2022 journal article

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


By: D. Monte*, M. Nethery n, H. Berman n, S. Keelara n, N. Lincopan*, P. Fedorka-Cray n, R. Barrangou n, M. Landgraf*

co-author countries: Brazil 🇧🇷 United States of America 🇺🇸
author keywords: antibiotic resistance; CRISPR; phylogeny; Salmonella Heidelberg; foodborne disease; WGS
Source: Web Of Science
Added: July 11, 2022

Salmonella enterica subsp. enterica serovar Heidelberg has been associated with a broad host range, such as poultry, dairy calves, swine, wild birds, environment, and humans. The continuous evolution of S . Heidelberg raises a public health concern since there is a global dispersal of lineages harboring a wide resistome and virulome on a global scale. Here, we characterized the resistome, phylogenetic structure and clustered regularly interspaced short palindromic repeats (CRISPR) array composition of 81 S . Heidelberg strains isolated from broiler farms ( n = 16), transport and lairage ( n = 5), slaughterhouse ( n = 22), and retail market ( n = 38) of the poultry production chain in Brazil, between 2015 and 2016 using high-resolution approaches including whole-genome sequencing (WGS) and WGS-derived CRISPR genotyping. More than 91% of the S . Heidelberg strains were multidrug-resistant. The total antimicrobial resistance (AMR) gene abundances did not vary significantly across regions and sources suggesting the widespread distribution of antibiotic-resistant strains from farm to market. The highest AMR gene abundance was observed for fosA7 , aac(6′)-Iaa , sul2 , tet(A) , gyrA , and parC for 100% of the isolates, followed by 88.8% for bla CMY –2 . The β-lactam resistance was essentially driven by the presence of the plasmid-mediated AmpC (pAmpC) bla CMY –2 gene, given the isolates which did not carry this gene were susceptible to cefoxitin (FOX). Most S . Heidelberg strains were classified within international lineages, which were phylogenetically nested with Salmonella strains from European countries; while CRISPR genotyping analysis revealed that the spacer content was overall highly conserved, but distributed into 13 distinct groups. In summary, our findings underscore the potential role of S . Heidelberg as a key pathogen disseminated from farm to fork in Brazil and reinforce the importance of CRISPR-based genotyping for salmonellae. Hence, we emphasized the need for continuous mitigation programs to monitor the dissemination of this high-priority pathogen.