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Pearce ME, Langridge GC, Lauer AC, Grant K, Maiden MCJ, Chattaway MA. An evaluation of the species and subspecies of the genus Salmonella with whole genome sequence data: Proposal of type strains and epithets for novel S. enterica subspecies VII, VIII, IX, X and XI. Genomics 2021; 113:3152-3162. [PMID: 34242711 PMCID: PMC8426187 DOI: 10.1016/j.ygeno.2021.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 01/01/2023]
Abstract
Species and subspecies within the Salmonella genus have been defined for public health purposes by biochemical properties; however, reference laboratories have increasingly adopted sequence-based, and especially whole genome sequence (WGS), methods for surveillance and routine identification. This leads to potential disparities in subspecies definitions, routine typing, and the ability to detect novel subspecies. A large-scale analysis of WGS data from the routine sequencing of clinical isolates was employed to define and characterise Salmonella subspecies population structure, demonstrating that the Salmonella species and subspecies were genetically distinct, including those previously identified through phylogenetic approaches, namely: S. enterica subspecies londinensis (VII), subspecies brasiliensis (VIII), subspecies hibernicus (IX) and subspecies essexiensis (X). The analysis also identified an additional novel subspecies, reptilium (XI). Further, these analyses indicated that S. enterica subspecies arizonae (IIIa) isolates were divergent from the other S. enterica subspecies, which clustered together and, on the basis of ANI analysis, subspecies IIIa was sufficiently distinct to be classified as a separate species, S. arizonae. Multiple phylogenetic and statistical approaches generated congruent results, suggesting that the proposed species and subspecies structure was sufficiently biologically robust for routine application. Biochemical analyses demonstrated that not all subspecies were distinguishable by these means and that biochemical approaches did not capture the genomic diversity of the genus. We recommend the adoption of standardised genomic definitions of species and subspecies and a genome sequence-based approach to routine typing for the identification and definition of novel subspecies. A large-scale analysis of genomic data demonstrate Salmonella species and subspecies are genetically distinct. Biochemical analysis does not capture the genomic diversity of the Salmonella genus but routine species and subspecies identification can be achieved with rMLST Average Nucleotide Identify (ANI) with a 95% criteria was suitable to distinguish species and 98% to distinguish subspecies. Five novel S. enteric subspecies (VII-XI) type strains are defined. Reclassification of S. arizonae as a separate species is recommended.
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Affiliation(s)
- Madison E Pearce
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom; National Institute for Health Research, Health Protection Research Unit, Gastrointestinal Infections, University of Oxford, United Kingdom
| | - Gemma C Langridge
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom.
| | - A C Lauer
- Centers for Disease Control and Prevention, Enteric Diseases Laboratory Branch, 1600 Clifton RD NE, Atlanta, GA 30329, USA.
| | - Kathie Grant
- Public Health England, Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London NW9 5EQ, United Kingdom
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom; National Institute for Health Research, Health Protection Research Unit, Gastrointestinal Infections, University of Oxford, United Kingdom.
| | - Marie A Chattaway
- Public Health England, Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London NW9 5EQ, United Kingdom.
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Sharma RN, Matthew-Belmar V, Nicholas-Thomas R, Arya G, Holtslander B, Hariharan H, Amadi VA. Prevalence of Salmonella spp. in red-footed tortoises (Chelonoidis carbonaria) from Grenada, West Indies. INTERNATIONAL JOURNAL OF ONE HEALTH 2020. [DOI: 10.14202/ijoh.2020.12-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: There is currently no published information on the prevalence of Salmonella spp. in pet red-footed tortoises in Grenada. Monitoring is essential to understand the dynamics of the epidemiology of Salmonella. This study aimed to estimate the prevalence of Salmonella spp. from pet red-footed tortoises from Grenada and to test for antimicrobial drug resistance of the isolates.
Materials and Methods: Established bacterial culture, serotyping, and antimicrobial susceptibility methods were used. Fecal samples were obtained from 114 tortoises from five parishes of Grenada, and cultured for Salmonella using enrichment and selective culture techniques. The serotyping of isolated Salmonella was performed at the Office International des Epizooties Salmonella Reference Laboratory, Guelph, Ontario, Canada. The isolates were tested for antimicrobial susceptibility in the Microbiology Laboratory of the School of Veterinary Medicine, St. George's University, Grenada.
Results: Fifteen tortoises (13.2%) out of 114 were positive for Salmonella spp. Five serovars were identified: Salmonella Javiana (6.3%), Salmonella Rubislaw (6.3%), Salmonella Saintpaul (18.75%), Salmonella Glostrup (6.3%), and S. I: Rough.O;e,h:1,2 (62.5%). All isolates were sensitive to the 12 antimicrobial drugs.
Conclusion: Three serovars (S. Javiana, S. Saintpaul, and S. Rubislaw) are known pathogens causing disease in humans. Since tortoises included in the study were pets, the tortoises may be a possible source of transmission of Salmonella to their owners. The tortoise owners should be educated on the importance of hygienic raising of their pets. This is the first report of isolation of Salmonella spp. from pet red-footed tortoises in Grenada.
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Affiliation(s)
- Ravindra Nath Sharma
- Department of Pathobiology, School of Veterinary Medicine, St. George's University, Grenada, West Indies
| | - Vanessa Matthew-Belmar
- Department of Pathobiology, School of Veterinary Medicine, St. George's University, Grenada, West Indies
| | - Roxane Nicholas-Thomas
- Department of Pathobiology, School of Veterinary Medicine, St. George's University, Grenada, West Indies
| | - Gitanjali Arya
- Office International des Epizooties Salmonella Reference Laboratory, Public Health Agency of Canada, National Microbiology at Guelph, Guelph, Ontario, Canada
| | - Bob Holtslander
- Office International des Epizooties Salmonella Reference Laboratory, Public Health Agency of Canada, National Microbiology at Guelph, Guelph, Ontario, Canada
| | - Harry Hariharan
- Department of Pathobiology, School of Veterinary Medicine, St. George's University, Grenada, West Indies
| | - Victor A. Amadi
- Department of Pathobiology, School of Veterinary Medicine, St. George's University, Grenada, West Indies
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Hossain S, De Silva B, Dahanayake P, Shin GW, Heo GJ. MOLECULAR CHARACTERIZATION OF VIRULENCE, ANTIMICROBIAL RESISTANCE GENES, AND CLASS ONE INTEGRON GENE CASSETTES IN SALMONELLA ENTERICA SUBSP. ENTERICA ISOLATED FROM PET TURTLES IN SEOUL, KOREA. J Exot Pet Med 2019. [DOI: 10.1053/j.jepm.2018.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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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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Antimicrobial property of lemongrass ( Cymbopogon citratus) oil against pathogenic bacteria isolated from pet turtles. Lab Anim Res 2017; 33:84-91. [PMID: 28747972 PMCID: PMC5527151 DOI: 10.5625/lar.2017.33.2.84] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/07/2017] [Accepted: 03/16/2017] [Indexed: 11/30/2022] Open
Abstract
The usage of essential oils as antimicrobial agents is gaining attention. Besides, pet turtles were known to harbor a range of pathogenic bacteria while the turtle keeping is a growing trend worldwide.The current study examined the antimicrobial activity of lemon grass oil (LGO) against seven species of Gram negative bacteria namely; Aeromonas hydrophila, A. caviae, Citrobacter freundii, Salmonella enterica, Edwardsiella tarda, Pseudomonas aeruginosa, and Proteus mirabilis isolated from three popular species of pet turtles. Along with the results of disc diffusion, minimum inhibitory and minimum bactericidal concentration (MIC and MBC) tests, LGO was detected as effective against 6 species of bacteria excluding P. aeruginosa. MIC of LGO for the strains except P. aeruginosa ranged from 0.016 to 0.5% (V/V). The lowest MIC recorded in the E. tarda strain followed by A. hydrophilla, C. freundii, P. mirabilis, and S. enterica. Interestingly, all the bacterial species except E. tarda were showing high multiple antimicrobial resistance (MAR) index values ranging from 0.36 to 0.91 upon the 11 antibiotics tested although they were sensitive to LGO.
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Quinolone susceptibility and genetic characterization of Salmonella enterica subsp. enterica isolated from pet turtles. Lab Anim Res 2017; 33:49-56. [PMID: 28747968 PMCID: PMC5527147 DOI: 10.5625/lar.2017.33.2.49] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/07/2017] [Accepted: 03/16/2017] [Indexed: 01/02/2023] Open
Abstract
Turtle-borne Salmonella enterica owns significance as a leading cause in human salmonellosis. The current study aimed to determine the quinolone susceptibility and the genetic characteristics of 21 strains of S. enterica subsp. enterica isolated from pet turtles. Susceptibility of four antimicrobials including nalidixic acid, ciprofloxacin, ofloxacin, and levofloxacin was examined in disk diffusion and MIC tests where the majority of the isolates were susceptible to all tested quinolones. In genetic characterization, none of the isolates were positive for qnr or aac(6')-Ib genes and no any target site mutations could be detected in gyrA, gyrB, and parC quinolone resistance determining regions (QRDR). In addition, neighbor-joining phylogenetic tree derived using gyrA gene sequences exhibited two distinct clads comprising; first, current study isolates, and second, quinolone-resistant isolates of human and animal origin. All results suggest that studied strains of S. enterica subsp. enterica isolated from pet turtles are susceptible to quinolones and genetically more conserved with regards to gyrA gene region.
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Vercelli C, De Vito V, Salvadori M, Barbero R, Re G, Gennero MS, Giorgi M. Blood concentrations of marbofloxacin and its in vivo effect in yellow-bellied slider turtles (Trachemys scripta scripta) after a single intracoelomic injection at 3 dose rates. J Exot Pet Med 2016. [DOI: 10.1053/j.jepm.2016.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Prevalence of Salmonella spp. in pet turtles and their environment. Lab Anim Res 2016; 32:166-170. [PMID: 27729933 PMCID: PMC5057005 DOI: 10.5625/lar.2016.32.3.166] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/16/2016] [Accepted: 08/21/2016] [Indexed: 11/21/2022] Open
Abstract
Pet turtles are known as a source of Salmonella infection to humans when handled in captivity. Thirty four turtles purchased from pet shops and online markets in Korea were examined to determine whether the turtles and their environment were contaminated with Salmonella spp. Salmonella spp. were isolated from fecal samples of 17 turtles. These isolates were identified as S. enterica through 16S rRNA gene sequencing. The isolation rate of Salmonella spp. from the soil and water samples increased over time. We concluded that a high percentage of turtles being sold in pet shops were infected with Salmonella spp., and their environments tend to become contaminated over time unless they are maintained properly. These results indicate that pet turtles could be a potential risk of salmonellosis in Korea.
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Nowakiewicz A, Zięba P, Ziółkowska G, Gnat S, Muszyńska M, Tomczuk K, Majer Dziedzic B, Ulbrych Ł, Trościańczyk A. Free-Living Species of Carnivorous Mammals in Poland: Red Fox, Beech Marten, and Raccoon as a Potential Reservoir of Salmonella, Yersinia, Listeria spp. and Coagulase-Positive Staphylococcus. PLoS One 2016; 11:e0155533. [PMID: 27171434 PMCID: PMC4865137 DOI: 10.1371/journal.pone.0155533] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/29/2016] [Indexed: 12/01/2022] Open
Abstract
The objective of the study was to examine a population of free-living carnivorous mammals most commonly found in Poland (red fox, beech marten, and raccoon) for the occurrence of bacteria that are potentially pathogenic for humans and other animal species and to determine their virulence potential (the presence of selected virulence genes). From the total pool of isolates obtained (n = 328), we selected 90 belonging to species that pose the greatest potential threat to human health: Salmonella spp. (n = 19; 4.51%), Yersinia enterocolitica (n = 10; 2.37%), Listeria monocytogenes and L. ivanovii (n = 21), and Staphylococcus aureus (n = 40; 9.5%). The Salmonella spp. isolates represented three different subspecies; S. enterica subsp. enterica accounted for a significant proportion (15/19), and most of the serotypes isolated (S. Typhimurium, S. Infantis, S. Newport and S. Enteritidis) were among the 10 non-typhoidal Salmonella serotypes that are most often responsible for infections in Europe, including Poland. Y. enterococlitica was detected in the smallest percentage of animals, but 60% of strains among the isolates tested possessed the ail gene, which is responsible for attachment and invasion. Potentially pathogenic Listeria species were isolated from approx. 5% of the animals. The presence of all tested virulence genes was shown in 35% of L. monocytogenes strains, while in the case of the other strains, the genes occurred in varying numbers and configurations. The presence of the inlA, inlC, hlyA, and iap genes was noted in all strains, whereas the genes encoding PI-PLC, actin, and internalin Imo2821 were present in varying percentages (from 80% to 55%). S. aureus was obtained from 40 individuals. Most isolates possessed the hla, hld (95% for each), and hlb (32.5%) genes encoding hemolysins as well as the gene encoding leukotoxin lukED (70%). In a similar percentage of strains (77.5%), the presence of at least one gene encoding enterotoxin was found, with 12.5% exhibiting the presence of egc-like variants. In two animals, we also noted the gene encoding the TSST-1 toxin. The results of the study showed that free-living animals may be a significant reservoir of bacteria that are potentially pathogenic for humans. The results of the statistical analysis revealed that, among the animals species studied, the red fox constitutes the most important source of infections.
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Affiliation(s)
- Aneta Nowakiewicz
- Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine University of Life Sciences, Lublin, Poland
| | | | - Grażyna Ziółkowska
- Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine University of Life Sciences, Lublin, Poland
| | - Sebastian Gnat
- Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine University of Life Sciences, Lublin, Poland
| | | | - Krzysztof Tomczuk
- Sub-Department of Parasitology and Invasive Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Lublin, Poland
| | - Barbara Majer Dziedzic
- Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine University of Life Sciences, Lublin, Poland
| | | | - Aleksandra Trościańczyk
- Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine University of Life Sciences, Lublin, Poland
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Abstract
This study aimed to evaluate the incidence ofSalmonellaisolates from a wide variety of reptiles in Poland. A total of 374 faecal samples from chelonians, lizards and snakes were collected between 2009 and 2012. The nested, two-step PCR and multiplex PCR were performed to access the incidence and to characterizeSalmonellaisolates.Salmonellastrains were found in 122 of 374 samples (32.6%). Among the different reptilian species,Salmonellastrains were found in 58 samples from lizards (38.9%), 31 samples from snakes (28.7%) and 33 samples from chelonians (28.2%). Of the total of 122 strains, 72 belonged to the speciesSalmonella entericasubsp.enterica, 20 to the speciesS.entericasubs.salamaeorS.entericasubs.houtanae. The incidence ofS.entericasubs.diarizonaeandS.entericasubs.indicawas low, constituting less than 3.5% of the examined population. The findings show that reptiles can be considered as a reservoir forSalmonellaand hence could pose a zoonotic hazard. In addition, multiplex PCR assay is a rapid, specific and easy-to-perform method and might be applied for rapid screening of large numbers ofSalmonellasamples.
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Giorgi M, Rota S, Giorgi T, Capasso M, Briganti A. Blood Concentrations of Enrofloxacin and the Metabolite Ciprofloxacin in Yellow-Bellied Slider Turtles (Trachemys scripta scripta) After a Single Intracoelomic Injection of Enrofloxacin. J Exot Pet Med 2013. [DOI: 10.1053/j.jepm.2013.05.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Dipineto L, Capasso M, Maurelli MP, Russo TP, Pepe P, Capone G, Fioretti A, Cringoli G, Rinaldi L. Survey of co-infection by Salmonella and oxyurids in tortoises. BMC Vet Res 2012; 8:69. [PMID: 22640421 PMCID: PMC3488555 DOI: 10.1186/1746-6148-8-69] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 04/10/2012] [Indexed: 11/10/2022] Open
Abstract
Background Salmonella spp. and oxyurids are among the most prevalent bacterial and parasitic agents in reptiles. These organisms are routinely isolated in healthy tortoises, although heavy infections may cause significant pathology. Tortoises are considered a common source of reptile-associated salmonellosis, an important zoonosis reported worldwide. A survey of the prevalence of Salmonella spp. and oxyurids in 53 tortoises was conducted in southern Italy and a possible correlation between the two pathogens was therefore investigated. Results Salmonella spp. and oxyurids were detected with a prevalence of 49.1 and 81.1%, respectively. A significant positive correlation between Salmonella spp. and oxyurids was demonstrated. However, confounding factors related to husbandry could have been involved in determining this correlation. Conclusions Our results suggest that caution should be exercised in translocation, husbandry, and human contact with tortoises and other exotic pets. Further studies on the epidemiology, molecular characterization and pathogenesis of Salmonella and oxyurids are needed to assess the actual impact of these organisms, as single or associated infections, on tortoises and on other exotic pets.
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Affiliation(s)
- Ludovico Dipineto
- Department of Pathology and Animal Health, University of Naples Federico II, Napoli, Italy
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