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Nadin-Davis S, Pope L, Devenish J, Allain R, Ogunremi D. Evaluation of the use of CRISPR loci for discrimination of Salmonella enterica subsp. enterica serovar Enteritidis strains recovered in Canada and comparison with other subtyping methods. AIMS Microbiol 2022; 8:300-317. [PMID: 36317002 PMCID: PMC9576496 DOI: 10.3934/microbiol.2022022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/18/2022] [Accepted: 05/29/2022] [Indexed: 12/01/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Enteritidis remains one of the most important foodborne pathogens worldwide. To minimise its public health impact when outbreaks of the disease occur, timely investigation to identify and recall the contaminated food source is necessary. Central to this approach is the need for rapid and accurate identification of the bacterial subtype epidemiologically linked to the outbreak. While traditional methods of S. Enteritidis subtyping, such as pulsed field gel electrophoresis (PFGE) and phage typing (PT), have played an important role, the clonal nature of this organism has spurred efforts to improve subtyping resolution and timeliness through molecular based approaches. This study uses a cohort of 92 samples, recovered from a variety of sources, to compare these two traditional methods for S. Enteritidis subtyping with recently developed molecular techniques. These latter methods include the characterisation of two clustered regularly interspaced short palindromic repeats (CRISPR) loci, either in isolation or together with sequence analysis of virulence genes such as fimH. For comparison, another molecular technique developed in this laboratory involved the scoring of 60 informative single nucleotide polymorphisms (SNPs) distributed throughout the genome. Based on both the number of subtypes identified and Simpson's index of diversity, the CRISPR method was the least discriminatory and not significantly improved with the inclusion of fimH gene sequencing. While PT analysis identified the most subtypes, the SNP-PCR process generated the greatest index of diversity value. Combining methods consistently improved the number of subtypes identified, with the SNP/CRISPR typing scheme generating a level of diversity comparable with that of PT/PFGE. While these molecular methods, when combined, may have significant utility in real-world situations, this study suggests that CRISPR analysis alone lacks the discriminatory capability required to support investigations of foodborne disease outbreaks.
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Affiliation(s)
| | | | | | | | - Dele Ogunremi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
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KARAGÖZ A, ALTINTAŞ L, ARSLANTAŞ T, TUTUN H, KOÇAK N, ALTINTAŞ Ö. Phenotypic and molecular characterization of Salmonella Enteritidis isolates. ANKARA ÜNIVERSITESI VETERINER FAKÜLTESI DERGISI 2020. [DOI: 10.33988/auvfd.691746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Ziebell K, Chui L, King R, Johnson S, Boerlin P, Johnson RP. Subtyping of Canadian isolates of Salmonella Enteritidis using Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) alone and in combination with Pulsed-Field Gel Electrophoresis (PFGE) and phage typing. J Microbiol Methods 2017; 139:29-36. [PMID: 28456552 DOI: 10.1016/j.mimet.2017.04.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 10/19/2022]
Abstract
Salmonella enterica subspecies enterica serovar Enteritidis (SE) is one of the most common causes of human salmonellosis and in Canada currently accounts for over 40% of human cases. Reliable subtyping of isolates is required for outbreak detection and source attribution. However, Pulsed-Field Gel Electrophoresis (PFGE), the current standard subtyping method for Salmonella spp., is compromised by the high genetic homogeneity of SE. Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) was introduced to supplement PFGE, although there is a lack of data on the ability of MLVA to subtype Canadian isolates of SE. Three subtyping methods, PFGE, MLVA and phage typing were compared for their discriminatory power when applied to three panels of Canadian SE isolates: Panel 1: 70 isolates representing the diversity of phage types (PTs) and PFGE subtypes within these PTs; Panel 2: 214 apparently unrelated SE isolates of the most common PTs; and Panel 3: 27 isolates from 10 groups of epidemiologically related strains. For Panel 2 isolates, four MLVA subtypes were shared among 74% of unrelated isolates and in Panel 3 isolates, one MLVA subtype accounted for 62% of the isolates. For all panels, combining results from PFGE, MLVA and PT gave the best discrimination, except in Panel 1, where the combination of PT and PFGE was equally as high, due to the selection criteria for this panel. However, none of these methods is sufficiently discriminatory alone for reliable outbreak detection or source attribution, and must be applied together to achieve sufficient discrimination for practical purposes. Even then, some large clusters were not differentiated adequately. More discriminatory methods are required for reliable subtyping of this genetically highly homogeneous serovar. This need will likely be met by whole genome sequence analysis given the recent promising reports and as more laboratories implement this tool for outbreak response and surveillance.
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Affiliation(s)
- Kim Ziebell
- National Microbiology Laboratory at Guelph, PHAC, Guelph, ON, Canada
| | - Linda Chui
- Alberta Provincial Laboratory for Public Health, Edmonton, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Robin King
- Alberta Agriculture and Forestry, Edmonton, AB, Canada
| | - Suzanne Johnson
- National Microbiology Laboratory at Guelph, PHAC, Guelph, ON, Canada
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Roger P Johnson
- National Microbiology Laboratory at Guelph, PHAC, Guelph, ON, Canada.
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Development of a new molecular subtyping tool for Salmonella enterica serovar Enteritidis based on single nucleotide polymorphism genotyping using PCR. J Clin Microbiol 2014; 52:4275-85. [PMID: 25297333 DOI: 10.1128/jcm.01410-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The lack of a sufficiently discriminatory molecular subtyping tool for Salmonella enterica serovar Enteritidis has hindered source attribution efforts and impeded regulatory actions required to disrupt its food-borne transmission. The underlying biological reason for the ineffectiveness of current molecular subtyping tools such as pulsed-field gel electrophoresis (PFGE) and phage typing appears to be related to the high degree of clonality of S. Enteritidis. By interrogating the organism's genome, we previously identified single nucleotide polymorphisms (SNP) distributed throughout the chromosome and have designed a highly discriminatory PCR-based SNP typing test based on 60 polymorphic loci. The application of the SNP-PCR method to DNA samples from S. Enteritidis strains (n = 55) obtained from a variety of sources has led to the differentiation and clustering of the S. Enteritidis isolates into 12 clades made up of 2 to 9 isolates per clade. Significantly, the SNP-PCR assay was able to further differentiate predominant PFGE types (e.g., XAI.0003) and phage types (e.g., phage type 8) into smaller subsets. The SNP-PCR subtyping test proved to be an accurate, precise, and quantitative tool for evaluating the relationships among the S. Enteritidis isolates tested in this study and should prove useful for clustering related S. Enteritidis isolates involved in outbreaks.
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Zheng J, Pettengill J, Strain E, Allard MW, Ahmed R, Zhao S, Brown EW. Genetic diversity and evolution of Salmonella enterica serovar Enteritidis strains with different phage types. J Clin Microbiol 2014; 52:1490-500. [PMID: 24574287 PMCID: PMC3993623 DOI: 10.1128/jcm.00051-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 02/18/2014] [Indexed: 11/20/2022] Open
Abstract
Phage typing has been used for the epidemiological surveillance of Salmonella enterica serovar Enteritidis for over 2 decades. However, knowledge of the genetic and evolutionary relationships between phage types is very limited, making differences difficult to interpret. Here, single nucleotide polymorphisms (SNPs) identified from whole-genome comparisons were used to determine the relationships between some S. Enteritidis phage types (PTs) commonly associated with food-borne outbreaks in the United States. Emphasis was placed on the predominant phage types PT8, PT13a, and PT13 in North America. With >89,400 bp surveyed across 98 S. Enteritidis isolates representing 14 distinct phage types, 55 informative SNPs were discovered within 23 chromosomally anchored loci. To maximize the discriminatory and evolutionary partitioning of these highly homogeneous strains, sequences comprising informative SNPs were concatenated into a single combined data matrix and subjected to phylogenetic analysis. The resultant phylogeny allocated most S. Enteritidis isolates into two distinct clades (clades I and II) and four subclades. Synapomorphic (shared and derived) sets of SNPs capable of distinguishing individual clades/subclades were identified. However, individual phage types appeared to be evolutionarily disjunct when mapped to this phylogeny, suggesting that phage typing may not be valid for making phylogenetic inferences. Furthermore, the set of SNPs identified here represents useful genetic markers for strain differentiation of more clonal S. Enteritidis strains and provides core genotypic markers for future development of a SNP typing scheme with S. Enteritidis.
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Affiliation(s)
- Jie Zheng
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - James Pettengill
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Errol Strain
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Rafiq Ahmed
- National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, Winnipeg, MB, Canada
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Eric W. Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
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Scientific Opinion on the evaluation of molecular typing methods for major food‐borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications). EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3502] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Dewaele I, Heyndrickx M, Rasschaert G, Bertrand S, Wildemauwe C, Wattiau P, Imberechts H, Herman L, Ducatelle R, Van Weyenberg S, De Reu K. Phage and MLVA Typing ofSalmonellaEnteritidis Isolated from Layers and Humans in Belgium from 2000-2010, A Period in which Vaccination of Laying Hens was Introduced. Zoonoses Public Health 2013; 61:398-404. [DOI: 10.1111/zph.12084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Indexed: 11/26/2022]
Affiliation(s)
- I. Dewaele
- Institute for Agricultural and Fisheries Research (ILVO); Technology and Food Science Unit; Melle Belgium
| | - M. Heyndrickx
- Institute for Agricultural and Fisheries Research (ILVO); Technology and Food Science Unit; Melle Belgium
- Faculty of Veterinary Medicine; Department of Pathology, Bacteriology and Poultry Diseases; Ghent University; Merelbeke Belgium
| | - G. Rasschaert
- Institute for Agricultural and Fisheries Research (ILVO); Technology and Food Science Unit; Melle Belgium
| | - S. Bertrand
- National Reference Centre for Salmonella and Shigella; Bacterial Diseases Division; Scientific Institute of Public Health (IPH); Brussels Belgium
| | - C. Wildemauwe
- National Reference Centre for Salmonella and Shigella; Bacterial Diseases Division; Scientific Institute of Public Health (IPH); Brussels Belgium
| | - P. Wattiau
- Veterinary and Agrochemical Research Centre (CODA-CERVA); Brussels Belgium
| | - H. Imberechts
- Veterinary and Agrochemical Research Centre (CODA-CERVA); Brussels Belgium
| | - L. Herman
- Institute for Agricultural and Fisheries Research (ILVO); Technology and Food Science Unit; Melle Belgium
| | - R. Ducatelle
- Faculty of Veterinary Medicine; Department of Pathology, Bacteriology and Poultry Diseases; Ghent University; Merelbeke Belgium
| | - S. Van Weyenberg
- Institute for Agricultural and Fisheries Research (ILVO); Technology and Food Science Unit; Melle Belgium
| | - K. De Reu
- Institute for Agricultural and Fisheries Research (ILVO); Technology and Food Science Unit; Melle Belgium
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Ngoi ST, Thong KL. Molecular characterization showed limited genetic diversity among Salmonella Enteritidis isolated from humans and animals in Malaysia. Diagn Microbiol Infect Dis 2013; 77:304-11. [PMID: 24139970 DOI: 10.1016/j.diagmicrobio.2013.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 09/08/2013] [Accepted: 09/08/2013] [Indexed: 11/25/2022]
Abstract
Salmonella enterica serovar Enteritidis (S. Enteritidis) is the most common causative agent of non-typhoidal salmonellosis in Malaysia. We aimed to characterize S. Enteritidis isolated from humans and animals by analyzing their antimicrobial resistance profiles and genotypes. A total of 111 strains were characterized using multiple-locus variable-number tandem repeat analysis, pulsed-field gel electrophoresis, and antimicrobial susceptibility testing. Both typing methods revealed that genetically similar S. Enteritidis strains had persisted among human and animal populations within the period of study (2003-2008). Only 39% of the strains were multi-drug resistant (i.e., resistant to 3 or more classes of antimicrobial agents), with a majority (73%) of these in low-risk phase (multiple antibiotic resistant index <0.20). Limited genetic diversity among clinical and zoonotic S. Enteritidis suggested that animals are possible sources of human salmonellosis. The degree of multi-drug resistance among the strains was generally low during the study period.
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Affiliation(s)
- Soo Tein Ngoi
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; Laboratory of Biomedical Science and Molecular Microbiology, Institute of Graduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Dewaele I, Rasschaert G, Bertrand S, Wildemauwe C, Wattiau P, Imberechts H, Herman L, Ducatelle R, De Reu K, Heyndrickx M. Molecular characterization of Salmonella Enteritidis: comparison of an optimized multi-locus variable-number of tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis. Foodborne Pathog Dis 2013; 9:885-95. [PMID: 23035725 DOI: 10.1089/fpd.2012.1199] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Salmonella Enteritidis (SE) is a genetically homogenous serovar, which makes optimal subtype discrimination crucial for epidemiological research. This study describes the development and evaluation of an optimized multiple-locus variable number tandem-repeat assay (MLVA) for characterization of SE. The typeability and discriminatory power of this MLVA was determined on a selected collection of 60 SE isolates and compared with pulsed-field gel electrophoresis (PFGE) using restriction enzymes XbaI, NotI, or SfiI. In addition, the estimated Wallace coefficient (W) was calculated to assess the congruence of the typing methods. Selection of epidemiologically unrelated isolates and more related isolates (originating from layer farms) was also based on the given phage type (PT). When targeting six loci, MLVA generated 16 profiles, while PFGE produced 10, 9, and 16 pulsotypes using XbaI, NotI, and SfiI, respectively, for the entire strain collection. For the epidemiologically unrelated isolates, MLVA had the highest discriminatory power and showed good discrimination between isolates from different layer farms and among isolates from the same layer farm. MLVA performed together with PT showed higher discriminatory power compared to PFGE using one restriction enzyme together with PT. Results showed that combining PT with the optimized MLVA presented here provides a rapid typing tool with good discriminatory power for characterizing SE isolates of various origins and isolates originating from the same layer farm.
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Affiliation(s)
- Isabelle Dewaele
- Technology and Food Science Unit, Institute for Agricultural and Fisheries Research, Melle, Belgium
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Allard MW, Luo Y, Strain E, Pettengill J, Timme R, Wang C, Li C, Keys CE, Zheng J, Stones R, Wilson MR, Musser SM, Brown EW. On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004. PLoS One 2013; 8:e55254. [PMID: 23383127 PMCID: PMC3559427 DOI: 10.1371/journal.pone.0055254] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/21/2012] [Indexed: 12/20/2022] Open
Abstract
Facile laboratory tools are needed to augment identification in contamination events to trace the contamination back to the source (traceback) of Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis). Understanding the evolution and diversity within and among outbreak strains is the first step towards this goal. To this end, we collected 106 new S. Enteriditis isolates within S. Enteriditis Pulsed-Field Gel Electrophoresis (PFGE) pattern JEGX01.0004 and close relatives, and determined their genome sequences. Sources for these isolates spanned food, clinical and environmental farm sources collected during the 2010 S. Enteritidis shell egg outbreak in the United States along with closely related serovars, S. Dublin, S. Gallinarum biovar Pullorum and S. Gallinarum. Despite the highly homogeneous structure of this population, S. Enteritidis isolates examined in this study revealed thousands of SNP differences and numerous variable genes (n = 366). Twenty-one of these genes from the lineages leading to outbreak-associated samples had nonsynonymous (causing amino acid changes) changes and five genes are putatively involved in known Salmonella virulence pathways. While chromosome synteny and genome organization appeared to be stable among these isolates, genome size differences were observed due to variation in the presence or absence of several phages and plasmids, including phage RE-2010, phage P125109, plasmid pSEEE3072_19 (similar to pSENV), plasmid pOU1114 and two newly observed mobile plasmid elements pSEEE1729_15 and pSEEE0956_35. These differences produced modifications to the assembled bases for these draft genomes in the size range of approximately 4.6 to 4.8 mbp, with S. Dublin being larger (∼4.9 mbp) and S. Gallinarum smaller (4.55 mbp) when compared to S. Enteritidis. Finally, we identified variable S. Enteritidis genes associated with virulence pathways that may be useful markers for the development of rapid surveillance and typing methods, potentially aiding in traceback efforts during future outbreaks involving S. Enteritidis PFGE pattern JEGX01.0004.
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Affiliation(s)
- Marc W Allard
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America.
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