Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil

Abstract

Salmonella enterica Heidelberg is a serovar isolated from poultry-producing regions around the World. In Brazil, S. Heidelberg has been frequently detected in poultry flocks, slaughterhouses and chicken. The goal of the present study was to assess the population structure, recent temporal evolution and some important genetic characteristics of S. Heidelberg isolated from Brazilian poultry farms. Phylogenetic analysis of 68 S . Heidelberg genomes sequenced here and additional whole-genomes data from NCBI demonstrated that all isolates from the Brazilian poultry production chain clustered into a monophyletic group, here called S. Heidelberg Brazilian poultry lineage (SH-BPL). Bayesian analysis defined the time of the most recent common ancestor (tMRCA) as 2004 and the overall population size (N e ) constant until 2008, when a ∼10-fold N e increase was observed until circa 2013. SH-BPL presented at least two plasmids with replicons ColpVC ( n =68; 100%), IncX1 ( n =66; 97%), IncA/C2 ( n =65; 95.5%), ColRNAI ( n =43; 63.2%), IncI1 ( n =32; 47%), ColMG828, Col156, IncHI2A, IncHI2, IncQ1, IncX4, IncY and TrfA (each with n<4; <4% each). Antibiotic resistance genes were found, with high frequencies of fosA7 ( n =68; 100%), mdf A ( n =68; 100%), tet(34) ( n =68; 100%), sul2 ( n =64; 94.1%), blaCMY-2 ( n =56; 82.3%) and an overall multi-drug resistance (MDR) profile. Ten pathogenicity islands (SPI1-5, SPI9 and SPI11-14) and 139 virulence genes were also detected. SH-BPL profile was like other previous S. Heidelberg isolates from poultry around the world in the 1990s. In conclusion, the present study demonstrates the recent introduction (2004) and high level of dissemination of an MDR S. Heidelberg lineage in Brazilian poultry operations. IMPORTANCE S. Heidelberg is the most frequent serovar in several broiler farms from the main Brazilian poultry-producing regions. So avian-source foods (mainly chicken carcasses) commercialized in the country and exported to other continents are contaminated with this foodborne pathogen, generating several national and international economic losses. In addition, isolates of this serovar are usually resistant to antibiotics and can cause human invasive and septicemic infection, representing a public health concern. This study demonstrates the use of whole-genome sequencing (WGS) to obtain epidemiological information of one S. Heidelberg lineage highly spread among Brazilian poultry farms. This information will help to define biosecurity measures to control this important Salmonella serovar in Brazilian and worldwide poultry operations.

Clustered Regularly Interspaced Short Palindromic Repeats Genotyping of Multidrug-Resistant Salmonella Heidelberg Strains Isolated From the Poultry Production Chain Across Brazil

“…Consistent with observations obtained in our study, recent surveys strongly support that S. Heidelberg may originate from a common ancestor, which circulates and persists in the Brazilian poultry production chain since at least 2004 (Kipper et al, 2021). More importantly, these strains are also nested with strains isolated from several sources and countries around the world supporting the hypotheses of intercontinental spread, which demonstrate that probably the common ancestor underwent diversification through genetic changes over time (Supplementary Material).…”

“…One of the most important risk factors surrounding foodborne illness is the international food trade that has been circumstantially accompanied by Salmonellae dispersal beyond borders. In this context, there is a global dispersal of multidrugresistant lineages of serovar S. Heidelberg, reaching various countries in North America (Andrysiak et al, 2008;Centers for Disease Control and Prevention, 2014;Public Health Agency of Canada, 2014;Deblais et al, 2018;Cox et al, 2021), South America (Kipper et al, 2021), Europe (Liakopoulos et al, 2016b;Campos et al, 2018), and Asia (Wu et al, 2013). Therefore, the simultaneous increase and extended protraction of S. Heidelberg in many parts of the world have favored their genetic acquisition of virulence and antimicrobial resistance (AMR) genes through horizontal gene transfer (HGT), which has ultimately led to one of the most pressing global concerns.…”

Emergence, Dissemination and Antimicrobial Resistance of the Main Poultry-Associated Salmonella Serovars in Brazil

“…A study evaluating 930 WGS of different Salmonella serovars retrieved from the public database of the National Center for Biotechnology Information (NCBI) and published in the last four decades, demonstrated the prediction of the MDR phenotype in 58% (540/930) of the isolates, highlighting ciprofloxacin and nalidixic acid with the highest frequency rates [39]. Other recent reports have also demonstrated that MDR is frequent in Salmonella serovars Heidelberg and Minnesota isolated from broilers, layers, and poultry-derived food in Brazil [44,[49][50][51][52].…”

“…The prolonged use of antimicrobials has possibly increased Salmonella resistance to the most used classes in the poultry production chains [39,43,44]. Overall, 6 out of the 10 most frequently poultry-associated Salmonella serovars in the United States (Enteritidis, Montevideo, Schwarzengrund, Infantis, Thompson, and Mbandaka) have been demonstrated to be generally pan-susceptible or with resistance to few antimicrobials, whereas four (Heidelberg, Typhimurium, Kentucky, and Senftenberg) are more commonly reported as resistant to many of them [45].…”

“…Overall, 6 out of the 10 most frequently poultry-associated Salmonella serovars in the United States (Enteritidis, Montevideo, Schwarzengrund, Infantis, Thompson, and Mbandaka) have been demonstrated to be generally pan-susceptible or with resistance to few antimicrobials, whereas four (Heidelberg, Typhimurium, Kentucky, and Senftenberg) are more commonly reported as resistant to many of them [45]. Some Salmonella isolates from these last four serovars have also been reported as multidrug-resistant (MDR), which means, resistant to three or more antimicrobials classes [34,[44][45][46][47].…”