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Liu CC, Hsiao WWL. Large-scale comparative genomics to refine the organization of the global Salmonella enterica population structure. Microb Genom 2022; 8:mgen000906. [PMID: 36748524 PMCID: PMC9837569 DOI: 10.1099/mgen.0.000906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The White-Kauffmann-Le Minor (WKL) scheme is the most widely used Salmonella typing scheme for reporting the disease prevalence of the enteric pathogen. With the advent of whole-genome sequencing (WGS), in silico methods have increasingly replaced traditional serotyping due to reproducibility, speed and coverage. However, despite integrating genomic-based typing by in silico serotyping tools such as SISTR, in silico serotyping in certain contexts remains ambiguous and insufficiently informative. Specifically, in silico serotyping does not attempt to resolve polyphyly. Furthermore, in spite of the widespread acknowledgement of polyphyly from genomic studies, the prevalence of polyphyletic serovars is not well characterized. Here, we applied a genomics approach to acquire the necessary resolution to classify genetically discordant serovars and propose an alternative typing scheme that consistently reflect natural Salmonella populations. By accessing the unprecedented volume of bacterial genomic data publicly available in GenomeTrakr and PubMLST databases (>180 000 genomes representing 723 serovars), we characterized the global Salmonella population structure and systematically identified putative non-monophyletic serovars. The proportion of putative non-monophyletic serovars was estimated higher than previous reports, reinforcing the inability of antigenic determinants to depict the complexity of Salmonella evolutionary history. We explored the extent of genetic diversity masked by serotyping labels and found significant intra-serovar molecular differences across many clinically important serovars. To avoid false discovery due to incorrect in silico serotyping calls, we cross-referenced reported serovar labels and concluded a low error rate in in silico serotyping. The combined application of clustering statistics and genome-wide association methods demonstrated effective characterization of stable bacterial populations and explained functional differences. The collective methods adopted in our study have practical values in establishing genomic-based typing nomenclatures for an entire microbial species or closely related subpopulations. Ultimately, we foresee an improved typing scheme to be a hybrid that integrates both genomic and antigenic information such that the resolution from WGS is leveraged to improve the precision of subpopulation classification while preserving the common names defined by the WKL scheme.
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Affiliation(s)
- Chao Chun Liu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - William W. L. Hsiao
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada,*Correspondence: William W. L. Hsiao,
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2
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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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3
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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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4
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Nadin-Davis S, Pope L, Chmara J, Duceppe MO, Burke T, Devenish J, Andrievskaia O, Allain R, Ogunremi D. An Unusual Salmonella Enteritidis Strain Carrying a Modified Virulence Plasmid Lacking the prot6e Gene Represents a Geographically Widely Distributed Lineage. Front Microbiol 2020; 11:1322. [PMID: 32625191 PMCID: PMC7311658 DOI: 10.3389/fmicb.2020.01322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/25/2020] [Indexed: 12/02/2022] Open
Abstract
This study identifies a strain of Salmonella enterica subspecies enterica serovar Enteritidis that harbors a highly unusual virulence plasmid. During the characterisation of a group of S. Enteritidis isolates, 10 isolates recovered from Canadian duck production facilities, of which seven were phage type 9b and three were closely related atypical phage types, failed detection by a PCR targeting the prot6e gene, a marker located on the virulence plasmid often employed for identification of this serovar. Comparison to prot6e+ isolates by several standard genetic typing tools, further revealed their distinctive genomic makeup. Both short read and long read whole genome sequencing were completed on six of these isolates. In addition to loss of the prot6e gene, the virulence plasmid of each isolate was found to be exceptionally large (86.5 Kb) due to a 28 Kb insertion of S. Typhimurium plasmid sequence that encodes multiple genes of the incF operon. Interrogation of the chromosome sequence data of these isolates using a SNP-based typing tool and MLST both indicated their close genetic relatedness. One additional isolate carrying this plasmid was identified in an in-house collection of S. Enteritidis isolates. Finally, the identification of this unusual plasmid sequence in additional isolates submitted to public repositories of Salmonella sequence data was explored. All these analyses indicated that a very distinctive but rarely reported strain of S. Enteritidis was widely distributed across North America and the United Kingdom with one additional report involving a case from Brazil. With increased use of genetic methods for Salmonella identification, the loss of the prot6e sequence may confound correct identification of this serovar while also potentially altering the mode of transmission to humans given the gene’s role in facilitating propagation of this bacterium in eggs. Accordingly, this strain may present certain challenges with respect to public health investigations. Our studies also suggest this strain is often associated with duck hosts thereby providing a possible mechanism by which this strain has spread over an extensive geographical area.
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Affiliation(s)
- Susan Nadin-Davis
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Louise Pope
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Chmara
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Marc-Olivier Duceppe
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Teresa Burke
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Devenish
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Olga Andrievskaia
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Ray Allain
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Dele Ogunremi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
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5
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Kim S, Kim SH, Rahman M, Kim J. Characterization of a Salmonella Enteritidis bacteriophage showing broad lytic activity against Gram-negative enteric bacteria. J Microbiol 2018; 56:917-925. [PMID: 30361974 DOI: 10.1007/s12275-018-8310-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/16/2018] [Accepted: 08/28/2018] [Indexed: 01/03/2023]
Abstract
In this study, we sought to isolate Salmonella Enteritidis-specific lytic bacteriophages (phages), and we found a lytic phage that could lyse not only S. Enteritidis but also other Gramnegative foodborne pathogens. This lytic phage, SS3e, could lyse almost all tested Salmonella enterica serovars as well as other enteric pathogenic bacteria including Escherichia coli, Shigella sonnei, Enterobacter cloacae, and Serratia marcescens. This SS3e phage has an icosahedral head and a long tail, indicating belong to the Siphoviridae. The genome was 40,793 base pairs, containing 58 theoretically determined open reading frames (ORFs). Among the 58 ORFs, ORF49, and ORF25 showed high sequence similarity with tail spike protein and lysozyme-like protein of Salmonella phage SE2, respectively, which are critical proteins recognizing and lysing host bacteria. Unlike SE2 phage whose host restricted to Salmonella enterica serovars Enteritidis and Gallinarum, SS3e showed broader host specificity against Gram-negative enteric bacteria; thus, it could be a promising candidate for the phage utilization against various Gram-negative bacterial infection including foodborne pathogens.
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Affiliation(s)
- Shukho Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea
| | - Sung-Hun Kim
- CJ CheilJedang Research Institute of Biotechnology, Suwon, 16495, Republic of Korea
| | - Marzia Rahman
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea.,Present address: Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Jungmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea.
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MANDILARA G, VASSALOS CM, CHRISOSTOMOU A, KARADIMAS K, MATHIOUDAKI E, GEORGAKOPOULOU T, TSIODRAS S, MELLOU K. A severe gastroenteritis outbreak of Salmonella enterica serovar Enteritidis PT8, with PFGE profile XbaI.0024 and MLVA profile 2-9-7-3-2 following a christening reception, Greece, 2016. Epidemiol Infect 2018; 146:28-36. [PMID: 29198195 PMCID: PMC9134529 DOI: 10.1017/s0950268817002667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/18/2017] [Accepted: 11/03/2017] [Indexed: 11/05/2022] Open
Abstract
In June 2016, a Salmonella enterica serovar Enteritidis outbreak (n = 56) occurred after a christening reception in Central Greece, mainly affecting previously healthy adults; one related death caused media attention. Patients suffered from profuse diarrhoea, fever and frequent vomiting episodes requiring prolonged hospitalisation and sick leave from work, with a 54% hospital admission rate. The majority of cases experienced serious illness within <12 h of attending the party. We investigated the outbreak to identify the source(s) of infection and contributing factors to the disease severity. From the retrospective cohort study, the cheesy penne pasta was the most likely vehicle of infection (relative risk 7·8; 95% confidence interval 3·6-16·8), explaining 79% of the cases. S. enterica ser. Enteritidis isolates were typed as phage-type PT8, pulsed-field gel electrophoresis type XbaI.0024, multiple locus variable-number tandem repeat analysis-type 2-9-7-3-2. The strain did not share the single-nucleotide polymorphism address of the concurrent European S. enterica ser. Enteritidis PT8 outbreak clusters. Following five consecutive years with no documented S. enterica ser. Enteritidis outbreaks in Greece, this outbreak, likely associated with a virulent strain, prompted actions towards the enhancement of the national Salmonella molecular surveillance and control programmes including the intensification of training of food handlers for preventing similar outbreaks in the future. Advanced molecular techniques were useful in distinguishing unrelated outbreak strains.
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Affiliation(s)
- G. MANDILARA
- National Reference Centre for Salmonella, National School of Public Health, Central Public Health Laboratory/Hellenic Centre for Disease Control and Prevention, Vari, Attica, Greece
| | - C. M. VASSALOS
- European Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control, Stockholm, Sweden; Greek Health System, Athens, Greece
| | - A. CHRISOSTOMOU
- Hellenic Centre for Disease Control and Prevention, Athens, Greece
| | - K. KARADIMAS
- National Reference Centre for Salmonella, National School of Public Health, Central Public Health Laboratory/Hellenic Centre for Disease Control and Prevention, Vari, Attica, Greece
| | - E. MATHIOUDAKI
- Food Unit, Department of Microbiology, Central Public Health Laboratory, Vari, Attica, Greece
| | | | - S. TSIODRAS
- Department of Internal Medicine, Atticon University Hospital, National and Kapodistrian University of Athens, Greece
| | - K. MELLOU
- Hellenic Centre for Disease Control and Prevention, Athens, Greece
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7
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Ayala D, Nightingale K, Narvaez-Bravo C, Brashears MM. Molecular Characterization of Salmonella from Beef Carcasses and Fecal Samples from an Integrated Feedlot and Abattoir in Mexico. J Food Prot 2017; 80:1964-1972. [PMID: 29130766 DOI: 10.4315/0362-028x.jfp-17-157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nontyphoid Salmonella strains are some of the leading causes of foodborne illnesses worldwide; however, there is very limited information on the presence and characteristics of Salmonella in the food production chain in developing countries. In this study, pulsed-field gel electrophoresis (PFGE) was used for molecular subtyping and for monitoring the ecology and transmission of Salmonella isolates in a slaughter facility in Mexico in an attempt to determine specific steps that need to be improved to reduce Salmonella contamination in beef carcasses. A total of 94 isolates from a Salmonella stock culture collection originally obtained from a single vertically integrated feedlot and beef abattoir in Mexico were analyzed. A total of 26 unique PFGE patterns were identified, 38.5% of them corresponding to a single serotype. High concordance (88.4%) was found between serotype and PFGE banding subtype. Salmonella Kentucky and Salmonella Give were the most clonal subtypes in this study, and Salmonella Muenster was the most diverse, with 11 banding patterns identified. A total of 73.7, 70.6, and 85.7% of the PFGE subtypes identified from preevisceration, precooler, and chilled carcasses, respectively, were identified only at those specific points and not at any previous or subsequent steps of the slaughter process, suggesting that each step is in itself a source of Salmonella contamination. Salmonella Mbandaka was more likely to be recovered from feces than from any of the steps of the slaughter process. The genetic diversity and distribution of PFGE subtypes in the processing facility highlight the need to implement antimicrobial interventions and improve sanitation procedures at various points to avoid further Salmonella dissemination into the meat supply.
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Affiliation(s)
- Diana Ayala
- 1 International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Box 42141, Lubbock, Texas 79409, USA; and
| | - Kendra Nightingale
- 1 International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Box 42141, Lubbock, Texas 79409, USA; and
| | - Claudia Narvaez-Bravo
- 2 Department of Food Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Mindy M Brashears
- 1 International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Box 42141, Lubbock, Texas 79409, USA; and
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8
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Epidemiological Analysis Using Pulsed-Field Gel Electrophoresis of Salmonella enteritidis Outbreak in Factory Workers. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.14144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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9
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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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10
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Kjeldsen MK, Torpdahl M, Pedersen K, Nielsen EM. Development and comparison of a generic multiple-locus variable-number tandem repeat analysis with pulsed-field gel electrophoresis for typing of Salmonella enterica subsp. enterica. J Appl Microbiol 2016; 119:1707-17. [PMID: 26440858 DOI: 10.1111/jam.12965] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/10/2015] [Accepted: 09/17/2015] [Indexed: 11/28/2022]
Abstract
AIMS Salmonella enterica subsp. enterica causes salmonellosis in humans and animals. Serovar-specific multiple-locus variable-number tandem repeat analysis (MLVA) is widely used for Salmonella surveillance; however, isolates have to be serotyped prior to MLVA typing and only the most common serovars can be typed. We developed a MLVA scheme for high-discriminatory typing of Salmonella. METHODS AND RESULTS Sixty-six unique VNTRs were investigated and the polymorphisms of seven promising VNTRs were evaluated with a panel 163 diverse isolates of 14 serotypes of significance for human health. Five VNTRs were selected for MLVA analysis. The discriminatory power was evaluated within serovars by 163 isolates and MLVA yielded 79 genotypes (DI of 0·9790) and pulsed-field gel electrophoresis (PFGE) revealed 87 genotypes (DI of 0·9989). MLVA divided each serotype into 2-8 different profiles and identified six pairs of outbreak-related strains. CONCLUSIONS The technique showed a high-discriminatory power within most serotypes comparable with or better than that of PFGE. SIGNIFICANCE AND IMPACT OF THE STUDY This MLVA assay makes it possible to use a single typing method for Salmonella surveillance and outbreak investigations. This allows inexpensive and fast surveillance for laboratories without resources for both serotyping and molecular typing, e.g. PFGE or sequence-based methods, and thereby improve the effectiveness of epidemiological investigations of Salmonella infections globally.
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Affiliation(s)
- M K Kjeldsen
- The Unit for Foodborne Infections, Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.,National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - M Torpdahl
- The Unit for Foodborne Infections, Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - K Pedersen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - E M Nielsen
- The Unit for Foodborne Infections, Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
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11
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Papadopoulos T, Petridou E, Zdragas A, Mandilara G, Nair S, Peters T, Chattaway M, de Pinna E, Passiotou M, Vatopoulos A. Comparative study of all Salmonella enterica serovar Enteritidis strains isolated from food and food animals in Greece from 2008 to 2010 with clinical isolates. Eur J Clin Microbiol Infect Dis 2016; 35:741-6. [PMID: 26864044 DOI: 10.1007/s10096-016-2591-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 01/18/2016] [Indexed: 12/25/2022]
Abstract
The aim of the present work was to study the epidemiology of Salmonella enterica serovar Enteritidis (S. Enteritidis) in Greece, comparing all the food and food animal isolates during a 3-year period with clinical isolates. Submission of the generated data to the PulseNet Europe database was carried out in order to study the population structure of this particular serovar and indicate possible connections with European strains. One hundred and sixty-eight (168) S. Enteritidis strains of human, animal, and food origin, isolated during the period 2008-2010 in Greece, were studied. Strains were characterized by phenotypic (antibiotic resistance) and molecular [pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST)] methods. PFGE revealed 39 XbaI, 48 BlnI, and 80 XbaI-BlnI distinct pulsotypes, suggesting several clones circulating through the food chain and multiple sources of transmission. Submission to the PulseNet Europe database indicated that PFGE profile SENTXB.0001, the most common PFGE profile in Europe, was also predominant in Greece (33.3 %). MLST showed that all the strains studied shared the same sequence type (ST11), representing the most common ST in Europe. High rates of resistance to nalidixic acid were observed among human and poultry isolates (~25 %), indicating the potential fluoroquinolone treatment failure. Our data suggest that strains originating from multiple reservoirs circulated in Greece through the food chain during the study period. Predominant profiles in Greece were common to PulseNet Europe profiles, indicating similarities between the S. Enteritidis populations in Greece and Europe.
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Affiliation(s)
- T Papadopoulos
- Laboratory of Microbiology, School of Veterinary Medicine, Aristotle University, AUTH Campus, 54124, Thessaloniki, Greece.
| | - E Petridou
- Laboratory of Microbiology, School of Veterinary Medicine, Aristotle University, AUTH Campus, 54124, Thessaloniki, Greece
| | - A Zdragas
- Veterinary Research Institute of Thessaloniki, National Agricultural Research Foundation, NAGREF Campus, 57001, Thermi, Greece
| | - G Mandilara
- National Reference Centre for Salmonella, National School of Public Health & Central Public Health Laboratory, Hellenic Centre of Disease Control and Prevention, 16672, Vari, Greece
| | - S Nair
- Salmonella Reference Service, Public Health England, Colindale, London, NW9 5EQ, UK
| | - T Peters
- Salmonella Reference Service, Public Health England, Colindale, London, NW9 5EQ, UK
| | - M Chattaway
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, NW9 5EQ, UK
| | - E de Pinna
- Salmonella Reference Service, Public Health England, Colindale, London, NW9 5EQ, UK
| | - M Passiotou
- Veterinary Laboratory of Chalkis, Veterinary National Reference Laboratory for Salmonella, 34100, Chalkis, Greece
| | - A Vatopoulos
- National Reference Centre for Salmonella, National School of Public Health & Central Public Health Laboratory, Hellenic Centre of Disease Control and Prevention, 16672, Vari, Greece
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12
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Complete Genome and Plasmid Sequences of Three Canadian Strains of Salmonella enterica subsp. enterica Serovar Enteritidis Belonging to Phage Types 8, 13, and 13a. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01017-15. [PMID: 26404595 PMCID: PMC4582571 DOI: 10.1128/genomea.01017-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Salmonella enterica subsp. enterica serovar Enteritidis is a prominent cause of human salmonellosis frequently linked to poultry products. In Canada, S. Enteritidis phage types 8, 13, and 13a predominate among both clinical and poultry isolates. Here, we report the complete genome and plasmid sequences of poultry isolates of these three phage types.
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13
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De Cesare A, Krishnamani K, Parisi A, Ricci A, Luzzi I, Barco L, Lucchi A, Miccolupo A, Manfreda G. Comparison between Salmonella enterica Serotype Enteritidis Genotyping Methods and Phage Type. J Clin Microbiol 2015; 53:3021-31. [PMID: 26135859 PMCID: PMC4540901 DOI: 10.1128/jcm.01122-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/21/2015] [Indexed: 11/20/2022] Open
Abstract
A quantitative comparison between discriminatory indexes and concordance among multilocus variable-number tandem-repeat analysis (MLVA), pulsed-field gel electrophoresis (PFGE), automated ribotyping, and phage typing has been performed, testing 238 Salmonella enterica serotype Enteritidis isolates not epidemiologically correlated. The results show that MLVA is the best choice, but each typing method provides a piece of information for establishing clonal relationships between the isolates.
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Affiliation(s)
| | | | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Putignano, Bari, Italy
| | - Antonia Ricci
- OIE/National Reference Laboratory for Salmonella-Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Ida Luzzi
- Istituto Superiore di Sanità, Rome, Italy
| | - Lisa Barco
- OIE/National Reference Laboratory for Salmonella-Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, Ozzano dell'Emilia, Italy
| | - Angela Miccolupo
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Putignano, Bari, Italy
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, Ozzano dell'Emilia, Italy
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Evaluation of a Salmonella Enteritidis vaccine and related ELISA for respective induction and assessment of acquired immunity to the vaccine and/or Echinacea purpurea in Awassi Ewes. Vaccine 2015; 33:2228-2231. [PMID: 25820070 DOI: 10.1016/j.vaccine.2015.03.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/12/2015] [Indexed: 11/22/2022]
Abstract
The aim of this study was to evaluate an experimental Salmonella Enteritidis (SE) bacterin and an indirect ELISA system to assess quantitatively the acquired immunity in Awassi ewes to the vaccine and/or Echinacea purpurea (EP) dried roots. Four treatments of the ewes were included in the experimental design, with 6 ewes/treatment. The first treatment (T1) had the controls that were non-vaccinated and non-treated with EP. The T2 ewes were only treated with EP. The T3 and T4 ewes were vaccinated at D1 (initiation of trial) and D10, while the T4 ewes were additionally administered the EP dried roots. Blood was collected from the jugular vein of all ewes at D1, D10, D21 and D45. The construction of the vaccine and the ELISA are detailed within the manuscript. The ELISA was able to detect quantitatively the significant acquired primary and secondary immunity to the vaccine in T3 and T4 ewes, compared to their low level of background immunities at initiation of the experiment (p<0.05). In addition, the ELISA detected the absence of seroconversion at all blood sampling times (p>0.05) in T1 control ewes, and in the T2 ewes that were given only the (EP) (p>0.05). Moreover, the ELISA was able to uncover the significant seroconversion of secondary immune response in T4 ewes at D21 compared to that at D10 (p<0.05), and the absence of significant seroconversion of secondary response in T3 ewes. This is the first work in literature that reports the need to supplement the vaccination by the experimental SE bacterin with daily oral intake of 250mg of EP-dried roots, effective the first vaccination day and up to 21 days, for obtaining a statistically significant seroconversion.
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Byrne L, Fisher I, Peters T, Mather A, Thomson N, Rosner B, Bernard H, McKeown P, Cormican M, Cowden J, Aiyedun V, Lane C. A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012. ACTA ACUST UNITED AC 2014; 19:6-13. [PMID: 25138971 DOI: 10.2807/1560-7917.es2014.19.31.20866] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In November 2011, the presence of Salmonella Newport in a ready-to-eat watermelon slice was confirmed as part of a local food survey in England. In late December 2011, cases of S. Newport were reported in England, Wales, Northern Ireland, Scotland, Ireland and Germany. During the outbreak, 63 confirmed cases of S. Newport were reported across all six countries with isolates indistinguishable by pulsed-field gel electrophoresis from the watermelon isolate.A subset of outbreak isolates were whole-genome sequenced and were identical to, or one single nucleotide polymorphism different from the watermelon isolate.In total, 46 confirmed cases were interviewed of which 27 reported watermelon consumption. Further investigations confirmed the outbreak was linked to the consumption of watermelon imported from Brazil.Although numerous Salmonella outbreaks associated with melons have been reported in the United States and elsewhere, this is the first of its kind in Europe.Expansion of the melon import market from Brazil represents a potential threat for future outbreaks. Whole genome sequencing is rapidly becoming more accessible and can provide a compelling level of evidence of linkage between human cases and sources of infection,to support public health interventions in global food markets.
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Affiliation(s)
- L Byrne
- Gastrointestinal, Emerging and Zoonotic Infections, Centre for Infectious Disease Surveillance and Control, Public Health England, Colindale, London, United Kingdom
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Multi‐country outbreak of Salmonella Enteritidis infections associated with consumption of eggs from Germany. ACTA ACUST UNITED AC 2014. [DOI: 10.2903/sp.efsa.2014.en-646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Kjeldsen M, Torpdahl M, Campos J, Pedersen K, Nielsen E. Multiple-locus variable-number tandem repeat analysis of Salmonella enterica
subsp. enterica
serovar Dublin. J Appl Microbiol 2014; 116:1044-54. [DOI: 10.1111/jam.12441] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/21/2013] [Accepted: 01/02/2014] [Indexed: 11/29/2022]
Affiliation(s)
- M.K. Kjeldsen
- Department of Microbiology and Infection Control; Foodborne Pathogens; Statens Serum Institut; Copenhagen Denmark
- National Food Institute; Technical University of Denmark; Mørkhøj Denmark
| | - M. Torpdahl
- Department of Microbiology and Infection Control; Foodborne Pathogens; Statens Serum Institut; Copenhagen Denmark
| | - J. Campos
- Servicio Enterobacterias; ANLIS-Instituto Carlos G. Malbrán; CABA; Buenos Aires Argentina
| | - K. Pedersen
- National Food Institute; Technical University of Denmark; Mørkhøj Denmark
| | - E.M. Nielsen
- Department of Microbiology and Infection Control; Foodborne Pathogens; Statens Serum Institut; Copenhagen Denmark
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Campos MJ, Palomo G, Hormeño L, Ugarte M, Porrero MC, Herrera-León S, Vadillo S, Píriz S, Quesada A. Co-Occurrence of ACSSuT and Cephalosporin Resistance Phenotypes Is Mediated by int1-Associated Elements in Nontyphoidal Salmonella enterica from Human Infections in Spain. Microb Drug Resist 2013; 19:384-91. [DOI: 10.1089/mdr.2012.0261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Maria Jorge Campos
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
- Grupo de Investigação em Recursos Marinhos (GIRM), Instituto Politécnico de Leiria (IPL), Peniche, Portugal
| | - Gonzalo Palomo
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Lorena Hormeño
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - María Ugarte
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - María Concepción Porrero
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Silvia Herrera-León
- Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Santiago Vadillo
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Segundo Píriz
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Alberto Quesada
- Departamento de Bioquímica, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
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Resistance genes, phage types and pulsed field gel electrophoresis pulsotypes in Salmonella enterica strains from laying hen farms in southern Italy. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2013; 10:3347-62. [PMID: 23924880 PMCID: PMC3774442 DOI: 10.3390/ijerph10083347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/11/2013] [Accepted: 07/29/2013] [Indexed: 11/17/2022]
Abstract
Twenty-four Salmonella enterica isolates (13 serovar Enteritidis and 11 Typhimurium) isolated from 5,600 samples from intensive laying hen farms in Italy in 1998-2007 were characterized for antimicrobial resistance genes, pulsotype and phage type. Most of S. Typhimurium strains were pulsotype STYMXB.0147 (81.8%), phage type DT143 and resistant to sulfamethoxazole encoded by sul2. Two multidrug resistant (MDR) strains were identified. One strain, STYMXB.0061, was resistant to ampicillin (A), chloramphenicol (C), streptomycin (S), sulfamethoxazole (Su) and tetracycline (T) encoded by the Salmonella Genomic Island SGI1. The second MDR strain, STYMXB.0110, was resistant to SSuT encoded by sul1 and sul2, aadA1 and tet(C)-flanked by an IS26 element, respectively. The tet(C) gene has been reported to confer low levels of resistance and it has very rarely been detected in S. Typhimurium from poultry. In the current study, the MIC value (32 µg/mL) was consistent with the breakpoint (≥16 µg/mL) reported for Enterobacteriaceae. Most of the S. Enteritidis strains were resistant to Su (encoded by sul2). One MDR strain (ANxSSuT) was identified. With the exception of nalidixic acid (Nx), the resistances were respectively encoded by bla(TEM), strAB, sul2 and tet(A) harbored by an IncN conjugative plasmid. All isolates were pulsotype SENTXB.0001 with PT14b being the most prevalent identified phage type (57.1%). In Europe, SENTXB.0001 is the predominant PFGE profile from clinical cases and the identification of PT14b has steadily been on the increase since 2001. The findings presented in this study highlight the potential spread of S. Enteritidis phage types PT14b and S. Typhimurium DT143 in a field of particular relevance for zoonoses. Additional, the presence of resistance genes and genetic elements (conjugative plasmid and IS element) underlines the need to assess routinely studies in field, such as poultry farms, relevant fot the public health and suitable for the storage and diffusion of antimicrobial resistance.
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Paranthaman K, Haroon S, Latif S, Vinnyey N, de Souza V, Welfare W, Tahir M, Cooke E, Stone K, Lane C, Peters T, Puleston R. Emergence of a multidrug-resistant (ASSuTTm) strain of Salmonella enterica serovar Typhimurium DT120 in England in 2011 and the use of multiple-locus variable-number tandem-repeat analysis in supporting outbreak investigations. Foodborne Pathog Dis 2013; 10:850-5. [PMID: 23869962 DOI: 10.1089/fpd.2013.1513] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In summer 2011, two outbreaks of a unique, multidrug-resistant strain of Salmonella enterica serovar Typhimurium phage type 120 (DT120) occurred mainly in the Midlands, England. The first outbreak occurred among guests attending a wedding in July 2011 ('Wedding outbreak'), followed by a more geographically dispersed outbreak in August and September 2011 ('Midlands outbreak'). Fifty-one cases were confirmed. Detailed epidemiological and environmental health investigations suggested that pork was the most likely source of both outbreaks. All human samples and one pork sample showed the specific multiple-locus variable-number tandem-repeat analysis (MLVA) profile 3-11-12-NA-0211, with at most two loci variations. Trace-back investigations suggested a link to a butcher's shop and a pig farm in the East Midlands. The investigations highlight the utility of molecular analysis (MLVA) in supporting epidemiological investigations of outbreaks caused by S. Typhimurium DT120. Safe handling and cooking of pork by food business operators and consumers are key interventions to prevent future outbreaks.
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Dewaele I, Rasschaert G, Wildemauwe C, Van Meirhaeghe H, Vanrobaeys M, De Graef E, Herman L, Ducatelle R, Heyndrickx M, De Reu K. Polyphasic characterization of Salmonella Enteritidis isolates on persistently contaminated layer farms during the implementation of a national control program with obligatory vaccination: A longitudinal study. Poult Sci 2012; 91:2727-35. [DOI: 10.3382/ps.2012-02218] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Tankouo-Sandjong B, Kinde H, Wallace I. Development of a sequence typing scheme for differentiation of Salmonella Enteritidis strains. FEMS Microbiol Lett 2012; 331:165-75. [PMID: 22486191 DOI: 10.1111/j.1574-6968.2012.02568.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 04/03/2012] [Accepted: 04/04/2012] [Indexed: 11/30/2022] Open
Abstract
A DNA sequence typing scheme based on the caiC and SEN0629 loci was developed for differentiation of Salmonella Enteritidis strains and validated using a diverse collection of 102 isolates representing 38 phage types from different sources, year of isolation, geographical locations and epidemiological backgrounds. caiC encodes a probable crotonobetaine/carnitine-CoA ligase, and SEN0629 is a pseudogene. Our system allowed for discrimination of 16 sequence types (STs) among the 102 isolates analysed and intraphage type differentiation. Our findings also suggested that the stability of phage typing may be adversely affected by the occurrence of phage type conversion events. During a confirmatory phage typing analysis performed by a reference laboratory, 13 of 31 S. Enteritidis strains representing nine phage types were assigned phage types that differed from the ones originally determined by the same reference laboratory. It is possible that this phenomenon passes largely unrecognized in reference laboratories performing routine phage typing analyses. Our results demonstrate that phage typing is an unstable system displaying limited reproducibility and that the two-loci sequence typing scheme is highly discriminatory, stable, truly portable and has the potential to become the new gold standard for epidemiological typing of S . Enteritidis strains.
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Affiliation(s)
- Bertrand Tankouo-Sandjong
- California Animal Health and Food Safety Laboratory System, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
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23
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Campos J, Pichel M, Vaz T, Tavechio A, Fernandes S, Muñoz N, Rodriguez C, Realpe M, Moreno J, Araya P, Fernández J, Fernández A, Campos E, Duarte F, Gustafson NW, Binsztein N, Gutierrez EP. Building PulseNet Latin America and Caribbean Salmonella regional database: First conclusions of genetic subtypes of S. Typhi, S. Typhimurium and S. Enteritidis circulating in six countries of the region. Food Res Int 2012. [DOI: 10.1016/j.foodres.2011.10.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Multiple-locus variable-number tandem-repeat analysis for discriminating within Salmonella enterica serovar Typhimurium definitive types and investigation of outbreaks. Epidemiol Infect 2010; 139:1050-9. [PMID: 20822575 DOI: 10.1017/s0950268810002025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The discriminatory power of multiple-locus variable-number tandem-repeat analysis (MLVA) needs to be evaluated for all Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) phage types so that the power of this methodology is understood and results can be interpreted correctly during outbreak investigations. We evaluated the ability of MLVA to characterize four definitive phage types (DT) problematic in New Zealand. MLVA discriminated between DT104 isolates although there was very limited variation in the MLVA profiles for isolates with an RDNC phage type (reacts but does not conform to a recognized Typhimurium phage pattern) first observed in New Zealand's Enteric Reference Laboratory in May 2006. Most DT101 isolates had indistinguishable MLVA profiles or profiles that differed at one or two loci. This was also observed in DT160 isolates. MLVA may not identify all common-source outbreaks although it provided valuable data when applied to case isolates from two S. Typhimurium outbreaks.
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Vaz C, Streck A, Michael G, Marks F, Rodrigues D, dos Reis E, Cardoso M, Canal C. Antimicrobial resistance and subtyping of Salmonella enterica subspecies enterica serovar Enteritidis isolated from human outbreaks and poultry in southern Brazil. Poult Sci 2010; 89:1530-6. [DOI: 10.3382/ps.2009-00453] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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26
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Betancor L, Yim L, Fookes M, Martinez A, Thomson NR, Ivens A, Peters S, Bryant C, Algorta G, Kariuki S, Schelotto F, Maskell D, Dougan G, Chabalgoity JA. Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates. BMC Microbiol 2009; 9:237. [PMID: 19922635 PMCID: PMC2784474 DOI: 10.1186/1471-2180-9-237] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 11/18/2009] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Salmonella enterica serovar Enteritidis (S. Enteritidis) has caused major epidemics of gastrointestinal infection in many different countries. In this study we investigate genome divergence and pathogenic potential in S. Enteritidis isolated before, during and after an epidemic in Uruguay. RESULTS 266 S. Enteritidis isolates were genotyped using RAPD-PCR and a selection were subjected to PFGE analysis. From these, 29 isolates spanning different periods, genetic profiles and sources of isolation were assayed for their ability to infect human epithelial cells and subjected to comparative genomic hybridization using a Salmonella pan-array and the sequenced strain S. Enteritidis PT4 P125109 as reference. Six other isolates from distant countries were included as external comparators.Two hundred and thirty three chromosomal genes as well as the virulence plasmid were found as variable among S. Enteritidis isolates. Ten out of the 16 chromosomal regions that varied between different isolates correspond to phage-like regions. The 2 oldest pre-epidemic isolates lack phage SE20 and harbour other phage encoded genes that are absent in the sequenced strain. Besides variation in prophage, we found variation in genes involved in metabolism and bacterial fitness. Five epidemic strains lack the complete Salmonella virulence plasmid. Significantly, strains with indistinguishable genetic patterns still showed major differences in their ability to infect epithelial cells, indicating that the approach used was insufficient to detect the genetic basis of this differential behaviour. CONCLUSION The recent epidemic of S. Enteritidis infection in Uruguay has been driven by the introduction of closely related strains of phage type 4 lineage. Our results confirm previous reports demonstrating a high degree of genetic homogeneity among S. Enteritidis isolates. However, 10 of the regions of variability described here are for the first time reported as being variable in S. Enteritidis. In particular, the oldest pre-epidemic isolates carry phage-associated genetic regions not previously reported in S. Enteritidis. Overall, our results support the view that phages play a crucial role in the generation of genetic diversity in S. Enteritidis and that phage SE20 may be a key marker for the emergence of particular isolates capable of causing epidemics.
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Affiliation(s)
- Laura Betancor
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. A, Navarro 3051, CP 11600, Montevideo, Uruguay
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. A, Navarro 3051, CP 11600, Montevideo, Uruguay
| | - Lucia Yim
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. A, Navarro 3051, CP 11600, Montevideo, Uruguay
| | - Maria Fookes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Araci Martinez
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. A, Navarro 3051, CP 11600, Montevideo, Uruguay
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. A, Navarro 3051, CP 11600, Montevideo, Uruguay
| | - Nicholas R Thomson
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alasdair Ivens
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah Peters
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Clare Bryant
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Gabriela Algorta
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. A, Navarro 3051, CP 11600, Montevideo, Uruguay
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Reserch Institute, Nairobi, Kenya
| | - Felipe Schelotto
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. A, Navarro 3051, CP 11600, Montevideo, Uruguay
| | - Duncan Maskell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jose A Chabalgoity
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. A, Navarro 3051, CP 11600, Montevideo, Uruguay
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Report of the Task Force on Zoonoses Data Collection on the availability of molecular typing methods for Salmonella, Campylobacter, verotoxigenic Escherichia coli, Listeria monocytogenes and Staphylococcus aureus isolates from food, animals and feedingstuffs in European Union Member States (and in some other reporting countries). EFSA J 2009. [DOI: 10.2903/j.efsa.2009.272r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Abstract
Foodborne diseases due to well-recognized pathogens have emerged as an important and growing public health problem with a significant impact on health. Molecular methods for subtyping these microorganisms have become a valid adjunct to the traditional techniques employed in most laboratories. One such molecular technique for the detection and identification of food pathogens is pulsed-field gel electrophoresis (PFGE). This method separates large DNA molecules by the use of an alternating electrical field, such that greater size resolution can be obtained when compared to normal agarose gel electrophoresis. PFGE is often employed to track pathogens, such as Salmonella, Shigella, Escherichia coli (including O157), Campylobacter, and Listeria species through the food chain. The contour-clamped homogeneous electric field (CHEF) PFGE system is considered to be the gold standard for use in epidemiological studies of these organisms.
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Affiliation(s)
- Tansy M Peters
- Health Protection Agency, Centre for Infections, 61 Colindale Avenue, London, UK
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Malorny B, Junker E, Helmuth R. Multi-locus variable-number tandem repeat analysis for outbreak studies of Salmonella enterica serotype Enteritidis. BMC Microbiol 2008; 8:84. [PMID: 18513386 PMCID: PMC2430564 DOI: 10.1186/1471-2180-8-84] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 05/30/2008] [Indexed: 01/08/2023] Open
Abstract
Background Salmonella enterica subsp. enterica serotype Enteritidis is known as an important and pathogenic clonal group which continues to cause worldwide sporadic cases and outbreaks in humans. Here a new multiple-locus variable-number tandem repeat analysis (MLVA) method is reported for highly-discriminative subtyping of Salmonella Enteritidis. Emphasis was given on the most predominant phage types PT4 and PT8. The method comprises multiplex PCR specifically amplifying repeated sequences from nine different loci followed by an automatic fragment size analysis using a multicolor capillary electrophoresis instrument. A total of 240 human, animal, food and environmental isolates of S. Enteritidis including 23 definite phage types were used for development and validation. Furthermore, the MLVA types were compared to the phage types of several isolates from two recent outbreaks to determine the concordance between both methods and to estimate their in vivo stability. The in vitro stability of the two MLVA types specifically for PT4 and PT8 strains were determined by multiple freeze-thaw cycles. Results Seventy-nine different MLVA types were identified in 240 S. Enteritidis strains. The Simpson's diversity index for the MLVA method was 0.919 and Nei diversity values for the nine VNTR loci ranged from 0.07 to 0.65. Twenty-four MLVA types could be assigned to 62 PT4 strains and 21 types to 81 PT8 strains. All outbreak isolates had an indistinguishable outbreak specific MLVA type. The in vitro stability experiments showed no changes of the MLVA type compared to the original isolate. Conclusion This MLVA method is useful to discriminate S. Enteritidis strains even within a single phage type. It is easy in use, fast, and cheap compared to other high-resolution molecular methods and therefore an important tool for surveillance and outbreak studies for S. Enteritidis.
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Affiliation(s)
- Burkhard Malorny
- Federal Institute for Risk Assessment, National Salmonella Reference LaboratoryDiedersdorfer Weg 1, D-12277 Berlin, Germany.
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