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Guzinski J, Tang Y, Chattaway MA, Dallman TJ, Petrovska L. Development and validation of a random forest algorithm for source attribution of animal and human Salmonella Typhimurium and monophasic variants of S. Typhimurium isolates in England and Wales utilising whole genome sequencing data. Front Microbiol 2024; 14:1254860. [PMID: 38533130 PMCID: PMC10963456 DOI: 10.3389/fmicb.2023.1254860] [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] [Received: 07/07/2023] [Accepted: 12/22/2023] [Indexed: 03/28/2024] Open
Abstract
Source attribution has traditionally involved combining epidemiological data with different pathogen characterisation methods, including 7-gene multi locus sequence typing (MLST) or serotyping, however, these approaches have limited resolution. In contrast, whole genome sequencing data provide an overview of the whole genome that can be used by attribution algorithms. Here, we applied a random forest (RF) algorithm to predict the primary sources of human clinical Salmonella Typhimurium (S. Typhimurium) and monophasic variants (monophasic S. Typhimurium) isolates. To this end, we utilised single nucleotide polymorphism diversity in the core genome MLST alleles obtained from 1,061 laboratory-confirmed human and animal S. Typhimurium and monophasic S. Typhimurium isolates as inputs into a RF model. The algorithm was used for supervised learning to classify 399 animal S. Typhimurium and monophasic S. Typhimurium isolates into one of eight distinct primary source classes comprising common livestock and pet animal species: cattle, pigs, sheep, other mammals (pets: mostly dogs and horses), broilers, layers, turkeys, and game birds (pheasants, quail, and pigeons). When applied to the training set animal isolates, model accuracy was 0.929 and kappa 0.905, whereas for the test set animal isolates, for which the primary source class information was withheld from the model, the accuracy was 0.779 and kappa 0.700. Subsequently, the model was applied to assign 662 human clinical cases to the eight primary source classes. In the dataset, 60/399 (15.0%) of the animal and 141/662 (21.3%) of the human isolates were associated with a known outbreak of S. Typhimurium definitive type (DT) 104. All but two of the 141 DT104 outbreak linked human isolates were correctly attributed by the model to the primary source classes identified as the origin of the DT104 outbreak. A model that was run without the clonal DT104 animal isolates produced largely congruent outputs (training set accuracy 0.989 and kappa 0.985; test set accuracy 0.781 and kappa 0.663). Overall, our results show that RF offers considerable promise as a suitable methodology for epidemiological tracking and source attribution for foodborne pathogens.
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Affiliation(s)
- Jaromir Guzinski
- Animal and Plant Health Agency, Bacteriology Department, Addlestone, United Kingdom
| | - Yue Tang
- Animal and Plant Health Agency, Bacteriology Department, Addlestone, United Kingdom
| | - Marie Anne Chattaway
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency, London, United Kingdom
| | - Timothy J. Dallman
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency, London, United Kingdom
| | - Liljana Petrovska
- Animal and Plant Health Agency, Bacteriology Department, Addlestone, United Kingdom
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Uelze L, Borowiak M, Deneke C, Fischer J, Flieger A, Simon S, Szabó I, Tausch SH, Malorny B. Comparative genomics of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) reveals lineage-specific host adaptation of ST432. Microb Genom 2021; 7. [PMID: 34338625 PMCID: PMC8549363 DOI: 10.1099/mgen.0.000604] [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] [Indexed: 11/18/2022] Open
Abstract
Unlike most Salmonella enterica subsp. diarizonae, which are predominantly associated with cold-blooded animals such as reptiles, the serovar IIIb 61:k:1,5,(7) (termed SASd) is regarded as host-adapted to sheep. The bacterium is rarely associated with disease in humans but, nevertheless, SASd isolates are sporadically obtained from human clinical samples. It is unclear whether these transmissions are directly linked to sheep or whether transmissions may, for example, occur through other domestic animals also carrying SASd. For this reason, we utilized whole-genome sequencing to investigate a set of 119 diverse SASd isolates, including sheep-associated and human-associated isolates, as well as isolates obtained from other matrices. We discovered that serovar IIIb 61:k:1,5,(7) is composed of two distinct lineages defined by their sequence types ST432 and ST439. These two lineages are distinguished by a number of genetic features, as well as their prevalence and reservoir. ST432 appears to be the more prevalent sequence type, with the majority of isolates investigated in this study belonging to ST432. In contrast, only a small number of isolates were attributed to ST439. While ST432 isolates were of sheep, human or other origin, all ST439 isolates with source information available, were obtained from human clinical samples. Regarding their genetic features, lineage ST432 shows increased pseudogenization, harbours a virB/D4 plasmid that encodes a type IV secretion system (T4SS) and does not possess the iro gene cluster, which encodes a salmochelin siderophore for iron acquisition. These characteristics likely contribute to the ability of ST432 to persistently colonize the intestines of sheep. Furthermore, we found isolates of the lineage ST432 to be highly clonal, with little variation over the sampling period of almost 20 years. We conclude from the genomic comparisons that SASd underlies a microevolutionary process and that it is specifically lineage ST432 that should be considered as host-adapted to sheep.
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Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Antje Flieger
- Unit for Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute (RKI), Burgstraße 37, 38855 Wernigerode, Germany
| | - Sandra Simon
- Unit for Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute (RKI), Burgstraße 37, 38855 Wernigerode, Germany
| | - István Szabó
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
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Hyeon JY, Helal ZH, Polkowski R, Heishima M, Kim J, Lee DH, Risatti GR. Genetic features of Salmonella enterica subspecies diarizonae serovar 61:k:1,5 isolated from abortion cases in sheep, United States, 2020. Res Vet Sci 2021; 138:125-136. [PMID: 34139624 DOI: 10.1016/j.rvsc.2021.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/13/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022]
Abstract
Salmonella enterica subspecies diarizonae serovar 61:(k):1, 5, (7) (sheep associated S. diarizonae, SASd) is the most common Salmonella serotype identified in sheep flocks. Despite the involvement with animal and human infections, there is limited information regarding virulence profiles of SASds and their antibiotic resistance gene complement, particularly for those circulating in the U.S. In this study, we genetically characterized three SASds, 20-265, 20-269, and 20-312, isolated from sheep placental tissues during an abortion storm affecting a flock in Connecticut during 2020. SASds were the only bacteria isolated from analyzed sheep tissues. The isolates were sensitive to all the antibiotics tested, but all these SASd isolates carry the aminoglycoside resistance gene, aac(6')-Iaa, and a chromosomal substitution in the parC gene. The proportion of pseudogenes (5.3-5.5%) was similar among the isolates, and these SASds carry IncX1 type plasmids. Comparing with the SASds isolates from Enterobase, the three isolates showed an identical genomic virulence profile carrying virulence genes in the conserved set of other SASd isolates except for steC, iagB, iacP, sseI, and slrP genes. In the SNP-based phylogenetic analysis, SASd sequences were grouped into group A-C, and the group C was further subdivided into subgroup C1-C6. The three isolates clustered with other SASd isolates from the U.S. and Canada in subgroup C6. SASd isolates in the identical phylogenetic groups tended to have similar geographical origin. The results of our study did not provide conclusive evidence about which are the genetic traits that trigger SASds to become virulent in sheep, but our data will provide a point for comparative studies of this Salmonella serovar.
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Affiliation(s)
- Ji-Yeon Hyeon
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA; Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Zeinab H Helal
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA; Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Robert Polkowski
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Mizuki Heishima
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Junwon Kim
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA.
| | - Guillermo R Risatti
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA; Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA.
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Giner-Lamia J, Vinuesa P, Betancor L, Silva C, Bisio J, Soleto L, Chabalgoity JA, Puente JL, García-del Portillo F. Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256. BMC Genomics 2019; 20:99. [PMID: 30704413 PMCID: PMC6357384 DOI: 10.1186/s12864-018-5352-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 12/05/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environment, cold-blooded reptiles, sheep and humans; however only a few studies describe the isolation of this subspecies from invasive human infections. The factors contributing to this unusual behavior are currently unknown. RESULTS We report here the genome features of two diarizonae strains, SBO13 and SBO27, isolated from endocervical tissue collected post-abortion and from cerebrospinal fluid of a newborn child, respectively, in the city of Santa Cruz, Bolivia. Although isolated six years apart, SBO27 in 2008 and SBO13 in 2014, both strains belong to the same sequence type 1256 (ST1256) and show a high degree of genome conservation sharing more than 99% of their genes, including the conservation of a ~ 10 kb plasmid. A prominent feature of the two genomes is the presence of 24 genomic islands (GIs), in addition to 10 complete Salmonella pathogenicity islands (SPI) and fragments of SPI-7, a pathogenicity island first reported in the human-adapted serovar Typhi. Some of the GIs identified in SBO13 and SBO27 harbor genes putatively encoding auto-transporters involved in adhesion, lipopolysaccharide modifying enzymes, putative toxins, pili-related proteins, efflux pumps, and several putative membrane cation transport related-genes, among others. These two Bolivian isolates also share genes encoding the type-III secretion system effector proteins SseK2, SseK3 and SlrP with other diarizonae sequence types (ST) mainly-associated with infections in humans. The sseK2, sseK3 and slrP genes were either absent or showing frameshift mutations in a significant proportion of genomes from environmental diarizonae isolates. CONCLUSIONS The comparative genomic study of two diarizonae strains isolated in Bolivia from human patients uncovered the presence of many genes putatively related to virulence. The statistically-significant acquisition of a unique combination of these functions by diarizonae strains isolated from humans may have impacted the ability of these isolates to successfully infect the human host.
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Affiliation(s)
- Joaquín Giner-Lamia
- Laboratorio de Patógenos Bacterianos Intracelulares, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Laura Betancor
- Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Claudia Silva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Julieta Bisio
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Lorena Soleto
- Ministerio de Salud de Bolivia, Centro Nacional de Enfermedades Tropicales (CENETROP), Santa Cruz, Bolivia
- Universidad Autónoma Gabriel René Moreno, Santa Cruz, Bolivia
| | - José A. Chabalgoity
- Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - José Luis Puente
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Francisco García-del Portillo
- Laboratorio de Patógenos Bacterianos Intracelulares, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
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Methner U, Moog U. Occurrence and characterisation of Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) in sheep in the federal state of Thuringia, Germany. BMC Vet Res 2018; 14:401. [PMID: 30558604 PMCID: PMC6296128 DOI: 10.1186/s12917-018-1741-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 12/07/2018] [Indexed: 11/28/2022] Open
Abstract
Background The occurrence of Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) (SASd) and other Salmonella organisms in sheep in the German federal state of Thuringia was examined for the first time. Pooled faecal samples from 90 flocks located in this state were monitored. Results Only SASd was detected in 74 (82.2%) out of the 90 sheep herds, other Salmonella serovars were not identified. A positive correlation was found between the flock size and the detection probability of SASd. Despite the agent’s high prevalence, clinical symptoms of a disease exclusively due to SASd have not been observed. The SASd strains were characterised by macrorestriction analysis, antimicrobial testing and the biochemical profile. All strains were sensitive to 13 out of 14 antimicrobial substances and resistant to only sulfamethoxazole. The high number of macrorestriction groups of SASd strains indicated a low clonality of the serovar. Conclusions Data from sheep derived foods and public health data in Germany strongly suggest that the significance of SASd for public health is considerably lower than that of serovars belonging to Salmonella enterica subspecies enterica. For this reason and because of the low disease-causing potential of SASd in sheep, it is worthwile to consider a reduction in ongoing activities from combating to monitoring serovar 61: k: 1, 5, (7) in the sheep population.
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Affiliation(s)
- Ulrich Methner
- Institute of Bacterial Infections and Zoonoses at the Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Naumburger Str. 96a, 07743, Jena, Germany.
| | - Udo Moog
- Thuringian Animal Diseases Fund, Victor-Goerttler-Str. 4, 07745, Jena, Germany
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Schnydrig P, Overesch G, Regli W, Bee A, Rodriguez-Campos S. Salmonella enterica subspecies diarizonae serovar 61:(k):1,5,(7) as cause of caprine abortion. Small Rumin Res 2018. [DOI: 10.1016/j.smallrumres.2018.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Lamas A, Miranda JM, Regal P, Vázquez B, Franco CM, Cepeda A. A comprehensive review of non-enterica subspecies of Salmonella enterica. Microbiol Res 2018; 206:60-73. [DOI: 10.1016/j.micres.2017.09.010] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/22/2017] [Accepted: 09/26/2017] [Indexed: 12/11/2022]
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Røssvoll E, Røtterud OJ, Hauge SJ, Alvseike O. A comparison of two evisceration methods on hygienic quality in the pelvic area of sheep carcasses. Meat Sci 2017; 137:134-138. [PMID: 29179139 DOI: 10.1016/j.meatsci.2017.11.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 10/18/2022]
Abstract
The aim was to compare the effects of two evisceration methods under operational conditions, on the pelvic hygiene of sheep carcasses. Method 1: rectum sealed with plastic bag and pushed through the pelvic cavity. Method 2: rectum cut, placed back inside and pulled out from the carcass. The 18 largest Norwegian sheep abattoirs participated. Sampling areas were i) 400cm2 inside the pelvic cavity (n=623), ii) 100cm2 outside the circum-anal incision (n=622). There were pooled samples by swabbing the same area of five carcasses, representing totally 3115 carcasses. Mean E. coli results from Method 1: -1.61logCFU/cm2 inside and -0.25logCFU/cm2 for the outside area. Results from Method 2: -1.56logCFU/cm2 inside and -0.42logCFU/cm2 outside. There were no significant differences between the two methods. Both evisceration methods can produce carcasses that are of practically identical high hygienic quality.
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Affiliation(s)
- Elin Røssvoll
- Animalia - Norwegian Meat and Poultry Research Centre, P.O. Box 396 Økern, N-0513 Oslo, Norway
| | - Ole-Johan Røtterud
- Animalia - Norwegian Meat and Poultry Research Centre, P.O. Box 396 Økern, N-0513 Oslo, Norway
| | - Sigrun J Hauge
- Animalia - Norwegian Meat and Poultry Research Centre, P.O. Box 396 Økern, N-0513 Oslo, Norway.
| | - Ole Alvseike
- Animalia - Norwegian Meat and Poultry Research Centre, P.O. Box 396 Økern, N-0513 Oslo, Norway
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Lacasta D, Figueras L, Bueso J, De las Heras M, Ramos J, Ferrer L, González J, Ruíz de Arcaute M, Ortín A, Marteles D, Navarro T, Fernández A. Experimental infection with Salmonella enterica subsp. diarizonae serotype 61:k:1,5,(7) in sheep: Study of cell mediated immune response. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Draft Genome Sequence of Salmonella enterica subsp. diarizonae Serovar 61:k:1,5,(7) Strain CRJJGF_00165 (Phylum Gammaproteobacteria). GENOME ANNOUNCEMENTS 2016; 4:4/6/e01322-16. [PMID: 27881547 PMCID: PMC5122689 DOI: 10.1128/genomea.01322-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report a 4.78-Mb draft genome sequence of the Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) strain CRJJGF_00165 [also called S. enterica subsp. IIIb serovar 61:k:1,5,(7) strain CRJJGF_00165], isolated from ground beef in 2007.
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Amagliani G, Petruzzelli A, Carloni E, Tonucci F, Foglini M, Micci E, Ricci M, Di Lullo S, Rotundo L, Brandi G. Presence of Escherichia coli O157, Salmonella spp., and Listeria monocytogenes in Raw Ovine Milk Destined for Cheese Production and Evaluation of the Equivalence Between the Analytical Methods Applied. Foodborne Pathog Dis 2016; 13:626-632. [DOI: 10.1089/fpd.2016.2159] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Giulia Amagliani
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Urbino (PU), Italy
| | | | - Elisa Carloni
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Urbino (PU), Italy
| | - Franco Tonucci
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Pesaro, Italy
| | - Martina Foglini
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Pesaro, Italy
| | - Eleonora Micci
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Pesaro, Italy
| | - Mariagrazia Ricci
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Pesaro, Italy
| | - Stefania Di Lullo
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Pesaro, Italy
| | - Luca Rotundo
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Urbino (PU), Italy
| | - Giorgio Brandi
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Urbino (PU), Italy
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Sörén K, Lindblad M, Jernberg C, Eriksson E, Melin L, Wahlström H, Lundh M. Changes in the risk management of Salmonella enterica subspecies diarizonae serovar 61:(k):1, 5, (7) in Swedish sheep herds and sheep meat due to the results of a prevalence study 2012. Acta Vet Scand 2015; 57:6. [PMID: 25644506 PMCID: PMC4324828 DOI: 10.1186/s13028-015-0096-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 01/15/2015] [Indexed: 11/16/2022] Open
Abstract
Background The prevalence of Salmonella in food producing animals is very low in Sweden due to rigorous control programmes. However, no active surveillance is in place in sheep. The authorities decided to perform a prevalence study in sheep herds because findings at slaughter indicated that sheep associated S. diarizonae (S. enterica subspecies diarizonae serovar 61:(k):1, 5, (7)) might be common in sheep. Sampling was stratified by herd size in two groups, small herds with ≤ 30 animals and large herds with > 30 animals. In each stratum, 237 herds were selected at random. Faecal samples received from 244 out of the 474 randomly selected herds were analysed. Results A total of 40 of 100 (40%) of large herds and 17 of 144 (12%) of small herds were positive. The overall adjusted prevalence was 17.6% (95% CI, 12.9-22.2). Sheep associated S. diarizonae was detected in all counties (n = 21). Scientific opinions and an evaluation of on-farm control measures performed concluded that the impact of sheep associated S. diarizonae on human health is very low, and that risk management measures applied in response to findings of sheep associated S. diarizonae in sheep or sheep meat can be expected to have very little impact on reducing risks to human health. As a result, Swedish authorities decided to make an exemption for sheep associated Salmonella diarizonae in sheep and sheep meat in the current Salmonella control measures. Conclusions Sheep associated S. diarizonae is endemic in Swedish sheep herds. It is more common in large herds and not limited to certain parts of the country. The responsible authorities concluded that current risk management actions regarding sheep associated S. diarizonae in sheep and sheep meat are not proportional to the risk. This is the first time in the history of the Swedish Salmonella control programme that an exemption from the legislation has been made for a specific serovar. If there is any future indication of an increasing risk, due to e.g. change in the pathogenicity or development of antimicrobial resistance, the risk assessment will be re-evaluated and control measures reinforced if needed.
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A Pilot Study for Identification of Salmonella in Food Processing Plants by Real-Time PCR Screening. FOOD ANAL METHOD 2011. [DOI: 10.1007/s12161-011-9352-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Thiolet J, Jourdan-Da Silva N, Reggiani A, De Valk H, Coignard B, Weill F. Nationwide pseudo-outbreak of Salmonella enterica ssp. diarizonae, France. Clin Microbiol Infect 2011; 17:915-8. [DOI: 10.1111/j.1469-0691.2010.03343.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Subspecies IIIa and IIIb Salmonellae are defective for colonization of murine models of salmonellosis compared to Salmonella enterica subsp. I serovar typhimurium. J Bacteriol 2009; 191:2843-50. [PMID: 19218378 DOI: 10.1128/jb.01223-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Non-subspecies I salmonellae are commensals of cold-blooded vertebrates and cause sporadic disease in mammals. The reasons why non-subspecies I salmonellae do not circulate in populations of warm-blooded vertebrates, but instead only cause occasional disease in this niche, are unknown. We examined the ability of Salmonella enterica subsp. IIIa (subsp. arizonae) and subsp. IIIb (subsp. diarizonae) isolates to grow competitively with subspecies I (serovar Typhimurium) ATCC 14028 in vitro, to colonize Salmonella-sensitive BALB/c mice, and to persist in the intestine of Salmonella-resistant CBA/J mice in competitive infections. Subspecies IIIa had severely reduced intestinal colonization, intestinal persistence, and systemic spread in mice. Subspecies IIIa is nonmotile on swarming agar and thus may also have reduced motility under viscous conditions in vivo. Surprisingly, subspecies IIIb colonizes the intestinal tract of BALB/c mice normally yet does not spread systemically. Subspecies IIIb colonization of the intestine of CBA/J mice is reduced late in infection. In order to understand why these isolates do not colonize systemic sites, we determined that subspecies IIIa and IIIb are not internalized well and do not replicate in J774-A.1 murine macrophages, despite normal adherence to these cells. We further show that selected effectors of both type III secretion systems 1 and 2 are secreted by subspecies IIIa and IIIb in vitro but that each of these isolates secretes a different combination of effectors. We outline the phenotypic differences between these subspecies and subspecies I and provide a possible explanation for the inability of these strains to spread systemically in murine models.
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