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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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Molecular Characteristics and Antimicrobial Resistance of Salmonella enterica Serovar Schwarzengrund from Chicken Meat in Japan. Antibiotics (Basel) 2021; 10:antibiotics10111336. [PMID: 34827274 PMCID: PMC8615118 DOI: 10.3390/antibiotics10111336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022] Open
Abstract
Our previous study revealed that Salmonella enterica serovar Schwarzengrund-contaminated areas of broiler chickens have expanded from West Japan to East Japan. The present study investigated the antimicrobial resistance and molecular characteristics of 124 S. Schwarzengrund isolates obtained from chicken meat produced in East and West Japan from 2008 to 2019. Comparing the isolates obtained in 2008 and 2015–2019, an increase in the proportion of those resistant to kanamycin [51.4–89.7% (p < 0.001)] was observed. In contrast, the proportion of isolates resistant to both streptomycin and tetracycline and those that harbored a 1.0-kb class 1 integron, aadA1, and tetA, significantly decreased from 100% in 2008 to 47.1% in 2015–2019 (p < 0.001). A 1.0-kb class 1 integron containing aadA1, harbored by 78 isolates, was different from that reported in globally distributed S. Schwarzengrund strains (1.9 kb, containing the dfrA12-aadA2 gene cassette). Twenty-five isolates from different product districts and years of isolation were typed as sequence type (ST) 241 with multilocus sequence typing. Our results suggest that S. Schwarzengrund, which contaminates chicken meat in Japan, shares a common ancestor regardless of the product district from 2008 to recent years. Moreover, S. Schwarzengrund ST241 may have spread from western to eastern Japan.
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AT Homopolymer Strings in Salmonella enterica Subspecies I Contribute to Speciation and Serovar Diversity. Microorganisms 2021; 9:microorganisms9102075. [PMID: 34683396 PMCID: PMC8538453 DOI: 10.3390/microorganisms9102075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/08/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Adenine and thymine homopolymer strings of at least 8 nucleotides (AT 8+mers) were characterized in Salmonella enterica subspecies I. The motif differed between other taxonomic classes but not between Salmonella enterica serovars. The motif in plasmids was possibly associated with serovar. Approximately 12.3% of the S. enterica motif loci had mutations. Mutability of AT 8+mers suggests that genomes undergo frequent repair to maintain optimal gene content, and that the motif facilitates self-recognition; in addition, serovar diversity is associated with plasmid content. A theory that genome regeneration accounts for both persistence of predominant Salmonella serovars and serovar diversity provides a new framework for investigating root causes of foodborne illness.
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Achtman M, Zhou Z, Alikhan NF, Tyne W, Parkhill J, Cormican M, Chiou CS, Torpdahl M, Litrup E, Prendergast DM, Moore JE, Strain S, Kornschober C, Meinersmann R, Uesbeck A, Weill FX, Coffey A, Andrews-Polymenis H, Curtiss 3rd R, Fanning S. Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project. Wellcome Open Res 2021; 5:223. [PMID: 33614977 PMCID: PMC7869069 DOI: 10.12688/wellcomeopenres.16291.2] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.
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Affiliation(s)
- Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | | | - William Tyne
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Martin Cormican
- National Salmonella, Shigella and Listeria Reference Laboratory, Galway, H91 YR71, Ireland
| | - Chien-Shun Chiou
- Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, None, Taiwan
| | - Mia Torpdahl
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Eva Litrup
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Deirdre M. Prendergast
- Backweston complex, Department of Agriculture, Food and the Marine (DAFM), Celbridge, Co. Kildare, W23 X3PH, Ireland
| | - John E. Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, BT9 7AD, UK
| | - Sam Strain
- Animal Health and Welfare NI, Dungannon, BT71 6JT, UK
| | - Christian Kornschober
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Graz, 8010, Austria
| | - Richard Meinersmann
- US National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Alexandra Uesbeck
- Institute for Medical Microbiology, Immunology, and Hygiene, University of Cologne, Cologne, 50935, Germany
| | - François-Xavier Weill
- Unité des bactéries pathogènes entériques, Institut Pasteur, Paris, cedex 15, France
| | - Aidan Coffey
- Cork Institute of Technology, Cork, T12P928, Ireland
| | - Helene Andrews-Polymenis
- Dept. of Microbial Pathogenesis and Immunology, College of Medicine Texas A&M University, Bryan, TX, 77807, USA
| | - Roy Curtiss 3rd
- Dept. of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, 32611, USA
| | - Séamus Fanning
- UCD-Centre for Food Safety, University College Dublin, Dublin, D04 N2E5, Ireland
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Achtman M, Zhou Z, Alikhan NF, Tyne W, Parkhill J, Cormican M, Chiou CS, Torpdahl M, Litrup E, Prendergast DM, Moore JE, Strain S, Kornschober C, Meinersmann R, Uesbeck A, Weill FX, Coffey A, Andrews-Polymenis H, Curtiss 3rd R, Fanning S. Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project. Wellcome Open Res 2020; 5:223. [PMID: 33614977 PMCID: PMC7869069 DOI: 10.12688/wellcomeopenres.16291.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 01/25/2023] Open
Abstract
Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.
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Affiliation(s)
- Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | | | - William Tyne
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Martin Cormican
- National Salmonella, Shigella and Listeria Reference Laboratory, Galway, H91 YR71, Ireland
| | - Chien-Shun Chiou
- Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, None, Taiwan
| | - Mia Torpdahl
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Eva Litrup
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Deirdre M. Prendergast
- Backweston complex, Department of Agriculture, Food and the Marine (DAFM), Celbridge, Co. Kildare, W23 X3PH, Ireland
| | - John E. Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, BT9 7AD, UK
| | - Sam Strain
- Animal Health and Welfare NI, Dungannon, BT71 6JT, UK
| | - Christian Kornschober
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Graz, 8010, Austria
| | - Richard Meinersmann
- US National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Alexandra Uesbeck
- Institute for Medical Microbiology, Immunology, and Hygiene, University of Cologne, Cologne, 50935, Germany
| | - François-Xavier Weill
- Unité des bactéries pathogènes entériques, Institut Pasteur, Paris, cedex 15, France
| | - Aidan Coffey
- Cork Institute of Technology, Cork, T12P928, Ireland
| | - Helene Andrews-Polymenis
- Dept. of Microbial Pathogenesis and Immunology, College of Medicine Texas A&M University, Bryan, TX, 77807, USA
| | - Roy Curtiss 3rd
- Dept. of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, 32611, USA
| | - Séamus Fanning
- UCD-Centre for Food Safety, University College Dublin, Dublin, D04 N2E5, Ireland
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Salmonella inactivation and cross-contamination on cherry and grape tomatoes under simulated wash conditions. Food Microbiol 2020; 87:103359. [DOI: 10.1016/j.fm.2019.103359] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/31/2019] [Accepted: 11/01/2019] [Indexed: 11/24/2022]
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Galbraith P, Henry R, McCarthy DT. Rise of the killer plants: investigating the antimicrobial activity of Australian plants to enhance biofilter-mediated pathogen removal. J Biol Eng 2019; 13:52. [PMID: 31182974 PMCID: PMC6555726 DOI: 10.1186/s13036-019-0175-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/06/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biofilters are soil-plant based passive stormwater treatment systems which demonstrate promising, although inconsistent, removal of faecal microorganisms. Antimicrobial-producing plants represent a safe, inexpensive yet under-researched biofilter design component that may enhance treatment reliability. The mechanisms underlying plant-mediated microbial removal in biofilters have not been fully elucidated, particularly with respect to antimicrobial production. The aim of this study was therefore to inform biofilter vegetation selection guidelines for optimal pathogen treatment by conducting antimicrobial screening of biofilter-suitable plant species. This involved: (1) selecting native plants suitable for biofilters (17 species) in a Victorian context (southeast Australia); and (2) conducting antimicrobial susceptibility testing of selected plant methanolic extracts (≥ 5 biological replicates/species; 86 total) against reference stormwater faecal bacteria (Salmonella enterica subsp. enterica ser. Typhimurium, Enterococcus faecalis and Escherichia coli). RESULTS The present study represents the first report on the inhibitory activity of polar alcoholic extracts from multiple tested species. Extracts of plants in the Myrtaceae family, reputed for their production of antimicrobial oils, demonstrated significantly lower minimum inhibitory concentrations (MICs) than non-myrtaceous candidates (p < 0.0001). Melaleuca fulgens (median MIC: 8 mg/mL; range: [4-16 mg/mL]), Callistemon viminalis (16 mg/mL, [2-16 mg/mL]) and Leptospermum lanigerum (8 mg/mL, [4-16 mg/mL]) exhibited the strongest inhibitory activity against the selected bacteria (p < 0.05 compared to each tested non-myrtaceous candidate). In contrast, the Australian biofilter gold standard Carex appressa demonstrated eight-fold lower activity than the highest performer M. fulgens (64 mg/mL, [32-64 mg/mL]). CONCLUSION Our results suggest that myrtaceous plants, particularly M. fulgens, may be more effective than the current vegetation gold standard in mediating antibiosis and thus improving pathogen treatment within biofilters. Further investigation of these plants in biofilter contexts is recommended to refine biofilter vegetation selection guidelines.
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Affiliation(s)
- P. Galbraith
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Monash Water for Liveability, Department of Civil Engineering, Monash University, Wellington Road, Clayton, Victoria 3800 Australia
| | - R. Henry
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Monash Water for Liveability, Department of Civil Engineering, Monash University, Wellington Road, Clayton, Victoria 3800 Australia
| | - D. T. McCarthy
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Monash Water for Liveability, Department of Civil Engineering, Monash University, Wellington Road, Clayton, Victoria 3800 Australia
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Guo X, Wang H, Cheng Y, Zhang W, Luo Q, Wen G, Wang G, Shao H, Zhang T. Quinolone resistance phenotype and genetic characterization of Salmonella enterica serovar Pullorum isolates in China, during 2011 to 2016. BMC Microbiol 2018; 18:225. [PMID: 30587131 PMCID: PMC6307136 DOI: 10.1186/s12866-018-1368-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/06/2018] [Indexed: 12/15/2022] Open
Abstract
Background Pullorum disease, caused by Salmonella enterica serovar Pullorum (S. Pullorum), is one of the most important bacterial infections in the poultry industry in developing countries, including China. To examine the prevalence and characteristics of S. Pullorum, the Multilocus Sequence Typing (MLST) genotypes, fluoroquinolones resistance, and biofilm-forming abilities of S. Pullorum isolates were investigated, collected from 2011 to 2016 in China. Results Thirty S. Pullorum isolates collected from 2011 to 2016 were analyzed. Quinolones susceptibility testing showed that 90% of the isolates were resistant to the first generation of quinolines nalidixic acid, but the resistance rates to different fluoroquinolones agents were lower than 13.3%; for some there was even no resistance. Multilocus sequence typing (MLST) showed that ST-92 was the dominating genotype, accounting for 90.0% of all S. pullorum strains. The remaining three isolates were of the new reported sequence type ST-2151. Interestingly, the Asp87Gly substitution in quinolone resistance-determining regions (QRDR) of GyrA was only observed in the three strains of ST-2151, suggesting a potential correlation between Asp87Gly substitution and sequence type (p < 0.05). However, Asp87Gly substitution could not confer the resistant to ofloxacin and ciprofloxacin of these isolates. The plasmid-mediated quinolone resistance (PMQR) gene was not found in any of the tested isolates. Furthermore, an assay measuring biofilm-forming abilities showed that 46.7% of the isolates were non-biofilm producers, while 53.3% could form very weak biofilms, which might explain the relatively lower resistance to fluoroquinolones. Conclusions We reported a high resistance rate to the first generation of quinolines nalidixic acid and relatively low resistance rates to fluoroquinolones in S. Pullorum isolates. In addition, weak biofilm-forming abilities were found, which might be an important reason of the low fluoroquinolones resistance rates of S. Pullorum isolates. ST-92 was the dominating genotype demonstrated by MLST, and the new sequence type ST-2151 showed a potential correlation with Asp87Gly substitution in QRDR of GyrA. We believe the characterization of these S. Pullorum isolates will be helpful to develop prevention and control strategies. Electronic supplementary material The online version of this article (10.1186/s12866-018-1368-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaodong Guo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China.,College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Honglin Wang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China.,Hubei Engineering Technology Center of Veterinary Diagnostic products, Wuhan, 430070, China
| | - Yiluo Cheng
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China.,Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal and Veterinary Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wenting Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China.,Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal and Veterinary Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qingping Luo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China.,Hubei Engineering Technology Center of Veterinary Diagnostic products, Wuhan, 430070, China
| | - Guoyuan Wen
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China.,Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal and Veterinary Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guijun Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Huabin Shao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China. .,Hubei Engineering Technology Center of Veterinary Diagnostic products, Wuhan, 430070, China.
| | - Tengfei Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China. .,Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal and Veterinary Science, Hubei Academy of Agricultural Sciences, Wuhan, China.
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9
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Luo Y, Yi W, Yao Y, Zhu N, Qin P. Characteristic diversity and antimicrobial resistance of Salmonella from gastroenteritis. J Infect Chemother 2017; 24:251-255. [PMID: 29208344 DOI: 10.1016/j.jiac.2017.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
Abstract
Salmonella is a leading cause of foodborne disease worldwide and may cause to gastroenteritis. The aim of this study was to determine the prevalence, serotypes, virulence genes, molecular subtyping, and antibiotic resistance phenotype of Salmonella from gastroenteritis in Hubei, China. Of 500 patients stools samples collected from January 2015 to January 2016, 52 (10.40%) samples were contaminated by Salmonella. The results showed that most of the isolates were positive for eight virulence genes that appear on pathogenicity islands, prophages, plasmid, and fimbrial. A total of twelve serotypes were found. Antimicrobial susceptibility results indicated that most strains were resistant to ampicillin (57.69%), kanamycin (53.85%), and tetracycline (40.38%). There were 33 STs on MLST types, and were grouped into two clusters. Thus, our findings provided insights into the dissemination of antibiotic resistant strains, genetic diversity, and improved our knowledge of microbiological risk assessment in Salmonella from gastroenteritis.
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Affiliation(s)
- Yunchun Luo
- The First College of Clinical Medical Science, China Three Gorges University and the Department of Anorectal, Yichang Center People's Hospital, Yichang, China.
| | - Wen Yi
- The First College of Clinical Medical Science, China Three Gorges University and the Department of Anorectal, Yichang Center People's Hospital, Yichang, China
| | - Yuzhou Yao
- The First College of Clinical Medical Science, China Three Gorges University and the Department of Anorectal, Yichang Center People's Hospital, Yichang, China
| | - Ni Zhu
- The First College of Clinical Medical Science, China Three Gorges University and the Department of Anorectal, Yichang Center People's Hospital, Yichang, China
| | - Pengfei Qin
- The First College of Clinical Medical Science, China Three Gorges University and the Department of Anorectal, Yichang Center People's Hospital, Yichang, China
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10
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Furukawa M, Goji N, Janzen TW, Thomas MC, Ogunremi D, Blais B, Misawa N, Amoako KK. Rapid detection and serovar identification of common Salmonella enterica serovars in Canada using a new pyrosequencing assay. Can J Microbiol 2017; 64:75-86. [PMID: 29088546 DOI: 10.1139/cjm-2017-0496] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Serotyping of Salmonella enterica subsp. enterica is a critical step for foodborne salmonellosis investigation. To identify Salmonella enterica subsp. enterica serovars, we have developed a new assay based on a triplex polymerase chain reaction (PCR) with pyrosequencing for amplicon confirmation and phylogenetic discrimination of strains. The top 54 most prevalent serovars of S. enterica in Canada were examined with a total of 23 single-nucleotide polymorphisms (SNPs) and (or) single-nucleotide variations (SNVs) located on 3 genes (fliD, sopE2, and spaO). Seven of the most common serovars, Newport, Typhi, Javiana, Infantis, Thompson, Heidelberg, and Enteritidis, were successfully distinguished from the other serovars based on their unique SNP-SNV combinations. The remaining serovars, including Typhimurium, ssp I:4,[5],12:i:-, and Saintpaul, were further divided into 47 subgroups that demonstrate the relatedness to phylogenetic classifications of each serovar. This pyrosequencing assay is not only cost-effective, rapid, and user-friendly, but also provides phylogenetic information by analyzing 23 selected SNPs. With the added layer of confidence in the PCR results and the accuracy and speed of pyrosequencing, this novel method would benefit the food industry and provides a tool for rapid outbreak investigation through quick detection and identification of common S. enterica serovars in Canada.
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Affiliation(s)
- Maika Furukawa
- a Canadian Food Inspection Agency (CFIA) National Centres for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, AB T1J 3Z4, Canada.,b Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, 889-2192, Japan
| | - Noriko Goji
- a Canadian Food Inspection Agency (CFIA) National Centres for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, AB T1J 3Z4, Canada
| | - Timothy W Janzen
- a Canadian Food Inspection Agency (CFIA) National Centres for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, AB T1J 3Z4, Canada
| | - Matthew C Thomas
- a Canadian Food Inspection Agency (CFIA) National Centres for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, AB T1J 3Z4, Canada
| | - Dele Ogunremi
- c Canadian Food Inspection Agency (CFIA) Ontario Laboratory Network, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada
| | - Burton Blais
- d Canadian Food Inspection Agency (CFIA) Ontario Laboratory Network, Building 22, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Naoaki Misawa
- b Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, 889-2192, Japan.,e Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, 889-2192, Japan
| | - Kingsley K Amoako
- a Canadian Food Inspection Agency (CFIA) National Centres for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, AB T1J 3Z4, Canada
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11
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Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovars Typhimurium, Saintpaul, and Stanleyville from the SARA/SARB Collection. GENOME ANNOUNCEMENTS 2017; 5:5/11/e00031-17. [PMID: 28302778 PMCID: PMC5356055 DOI: 10.1128/genomea.00031-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this announcement, we report the complete genome and methylome sequences of three Salmonella enterica strains from the SARA and SARB collection: S. enterica subsp. enterica serovar Typhimurium (SARA13), S. enterica subsp. enterica serovar Saintpaul (SARA26), and S. enterica subsp. enterica serovar Stanleyville (SARB61).
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12
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Yamazaki W, Uemura R, Sekiguchi S, Dong JB, Watanabe S, Kirino Y, Mekata H, Nonaka N, Norimine J, Sueyoshi M, Goto Y, Horii Y, Kurogi M, Yoshino S, Misawa N. Campylobacter and Salmonella are prevalent in broiler farms in Kyushu, Japan: results of a 2-year distribution and circulation dynamics audit. J Appl Microbiol 2016; 120:1711-22. [PMID: 27005691 DOI: 10.1111/jam.13141] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/16/2016] [Accepted: 03/16/2016] [Indexed: 12/22/2022]
Abstract
AIM To elucidate the distribution and circulation dynamics of Campylobacter and Salmonella in Japanese chicken broiler flocks. METHODS AND RESULTS A 2-year investigation of the distribution of Campylobacter and Salmonella was conducted in 25 broiler flocks at nine farms in Japan from 2013 to 2014. Campylobacter and Salmonella tested positive in 11 (44·0%) and 24 (96·0%) broiler flocks respectively. One hundred and ninety-five Campylobacter and 184 Salmonella isolates were characterized into 12 Campylobacter (including two novel genotypes) and three Salmonella MLST genotypes. Only Salmonella isolation between caecal and environmental samples were significantly correlated. Further, one litter sample tested positive for Salmonella before new chicks were introduced. The Campylobacter strains rapidly lost culturability within 2-18 days; in contrast, the Salmonella strains survived from 64-211 days in artificially inoculated water samples. CONCLUSION No persistent circulation-mediated Campylobacter contamination was observed. In contrast, circulation of Salmonella in broiler houses was seen, apparently due to the litter excreted from broiler flocks, as well as Salmonella-contaminated water and feed. SIGNIFICANCE AND IMPACT OF THE STUDY This paper provides the distribution, genotypic data and circulation dynamics of Campylobacter and Salmonella as recently observed in Japanese chicken broiler farms.
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Affiliation(s)
- W Yamazaki
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - R Uemura
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - S Sekiguchi
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - J-B Dong
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - S Watanabe
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Y Kirino
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - H Mekata
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - N Nonaka
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - J Norimine
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - M Sueyoshi
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Y Goto
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Y Horii
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - M Kurogi
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | - S Yoshino
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | - N Misawa
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
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13
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Prevalence, antimicrobial resistance and genetic diversity of Salmonella isolated from retail ready-to-eat foods in China. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.07.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing. J Clin Microbiol 2015; 53:2530-8. [PMID: 26019201 DOI: 10.1128/jcm.03407-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 05/25/2015] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing foodborne infections in Australia and many other countries. Twenty-one S. Typhimurium strains from Salmonella reference collection A (SARA) were analyzed using Illumina high-throughput genome sequencing. Single nucleotide polymorphisms (SNPs) in 21 SARA strains ranged from 46 to 11,916 SNPs, with an average of 1,577 SNPs per strain. Together with 47 strains selected from publicly available S. Typhimurium genomes, the S. Typhimurium core genes (STCG) were determined. The STCG consist of 3,846 genes, a set that is much larger than that of the 2,882 Salmonella core genes (SCG) found previously. The STCG together with 1,576 core intergenic regions (IGRs) were defined as the S. Typhimurium core genome. Using 93 S. Typhimurium genomes from 13 epidemiologically confirmed community outbreaks, we demonstrated that typing based on the S. Typhimurium core genome (STCG plus core IGRs) provides superior resolution and higher discriminatory power than that based on SCG for outbreak investigation and molecular epidemiology of S. Typhimurium. STCG and STCG plus core IGR typing achieved 100% separation of all outbreaks compared to that of SCG typing, which failed to separate isolates from two outbreaks from background isolates. Defining the S. Typhimurium core genome allows standardization of genes/regions to be used for high-resolution epidemiological typing and genomic surveillance of S. Typhimurium.
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15
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Yun YS, Chae SJ, Na HY, Chung GT, Yoo CK, Lee DY. Modified Method of Multilocus Sequence Typing (MLST) for Serotyping inSalmonellaSpecies. ACTA ACUST UNITED AC 2015. [DOI: 10.4167/jbv.2015.45.4.314] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Young-Sun Yun
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
| | - Su-Jin Chae
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
| | - Hye-Young Na
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
| | - Gyung Tae Chung
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
| | - Cheon-Kwon Yoo
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
| | - Deog-Yong Lee
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
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16
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Maier L, Barthel M, Stecher B, Maier RJ, Gunn JS, Hardt WD. Salmonella Typhimurium strain ATCC14028 requires H2-hydrogenases for growth in the gut, but not at systemic sites. PLoS One 2014; 9:e110187. [PMID: 25303479 PMCID: PMC4193879 DOI: 10.1371/journal.pone.0110187] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/11/2014] [Indexed: 11/23/2022] Open
Abstract
Salmonella enterica is a common cause of diarrhea. For eliciting disease, the pathogen has to colonize the gut lumen, a site colonized by the microbiota. This process/initial stage is incompletely understood. Recent work established that one particular strain, Salmonella enterica subspecies 1 serovar Typhimurium strain SL1344, employs the hyb H2-hydrogenase for consuming microbiota-derived H2 to support gut luminal pathogen growth: Protons from the H2-splitting reaction contribute to the proton gradient across the outer bacterial membrane which can be harvested for ATP production or for import of carbon sources. However, it remained unclear, if other Salmonella strains would use the same strategy. In particular, earlier work had left unanswered if strain ATCC14028 might use H2 for growth at systemic sites. To clarify the role of the hydrogenases, it seems important to establish if H2 is used at systemic sites or in the gut and if Salmonella strains may differ with respect to the host sites where they require H2 in vivo. In order to resolve this, we constructed a strain lacking all three H2-hydrogenases of ATCC14028 (14028hyd3) and performed competitive infection experiments. Upon intragastric inoculation, 14028hyd3 was present at 100-fold lower numbers than 14028WT in the stool and at systemic sites. In contrast, i.v. inoculation led to equivalent systemic loads of 14028hyd3 and the wild type strain. However, the pathogen population spreading to the gut lumen featured again up to 100-fold attenuation of 14028hyd3. Therefore, ATCC14028 requires H2-hydrogenases for growth in the gut lumen and not at systemic sites. This extends previous work on ATCC14028 and supports the notion that H2-utilization might be a general feature of S. Typhimurium gut colonization.
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Affiliation(s)
- Lisa Maier
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Manja Barthel
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Bärbel Stecher
- Max von Pettenkofer-Institut, München, Germany
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
| | - Robert J. Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - John S. Gunn
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, Biomedical Research Tower, The Ohio State University, Columbus, Ohio, United States of America
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17
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Soler-García AA, De Jesús AJ, Taylor K, Brown EW. Differentiation of Salmonella strains from the SARA, SARB and SARC reference collections by using three genes PCR-RFLP and the 2100 Agilent Bioanalyzer. Front Microbiol 2014; 5:417. [PMID: 25157247 PMCID: PMC4127528 DOI: 10.3389/fmicb.2014.00417] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/22/2014] [Indexed: 11/13/2022] Open
Abstract
Rapid molecular typing methods are important tools in surveillance and outbreak investigations of human Salmonella infections. Here we described the development of a three-genes PCR-RFLP typing method for the differentiation of Salmonella species, subspecies and serovars using the Agilent 2100 Bioanalyzer. The fliC, gnd, and mutS genes were PCR-amplified in 160 Salmonella strains representing the two Salmonella species, six subspecies, and 41 different serovars of S. enterica subspecies enterica. PCR products were individually cut with two different restriction enzymes and the resulting 930 restriction patterns were collected using the Agilent 2100 Bioanalyzer followed by cluster analysis. Both species of Salmonella were differentiated by conventional PCR. All of S. bongori tested were gnd PCR negative due to a mismatch at the 3'-end in one the PCR primers. Salmonella subspecies were differentiated into third-teen homogeneous groups representing each of the six subspecies by cluster analysis of restriction patterns generated from the mutS gene cut with AciI. S. enterica subspecies enterica serovars were further differentiated by the combination of the three target genes and five out the six sets of restriction patterns with a discriminatory power of 0.9725 by cluster analysis. The combined RFLP results of five sets of restriction patterns allowed us to assign each of the 160 strains to one of 128 restriction types. During inoculation studies we were able to identify S. Saintpaul and Typhimurium from 24 h pre-enrichment samples using the described method. The use of fliC, gnd, and mutS PCR-RFLP with the Agilent 2100 Bioanalyzer can provide an accessible and automated alternative method for differentiation of Salmonella pathogens.
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Affiliation(s)
- Angel A Soler-García
- Molecular Methods and Subtyping Branch, Division of Microbiology, Center for Food Safety and Applied Nutrition, US Food and Drug Administration College Park, MD, USA
| | - Antonio J De Jesús
- Molecular Methods and Subtyping Branch, Division of Microbiology, Center for Food Safety and Applied Nutrition, US Food and Drug Administration College Park, MD, USA
| | - Kishana Taylor
- Molecular Methods and Subtyping Branch, Division of Microbiology, Center for Food Safety and Applied Nutrition, US Food and Drug Administration College Park, MD, USA
| | - Eric W Brown
- Molecular Methods and Subtyping Branch, Division of Microbiology, Center for Food Safety and Applied Nutrition, US Food and Drug Administration College Park, MD, USA
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