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Gopinath GR, Jang H, Beaubrun JJG, Gangiredla J, Mammel MK, Müller A, Tamber S, Patel IR, Ewing L, Weinstein LM, Wang CZ, Finkelstein S, Negrete F, Muruvanda T, Allard M, Sockett DC, Pagotto F, Tall BD, Stephan R. Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes. Microorganisms 2022; 10:microorganisms10061199. [PMID: 35744717 PMCID: PMC9228720 DOI: 10.3390/microorganisms10061199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains analyzed by k-mer-binning based strategy, contained a conserved core genome backbone with a different evolutionary lineage as compared to strains comprising the other cluster (ST150). In addition, the assortment of genotypic features contributing to pathogenesis and persistence, such as antimicrobial resistance, prophage, plasmid, and virulence factor genes, were assessed to understand the emerging characteristics of this serovar that are relevant clinically and for food safety concerns. The phylogenomic profiling of polyphyletic S. Bovismorbificans in this study corresponds to intra-serovar variations observed in S. Napoli and S. Newport serovars using similar high-resolution genomic profiling approaches and contributes to the understanding of the evolution and sequence divergence of foodborne Salmonellae. These intra-serovar differences may have to be thoroughly understood for the accurate classification of foodborne Salmonella strains needed for the uniform development of future food safety mitigation strategies.
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Affiliation(s)
- Gopal R. Gopinath
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
- Correspondence: ; Tel.: +1-240-402-3612
| | - Hyein Jang
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Junia Jean-Gilles Beaubrun
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
- Biological Analysis Division, Public Health Command Europe Laboratory Sciences, Room 102, Bldg 3810, Kirchberg Kaserne, RP 66849 Landstuhl, Germany
| | - Jayanthi Gangiredla
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Mark K. Mammel
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Andrea Müller
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.M.); (R.S.)
| | - Sandeep Tamber
- Food Directorate, Bureau of Microbial Hazards/Health Canada, Ottawa, ON K1A 0K9, Canada; (S.T.); (F.P.)
| | - Isha R. Patel
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Laura Ewing
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Leah M. Weinstein
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Caroline Z. Wang
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Samantha Finkelstein
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Flavia Negrete
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Tim Muruvanda
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA; (T.M.); (M.A.)
| | - Marc Allard
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA; (T.M.); (M.A.)
| | - Donald C. Sockett
- Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Franco Pagotto
- Food Directorate, Bureau of Microbial Hazards/Health Canada, Ottawa, ON K1A 0K9, Canada; (S.T.); (F.P.)
| | - Ben D. Tall
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.M.); (R.S.)
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Blaylock M, Blackwell R, Merid S, Jackson S, Kotewicz M, Gopinath G, Ayers SL, Abbott J, Sabo J, Ewing L, Gangiredla J, Gebru S, Patel I, Jones B, Dudley K, Jarvis K, Hanes DE, Diallo AA, Jean-Gilles Beaubrun J. Comparison of Salmonella enterica serovar Bovismorbificans 2011 hummus outbreak strains with non-outbreak strains. Food Microbiol 2015; 46:627-634. [DOI: 10.1016/j.fm.2014.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 02/04/2014] [Accepted: 02/18/2014] [Indexed: 10/25/2022]
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