing of closely related multidrug-resistant Salmonella enterica serovar Heidelberg isolates from imported poultry meat in the Netherlands

Abstract

Multidrug-resistant Salmonella enterica serovar Heidelberg isolates are frequently recovered in the Netherlands from poultry meat imported from South America. Our aim was to retrospectively assess the characteristics of the antimicrobial determinants, gene content and the clonal relatedness of 122 unique S . Heidelberg isolates from chicken meat from Brazil (n = 119) and Argentina (n = 3) that were imported between 2010 and 2015. These isolates were subjected to antimicrobial susceptibility testing, PCR and Illumina HiSeq2500 whole genome sequencing. Draft genomes were assembled to assess the gene content, and the phylogenetic relationships between isolates were determined using single nucleotide polymorphisms. Ciprofloxacin-resistance was identified in 98.4% of the isolates and 83.7% isolates showed resistance to the extended-spectrum cephalosporins cefotaxime and ceftazidime (83.6% and 82.8% respectively). Of the latter, 97.1% exhibited an AmpC phenotype and contained bla CMY-2 , whereas the remaining three isolates contained an extended spectrum beta-lactamase. Of the 99 extended-spectrum cephalosporins-resistant isolates harboring CMY-2 plasmids, 56.6% contained the incompatibility group I1 replicon. Phylogenetic cluster analysis showed that all isolates from Brazil clustered together, with 49% occurring in clusters larger than 5 isolates that revealed intra-cluster similarities based on geographical location and/or resistance profiles. The remaining isolates were classified in smaller clusters or as singletons, highlighting the large diversity of S . Heidelberg in the poultry chain in Brazil that was revealed by this study. Considering the potential public health risk associated with multidrug-resistant S . Heidelberg in imported poultry, collaborative whole genome sequencing-based surveillance is needed to monitor the spread, pathogenic properties and epidemiological distribution of these isolates.

Molecular Characterization and Survive Abilities of Salmonella Heidelberg Strains of Poultry Origin in Brazil

“…The four identified resistomes (Table 1) revealed a high level of resistance to amoxicillin, ampicillin and/or ceftriaxone. Although the bla CTX−M gene is reported with a higher incidence of Salmonella in poultry products (Moura et al, 2018;Perin et al, 2020), our study shows that its frequency was low (2/20-10%) and corroborates with recent studies carried out with samples Brazilian samples (van den Berg et al, 2019;Souza et al, 2020). Gram-negative ESBL-producing and hyper-producing AmpC bacteria have also stood out for their resistance to carbapenems, such as meropenem, identified in 20% (4/20) of our strains, when associated with other mechanisms, such as hyper expressed efflux systems (Andrade and Darini, 2017).…”

“…The presence of the bla CMY−2 gene is consistent with this phenotype, due to the overproduction of AmpC induced by the presence of cephalosporin and cephamycin that exhibit resistance to extended-spectrum cephalosporins, such as ceftriaxone, and to cefoxitin (identified in four of the 20 strains -data not shown) (De Angelis et al, 2020). The high prevalence of SH AmpC strains highlights the endemic occurrence of β-lactam resistance in North and South America (Edirmanasinghe et al, 2017;Monte et al, 2019;van den Berg et al, 2019;Souza et al, 2020).…”

Molecular characterization and antimicrobial resistance profiles of Salmonella Heidelberg isolates from poultry

“…Similar results have been reported in S. Heidelberg isolates from humans (Cejas et al, 2014) and poultry (Castellanos et al, 2018;Souza et al, 2020). Moreover, the isolates show high prevalence of resistance to nalidixic acid and ciprofloxacin (FQ), a fact also observed by other authors in isolates from poultry (Casas et al, 2016;van den Berg et al, 2019). Similarly, an increasing number of isolates have been characterized as MDR to many antimicrobials by several authors (Giuriatti et al, 2017).…”

Salmonella in Pig Farms and on Pig Meat in Suriname

“…This combination of replicons, together with an IncN replicon, has also been found in E. coli. This plasmid carried an mcr-gene encoding colistin resistance [41]. A plasmid with exactly the same sequences was found in S. Brandenburg and S. Ohio from two different farms, indicating its spread amongst Salmonella in Suriname.…”