Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000-2016

Daniel F Monte; Nilton Lincopan; Hanna Berman; Louise Cerdeira; Shivaramu Keelara; Siddhartha Thakur; Paula J Fedorka-Cray; Mariza Landgraf

doi:10.1038/s41598-019-45838-0

Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000-2016

Sci Rep. 2019 Jul 30;9(1):11058. doi: 10.1038/s41598-019-45838-0.

Authors

Daniel F Monte^{1

2}, Nilton Lincopan^{3

4}, Hanna Berman⁵, Louise Cerdeira⁴, Shivaramu Keelara⁵, Siddhartha Thakur⁵, Paula J Fedorka-Cray⁵, Mariza Landgraf⁶

Affiliations

¹ Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil. monte_dfm@usp.br.
² Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA. monte_dfm@usp.br.
³ Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
⁴ Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
⁵ Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA.
⁶ Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil. landgraf@usp.br.

Abstract

Multidrug-resistant (MDR) Salmonella enterica has been deemed a high-priority pathogen by the World Health Organization. Two hundred and sixty-four Salmonella enterica isolates recovered over a 16-year period (2000 to 2016) from the poultry and swine production chains, in Brazil, were investigated by whole-genome sequencing (WGS). Most international lineages belonging to 28 serovars, including, S. enterica serovars S. Schwarzengrund ST96, S. Typhimurium ST19, S. Minnesota ST548, S. Infantis ST32, S. Heidelberg ST15, S. Newport ST45, S. Brandenburg ST65 and S. Kentucky ST198 displayed MDR and virulent genetic backgrounds. In this regard, resistome analysis revealed presence of qnrE1 (identified for the first time in S. Typhimurium from food chain), qnrB19, qnrS1, bla_CTX-M-8, bla_CTX-M-2 and bla_CMY-2 genes, as well as gyrA mutations; whereas ColpVC, IncHI2A, IncHI2, IncFIA, Incl1, IncA/C2, IncR, IncX1 and po111 plasmids were detected. In addition, phylogenetic analysis revealed multiple independent lineages such as S. enterica serovars S. Infantis, S. Schwarzengrund, S. Minnesota, S. Kentucky and S. Brandenburg. In brief, ocurrence and persistence of international lineages of S. enterica serovars in food production chain is supported by conserved genomes and wide virulome and resistome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Agriculture
Animals
Brazil
Drug Resistance, Multiple, Bacterial / genetics*
Poultry
Salmonella Infections, Animal / diagnosis*
Salmonella Infections, Animal / genetics
Salmonella enterica / isolation & purification*
Serogroup
Swine