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Xiong D, Yuan L, Song L, Jiao X, Pan Z. A new multiplex PCR for the accurate identification and differentiation of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum. Front Microbiol 2022; 13:983942. [PMID: 36147848 PMCID: PMC9485580 DOI: 10.3389/fmicb.2022.983942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Salmonella enterica serovar Gallinarum biovars Gallinarum and Pullorum cause severe chicken salmonellosis, a disease associated with high mortality and morbidity among chickens worldwide. The conventional serotyping and biochemical reactions have been used to identify Salmonella serovars. However, the conventional methods are complicated, time-consuming, laborious, and expensive. Furthermore, it is challenging to distinguish S. Gallinarum and S. Pullorum via biochemical assays and serotyping because of their antigenic similarity. Although various PCR methods were established, a PCR protocol to detect and discriminate S. Gallinarum and S. Pullorum simultaneously is lacking. Herein, a one-step multiplex PCR method was established for the accurate identification and discrimination of S. Pullorum and S. Gallinarum. Three specific genes were used for the multiplex PCR method, with the I137_14445 and ybgL genes being the key targets to identify and differentiate S. Gallinarum and S. Pullorum, and stn being included as a reference gene for the Salmonella genus. In silico analysis showed that the I137_14445 gene is present in all Salmonella serovars, except for S. Gallinarum, and could therefore be used for the identification of S. Gallinarum. A 68-bp sequence deficiency in ybgL was found only in S. Pullorum compared to other Salmonella serovars, and this could therefore be used for the specific identification of S. Pullorum. The developed PCR assay was able to distinguish S. Gallinarum and S. Pullorum among 75 various Salmonella strains and 43 various non-Salmonella pathogens with excellent specificity. The detection limit for the genomic DNA of S. Gallinarum and S. Pullorum was 21.4 pg./μL, and the detectable limit for bacterial cells was 100 CFU. The developed PCR method was used for the analysis of Salmonella isolates in a chicken farm. This PCR system successfully discriminated S. Gallinarum and S. Pullorum from other different Salmonella serovars. The PCR results were confirmed by the conventional serotyping method. The newly established multiplex PCR is a simple, accurate, and cost-effective method for the timely identification and differentiation of S. Pullorum and S. Gallinarum.
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Affiliation(s)
- Dan Xiong
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Li Yuan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Li Song
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- *Correspondence: Xinan Jiao,
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Zhiming Pan,
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Municipal Wastewater Surveillance Revealed a High Community Disease Burden of a Rarely Reported and Possibly Subclinical Salmonella enterica Serovar Derby Strain. Appl Environ Microbiol 2020; 86:AEM.00814-20. [PMID: 32591375 DOI: 10.1128/aem.00814-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/09/2020] [Indexed: 01/26/2023] Open
Abstract
Clinical surveillance of enteric pathogens like Salmonella is integral to track outbreaks and endemic disease trends. However, clinic-centered disease monitoring biases toward detection of severe cases and underestimates the incidence of self-limiting gastroenteritis and asymptomatic strains. Monitoring pathogen loads and diversity in municipal wastewater (MW) can provide insight into asymptomatic or subclinical infections which are not reflected in clinical cases. Subclinical infection patterns may explain the unusual observation from a year-long sampling campaign in Hawaii: Salmonella enterica serovar Derby was the most abundant pulsotype in MW but was detected infrequently in clinics over the sampling period. Using whole-genome sequencing data of Salmonella isolates from MW and public databases, we demonstrate that the Derby serovar has lower virulence potential than other clinical serovars, particularly based on its reduced profile of genes linked with immune evasion and symptom production, suggesting its potential as a subclinical salmonellosis agent. Furthermore, MW had high abundance of a rare Derby sequence type (ST), ST-72 (rather than the more common ST-40). ST-72 isolates had higher frequencies of fimbrial adherence genes than ST-40 isolates; these are key virulence factors involved in colonization and persistence of infections. However, ST-72 isolates lack the Derby-specific Salmonella pathogenicity island 23 (SPI-23), which invokes host immune responses. In combination, ST-72's genetic features may lead to appreciable infection rates without obvious symptom production, allowing for subclinical persistence in the community. This study demonstrated wastewater's capability to provide community infectious disease information-such as background infection rates of subclinical enteric illness-which is otherwise inaccessible through clinical approaches.IMPORTANCE Wastewater-based epidemiology (WBE) has been conventionally used to analyze community health via the detection of chemicals, such as legal and illicit drugs; however, municipal wastewater contains microbiological determinants of health and disease as well, including enteric pathogens. Here, we demonstrate that WBE can be used to examine subclinical community salmonellosis patterns. Derby was the most abundant Salmonella serovar detected in Hawaii wastewater over a year-long sampling study, with few corresponding clinical cases. Comparative genomics analyses indicate that the normally rare strain of S Derby found in wastewater has a unique combination of genes which allow it to persist as a subclinical infection without producing symptoms of severe gastroenteritis. This study shows that WBE can be used to explore trends in community infectious disease patterns which may not be reflected in clinical monitoring, shedding light on overall enteric disease burden and rates of asymptomatic cases.
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Vico JP, Lorenzutti AM, Zogbi AP, Aleu G, Sánchez IC, Caffer MI, Rosmini MR, Mainar-Jaime RC. Prevalence, associated risk factors, and antimicrobial resistance profiles of non-typhoidal Salmonella in large scale swine production in Córdoba, Argentina. Res Vet Sci 2020; 130:161-169. [PMID: 32193003 DOI: 10.1016/j.rvsc.2020.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/04/2020] [Accepted: 03/02/2020] [Indexed: 11/15/2022]
Abstract
Non-typhoidal Salmonella is considered a major public health concern. The growing relevance of pigs as reservoir of Salmonella spp. has prompted several countries to set up surveillance and control programs to fight Salmonella infection in swine and reduce public health risk. In the last decade, pork production in Córdoba increased significantly to become one of the most important pig production provinces in Argentina. The aim of this study was to estimate Salmonella spp. prevalence and associated risk factors in large scale-farms in this province. Mesenteric lymph nodes (MLN) of 580 pigs from 20 finishing large-scale farms were collected between 2014 and 2015 to estimate Salmonella infection. A prevalence of 41.5% (95%CI: 37.6-45.6%) was observed. Two major risk factors were significantly associated with Salmonella infection, both related to the pre-slaughter period (distance from the farm to the slaughterhouse and lairage time), highlighting the need to pay special attention to pre-slaughter practices in the province. Shortening transport times and complying with national regulations for lairage time at slaughter may help to reduce the prevalence of infection. Sixteen different serovars were identified, being S. Anatum and S. Typhimurium the most prevalent ones. Moreover, two isolate of the monophasic variant of Salmonella Typhimurium (I 4,5,12:i:-) resistant to enrofloxacin and which also displayed multidrug resistance was isolated for first time from pigs in Córdoba. The moderate to high levels of antimicrobial resistance detected for antibiotics commonly used in the pig sector suggested the need for implementing a plan to limit their use in the province.
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Affiliation(s)
- J P Vico
- Instituto de Investigaciones en Recursos Humanos y Sustentabilidad, José Sánchez Labrador S.J IRNASUS-Conicet-Univesidad Católica de Córdoba, Facultad de Ciencias Agropecuarias, Veterinaria, Universidad Católica de Córdoba, Av. Armada Argentina 3555, X5016DHK Córdoba, Argentina.
| | - A M Lorenzutti
- Instituto de Investigaciones en Recursos Humanos y Sustentabilidad, José Sánchez Labrador S.J IRNASUS-Conicet-Univesidad Católica de Córdoba, Facultad de Ciencias Agropecuarias, Veterinaria, Universidad Católica de Córdoba, Av. Armada Argentina 3555, X5016DHK Córdoba, Argentina
| | - A P Zogbi
- Instituto de Investigaciones en Recursos Humanos y Sustentabilidad, José Sánchez Labrador S.J IRNASUS-Conicet-Univesidad Católica de Córdoba, Facultad de Ciencias Agropecuarias, Veterinaria, Universidad Católica de Córdoba, Av. Armada Argentina 3555, X5016DHK Córdoba, Argentina
| | - G Aleu
- Instituto de Investigaciones en Recursos Humanos y Sustentabilidad, José Sánchez Labrador S.J IRNASUS-Conicet-Univesidad Católica de Córdoba, Facultad de Ciencias Agropecuarias, Veterinaria, Universidad Católica de Córdoba, Av. Armada Argentina 3555, X5016DHK Córdoba, Argentina
| | - I C Sánchez
- Instituto de Investigaciones en Recursos Humanos y Sustentabilidad, José Sánchez Labrador S.J IRNASUS-Conicet-Univesidad Católica de Córdoba, Facultad de Ciencias Agropecuarias, Veterinaria, Universidad Católica de Córdoba, Av. Armada Argentina 3555, X5016DHK Córdoba, Argentina
| | - M I Caffer
- Servicio de Enterobacterias, Instituto Nacional de Enfermedades Infecciosas (INEI) - ANLIS "Dr. Carlos G. Malbrán", Avenida Velez Sarfield 563, C1282AFF Ciudad Autónoma de Buenos Aires, Argentina
| | - M R Rosmini
- Universidad Nacional del Litoral, Facultad de Ciencias Veterinarias, R.P. Kreder 2805, S3080HOF Esperanza, Santa Fe, Argentina
| | - R C Mainar-Jaime
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Calle de Miguel Servet 177, 50013 Zaragoza, Spain
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Mughini-Gras L, Kooh P, Fravalo P, Augustin JC, Guillier L, David J, Thébault A, Carlin F, Leclercq A, Jourdan-Da-Silva N, Pavio N, Villena I, Sanaa M, Watier L. Critical Orientation in the Jungle of Currently Available Methods and Types of Data for Source Attribution of Foodborne Diseases. Front Microbiol 2019; 10:2578. [PMID: 31798549 PMCID: PMC6861836 DOI: 10.3389/fmicb.2019.02578] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/24/2019] [Indexed: 12/29/2022] Open
Abstract
With increased interest in source attribution of foodborne pathogens, there is a need to sort and assess the applicability of currently available methods. Herewith we reviewed the most frequently applied methods for source attribution of foodborne diseases, discussing their main strengths and weaknesses to be considered when choosing the most appropriate methods based on the type, quality, and quantity of data available, the research questions to be addressed, and the (epidemiological and microbiological) characteristics of the pathogens in question. A variety of source attribution approaches have been applied in recent years. These methods can be defined as top–down, bottom–up, or combined. Top–down approaches assign the human cases back to their sources of infection based on epidemiological (e.g., outbreak data analysis, case-control/cohort studies, etc.), microbiological (i.e., microbial subtyping), or combined (e.g., the so-called ‘source-assigned case-control study’ design) methods. Methods based on microbial subtyping are further differentiable according to the modeling framework adopted as frequency-matching (e.g., the Dutch and Danish models) or population genetics (e.g., Asymmetric Island Models and STRUCTURE) models, relying on the modeling of either phenotyping or genotyping data of pathogen strains from human cases and putative sources. Conversely, bottom–up approaches like comparative exposure assessment start from the level of contamination (prevalence and concentration) of a given pathogen in each source, and then go upwards in the transmission chain incorporating factors related to human exposure to these sources and dose-response relationships. Other approaches are intervention studies, including ‘natural experiments,’ and expert elicitations. A number of methodological challenges concerning all these approaches are discussed. In absence of an universally agreed upon ‘gold’ standard, i.e., a single method that satisfies all situations and needs for all pathogens, combining different approaches or applying them in a comparative fashion seems to be a promising way forward.
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Affiliation(s)
- Lapo Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands.,Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Pauline Kooh
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Philippe Fravalo
- Research Chair in Meat-Safety, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | | | - Laurent Guillier
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Julie David
- Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety, Ploufragan, France
| | - Anne Thébault
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Frederic Carlin
- UMR 408 SQPOV "Sécurité et Qualité des Produits d'Origine Végétale" INRA, Avignon Université, Avignon, France
| | - Alexandre Leclercq
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France
| | | | - Nicole Pavio
- Laboratory for Animal Health, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Isabelle Villena
- Laboratory of Parasitology-Mycology, EA ESCAPE, University of Reims Champagne-Ardenne, Reims, France
| | - Moez Sanaa
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Laurence Watier
- Department of Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI), Institut National de la Santé et de la Recherche Médicale (INSERM), UVSQ, Institut Pasteur, Université Paris-Saclay, Paris, France
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Sévellec Y, Vignaud ML, Granier SA, Lailler R, Feurer C, Le Hello S, Mistou MY, Cadel-Six S. Polyphyletic Nature of Salmonella enterica Serotype Derby and Lineage-Specific Host-Association Revealed by Genome-Wide Analysis. Front Microbiol 2018; 9:891. [PMID: 29867804 PMCID: PMC5966662 DOI: 10.3389/fmicb.2018.00891] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/18/2018] [Indexed: 12/17/2022] Open
Abstract
In France, Salmonella Derby is one of the most prevalent serotypes in pork and poultry meat. Since 2006, it has ranked among the 10 most frequent Salmonella serotypes isolated in humans. In previous publications, Salmonella Derby isolates have been characterized by pulsed field gel electrophoresis (PFGE) and antimicrobial resistance (AMR) profiles revealing the existence of different pulsotypes and AMR phenotypic groups. However, these results suffer from the low discriminatory power of these typing methods. In the present study, we built a collection of 140 strains of S. Derby collected in France from 2014 to 2015 representative of the pork and poultry food sectors. The whole collection was characterized using whole genome sequencing (WGS), providing a significant contribution to the knowledge of this underrepresented serotype, with few genomes available in public databases. The genetic diversity of the S. Derby strains was analyzed by single-nucleotide polymorphism (SNP). We also investigated AMR by both genome and phenotype, the main Salmonella pathogenicity island (SPI) and the fimH gene sequences. Our results show that this S. Derby collection is spread across four different lineages genetically distant by an average of 15k SNPs. These lineages correspond to four multilocus sequence typing (MLST) types (ST39, ST40, ST71, and ST682), which were found to be associated with specific animal hosts: pork and poultry. While the ST71 and ST682 strains are pansusceptible, ST40 isolates are characterized by the multidrug resistant profile STR-SSS-TET. Considering virulence determinants, only ST39 and ST40 present the SPI-23, which has previously been associated with pork enterocyte invasion. Furthermore, the pork ST682 isolates were found to carry mutations in the fimH sequence that could participate in the host tropism of this group. Our phylogenetic analysis demonstrates the polyphyletic nature of the Salmonella serotype Derby and provides an opportunity to identify genetic factors associated with host adaptation and markers for the monitoring of these different lineages within the corresponding animal sectors. The recognition of these four lineages is of primary importance for epidemiological surveillance throughout the food production chains and constitutes the first step toward refining monitoring and preventing dispersal of this pathogen.
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Affiliation(s)
- Yann Sévellec
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Marie-Léone Vignaud
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Sophie A. Granier
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Renaud Lailler
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Carole Feurer
- French Institute for Pig and Pork Industry, Le Rheu, France
| | - Simon Le Hello
- Centre National de Référence des Salmonella, Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France
| | - Michel-Yves Mistou
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Sabrina Cadel-Six
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
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Arruda PHE, Madson DM, Ramirez A, Rowe EW, Songer JG. Bacterial probiotics as an aid in the control of Clostridium difficile disease in neonatal pigs. THE CANADIAN VETERINARY JOURNAL = LA REVUE VETERINAIRE CANADIENNE 2016; 57:183-188. [PMID: 26834271 PMCID: PMC4712999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Although Clostridium difficile infection (CDI) is a common disease in swine, there is a lack of prevention strategies. The objectives of this study were to evaluate: i) the effectiveness of Lactobacillus spp. and ii) non-toxigenic C. difficile (NTCD) as prevention for the development of CDI in piglets. Cesarean-derived piglets (N = 150) were randomly assigned to 6 groups: GROUP 1 - negative control (n = 10); GROUP 2 - NTCD only (n = 13); GROUP 3 - Lactobacillus spp. only (n = 14); GROUP 4 - positive control (challenged with toxigenic C. difficile strain) (n = 35); GROUP 5 - NTCD and challenged with the toxigenic C. difficile strain (n = 34); and GROUP 6 - Lactobacillus spp. and challenged with the toxigenic C. difficile strain (n = 44). Piglets which received NTCD showed lower prevalence of toxin-positive feces, mesocolonic edema, and microscopic lesions compared with positive control piglets. Administration of Lactobacillus spp. did not reveal clear benefits.
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Albino LA, Rostagno MH, Húngaro HM, Mendonça RC. Isolation, Characterization, and Application of Bacteriophages for Salmonella spp. Biocontrol in Pigs. Foodborne Pathog Dis 2014; 11:602-9. [DOI: 10.1089/fpd.2013.1600] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Luiz A.A. Albino
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcos H. Rostagno
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - Humberto M. Húngaro
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Regina C.S. Mendonça
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Shariat N, DiMarzio MJ, Yin S, Dettinger L, Sandt CH, Lute JR, Barrangou R, Dudley EG. The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella enterica subsp. enterica serovar Enteritidis. Food Microbiol 2012; 34:164-73. [PMID: 23498194 DOI: 10.1016/j.fm.2012.11.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 11/16/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
Abstract
Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is a major cause of foodborne salmonellosis. Rapid, efficient and accurate methods for identification are required to track specific strains of S. Enteritidis during outbreaks of human salmonellosis. By exploiting the hypervariable nature of virulence genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs), we previously developed a powerful sequence-based subtyping approach, designated CRISPR-MVLST. To substantiate the applicability of CRISPR-MVLST, we analyzed a broad set of S. Enteritidis isolates collected over a six-year period. Among 141 isolates we defined 22 Enteritidis Sequence Types (ESTs), the majority of which were novel. Notably, strains exhibiting the common PFGE pattern, JEGX01.0004 (characteristic of ∼40% of S. Enteritidis isolates in the United States), were separated into twelve distinct sequence types. Conversely, isolates of EST4, the most predominant EST we observed, comprised eight different PFGE patterns. Importantly, we showed that some genotypes that were previously associated with the food supply chain at the farm level have now been identified in clinical samples. CRISPR sequence data shows subtle but distinct differences among different alleles of S. Enteritidis, suggesting that evolution of these loci occurs vertically, as opposed to previously reported evolution by spacer acquisition in other bacteria.
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Affiliation(s)
- Nikki Shariat
- Department of Food Science, 326 Food Science Building, The Pennsylvania State University, University Park, PA 16802, USA
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