AUTHOR=Monte Daniel F. M. , Nethery Matthew A. , Berman Hanna , Keelara Shivaramu , Lincopan Nilton , Fedorka-Cray Paula J. , Barrangou Rodolphe , Landgraf Mariza 

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

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.867278

DOI=10.3389/fmicb.2022.867278

ISSN=1664-302X

ABSTRACT=<p><italic>Salmonella enterica</italic> subsp. <italic>enterica</italic> 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 <italic>S</italic>. 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 <italic>S</italic>. Heidelberg strains isolated from broiler farms (<italic>n</italic> = 16), transport and lairage (<italic>n</italic> = 5), slaughterhouse (<italic>n</italic> = 22), and retail market (<italic>n</italic> = 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 <italic>S</italic>. 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 <italic>fosA7</italic>, <italic>aac(6′)-Iaa</italic>, <italic>sul2</italic>, <italic>tet(A)</italic>, <italic>gyrA</italic>, and <italic>parC</italic> for 100% of the isolates, followed by 88.8% for <italic>bla</italic><sub><italic>CMY</italic>–2</sub>. The β-lactam resistance was essentially driven by the presence of the plasmid-mediated AmpC (pAmpC) <italic>bla</italic><sub><italic>CMY</italic>–2</sub> gene, given the isolates which did not carry this gene were susceptible to cefoxitin (FOX). Most <italic>S</italic>. Heidelberg strains were classified within international lineages, which were phylogenetically nested with <italic>Salmonella</italic> 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 <italic>S</italic>. 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.</p>