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Thomas C, Methner U, Marz M, Linde J. Oxford nanopore technologies-a valuable tool to generate whole-genome sequencing data for in silico serotyping and the detection of genetic markers in Salmonella. Front Vet Sci 2023; 10:1178922. [PMID: 37323838 PMCID: PMC10267320 DOI: 10.3389/fvets.2023.1178922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023] Open
Abstract
Bacteria of the genus Salmonella pose a major risk to livestock, the food economy, and public health. Salmonella infections are one of the leading causes of food poisoning. The identification of serovars of Salmonella achieved by their diverse surface antigens is essential to gain information on their epidemiological context. Traditionally, slide agglutination has been used for serotyping. In recent years, whole-genome sequencing (WGS) followed by in silico serotyping has been established as an alternative method for serotyping and the detection of genetic markers for Salmonella. Until now, WGS data generated with Illumina sequencing are used to validate in silico serotyping methods. Oxford Nanopore Technologies (ONT) opens the possibility to sequence ultra-long reads and has frequently been used for bacterial sequencing. In this study, ONT sequencing data of 28 Salmonella strains of different serovars with epidemiological relevance in humans, food, and animals were taken to investigate the performance of the in silico serotyping tools SISTR and SeqSero2 compared to traditional slide agglutination tests. Moreover, the detection of genetic markers for resistance against antimicrobial agents, virulence, and plasmids was studied by comparing WGS data based on ONT with WGS data based on Illumina. Based on the ONT data from flow cell version R9.4.1, in silico serotyping achieved an accuracy of 96.4 and 92% for the tools SISTR and SeqSero2, respectively. Highly similar sets of genetic markers comparing both sequencing technologies were identified. Taking the ongoing improvement of basecalling and flow cells into account, ONT data can be used for Salmonella in silico serotyping and genetic marker detection.
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Affiliation(s)
- Christine Thomas
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
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2
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Stevens EL, Carleton HA, Beal J, Tillman GE, Lindsey RL, Lauer AC, Pightling A, Jarvis KG, Ottesen A, Ramachandran P, Hintz L, Katz LS, Folster JP, Whichard JM, Trees E, Timme RE, McDERMOTT P, Wolpert B, Bazaco M, Zhao S, Lindley S, Bruce BB, Griffin PM, Brown E, Allard M, Tallent S, Irvin K, Hoffmann M, Wise M, Tauxe R, Gerner-Smidt P, Simmons M, Kissler B, Defibaugh-Chavez S, Klimke W, Agarwala R, Lindsay J, Cook K, Austerman SR, Goldman D, McGARRY S, Hale KR, Dessai U, Musser SM, Braden C. Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States. J Food Prot 2022; 85:755-772. [PMID: 35259246 DOI: 10.4315/jfp-21-437] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/22/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety. HIGHLIGHTS
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Affiliation(s)
- Eric L Stevens
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Heather A Carleton
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jennifer Beal
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Glenn E Tillman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Rebecca L Lindsey
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - A C Lauer
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Arthur Pightling
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Karen G Jarvis
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Andrea Ottesen
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Padmini Ramachandran
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Leslie Hintz
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Lee S Katz
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jason P Folster
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jean M Whichard
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eija Trees
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Ruth E Timme
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Patrick McDERMOTT
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Beverly Wolpert
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Michael Bazaco
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Sabina Lindley
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Beau B Bruce
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Patricia M Griffin
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eric Brown
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Marc Allard
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Sandra Tallent
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Kari Irvin
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Maria Hoffmann
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Matt Wise
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Robert Tauxe
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Mustafa Simmons
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Bonnie Kissler
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | | | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Richa Agarwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - James Lindsay
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Kimberly Cook
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Suelee Robbe Austerman
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Ames, Iowa 50010, USA
| | - David Goldman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Sherri McGARRY
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Kis Robertson Hale
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Uday Dessai
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Steven M Musser
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Chris Braden
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
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3
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Application of a High-Throughput Targeted Sequence AmpliSeq Procedure to Assess the Presence and Variants of Virulence Genes in Salmonella. Microorganisms 2022; 10:microorganisms10020369. [PMID: 35208824 PMCID: PMC8879106 DOI: 10.3390/microorganisms10020369] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 01/27/2023] Open
Abstract
We have developed a targeted, amplicon-based next-generation sequencing method to detect and analyze 227 virulence genes (VG) of Salmonella (AmpliSeqSalm_227VG) for assessing the pathogenicity potential of Salmonella. The procedure was developed using 80 reference genomes representing 75 epidemiologically-relevant serovars associated with human salmonellosis. We applied the AmpliSeqSalm_227VG assay to (a) 35 previously characterized field strains of Salmonella consisting of serovars commonly incriminated in foodborne illnesses and (b) 34 Salmonella strains with undisclosed serological or virulence attributes, and were able to divide Salmonella VGs into two groups: core VGs and variable VGs. The commonest serovars causing foodborne illnesses such as Enteritidis, Typhimurium, Heidelberg and Newport had a high number of VGs (217–227). In contrast, serovars of subspecies not commonly associated with human illnesses, such as houtenae, arizonae and salame, tended to have fewer VGs (177–195). Variable VGs were not only infrequent but, when present, displayed considerable sequence variation: safC, sseL, sseD, sseE, ssaK and stdB showed the highest variation and were linked to strain pathogenicity. In a chicken infection model, VGs belonging to rfb and sse operons showed differences and were linked with pathogenicity. The high-throughput, targeted NGS-based AmpliSeqSalm_227VG procedure provided previously unknown information about variation in select virulence genes that can now be applied to a much larger population of Salmonella for evaluating pathogenicity of various serovars of Salmonella and for risk assessment of foodborne salmonellosis.
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4
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Development of a multiplex-PCR serotyping assay for characterizing Legionella pneumophila serogroups based on the diversity of LPS biosynthetic loci. J Clin Microbiol 2021; 59:e0015721. [PMID: 34379526 DOI: 10.1128/jcm.00157-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Legionella pneumophila, which is the main cause of Legionnaires' disease, comprises at least 15 serogroups (SGs). We show here the diversity of LPS biosynthetic loci among serogroups and describe the development of a PCR serotyping assay for 15 SGs based on the sequences of LPS biosynthetic loci. Using this multiplex-PCR (M-PCR) system, serogroup(s) were detected using primers that specifically amplify the sequences of SG1, SG2, SG5, SG7, SG8, SG9, SG11, SG13, SG3/15, and SG6/12. When PCR products of the expected sizes were not detected, we used primers that identified SG4/10/14. The PCR serotyping system specifically amplified the sequences corresponding SGs of 238 L. pneumophila strains. This method will be very useful for conducting epidemiological studies and investigating outbreak of Legionnaires' disease.
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5
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A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium. Food Microbiol 2020; 91:103534. [PMID: 32539977 DOI: 10.1016/j.fm.2020.103534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/22/2020] [Indexed: 11/23/2022]
Abstract
Humans are mostly contaminated by Salmonella through the consumption of pork- and poultry-derived food products. Therefore, a strict monitoring of Salmonella serotypes in food-producing animals is needed to limit the transmission of the pathogen to humans. Additionally, Salmonella can lead to economic loss in the food sector. Previously, a genoserotyping method using the MOL-PCR and Luminex technology was developed for the identification of the 6 Salmonella serotypes, and their variants, subjected to an official control in the Belgian food sector. In this study, 3 additional assays using the same technology were developed for the rapid and cost-effective detection of 13 dangerous highly invasive serotypes or other serotypes frequently isolated from the Belgian poultry and pork sector, i.e. Agona, Anatum, Brandenburg, Choleraesuis, Derby, Enteritidis vaccine strains, Gallinarum var. Gallinarum/Pullorum, Livingstone, Mbandaka, Minnesota, Ohio, Rissen and Senftenberg. Moreover, the previously developed first MOL-PCR assay was improved for S. Paratyphi B and serogroup O:3 detection. Finally, a Decision Support System hosted by a web application was created for an automatic and objective interpretation of the Luminex raw data. The 3 new assays and the modifications of the first assay were validated with a 100% accuracy, using 553 Salmonella and non-Salmonella strains in total.
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6
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Gand M, Mattheus W, Roosens NHC, Dierick K, Marchal K, De Keersmaecker SCJ, Bertrand S. A multiplex oligonucleotide ligation-PCR method for the genoserotyping of common Salmonella using a liquid bead suspension assay. Food Microbiol 2019; 87:103394. [PMID: 31948635 DOI: 10.1016/j.fm.2019.103394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/21/2019] [Accepted: 11/20/2019] [Indexed: 01/14/2023]
Abstract
Salmonella is a major pathogen having a public health and economic impact in both humans and animals. Six serotypes of the Salmonella genus are mentioned in the Belgian and European regulation as to be rapidly excluded from the food chain (EU regulation N°2160/2003, Belgian royal decree 27/04/2017). The reference method for Salmonella serotyping, including slide-agglutination and biochemical tests, is time-consuming, expensive, not always objective, and therefore does not match the fast identification criteria required by the legislation. In this study, a molecular method, using genetic markers detected by Multiplex Oligonucleotide Ligation - PCR and Luminex technology, was developed for the identification of the 6 Salmonella serotypes and their variants subjected to an official control. The resulting method was validated with the analysis of 971 Salmonella isolated from different matrixes (human, animal, food or environment) and 33 non-Salmonella strains. The results were compared with the reference identifications, achieving an accuracy of 99.7%. The cost-effective high-throughput genoserotyping assay is performed in 1 day and generates objective results, thanks to the automatic interpretation of raw data using a barcode system. In conclusion, it is fully adapted to the implementation in first line laboratories and meets the requirements of the regulation.
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Affiliation(s)
- Mathieu Gand
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, B-1180 Brussels, Belgium; Department of Information Technology, IDLab, Imec, Ghent University, B-9052 Ghent, Belgium
| | - Wesley Mattheus
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, B-1180 Brussels, Belgium.
| | - Nancy H C Roosens
- Sciensano, Transversal Activities in Applied Genomics, B-1050 Brussels, Belgium
| | - Katelijne Dierick
- Sciensano, Infectious Diseases in Humans, Food Pathogen, B-1050 Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Imec, Ghent University, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
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7
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Robertson J, Lin J, Wren-Hedgus A, Arya G, Carrillo C, Nash JHE. Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella. PLoS One 2019; 14:e0218638. [PMID: 31738764 PMCID: PMC6860452 DOI: 10.1371/journal.pone.0218638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/01/2019] [Indexed: 11/29/2022] Open
Abstract
Due to the public health importance of flagellar genes for typing, it is important to understand mechanisms that could alter their expression or presence. Phenotypic novelty in flagellar genes arise predominately through accumulation of mutations but horizontal transfer is known to occur. A linear plasmid termed pBSSB1 previously identified in Salmonella Typhi, was found to encode a flagellar operon that can mediate phase variation, which results in the rare z66 flagella phenotype. The identification and tracking of homologs of pBSSB1 is limited because it falls outside the normal replicon typing schemes for plasmids. Here we report the generation of nine new pBSSB1-family sequences using Illumina and Nanopore sequence data. Homologs of pBSSB1 were identified in 154 genomes representing 25 distinct serotypes from 67,758 Salmonella public genomes. Pangenome analysis of pBSSB1-family contigs was performed using roary and we identified three core genes amenable to a minimal pMLST scheme. Population structure analysis based on the newly developed pMLST scheme identified three major lineages representing 35 sequence types, and the distribution of these sequence types was found to span multiple serovars across the globe. This in silico pMLST scheme has shown utility in tracking and subtyping pBSSB1-family plasmids and it has been incorporated into the plasmid MLST database under the name “pBSSB1-family”.
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Affiliation(s)
- James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Janet Lin
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Amie Wren-Hedgus
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gitanjali Arya
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Catherine Carrillo
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - John H. E. Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Toronto, Ontario, Canada
- * E-mail:
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8
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Kasturi KN. A real-time PCR for rapid identification of Salmonella enterica Gaminara serovar. J Microbiol Methods 2019; 169:105729. [PMID: 31711901 DOI: 10.1016/j.mimet.2019.105729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/13/2019] [Accepted: 09/21/2019] [Indexed: 12/17/2022]
Abstract
Salmonella is one of the leading causes of foodborne illnesses in the USA. When a Salmonella outbreak occurs, rapid identification of the causative serovar is important for tracing the source of contamination and for preventing the further spread of the illness. Each serovar is characterized by the presence of a group-specific somatic O-antigen(s) and an assortment of flagellar phase-1 and phase-2 antigens. As the traditional serotyping protocol is time consuming, labor intensive, and expensive, faster and less expensive molecular diagnostic methods are needed. This report outlines the development of a rapid multiplex real-time PCR procedure that facilitates the identification of Salmonella serogroup I and the serovars of the group. Using Salmonella Gaminara serovar (O16:d:1,7) as an example, first the gene(s) responsible for expression of the somatic O antigen, O16, and the nucleotide sequence of the variable-region of genes encoding the flagellar phase-1 (d) and phase-2 (1,7) antigens were identified. Then, a multiplex real-time PCR was designed that incorporated primers and probes specific for the three target genes and confirmed the specificity. The assay had 100% inclusivity for all three gene targets, detecting 2 genomic DNA copies of O16 and 1,7 gene targets and 10 copies of d gene target. Importance: Rapid molecular methods to identify Salmonella serovars should increase the precision of routine surveillance of clinically important serovars and promote public health.
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Affiliation(s)
- Kuppuswamy N Kasturi
- U. S. Food and Drug Administration, Office of Regulatory Affairs, Office of Regulatory Science, Northeast Food and Feed Laboratory, Jamaica, New York 11433, USA.
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9
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Moore MM, Nucci MJ, Madson SM, Wagley GS, Keys CE, Brown EW, McQUISTON JR, Fields PI. Evaluation of a Bead-Based Salmonella Molecular Serotyping Method for Salmonella Isolated from Food and Environmental Samples. J Food Prot 2019; 82:1973-1987. [PMID: 31644335 DOI: 10.4315/0362-028x.jfp-18-600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Salmonella is a leading cause of foodborne illness worldwide, and foods containing Salmonella (except raw meat and poultry products) are considered adulterated. Serotyping of Salmonella is an essential part of surveillance and investigation of outbreaks. This study evaluated a bead-based Salmonella molecular serotyping (SMS) method, which included the O-group 1, H-antigen, alternate target, and O-group 2 assays, compared with traditional serotyping. Salmonella was isolated from food, pet food, and environmental samples or were reference strains. A total of 572 isolates were analyzed by using two formats of the SMS method in comparison with traditional methods: 485 were analyzed by using Radix SMS (a custom user-mixed format), 218 were analyzed by using Luminex SMS (a commercial kit format), and 131 of the total isolates were analyzed by both formats for comparison. The SMS method was evaluated on the basis of the successful identification of antigens by the probes included in the method. The method identified 550 (96.2%) isolates as expected, 6 (1.0%) isolates were not identified as initially expected but were shown to be correctly identified by SMS after reanalysis by traditional serotyping, and 16 (2.8%) isolates not identified as expected possessed an antigen that should have been detected by the method but was not. Among the isolates considered correctly identified, 255 (44.6%) were identified to a single serovar, 44 (7.7%) required additional biochemical testing to differentiate variants or subspecies, and 251 (43.9%) were partially serotyped because probes for some antigens were not in the assay or had allelic variation for known serovars. Whole genome sequencing, SeqSero, and the Salmonella In Silico Typing Resource gave added confirmation for three isolates. Addition of the O-group 2 assay enabled the identification of 55 (9.6%) of 572 isolates. The SMS method could fully or partially serotype most isolates within a day. The SMS method should be a valuable tool when faster screening methods are needed, such as outbreaks and screening large numbers of environmental isolates.
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Affiliation(s)
- M M Moore
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Pacific Northwest Laboratory, Applied Technology Center, Bothell, Washington 98021
| | - M J Nucci
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Denver Laboratory, Lakewood, Colorado 80225
| | - S M Madson
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Arkansas Laboratory, Jefferson, Arkansas 72079
| | - G S Wagley
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Southeast Food and Feed Laboratory, Atlanta, Georgia 30309
| | - C E Keys
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, Maryland 20740
| | - E W Brown
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, Maryland 20740
| | - J R McQUISTON
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Atlanta, Georgia 30333, USA
| | - P I Fields
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Atlanta, Georgia 30333, USA
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10
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Sequence-Specific End Labeling of Oligonucleotides (SSELO)-Based Microbial Detection. Methods Mol Biol 2019; 1918:47-56. [PMID: 30580398 DOI: 10.1007/978-1-4939-9000-9_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The sequence-specific end labeling of oligonucleotides (SSELO) is an alternative labelling approach for the short-oligonucleotide diagnostic microarrays that was firstly described by Rudi and coworkers (ScientificWorldJournal 3:578-584, 2003). SSELO approach is unique in a way that it shifts the specificity determining step from hybridization to labeling, ensuring both high specificity (with careful probe design even single nucleotide polymorphisms (SNPs) can be detected) and sensitivity (detection sensitivity in the range of 0.1% relative abundance has been demonstrated) of the diagnostic system. These features make SSELO approach a perfect choice for the development of microbial diagnostic microarrays, in particular in the frame of foodborne bacterial pathogen detection.
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11
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Gand M, Mattheus W, Saltykova A, Roosens N, Dierick K, Marchal K, De Keersmaecker SCJ, Bertrand S. Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java. Appl Microbiol Biotechnol 2019; 103:4987-4996. [PMID: 31062054 PMCID: PMC6536469 DOI: 10.1007/s00253-019-09854-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/09/2019] [Accepted: 04/14/2019] [Indexed: 11/30/2022]
Abstract
Discriminating between D-tartrate fermenting and non-fermenting strains of Salmonella enterica subsp. enterica serotype Paratyphi B is of major importance as these two variants have different pathogenic profiles. While D-tartrate non-fermenting S. Paratyphi B isolates are the causative agent of typhoid-like fever, D-tartrate fermenting isolates (also called variant Java) of the same serotype trigger the less dangerous gastroenteritis. The determination of S. Paratyphi B variants requires a time-consuming process and complex biochemical tests. Therefore, a quadruplex real-time PCR method, based on the allelic discrimination of molecular markers selected from the scientific literature and from whole genome sequencing data produced in-house, was developed in this study, to be applied to Salmonella isolates. This method was validated with the analysis of 178 S. Paratyphi B (D-tartrate fermenting and non-fermenting) and other serotypes reaching an accuracy, compared with the classical methods, of 98% for serotyping by slide agglutination and 100% for replacement of the biochemical test. The developed real-time PCR permits to save time and to obtain an accurate identification of a S. Paratyphi B serotype and its D-tartrate fermenting profile, which is needed in routine laboratories for fast and efficient diagnostics.
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Affiliation(s)
- Mathieu Gand
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, Rue Engeland 642, 1180, Brussels, Belgium
- Department of Information Technology, IDLab, imec, Ghent University, 9052, Ghent, Belgium
| | - Wesley Mattheus
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, Rue Engeland 642, 1180, Brussels, Belgium.
| | - Assia Saltykova
- Department of Information Technology, IDLab, imec, Ghent University, 9052, Ghent, Belgium
- Sciensano, Transversal Activities in Applied Genomics, 1050, Brussels, Belgium
| | - Nancy Roosens
- Sciensano, Transversal Activities in Applied Genomics, 1050, Brussels, Belgium
| | - Katelijne Dierick
- Sciensano, Infectious Diseases in Humans, Food Pathogen, 1050, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, imec, Ghent University, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
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12
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Quintela IA, de Los Reyes BG, Lin CS, Wu VCH. Simultaneous Colorimetric Detection of a Variety of Salmonella spp. in Food and Environmental Samples by Optical Biosensing Using Oligonucleotide-Gold Nanoparticles. Front Microbiol 2019; 10:1138. [PMID: 31214132 PMCID: PMC6554661 DOI: 10.3389/fmicb.2019.01138] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/06/2019] [Indexed: 01/17/2023] Open
Abstract
Optical biosensors for rapid detection of significant foodborne pathogens are steadily gaining popularity due to its simplicity and sensitivity. While nanomaterials such as gold nanoparticles (AuNPs) are commonly used as signal amplifiers for optical biosensors, AuNPs can also be utilized as a robust biosensing platform. Many reported optical biosensors were designed for individual pathogen detection in a single assay and have high detection limit (DL). Salmonella spp. is one of the major causative agents of foodborne sickness, hospitalization and deaths. Unfortunately, there are around 2,000 serotypes of Salmonella worldwide, and rapid and simultaneous detection of multiple strains in a single assay is lacking. In this study, a comprehensive and highly sensitive simultaneous colorimetric detection of nineteen (19) environmental and outbreak Salmonella spp. strains was achieved by a novel optical biosensing platform using oligonucleotide-functionalized AuNPs. A pair of newly designed single stranded oligonucleotides (30-mer) was displayed onto the surface of AuNPs (13 nm) as detection probes to hybridize with a conserved genomic region (192-bases) of ttrRSBCA found on a broad range of Salmonella spp. strains. The sandwich hybridization (30 min, 55°C) resulted in a structural formation of highly stable oligonucleotide/AuNPs-DNA complexes which remained undisturbed even after subjecting to an increased salt concentration (2 M, final), thus allowing a direct discrimination via color change of target (red color) from non-target (purplish-blue color) reaction mixtures by direct observation using the naked eye. In food matrices (blueberries and chicken meat), nineteen different Salmonella spp. strains were concentrated using immunomagnetic separation and then simultaneously detected in a 96-well microplate by oligonucleotide-functionalized AuNPs after DNA preparation. Successful oligonucleotide/AuNPs-DNA hybridization was confirmed by gel electrophoresis while AuNPs aggregation in non-target and control reaction mixtures was verified by both spectrophotometric analysis and TEM images. Results showed that the optical AuNP biosensing platform can simultaneously screen nineteen (19) viable Salmonella spp. strains tested with 100% specificity and a superior detection limit of <10 CFU/mL or g for both pure culture and complex matrices setups. The highly sensitive colorimetric detection system can significantly improve the screening and detection of viable Salmonella spp. strains present in complex food and environmental matrices, therefore reducing the risks of contamination and incidence of foodborne diseases.
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Affiliation(s)
- Irwin A Quintela
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Services, Western Regional Research Center, Albany, CA, United States.,School of Food and Agriculture, University of Maine, Orono, ME, United States
| | | | - Chih-Sheng Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Vivian C H Wu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Services, Western Regional Research Center, Albany, CA, United States.,Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
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13
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Robertson J, Yoshida C, Gurnik S, McGrogan M, Davis K, Arya G, Murphy SA, Nichani A, Nash JHE. An improved DNA array-based classification method for the identification of Salmonella serotypes shows high concordance between traditional and genotypic testing. PLoS One 2018; 13:e0207550. [PMID: 30513098 PMCID: PMC6279050 DOI: 10.1371/journal.pone.0207550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/01/2018] [Indexed: 11/23/2022] Open
Abstract
Previously we developed and tested the Salmonella GenoSerotyping Array (SGSA), which utilized oligonucleotide probes for O- and H- antigen biomarkers to perform accurate molecular serotyping of 57 Salmonella serotypes. Here we describe the development and validation of the ISO 17025 accredited second version of the SGSA (SGSA v. 2) with reliable and unambiguous molecular serotyping results for 112 serotypes of Salmonella which were verified both in silico and in vitro. Improvements included an expansion of the probe sets along with a new classifier tool for prediction of individual antigens and overall serotype from the array probe intensity results. The array classifier and probe sequences were validated in silico to high concordance using 36,153 draft genomes of diverse Salmonella serotypes assembled from public repositories. We obtained correct and unambiguous serotype assignments for 31,924 (88.30%) of the tested samples and a further 3,916 (10.83%) had fully concordant antigen predictions but could not be assigned to a single serotype. The SGSA v. 2 can directly use bacterial colonies with a limit of detection of 860 CFU/mL or purified DNA template at a concentration of 1.0 x 10−1 ng/μl. The SGSA v. 2 was also validated in the wet laboratory and certified using panel of 406 samples representing 185 different serotypes with correct antigen and serotype determinations for 60.89% of the panel and 18.31% correctly identified but an ambiguous overall serotype determination.
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Affiliation(s)
- James Robertson
- Public Health Agency of Canada, National Microbiology Laboratory, Guelph, Ontario, Canada
- * E-mail:
| | - Catherine Yoshida
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Ontario, Canada
| | - Simone Gurnik
- Public Health Agency of Canada, National Microbiology Laboratory, Guelph, Ontario, Canada
| | - Madison McGrogan
- Public Health Agency of Canada, National Microbiology Laboratory, Guelph, Ontario, Canada
| | - Kristin Davis
- Public Health Agency of Canada, National Microbiology Laboratory, Guelph, Ontario, Canada
| | - Gitanjali Arya
- Public Health Agency of Canada, National Microbiology Laboratory, Guelph, Ontario, Canada
| | - Stephanie A. Murphy
- Public Health Agency of Canada, National Microbiology Laboratory, Guelph, Ontario, Canada
| | - Anil Nichani
- Public Health Agency of Canada, National Microbiology Laboratory, Guelph, Ontario, Canada
| | - John H. E. Nash
- Public Health Agency of Canada, National Microbiology Laboratory, Guelph, Ontario, Canada
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14
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Nadin-Davis S, Pope L, Ogunremi D, Brooks B, Devenish J. A real-time PCR regimen for testing environmental samples for Salmonella enterica subsp. enterica serovars of concern to the poultry industry, with special focus on Salmonella Enteritidis. Can J Microbiol 2018; 65:162-173. [PMID: 30395482 DOI: 10.1139/cjm-2018-0417] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A real-time PCR (qPCR) regimen, using up to six genetic targets, was developed to rapidly detect Salmonella and in particular identify Salmonella Enteritidis. The test regimen was first evaluated using a reference culture collection of Salmonella to confirm the appropriateness of the selected targets, which included up to three genetic markers for discrimination of Salmonella Enteritidis from other Salmonella serovars commonly found in poultry facilities. The qPCR procedure was then compared with culture methods used to detect Salmonella using a collection of enrichment broths previously generated from 239 environmental samples collected from a large number of hatchery facilities across Canada over several years. The qPCR regimen facilitated specific detection of Salmonella Enteritidis, and on a sample basis, it showed excellent agreement with the culture methods. Moreover, in many cases, qPCR detected Salmonella earlier in the culture process than did the culture method. Application of this method will significantly shorten test times and allow more timely identification of infected poultry premises, thereby improving present programmes aimed at controlling Salmonella Enteritidis at the environmental source.
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Affiliation(s)
- S Nadin-Davis
- Animal Health Microbiology, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada.,Animal Health Microbiology, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada
| | - L Pope
- Animal Health Microbiology, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada.,Animal Health Microbiology, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada
| | - D Ogunremi
- Animal Health Microbiology, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada
| | - B Brooks
- Animal Health Microbiology, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada
| | - J Devenish
- Animal Health Microbiology, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada.,Animal Health Microbiology, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada
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15
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Quantifying the Survival of Multiple Salmonella enterica Serovars In Vivo via Massively Parallel Whole-Genome Sequencing To Predict Zoonotic Risk. Appl Environ Microbiol 2018; 84:AEM.02262-17. [PMID: 29180370 PMCID: PMC5795071 DOI: 10.1128/aem.02262-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/14/2017] [Indexed: 01/24/2023] Open
Abstract
Salmonella enterica is an animal and zoonotic pathogen of worldwide importance. Salmonella serovars that differ in their host and tissue tropisms exist. Cattle are an important reservoir of human nontyphoidal salmonellosis, and contaminated bovine peripheral lymph nodes enter the food chain via ground beef. The relative abilities of different serovars to survive within the bovine lymphatic system are poorly understood and constrain the development of control strategies. This problem was addressed by developing a massively parallel whole-genome sequencing method to study mixed-serovar infections in vivo. Salmonella serovars differ genetically by naturally occurring single nucleotide polymorphisms (SNPs) in certain genes. It was hypothesized that these SNPs could be used as markers to simultaneously identify serovars in mixed populations and quantify the abundance of each member in a population. The performance of the method was validated in vitro using simulated pools containing up to 11 serovars in various proportions. It was then applied to study serovar survival in vivo in cattle challenged orally with the same 11 serovars. All the serovars successfully colonized the bovine lymphatic system, including the peripheral lymph nodes, and thus pose similar risks of zoonosis. This method enables the fates of multiple genetically unmodified strains to be evaluated simultaneously in a single animal. It could be useful in reducing the number of animals required to study mixed-strain infections and in testing the cross-protective efficacy of vaccines and treatments. It also has the potential to be applied to diverse bacterial species which possess shared but polymorphic alleles. IMPORTANCE While some Salmonella serovars are more frequently isolated from lymph nodes rather than the feces and environment of cattle, the relative abilities of serovars to survive within the lymphatic system of cattle remain ill defined. A sequencing-based method which used available information from sequenced Salmonella genomes to study the dynamics of mixed-serovar infections in vivo was developed. The main advantages of the method include the simultaneous identification and quantification of multiple strains without any genetic modification and minimal animal use. This approach could be used in vaccination trials or in epidemiological surveys where an understanding of the dynamics of closely related strains of a pathogen in mixed populations could inform the prediction of zoonotic risk and the development of intervention strategies.
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16
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CRISPR-based assay for the molecular identification of highly prevalent Salmonella serotypes. Food Microbiol 2017; 71:8-16. [PMID: 29366473 DOI: 10.1016/j.fm.2017.03.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/16/2017] [Accepted: 03/26/2017] [Indexed: 11/22/2022]
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17
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Ferrato C, Chui L, King R, Louie M. Utilization of a molecular serotyping method for Salmonella enterica in a routine laboratory in Alberta Canada. J Microbiol Methods 2017; 135:14-19. [PMID: 28159627 DOI: 10.1016/j.mimet.2017.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 01/30/2017] [Accepted: 01/30/2017] [Indexed: 10/20/2022]
Abstract
Salmonella is one of the most common enteric pathogens related to foodborne illness. Alberta's Provincial Laboratory for Public Health (ProvLab) provides Outbreak and Surveillance support by performing serotyping. The Check&Trace Salmonella™ (CTS) assay (Check-Points, Netherlands), a commercial DNA microarray system, can determine the serotype designation of a Salmonella isolate with automated interpretation. Here we evaluate 1028 Salmonella isolates of human clinical or environmental sources in Alberta, Canada with the CTS assay. CTS was able to assign a serovar to 98.7% of the most frequently occurring human clinical strains in Alberta (82.5% overall), and 71.7% of isolates which were inconclusive by conventional methods. There was 99.7% concordance in environmental isolates. The CTS database has potential to expand to identify rare serovars. With the anticipated shift to molecular methods for identification, CTS provides an easy transition and demonstrates ease-of-use and reduces the turn-around-time of a reported result significantly compared to classical serotyping.
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Affiliation(s)
- Christina Ferrato
- Alberta Provincial Laboratory for Public Health, Calgary and Edmonton, Alberta, Canada
| | - Linda Chui
- Alberta Provincial Laboratory for Public Health, Calgary and Edmonton, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada.
| | - Robin King
- Alberta Agriculture and Forestry, Government of Alberta, Edmonton, Canada
| | - Marie Louie
- Alberta Provincial Laboratory for Public Health, Calgary and Edmonton, Alberta, Canada; Department of Microbiology Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
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18
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Ogunremi D, Nadin-Davis S, Dupras AA, Márquez IG, Omidi K, Pope L, Devenish J, Burke T, Allain R, Leclair D. Evaluation of a Multiplex PCR Assay for the Identification of Salmonella Serovars Enteritidis and Typhimurium Using Retail and Abattoir Samples. J Food Prot 2017; 80:295-301. [PMID: 28221989 DOI: 10.4315/0362-028x.jfp-16-167] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A multiplex PCR was developed to identify the two most common serovars of Salmonella causing foodborne illness in Canada, namely, serovars Enteritidis and Typhimurium. The PCR was designed to amplify DNA fragments from four Salmonella genes, namely, invA gene (211-bp fragment), iroB gene (309-bp fragment), Typhimurium STM 4497 (523-bp fragment), and Enteritidis SE147228 (612-bp fragment). In addition, a 1,026-bp ribosomal DNA (rDNA) fragment universally present in bacterial species was included in the assay as an internal control fragment. The detection rate of the PCR was 100% among Salmonella Enteritidis (n = 92) and Salmonella Typhimurium (n = 33) isolates. All tested Salmonella isolates (n = 194) were successfully identified based on the amplification of at least one Salmonella -specific DNA fragment. None of the four Salmonella DNA amplicons were detected in any of the non- Salmonella isolates (n = 126), indicating an exclusivity rate of 100%. When applied to crude extracts of 2,001 field isolates of Salmonella obtained during the course of a national microbiological baseline study in broiler chickens and chicken products sampled from abattoir and retail outlets, 163 isolates, or 8.1%, tested positive for Salmonella Enteritidis and another 80 isolates, or 4.0%, tested as Salmonella Typhimurium. All isolates identified by serological testing as Salmonella Enteritidis in the microbiological study were also identified by using the multiplex PCR. The new test can be used to identify or confirm pure isolates of the two serovars and is also amenable for integration into existing culture procedures for accurate detection of Salmonella colonies.
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Affiliation(s)
- Dele Ogunremi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Susan Nadin-Davis
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Andrée Ann Dupras
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Imelda Gálvan Márquez
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Katayoun Omidi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Louise Pope
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - John Devenish
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Teresa Burke
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Ray Allain
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Daniel Leclair
- Food Safety Science Division, Floor 5, 1400 Merivale Road, Tower 2, Ottawa, Ontario, Canada K1A 0Y9
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19
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Acar S, Bulut E, Durul B, Uner I, Kur M, Avsaroglu MD, Kirmaci HA, Tel YO, Zeyrek FY, Soyer Y. Phenotyping and genetic characterization of Salmonella enterica isolates from Turkey revealing arise of different features specific to geography. Int J Food Microbiol 2017; 241:98-107. [DOI: 10.1016/j.ijfoodmicro.2016.09.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 11/25/2022]
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20
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Molecular detection assay of five Salmonella serotypes of public interest: Typhimurium, Enteritidis, Newport, Heidelberg, and Hadar. J Microbiol Methods 2016; 134:14-20. [PMID: 27993596 DOI: 10.1016/j.mimet.2016.12.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/12/2016] [Accepted: 12/12/2016] [Indexed: 01/14/2023]
Abstract
Foodborne illnesses due to Salmonella represent an important public-health concern worldwide. In the United States, a majority of Salmonella infections are associated with a small number of serotypes. Furthermore, some serotypes that are overrepresented among human disease are also associated with multi-drug resistance phenotypes. Rapid detection of serotypes of public-health concern might help reduce the burden of salmonellosis cases and limit exposure to multi-drug resistant Salmonella. We developed a two-step real-time PCR-based rapid method for the identification and detection of five Salmonella serotypes that are either overrepresented in human disease or frequently associated with multi-drug resistance, including serotypes Enteritidis, Typhimurium, Newport, Hadar, and Heidelberg. Two sets of four markers were developed to detect and differentiate the five serotypes. The first set of markers was developed as a screening step to detect the five serotypes; whereas, the second set was used to further distinguish serotypes Heidelberg, Newport and Hadar. The utilization of these markers on a two-step investigation strategy provides a diagnostic specificity of 97% for the detection of Typhimurium, Enteritidis, Heidelberg, Infantis, Newport and Hadar. The diagnostic sensitivity of the detection makers is >96%. The availability of this two-step rapid method will facilitate specific detection of Salmonella serotypes that contribute to a significant proportion of human disease and carry antimicrobial resistance.
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21
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Serogenotyping and antimicrobial susceptibility testing of Salmonella spp. isolated from retail meat samples in Lagos, Nigeria. Mol Cell Probes 2016; 30:189-194. [DOI: 10.1016/j.mcp.2016.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/22/2016] [Accepted: 04/24/2016] [Indexed: 11/24/2022]
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22
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Evaluation of Molecular Methods for Identification of Salmonella Serovars. J Clin Microbiol 2016; 54:1992-8. [PMID: 27194688 DOI: 10.1128/jcm.00262-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/10/2016] [Indexed: 11/20/2022] Open
Abstract
Classification by serotyping is the essential first step in the characterization of Salmonella isolates and is important for surveillance, source tracking, and outbreak detection. To improve detection and reduce the burden of salmonellosis, several rapid and high-throughput molecular Salmonella serotyping methods have been developed.The aim of this study was to compare three commercial kits, Salm SeroGen (Salm Sero-Genotyping AS-1 kit), Check&Trace (Check-Points), and xMAP (xMAP Salmonella serotyping assay), to the Salmonella genoserotyping array (SGSA) developed by our laboratory. They were assessed using a panel of 321 isolates that represent commonly reported serovars from human and nonhuman sources globally. The four methods correctly identified 73.8% to 94.7% of the isolates tested. The methods correctly identified 85% and 98% of the clinically important Salmonella serovars Enteritidis and Typhimurium, respectively. The methods correctly identified 75% to 100% of the nontyphoidal, broad host range Salmonella serovars, including Heidelberg, Hadar, Infantis, Kentucky, Montevideo, Newport, and Virchow. The sensitivity and specificity of Salmonella serovars Typhimurium and Enteritidis ranged from 85% to 100% and 99% to 100%, respectively.It is anticipated that whole-genome sequencing will replace serotyping in public health laboratories in the future. However, at present, it is approximately three times more expensive than molecular methods. Until consistent standards and methodologies are deployed for whole-genome sequencing, data analysis and interlaboratory comparability remain a challenge. The use of molecular serotyping will provide a valuable high-throughput alternative to traditional serotyping. This comprehensive analysis provides a detailed comparison of commercial kits available for the molecular serotyping of Salmonella.
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23
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Draft Whole-Genome Sequences of 25 Salmonella enterica Strains Representing 24 Serovars. GENOME ANNOUNCEMENTS 2016; 4:4/2/e01718-15. [PMID: 26941156 PMCID: PMC4777767 DOI: 10.1128/genomea.01718-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report the draft genome sequences of 25 Salmonella enterica strains representing 24 different serotypes, many of which were not available in public repositories during our selection process. These draft genomes will provide useful reference for the genetic variation between serotypes and aid in the development of molecular typing tools.
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24
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Zhou X, Zhang L, Shi C, Fratamico PM, Liu B, Paoli GC, Dan X, Zhuang X, Cui Y, Wang D, Shi X. Genome-Scale Screening and Validation of Targets for Identification of Salmonella enterica and Serovar Prediction. J Food Prot 2016; 79:376-83. [PMID: 26939647 DOI: 10.4315/0362-028x.jfp-15-286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Salmonella enterica is the most common foodborne pathogen worldwide, with 2,500 recognized serovars. Detection of S. enterica and its classification into serovars are essential for food safety surveillance and clinical diagnosis. The PCR method is useful for these applications because of its rapidity and high accuracy. We obtained 412 candidate detection targets for S. enterica using a comparative genomics mining approach. Gene ontology (GO) functional enrichment analysis of these candidate targets revealed that the GO term with the largest number of unigenes with known function (38 of 177, 21.5%) was significantly involved in pathogenesis (P < 10(-24)). All the candidate targets were then evaluated by PCR assays. Fifteen targets showed high specificity for the detection of S. enterica by verification with 151 S. enterica strains and 34 non-Salmonella strains. The phylogenetic trees of verified targets were highly comparable with those of housekeeping genes, especially for differentiating S. enterica strains into serovars. The serovar prediction ability was validated by sequencing one target (S9) for 39 S. enterica strains belonging to six serovars. Identical mutation sites existed in the same serovar, and different mutation sites were found in diverse serovars. Our findings revealed that 15 verified targets can be potentially used for molecular detection, and some of them can be used for serotyping of S. enterica strains.
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Affiliation(s)
- Xiujuan Zhou
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Lida Zhang
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Chunlei Shi
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Pina M Fratamico
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania 19038, USA
| | - Bin Liu
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Shaanxi Yangling, People's Republic of China
| | - George C Paoli
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania 19038, USA
| | - Xianlong Dan
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Xiaofei Zhuang
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Yan Cui
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Dapeng Wang
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Xianming Shi
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
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25
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Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VPJ, Nash JHE, Taboada EN. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PLoS One 2016; 11:e0147101. [PMID: 26800248 PMCID: PMC4723315 DOI: 10.1371/journal.pone.0147101] [Citation(s) in RCA: 320] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/29/2015] [Indexed: 11/28/2022] Open
Abstract
For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub-typing allows for continuity with historical serotyping data as we transition towards the increasing adoption of genomic analyses in epidemiology. The SISTR platform is freely available on the web at https://lfz.corefacility.ca/sistr-app/.
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Affiliation(s)
- Catherine E. Yoshida
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Peter Kruczkiewicz
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
| | - Chad R. Laing
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
| | - Erika J. Lingohr
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Victor P. J. Gannon
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
| | - John H. E. Nash
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Eduardo N. Taboada
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
- * E-mail:
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26
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Figueiredo R, Card R, Nunes C, AbuOun M, Bagnall MC, Nunez J, Mendonça N, Anjum MF, da Silva GJ. Virulence Characterization of Salmonella enterica by a New Microarray: Detection and Evaluation of the Cytolethal Distending Toxin Gene Activity in the Unusual Host S. Typhimurium. PLoS One 2015; 10:e0135010. [PMID: 26244504 PMCID: PMC4526557 DOI: 10.1371/journal.pone.0135010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/16/2015] [Indexed: 11/19/2022] Open
Abstract
Salmonella enterica is a zoonotic foodborne pathogen that causes acute gastroenteritis in humans. We assessed the virulence potential of one-hundred and six Salmonella strains isolated from food animals and products. A high through-put virulence genes microarray demonstrated Salmonella Pathogenicity Islands (SPI) and adherence genes were highly conserved, while prophages and virulence plasmid genes were variably present. Isolates were grouped by serotype, and virulence plasmids separated S. Typhimurium in two clusters. Atypical microarray results lead to whole genome sequencing (WGS) of S. Infantis Sal147, which identified deletion of thirty-eight SPI-1 genes. Sal147 was unable to invade HeLa cells and showed reduced mortality in Galleria mellonella infection model, in comparison to a SPI-1 harbouring S. Infantis. Microarray and WGS of S. Typhimurium Sal199, established for the first time in S. Typhimurium presence of cdtB and other Typhi-related genes. Characterization of Sal199 showed cdtB genes were upstream of transposase IS911, and co-expressed with other Typhi-related genes. Cell cycle arrest, cytoplasmic distension, and nuclear enlargement were detected in HeLa cells infected by Sal199, but not with S. Typhimurium LT2. Increased mortality of Galleria was detected on infection with Sal199 compared to LT2. Thus, Salmonella isolates were rapidly characterized using a high through-put microarray; helping to identify unusual virulence features which were corroborated by further characterisation. This work demonstrates that the use of suitable screening methods for Salmonella virulence can help assess the potential risk associated with certain Salmonella to humans. Incorporation of such methodology into surveillance could help reduce the risk of emergence of epidemic Salmonella strains.
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Affiliation(s)
- Rui Figueiredo
- Faculty of Pharmacy and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Roderick Card
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Carla Nunes
- Faculty of Pharmacy and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Mary C. Bagnall
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Javier Nunez
- Specialist Scientific Support, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Nuno Mendonça
- Faculty of Pharmacy and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Gabriela Jorge da Silva
- Faculty of Pharmacy and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
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27
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Yoshida C, Lingohr EJ, Trognitz F, MacLaren N, Rosano A, Murphy SA, Villegas A, Polt M, Franklin K, Kostic T, Kropinski AM, Card RM. Multi-laboratory evaluation of the rapid genoserotyping array (SGSA) for the identification of Salmonella serovars. Diagn Microbiol Infect Dis 2014; 80:185-90. [PMID: 25219780 DOI: 10.1016/j.diagmicrobio.2014.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/31/2014] [Accepted: 08/21/2014] [Indexed: 10/24/2022]
Abstract
Salmonella serotyping is an essential first step for identification of isolates associated with disease outbreaks. The Salmonella genoserotyping array (SGSA) is a microarray-based alternative to standard serotyping designed to rapidly identify 57 of the most commonly reported serovars through detection of the genes encoding surface O and H antigens and reporting the corresponding serovar in accordance with the existing White-Kaufmann-Le Minor serotyping scheme. In this study, we evaluated the SGSA at 4 laboratories in 3 countries by testing 1874 isolates from human and non-human sources. The SGSA correctly identified 96.7% of isolates from the target 57 serovars. For the prevalent and clinically important Salmonella serovars Enteritidis and Typhimurium, test specificity and sensitivity were greater than 98% and 99%, respectively. Due to its high-throughput nature, the SGSA is a rapid and cost-effective alternative to standard serotyping for identifying the most prevalent serovars of Salmonella.
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Affiliation(s)
- Catherine Yoshida
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4.
| | - Erika J Lingohr
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | | | - Nikki MacLaren
- Animal Health and Veterinary Laboratories Agency (AHVLA), New Haw, Addlestone, Surrey, United Kingdom KT15 3NB
| | - Andrea Rosano
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | - Stephanie A Murphy
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | - Andre Villegas
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | - Marlies Polt
- Austrian Institute of Technology (AIT), 3430 Tulln an der Donau, Austria
| | - Kristyn Franklin
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | - Tanja Kostic
- Austrian Institute of Technology (AIT), 3430 Tulln an der Donau, Austria
| | | | | | - Andrew M Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | - Roderick M Card
- Animal Health and Veterinary Laboratories Agency (AHVLA), New Haw, Addlestone, Surrey, United Kingdom KT15 3NB
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28
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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: 0.9] [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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29
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Strawn LK, Danyluk MD, Worobo RW, Wiedmann M. Distributions of Salmonella subtypes differ between two U.S. produce-growing regions. Appl Environ Microbiol 2014; 80:3982-91. [PMID: 24747908 PMCID: PMC4054229 DOI: 10.1128/aem.00348-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/16/2014] [Indexed: 11/20/2022] Open
Abstract
Salmonella accounts for approximately 50% of produce-associated outbreaks in the United States, several of which have been traced back to contamination in the produce production environment. To quantify Salmonella diversity and aid in identification of Salmonella contamination sources, we characterized Salmonella isolates from two geographically diverse produce-growing regions in the United States. Initially, we characterized the Salmonella serotype and subtype diversity associated with 1,677 samples collected from 33 produce farms in New York State (NYS). Among these 1,677 samples, 74 were Salmonella positive, yielding 80 unique isolates (from 147 total isolates), which represented 14 serovars and 23 different pulsed-field gel electrophoresis (PFGE) types. To explore regional Salmonella diversity associated with production environments, we collected a smaller set of samples (n = 65) from South Florida (SFL) production environments and compared the Salmonella diversity associated with these samples with the diversity found among NYS production environments. Among these 65 samples, 23 were Salmonella positive, yielding 32 unique isolates (from 81 total isolates), which represented 11 serovars and 17 different PFGE types. The most common serovars isolated in NYS were Salmonella enterica serovars Newport, Cerro, and Thompson, while common serovars isolated in SFL were Salmonella serovars Saphra and Newport and S. enterica subsp. diarizonae serovar 50:r:z. High PFGE type diversity (Simpson's diversity index, 0.90 ± 0.02) was observed among Salmonella isolates across both regions; only three PFGE types were shared between the two regions. The probability of three or fewer shared PFGE types was <0.000001; therefore, Salmonella isolates were considerably different between the two sampled regions. These findings suggest the potential for PFGE-based source tracking of Salmonella in production environments.
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Affiliation(s)
- Laura K Strawn
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Michelle D Danyluk
- Department of Food Science and Human Nutrition, Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, USA
| | - Randy W Worobo
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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30
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Baptista AAS, Donato TC, Garcia KCOD, Gonçalves GAM, Coppola MP, Okamoto AS, Sequeira JL, Andreatti Filho RL. Immune response of broiler chickens immunized orally with the recombinant proteins flagellin and the subunit B of cholera toxin associated with Lactobacillus spp. Poult Sci 2014; 93:39-45. [PMID: 24570421 DOI: 10.3382/ps.2013-03372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This study investigated the immune response of broiler chickens with oral treatment of a Lactobacillus spp. pool (PL) associated with microencapsulated recombinant proteins flagellin (FliC) and the subunit B of cholera toxin (CTB). Immune responses were evaluated by measuring IgA from intestinal fluid, serum IgY, and immunostaining of CD8(+) T lymphocytes present in the cecum. The evaluations were performed on d 0, 7, 14, 21, and 28 posttreatment. A significant increase (P < 0.05) was observed in IgA levels in all immunized groups, especially 3 wk after immunization. Treatments 2 (recombinant CTB) and 3 (recombinant FliC+CTB) showed the highest concentrations. Similarly, serum concentrations IgY (μg/mL) increased along the experiment, and the means for treatments 2 and 3 showed significant differences (P < 0.05) compared with controls, reaching concentrations of 533 and 540 μg/mL, respectively. The number of CD8(+) T lymphocytes in all treatments greatly differed (P < 0.05) compared with the negative control at 21 d posttreatment. However, only treatment 2 (recombinant CTB), 4 (PL), and 5 (recombinant FliC+ recombinant CTB + PL) remained significantly (P < 0.05) different from the control at 28 d posttreatment. Thus, it is concluded that the microencapsulated recombinant proteins administered orally to broiler chickens are capable of stimulating humoral and cellular immune response, and the combinations of these antigens with Lactobacillus spp. can influence the population of CD8(+) T cells residing in the cecum.
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Affiliation(s)
- A A S Baptista
- College of Veterinary Medicine and Animal Science, São Paulo State University, Botucatu, Sao Paulo, Brazil 18618-970
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31
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Zając M, Hoszowski A, Wasyl D. Identification of common, non-typable and autoagglutinating Salmonella strains with Premi®Test Salmonella assay. Acta Vet Hung 2013; 61:425-31. [PMID: 23974934 DOI: 10.1556/avet.2013.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Since Salmonella serotyping according to the White-Kauffmann-Le Minor scheme fails to identify rough and atypical serological variants, this study aimed at improving serovar identification with the commercially available Premi®Test Salmonella Assay. The array was validated against a set of Salmonella reference strains (n = 27) and field isolates of known serological structure (n = 112) showing up to 97.8% congruent results. Its diagnostic suitability was further verified with random field isolates (n = 52; 100% congruence). For 'rough' isolates (n = 54) and those with antigen expression failure (n = 19) the assay showed, respectively, 98.1% and 73.7% of serovar recognition. It considerably improved diagnostic capacity while typing troublesome isolates such as those failing to express flagellar antigens or showing autoagglutination. The method offers lower labour time compared to the traditional serotyping and does not require a broad range of diagnostic sera.
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Affiliation(s)
- Magdalena Zając
- 1 National Veterinary Research Institute Department of Microbiology, National Reference Laboratory for Salmonellosis Partyzantów 57 24-100 Puławy Poland
| | - Andrzej Hoszowski
- 1 National Veterinary Research Institute Department of Microbiology, National Reference Laboratory for Salmonellosis Partyzantów 57 24-100 Puławy Poland
| | - Dariusz Wasyl
- 1 National Veterinary Research Institute Department of Microbiology, National Reference Laboratory for Salmonellosis Partyzantów 57 24-100 Puławy Poland
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32
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Shi C, Singh P, Ranieri ML, Wiedmann M, Moreno Switt AI. Molecular methods for serovar determination of Salmonella. Crit Rev Microbiol 2013; 41:309-25. [PMID: 24228625 DOI: 10.3109/1040841x.2013.837862] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Salmonella is a diverse foodborne pathogen, which has more than 2600 recognized serovars. Classification of Salmonella isolates into serovars is essential for surveillance and epidemiological investigations; however, determination of Salmonella serovars, by traditional serotyping, has some important limitations (e.g. labor intensive, time consuming). To overcome these limitations, multiple methods have been investigated to develop molecular serotyping schemes. Currently, molecular methods to predict Salmonella serovars include (i) molecular subtyping methods (e.g. PFGE, MLST), (ii) classification using serovar-specific genomic markers and (iii) direct methods, which identify genes encoding antigens or biosynthesis of antigens used for serotyping. Here, we reviewed reported methodologies for Salmonella molecular serotyping and determined the "serovar-prediction accuracy", as the percentage of isolates for which the serovar was correctly classified by a given method. Serovar-prediction accuracy ranged from 0 to 100%, 51 to 100% and 33 to 100% for molecular subtyping, serovar-specific genomic markers and direct methods, respectively. Major limitations of available schemes are errors in predicting closely related serovars (e.g. Typhimurium and 4,5,12:i:-), and polyphyletic serovars (e.g. Newport, Saintpaul). The high diversity of Salmonella serovars represents a considerable challenge for molecular serotyping approaches. With the recent improvement in sequencing technologies, full genome sequencing could be developed into a promising molecular approach to serotype Salmonella.
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Affiliation(s)
- Chunlei Shi
- Department of Food Science, Cornell University , Ithaca, NY , USA and
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33
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Guo D, Liu B, Liu F, Cao B, Chen M, Hao X, Feng L, Wang L. Development of a DNA microarray for molecular identification of all 46 Salmonella O serogroups. Appl Environ Microbiol 2013; 79:3392-9. [PMID: 23524674 PMCID: PMC3648052 DOI: 10.1128/aem.00225-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/18/2013] [Indexed: 12/29/2022] Open
Abstract
Salmonella is a major cause of food-borne disease in many countries. Serotype determination of Salmonella is important for disease assessment, infection control, and epidemiological surveillance. In this study, a microarray system that targets the O antigen-specific genes was developed for simultaneously detecting and identifying all 46 Salmonella O serogroups. Of these, 40 serogroups can be confidently identified, and the remaining 6, in three pairs (serogroups O67 and B, E1 and E4, and A and D1), need to be further distinguished from each other using PCR methods or conventional serotyping methods. The microarray was shown to be highly specific when evaluated against 293 Salmonella strains, 186 Shigella strains, representative Escherichia coli strains, and 10 strains of other bacterial species. The assay correctly identified 288 (98%) of the Salmonella strains. The detection sensitivity was determined to be 50 ng genomic DNA per sample. By testing simulated samples in a tomato background, 2 to 8 CFU per gram inoculated could be detected after enrichment. This newly developed microarray assay is the first molecular protocol that can be used for the comprehensive detection and identification of all 46 Salmonella O serogroups. Compared to the traditional serogrouping method, the microarray provides a reliable, high-throughput, and sensitive approach that can be used for rapid identification of multiple Salmonella O serogroups simultaneously.
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Affiliation(s)
- Dan Guo
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
- The Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - Bin Liu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
- The Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - Fenxia Liu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
- The Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - Boyang Cao
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
- The Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA, Tianjin, People's Republic of China
- Tianjin Research Center for Functional Genomics and Biochip, TEDA, Tianjin, People's Republic of China
| | - Min Chen
- Shanghai Municipal Center For Disease Control and Prevention, Shanghai, People's Republic of China
| | - Xiyan Hao
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
- The Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - Lu Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
- The Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA, Tianjin, People's Republic of China
- Tianjin Research Center for Functional Genomics and Biochip, TEDA, Tianjin, People's Republic of China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
- The Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA, Tianjin, People's Republic of China
- Tianjin Research Center for Functional Genomics and Biochip, TEDA, Tianjin, People's Republic of China
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34
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Comparison of typing methods with a new procedure based on sequence characterization for Salmonella serovar prediction. J Clin Microbiol 2013; 51:1786-97. [PMID: 23554194 DOI: 10.1128/jcm.03201-12] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As the development of molecular serotyping approaches is critical for Salmonella spp., which include >2,600 serovars, we performed an initial evaluation of the ability to identify Salmonella serovars using (i) different molecular subtyping methods and (ii) a newly implemented combined PCR- and sequencing-based approach that directly targets O- and H-antigen-encoding genes. Initial testing was performed using 46 isolates that represent the top 40 Salmonella serovars isolated from human and nonhuman sources, as reported by the U.S. Centers for Disease Control and Prevention and the World Health Organization. Multilocus sequence typing (MLST) was able to accurately predict the serovars for 42/46 isolates and showed the best ability to predict serovars among the subtyping methods tested. Pulsed-field gel electrophoresis (PFGE), ribotyping, and repetitive extragenic palindromic sequence-based PCR (rep-PCR) were able to accurately predict the serovars for 35/46, 34/46, and 30/46 isolates, respectively. Among the methods, S. enterica subsp. enterica serovars 4,5,12:i:-, Typhimurium, and Typhimurium var. 5- were frequently not classified correctly, which is consistent with their close phylogenetic relationship. To develop a PCR- and sequence-based serotyping approach, we integrated available data sources to implement a combination PCR-based O-antigen screening and sequencing of internal fliC and fljB fragments. This approach correctly identified the serovars for 42/46 isolates in the initial set representing the most common Salmonella serovars, as well as for 54/63 isolates representing less common Salmonella serovars. Our study not only indicates that different molecular approaches show the potential to allow for rapid serovar classification of Salmonella isolates, but it also provides data that can help with the selection of molecular serotyping methods to be used by different laboratories.
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35
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Braun SD, Ziegler A, Methner U, Slickers P, Keiling S, Monecke S, Ehricht R. Fast DNA serotyping and antimicrobial resistance gene determination of salmonella enterica with an oligonucleotide microarray-based assay. PLoS One 2012; 7:e46489. [PMID: 23056321 PMCID: PMC3464306 DOI: 10.1371/journal.pone.0046489] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 09/04/2012] [Indexed: 01/21/2023] Open
Abstract
Salmonellosis caused by Salmonella (S.) belongs to the most prevalent food-borne zoonotic diseases throughout the world. Therefore, serotype identification for all culture-confirmed cases of Salmonella infection is important for epidemiological purposes. As a standard, the traditional culture method (ISO 6579:2002) is used to identify Salmonella. Classical serotyping takes 4–5 days to be completed, it is labor-intensive, expensive and more than 250 non-standardized sera are necessary to characterize more than 2,500 Salmonella serovars currently known. These technical difficulties could be overcome with modern molecular methods. We developed a microarray based serogenotyping assay for the most prevalent Salmonella serovars in Europe and North America. The current assay version could theoretically discriminate 28 O-antigens and 86 H-antigens. Additionally, we included 77 targets analyzing antimicrobial resistance genes. The Salmonella assay was evaluated with a set of 168 reference strains representing 132 serovars previously serotyped by conventional agglutination through various reference centers. 117 of 132 (81%) tested serovars showed an unique microarray pattern. 15 of 132 serovars generated a pattern which was shared by multiple serovars (e.g., S. ser. Enteritidis and S. ser. Nitra). These shared patterns mainly resulted from the high similarity of the genotypes of serogroup A and D1. Using patterns of the known reference strains, a database was build which represents the basis of a new PatternMatch software that can serotype unknown Salmonella isolates automatically. After assay verification, the Salmonella serogenotyping assay was used to identify a field panel of 105 Salmonella isolates. All were identified as Salmonella and 93 of 105 isolates (88.6%) were typed in full concordance with conventional serotyping. This microarray based assay is a powerful tool for serogenotyping.
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