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Lopez-Garcia AV, AbuOun M, Nunez-Garcia J, Nale JY, Gaylov EE, Phothaworn P, Sukjoi C, Thiennimitr P, Malik DJ, Korbsrisate S, Clokie MRJ, Anjum MF. Pathogen genomics and phage-based solutions for accurately identifying and controlling Salmonella pathogens. Front Microbiol 2023; 14:1166615. [PMID: 37234523 PMCID: PMC10206635 DOI: 10.3389/fmicb.2023.1166615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/03/2023] [Indexed: 05/28/2023] Open
Abstract
Salmonella is a food-borne pathogen often linked to poultry sources, causing gastrointestinal infections in humans, with the numbers of multidrug resistant (MDR) isolates increasing globally. To gain insight into the genomic diversity of common serovars and their potential contribution to disease, we characterized antimicrobial resistance genes, and virulence factors encoded in 88 UK and 55 Thai isolates from poultry; the presence of virulence genes was detected through an extensive virulence determinants database compiled in this study. Long-read sequencing of three MDR isolates, each from a different serovar, was used to explore the links between virulence and resistance. To augment current control methods, we determined the sensitivity of isolates to 22 previously characterized Salmonella bacteriophages. Of the 17 serovars included, Salmonella Typhimurium and its monophasic variants were the most common, followed by S. Enteritidis, S. Mbandaka, and S. Virchow. Phylogenetic analysis of Typhumurium and monophasic variants showed poultry isolates were generally distinct from pigs. Resistance to sulfamethoxazole and ciprofloxacin was highest in isolates from the UK and Thailand, respectively, with 14-15% of all isolates being MDR. We noted that >90% of MDR isolates were likely to carry virulence genes as diverse as the srjF, lpfD, fhuA, and stc operons. Long-read sequencing revealed the presence of global epidemic MDR clones in our dataset, indicating they are possibly widespread in poultry. The clones included MDR ST198 S. Kentucky, harboring a Salmonella Genomic Island-1 (SGI)-K, European ST34 S. 1,4,[5],12:i:-, harboring SGI-4 and mercury-resistance genes, and a S. 1,4,12:i:- isolate from the Spanish clone harboring an MDR-plasmid. Testing of all isolates against a panel of bacteriophages showed variable sensitivity to phages, with STW-77 found to be the most effective. STW-77 lysed 37.76% of the isolates, including serovars important for human clinical infections: S. Enteritidis (80.95%), S. Typhimurium (66.67%), S. 1,4,[5],12:i:- (83.3%), and S. 1,4,12: i:- (71.43%). Therefore, our study revealed that combining genomics and phage sensitivity assays is promising for accurately identifying and providing biocontrols for Salmonella to prevent its dissemination in poultry flocks and through the food chain to cause infections in humans.
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Affiliation(s)
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Javier Nunez-Garcia
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Janet Y. Nale
- Department of Veterinary and Animal Science, Scotland's Rural College, Inverness, United Kingdom
| | - Edouard E. Gaylov
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Preeda Phothaworn
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chutikarn Sukjoi
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Danish J. Malik
- Department of Chemical Engineering, Loughborough University, Loughborough, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
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Serotype Occurrence, Virulence Profiles, Antimicrobial Resistance and Molecular Characterization of Salmonella Isolated from Hospitalized Patients with Gastroenteritis in Great Tunisia between 2010 and 2020. Antibiotics (Basel) 2023; 12:antibiotics12030526. [PMID: 36978394 PMCID: PMC10044041 DOI: 10.3390/antibiotics12030526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
Non-typhoid Salmonella is one of the major causes of food-borne infections worldwide. The aim of the current study is to determine the serotype occurrence, virulence factors and antimicrobial resistance patterns of Salmonella isolated from hospitalized patients. The identification of Salmonella strains was performed according to REMIC, 2018. The susceptibility of Salmonella isolates was assessed against 20 antimicrobials using the disk diffusion method. Some virulence and antimicrobial resistance genes were identified using PCR. Among the 61 isolated Salmonella strains, seven serotypes were identified and all were positive for the virulence genes invA, mgtC and sirA. Critical resistance rates (>40%) were detected for tetracycline, nalidixic acid, amoxicillin and fluoroquinolones. However, resistances to ertapenem, ceftazidim, aztreonam and colistin were null. In addition, 33% of the isolated strains were multidrug-resistant (MDR). Moreover, 80% and 60% of S. Kentucky isolates were identified as fluoroquinolone-resistant and MDR strains, respectively. The qnrB gene was amplified in 63.2% of fluoroquinolone-resistant strains. The dfrA1 gene was identified in 20% (4/20) of the trimethoprim-sulfamethoxazole resistant strains and the integrase Class 2 gene was amplified in only 8.2% (5/61) of the isolates. Our findings highlight the emergence of MDR Salmonella isolates. A rationalization of antimicrobial use is urgently recommended in both human and veterinary medicine.
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Retamal P, Gaspar J, Benavides MB, Saenz L, Galarce N, Aravena T, Cornejo J, Lapierre L. Virulence and antimicrobial resistance factors in Salmonella enterica serotypes isolated from pigs and chickens in central Chile. Front Vet Sci 2022; 9:971246. [PMID: 36204291 PMCID: PMC9530323 DOI: 10.3389/fvets.2022.971246] [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: 06/16/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica is a food-borne pathogen with a wide host-range that during decades has been of public health concern in developed and developing countries. In Chile, the poultry and pig industries represent the biggest contribution of meat consumption in the population, and sanitary regulations have been imposed for Salmonella control. The aim of this work was to determine and characterize Salmonella strains isolated from pigs and chicken raised on commercials farms in Chile. For this, isolates belonging to pigs (n = 46) and poultry (n = 57) were genotyped by two multiplex PCR reactions and virulotyped by the PCR detection of virulence-associated genes. In addition, isolates were serotyped and analyzed by the Kirby Bauer assay to determine their antimicrobial resistance phenotypes. From these analyses 52 genotypes, six serotypes and several multidrug resistance phenotypes and different combinations of virulence-associated genes were detected. These results suggest that S. enterica in pigs and poultry in central Chile should be monitored due to potential consequences in public and animal health.
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Affiliation(s)
- Patricio Retamal
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Joaquim Gaspar
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Magister en Ciencias Animales y Veterinarias, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - María Belén Benavides
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Magister en Ciencias Animales y Veterinarias, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Leonardo Saenz
- Departamento de Ciencias Biológicas, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Nicolás Galarce
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Trinidad Aravena
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Javiera Cornejo
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Javiera Cornejo
| | - Lisette Lapierre
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- *Correspondence: Lisette Lapierre
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Nunez-Garcia J, AbuOun M, Storey N, Brouwer MS, Delgado-Blas JF, Mo SS, Ellaby N, Veldman KT, Haenni M, Châtre P, Madec JY, Hammerl JA, Serna C, Getino M, La Ragione R, Naas T, Telke AA, Glaser P, Sunde M, Gonzalez-Zorn B, Ellington MJ, Anjum MF. Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance. Sci Rep 2022; 12:14372. [PMID: 35999234 PMCID: PMC9396611 DOI: 10.1038/s41598-022-16760-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Abstract
Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, and detection of antimicrobial resistance (AMR). Numerous published methods and protocols exist, but a lack of harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital for global genomic diagnostics and surveillance. As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436 Escherichia coli were compared to their AMR phenotypes, with the latter used as gold-standard. The pipelines exploited previously known genotype–phenotype associations. No significant differences in software performance were observed. As a consequence, efforts to harmonise AMR predictions from sequence data should focus on: (1) establishing universal minimum to assess performance thresholds (e.g. a control isolate panel, minimum sensitivity/specificity thresholds); (2) standardising AMR gene identifiers in reference databases and gene nomenclature; (3) producing consistent genotype/phenotype correlations. The study also revealed limitations of in-silico technology on detecting resistance to certain antimicrobials due to lack of specific fine-tuning options in bioinformatics tool or a lack of representation of resistance mechanisms in reference databases. Lastly, we noted user friendliness of tools was also an important consideration. Therefore, our recommendations are timely for widespread standardisation of bioinformatics for genomic diagnostics and surveillance globally.
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Affiliation(s)
| | - M AbuOun
- Animal and Plant Health Agency (APHA), Weybridge, UK
| | - N Storey
- Animal and Plant Health Agency (APHA), Weybridge, UK
| | - M S Brouwer
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | | | - S S Mo
- Norwegian Veterinary Institute (NVI), Oslo, Norway
| | - N Ellaby
- Public Health England (PHE), London, UK
| | - K T Veldman
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - M Haenni
- Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Maisons-Alfort, France
| | - P Châtre
- Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Maisons-Alfort, France
| | - J Y Madec
- Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Maisons-Alfort, France
| | - J A Hammerl
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - C Serna
- Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - M Getino
- University of Surrey (UoS), Guildford, UK
| | | | - T Naas
- Assistance Publique Hopitaux de Paris, Paris, France
| | - A A Telke
- Norwegian Veterinary Institute (NVI), Oslo, Norway
| | - P Glaser
- Institute Pasteur, EERA Unit, Paris, France
| | - M Sunde
- Norwegian Veterinary Institute (NVI), Oslo, Norway
| | | | | | - M F Anjum
- Animal and Plant Health Agency (APHA), Weybridge, UK. .,University of Surrey (UoS), Guildford, UK.
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Oueslati W, Rjeibi MR, Benyedem H, Mamlouk A, Souissi F, Selmi R, Ettriqui A. Salmonella Broiler Meat's Contamination in Tunisia: Prevalence, Serotypes, Antimicrobial Resistance and Molecular Characterization of Isolated Strains. Curr Microbiol 2022; 79:208. [PMID: 35639195 DOI: 10.1007/s00284-022-02900-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/09/2022] [Indexed: 11/03/2022]
Abstract
This study was conducted in north-eastern Tunisia to estimate the contamination prevalence of Salmonella in broilers' meat, to rank serotypes and to characterize the isolated multidrug-resistant (MDR) strains. A total number of 1288 meat samples were collected from 322 broiler batches; Salmonella isolates were identified by the alternative technique VIDAS Easy Salmonella. The susceptibility of Salmonella isolates was assessed against 21 antimicrobials using the disc diffusion method on Mueller-Hinton agar. Some antimicrobial resistance genes were identified using Polymerase Chain Reaction (PCR). The prevalence rates of Salmonella in the neck skin and the breast muscle contamination were estimated at 11.8% (38/322) and 0.9% (3/322), respectively. The prevalence rate of Salmonella in meat cutting parts contamination was estimated at 5.1% (33/644). Eight serotypes of Salmonella were identified, namely S. Enteritidis, S. Kentucky, S. Anatum, S. Infantis, S. Mbandaka, S. Zanzibar, S. Hadar and S. Agona. High rate of resistance was identified against amoxicillin (91.9%), nalidixic acid (83.8%), tetracycline (75.7%), streptomycin (73%), ciprofloxacin (70%), sulfamides (68.9%), cefalotin (68.9%), cefotaxim (67.6%) and cefoxitin (60.8%). The majority (90.5%; 67/74) of isolated strains was recognized as MDR. Nine MDR strains were identified as Extended-Spectrum β-Lactamase (ESBL) producers. The blaCTX-M gene was identified by PCR in all the nine ESBL strains. TetA, tetB and dfrA1 genes were amplified in 3.6% (2/56), 1.8% (1/56) and 19.3% (5/26) of tetracycline and trimethoprim-resistant strains, respectively. The integrase gene (class 2) was identified in only 8.1% (6/74) of the Salmonella-isolated strains. Our findings highlight the emergence of MDR Salmonella isolates in Tunisia.
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Affiliation(s)
- Walid Oueslati
- Laboratory of Management of Animal Production's Health and Quality, National School of Veterinary Medicine of Sidi Thabet, University Manouba (LR14AGR03), 2010, La Manouba, Tunisia. .,Department of Animal Production, National Agronomic Institute, University Carthage, 1054, Carthage, Tunisia.
| | - Mohamed Ridha Rjeibi
- Laboratory of Parasitology, National School of Veterinary Medicine of Sidi Thabet, University Manouba, 2010, La Manouba, Tunisia.,Laboratory of Parasitology, Veterinary Research Institute, University de Tunis El Manar, 1068, Tunis, Tunisia
| | - Hayet Benyedem
- Laboratory of Parasitology, National School of Veterinary Medicine of Sidi Thabet, University Manouba, 2010, La Manouba, Tunisia
| | - Aymen Mamlouk
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University Manouba, 2010, La Manouba, Tunisia
| | - Fatma Souissi
- Laboratory of Management of Animal Production's Health and Quality, National School of Veterinary Medicine of Sidi Thabet, University Manouba (LR14AGR03), 2010, La Manouba, Tunisia
| | - Rachid Selmi
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University Manouba, 2010, La Manouba, Tunisia
| | - Abdelfettah Ettriqui
- Laboratory of Management of Animal Production's Health and Quality, National School of Veterinary Medicine of Sidi Thabet, University Manouba (LR14AGR03), 2010, La Manouba, Tunisia
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Antimicrobial Resistance and Virulence of Non-Typhoidal Salmonella from Retail Foods Marketed in Bangkok, Thailand. Foods 2022; 11:foods11050661. [PMID: 35267294 PMCID: PMC8909193 DOI: 10.3390/foods11050661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/12/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023] Open
Abstract
Nontyphoidal-Salmonella bacteria cause foodborne gastroenteritis that may lead to fatal bacteremia, osteomyelitis, and meningitis if not treated properly. The emergence of multidrug-resistant Salmonella strains is a global public health threat. Regular monitoring of genotypes and phenotypes of Salmonella isolated from humans, animals, foods, and environments is mandatory for effective reduction and control of this food-borne pathogen. In this study, antimicrobial-resistant and virulent genotypes and phenotypes of Salmonella isolated from retail food samples in Bangkok, Thailand, were investigated. From 252 raw food samples, 58 Salmonella strains that belonged only to serotype Enteritidis were isolated. Disc diffusion method showed that all isolates were still sensitive to amikacin and carbapenems. More than 30% of the isolates were resistant to ampicillin, tetracycline, and ciprofloxacin. Twenty isolates resist at least three antibiotic classes. Minimum inhibitory concentration tests showed that 12.07% of the isolates produced extended-spectrum β-Lactamase. Polymerase chain reaction indicated that 32.76, 81.03, 39.66, and 5.17% of the isolates carried blaTEM-1, tetA, sul2, and dfrA7, respectively. All isolates were positive for invasion-associated genes. Effective prevention and control of Salmonella (as well as other food-borne pathogens) is possible by increasing public awareness and applying food hygienic practices. Active and well harmonised “One Health” co-operation is required to effectively control food-borne zoonosis.
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Prevalence, Risk Factors, Antimicrobial Resistance and Molecular Characterization of Salmonella in Northeast Tunisia Broiler Flocks. Vet Sci 2021; 9:vetsci9010012. [PMID: 35051096 PMCID: PMC8780282 DOI: 10.3390/vetsci9010012] [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: 10/18/2021] [Revised: 11/27/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
This study was conducted in northeastern Tunisia to estimate both the prevalence and the risk factors of Salmonella in broiler flocks as well as to characterize the isolated multidrug-resistant (MDR) Salmonella strains. In the present study, a total number of 124 farms were sampled; Salmonella isolates were identified by the alternative technique VIDAS Easy Salmonella. The susceptibility of Salmonella isolates was assessed against 21 antimicrobials using the disk diffusion method on Mueller–Hinton agar using antimicrobial discs. Some antimicrobial resistance genes were identified using PCR. The prevalence rate of Salmonella infection, in the sampled farms, was estimated at 19.9% (64/322). Moreover, a total number of 13 different serotypes were identified. High rate of resistance was identified against nalidixic acid (82.85%), amoxicillin (81.25%), streptomycin (75%), and ciprofloxacin (75%). Alarming level of resistance to ertapenem (12.5%) was noticed. A total of 87.5% (56/64) of isolated strains were recognized as MDR. Three MDR strains were extended-spectrum β-lactamases (ESBL)-producers and three MDR strains were cephalosporinase-producers. The blaCTX-M gene was amplified in all the three ESBL strains. The qnrB gene was not amplified in fluoroquinolones-resistant strains. The tetA and tetB genes were amplified in 5% (2/40) and 2.5% (1/40) of tetracycline-resistant strains, respectively. The dfrA1 gene was amplified in five of the 20 trimethoprim-resistant strains. The mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5 genes were not amplified in any of the phenotypically colistin-resistant strains. In terms of integrase genes int1 and int2, only gene class 2 was amplified in 11% (7/64) of analyzed strains. Risk factors, such as the poor level of cleaning and disinfection, the lack of antimicrobial treatment at the start of the breeding, and a crawl space duration lower than 15 days, were associated with high Salmonella infection in birds. These data should be considered when preparing salmonellosis control programs in Tunisian broiler flocks.
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Dos Santos AMP, Ferrari RG, Panzenhagen P, Rodrigues GL, Conte-Junior CA. Virulence genes identification and characterization revealed the presence of the Yersinia High Pathogenicity Island (HPI) in Salmonella from Brazil. Gene 2021; 787:145646. [PMID: 33848574 DOI: 10.1016/j.gene.2021.145646] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/22/2021] [Accepted: 04/07/2021] [Indexed: 11/30/2022]
Abstract
Salmonella spp. is one of the major agents of foodborne disease worldwide, and its virulence genes are responsible for the main pathogenic mechanisms of this micro-organism. The whole-genome sequencing (WGS) of pathogens has become a lower-cost and more accessible genotyping tool providing many gene analysis possibilities. This study provided an in silico investigation of 129 virulence genes, including plasmidial and bacteriophage genes from Brazilian strains' public Salmonella genomes. The frequency analysis of the four most sequenced serovars and a temporal analysis over the past four decades was also performed. The NCBI sequence reads archive (SRA) database comprised 1077 Salmonella public whole-genome sequences of strains isolated in Brazil between 1968 and 2018. Among the 1077 genomes, 775 passed in Salmonella in silico Typing (SISTR) quality control, which also identified 41 different serovars in which the four most prevalent were S. Enteritidis, S. Typhimurium, S. Dublin, and S. Heidelberg. Among these, S. Heidelberg presented the most distinct virulence profile, besides presenting Yersinia High Pathogenicity Island (HPI), rare and first reported in Salmonella from Brazil. The genes mgtC, csgC, ssaI and ssaS were the most prevalent within the 775 genomes with more than 99% prevalence. On the other hand, the less frequent genes were astA, iucBCD, tptC and shdA, with less than 1% frequency. All of the plasmids and bacteriophages virulence genes presented a decreasing trend between the 2000 s and 2010 s decades, except for the phage gene grvA, which increased in this period. This study provides insights into Salmonella virulence genes distribution in Brazil using freely available bioinformatics tools. This approach could guide in vivo and in vitro studies besides being an interesting method for the investigation and surveillance of Salmonella virulence. Moreover, here we propose the genes mgtC, csgC, ssaI and ssaS as additional targets for PCR identification of Salmonella in Brazil due to their very high frequency in the studied genomes.
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Affiliation(s)
- Anamaria M P Dos Santos
- Molecular & Analytical Laboratory Center, Faculty of Veterinary, Department of Food Technology, Universidade Federal Fluminense, Niterói, Brazil; Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Center for Food Analysis (NAL-LADETEC), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafaela G Ferrari
- Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil.
| | - Pedro Panzenhagen
- Molecular & Analytical Laboratory Center, Faculty of Veterinary, Department of Food Technology, Universidade Federal Fluminense, Niterói, Brazil; Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Center for Food Analysis (NAL-LADETEC), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Grazielle L Rodrigues
- Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Center for Food Analysis (NAL-LADETEC), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos A Conte-Junior
- Molecular & Analytical Laboratory Center, Faculty of Veterinary, Department of Food Technology, Universidade Federal Fluminense, Niterói, Brazil; Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Center for Food Analysis (NAL-LADETEC), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; National Institute of Health Quality Control, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Lapierre L, Cornejo J, Zavala S, Galarce N, Sánchez F, Benavides MB, Guzmán M, Sáenz L. Phenotypic and Genotypic Characterization of Virulence Factors and Susceptibility to Antibiotics in Salmonella Infantis Strains Isolated from Chicken Meat: First Findings in Chile. Animals (Basel) 2020; 10:ani10061049. [PMID: 32570768 PMCID: PMC7341295 DOI: 10.3390/ani10061049] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 01/22/2023] Open
Abstract
Simple Summary Salmonella Infantis (S. Infantis) is a zoonotic pathogen that causes gastroenteritis in humans and animals, with poultry being its main reservoir. This pathogen has emerged over the last few decades in different countries, causing outbreaks in humans subsequent to foodborne transmission. It is important to be able to characterize this pathogen in order to establish control measures in the poultry industry. In this study, we investigated the presence of virulence genes, biofilm formation abilities, antibiotic resistance genes, and antibiotic susceptibility in S. Infantis. The results showed that the S. Infantis strains isolated from chicken meat for sale in supermarkets in Santiago, Chile are multidrug-resistant (MDR) and contain virulence genes, making them pathogenic. Thus, Salmonella Infantis should be under surveillance in the poultry food production chain with the aim of protecting public health. Abstract Salmonella Infantis is a zoonotic pathogen that causes gastroenteritis in humans and animals, with poultry being its main reservoir. In Chile, there are no data to characterize S. Infantis strains in poultry production. In this study, 87 S. Infantis strains were isolated from chicken meat for sale in supermarkets in Santiago, Chile, and characterized according to their virulence genes, biofilm formation abilities, antibiotic susceptibility, and resistance genes. Through polymerase chain reaction or PCR, the strains were analyzed to detect the presence of 11 virulence genes, 12 antibiotic resistance genes, and integrase genes. Moreover, disc diffusion susceptibility to 18 antimicrobials and the ability to form biofilm in vitro were evaluated. Results demonstrated six different virulence gene profiles. Ninety-four percent of the strains were multi-resistant to antibiotics with weak biofilm formation abilities, 63.2% of the strains were broad spectrum β- lactam resistant, and the blaCTX-M-65 gene was amplified in 13 strains. Only 3.4% of the strains were fluoroquinolone resistant, and the qnrB gene was amplified in two strains. Colistin resistance was exhibited in 28.7% of the strains, but mrc genes were not amplified in any strain under study. The isolated S. Infantis strains are pathogenic and antibiotic multi-resistant, and thus, this Salmonella serotype should be under surveillance in the poultry food production chain with the aim of protecting public health.
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Affiliation(s)
- Lisette Lapierre
- Department of Animal Preventive Medicine, Faculty of Veterinary and Animal Sciences, Universidad de Chile, Santiago 8820808, Chile; (J.C.); (S.Z.); (N.G.); (F.S.); (M.B.B.)
- Correspondence: ; Tel.: +56-229-785-615
| | - Javiera Cornejo
- Department of Animal Preventive Medicine, Faculty of Veterinary and Animal Sciences, Universidad de Chile, Santiago 8820808, Chile; (J.C.); (S.Z.); (N.G.); (F.S.); (M.B.B.)
| | - Sebastián Zavala
- Department of Animal Preventive Medicine, Faculty of Veterinary and Animal Sciences, Universidad de Chile, Santiago 8820808, Chile; (J.C.); (S.Z.); (N.G.); (F.S.); (M.B.B.)
| | - Nicolás Galarce
- Department of Animal Preventive Medicine, Faculty of Veterinary and Animal Sciences, Universidad de Chile, Santiago 8820808, Chile; (J.C.); (S.Z.); (N.G.); (F.S.); (M.B.B.)
| | - Fernando Sánchez
- Department of Animal Preventive Medicine, Faculty of Veterinary and Animal Sciences, Universidad de Chile, Santiago 8820808, Chile; (J.C.); (S.Z.); (N.G.); (F.S.); (M.B.B.)
| | - María Belén Benavides
- Department of Animal Preventive Medicine, Faculty of Veterinary and Animal Sciences, Universidad de Chile, Santiago 8820808, Chile; (J.C.); (S.Z.); (N.G.); (F.S.); (M.B.B.)
| | - Miguel Guzmán
- Laboratory of Avian Pathology, Faculty of Veterinary and Animal Sciences, Universidad de Chile, Santiago 8820808, Chile;
| | - Leonardo Sáenz
- Laboratory of Veterinary Vaccines, Department of Animal Biology, Faculty of Veterinary and Animal Science, Universidad de Chile, Santiago 8820808, Chile;
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Retamal P, Llanos-Soto S, Salas LM, López J, Vianna J, Hernández J, Medina-Vogel G, Castañeda F, Fresno M, González-Acuña D. Isolation of drug-resistant Salmonella enterica serovar enteritidis strains in gentoo penguins from Antarctica. Polar Biol 2017. [DOI: 10.1007/s00300-017-2163-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Anjum MF, Duggett NA, AbuOun M, Randall L, Nunez-Garcia J, Ellis RJ, Rogers J, Horton R, Brena C, Williamson S, Martelli F, Davies R, Teale C. Colistin resistance in Salmonella and Escherichia coli isolates from a pig farm in Great Britain. J Antimicrob Chemother 2016; 71:2306-13. [PMID: 27147305 DOI: 10.1093/jac/dkw149] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/31/2016] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The objective of this study was to characterize colistin-resistant bacteria isolated from pigs on a farm in Great Britain following identification of a plasmid-borne colistin resistance mechanism in Escherichia coli from China. METHODS Phenotypic antimicrobial susceptibility testing was undertaken by broth dilution and WGS was performed to detect the presence of genes encoding resistance and virulence. Transferable colistin resistance was investigated by conjugation. RESULTS Two E. coli and one Salmonella Typhimurium variant Copenhagen were shown to be MDR, including resistance to colistin, with one E. coli and the Salmonella carrying the mcr-1 gene; all three harboured chromosomal mutations in genes conferring colistin resistance and both E. coli harboured β-lactamase resistance. The Salmonella mcr-1 plasmid was highly similar to pHNSHP45, from China, while the E. coli mcr-1 plasmid only had the ISApII and mcr-1 genes in common. The frequency of mcr-1 plasmid transfer by conjugation to recipient Enterobacteriaceae from Salmonella was low, lying between 10(-7) and 10(-9) cfu/recipient cfu. We were unable to demonstrate mcr-1 plasmid transfer from the E. coli. Plasmid profiling indicated transfer of multiple plasmids from the Salmonella resulting in some MDR transconjugants. CONCLUSIONS Identification of the mcr-1 gene in Enterobacteriaceae from pigs confirms its presence in livestock in Great Britain. The results suggest dissemination of resistance through different horizontally transferable elements. The in vitro transfer of multiple plasmids carrying colistin and other resistances from the Salmonella isolate underlines the potential for wider dissemination and recombination.
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Affiliation(s)
- Muna F Anjum
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Nicholas A Duggett
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Luke Randall
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Javier Nunez-Garcia
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Richard J Ellis
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Jon Rogers
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Robert Horton
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Camilla Brena
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Susanna Williamson
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Francesca Martelli
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Robert Davies
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Christopher Teale
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
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Perry JJ, Yousef AE. Salmonella enteritidis in shell eggs: evolving concerns and innovative control measures. ADVANCES IN APPLIED MICROBIOLOGY 2016; 81:243-74. [PMID: 22958532 DOI: 10.1016/b978-0-12-394382-8.00007-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The issue of egg contamination with Salmonella enterica serovar Enteritidis rose to prominence several decades ago with increasing rate of infection around the world. Recent outbreaks have assured that this problem maintains a place in the public consciousness. Extensive research has been conducted to investigate the factors precipitating contamination events, their avoidance, and mitigation of the threat of contaminated eggs; consequently, regulations have been put in place to increase the safety of shell eggs. Despite these measures, rate of illness remains significantly higher than projected goals. This chapter includes information regarding the contraction of Salmonella species by laying hens and the subsequent deposition of these cells in shell eggs. Particular attention will be given to the prevalence of Salmonella Enteritidis in eggs and egg-containing products relative to other salmonellae. Research has been conducted to elucidate the mechanisms behind the fitness of Salmonella Enteritidis strains for this environment, but a consensus has yet to be reached. Novel methods of sanitizing shell eggs also are reviewed.
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Retamal P, Fresno M, Dougnac C, Gutierrez S, Gornall V, Vidal R, Vernal R, Pujol M, Barreto M, González-Acuña D, Abalos P. Genetic and phenotypic evidence of the Salmonella enterica serotype Enteritidis human-animal interface in Chile. Front Microbiol 2015; 6:464. [PMID: 26029196 PMCID: PMC4432690 DOI: 10.3389/fmicb.2015.00464] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/28/2015] [Indexed: 12/26/2022] Open
Abstract
Salmonella enterica serotype Enteritidis is a worldwide zoonotic agent that has been recognized as a very important food-borne bacterial pathogen, mainly associated with consumption of poultry products. The aim of this work was to determine genotypic and phenotypic evidence of S. Enteritidis transmission among seabirds, poultry and humans in Chile. Genotyping was performed using PCR-based virulotyping, pulse-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Pathogenicity-associated phenotypes were determined with survival to free radicals, acidic pH, starvation, antimicrobial resistance, and survival within human dendritic cells. As result of PCR and PFGE assays, some isolates from the three hosts showed identical genotypic patterns, and through MLST it was determined that all of them belong to sequence type 11. Phenotypic assays show diversity of bacterial responses among isolates. When results were analyzed according to bacterial host, statistical differences were identified in starvation and dendritic cells survival assays. In addition, isolates from seabirds showed the highest rates of resistance to gentamycin, tetracycline, and ampicillin. Overall, the very close genetic and phenotypic traits shown by isolates from humans, poultry, and seabirds suggest the inter-species transmission of S. Enteritidis bacteria between hosts, likely through anthropogenic environmental contamination that determines infection of seabirds with bacteria that are potentially pathogenic for other susceptible organism, including humans.
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Affiliation(s)
- Patricio Retamal
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile Santiago, Chile ; Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile Santiago, Chile
| | - Marcela Fresno
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile Santiago, Chile
| | - Catherine Dougnac
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile Santiago, Chile
| | - Sindy Gutierrez
- Departamento de Medicina Preventiva, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile Santiago, Chile
| | - Vanessa Gornall
- Departamento de Medicina Preventiva, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile Santiago, Chile
| | - Roberto Vidal
- Emerging and Remerging Zoonosis Research Network Santiago, Chile ; Programa de Microbiología, Facultad de Medicina, Universidad de Chile Santiago, Chile
| | - Rolando Vernal
- Departamento de Odontología Conservadora, Facultad de Odontología, Universidad de Chile Santiago, Chile
| | - Myriam Pujol
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile Santiago, Chile
| | - Marlen Barreto
- Facultad de Ciencias de la Salud, Universidad Autónoma Santiago, Chile
| | - Daniel González-Acuña
- Emerging and Remerging Zoonosis Research Network Santiago, Chile ; Facultad de Ciencias Veterinarias, Universidad de Concepción Chillán, Chile
| | - Pedro Abalos
- Departamento de Medicina Preventiva, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile Santiago, Chile ; Emerging and Remerging Zoonosis Research Network Santiago, Chile
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Temperature and oxygen dependent metabolite utilization by Salmonella enterica serovars Derby and Mbandaka. PLoS One 2015; 10:e0120450. [PMID: 25798944 PMCID: PMC4370486 DOI: 10.1371/journal.pone.0120450] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/22/2015] [Indexed: 12/23/2022] Open
Abstract
Salmonella enterica is a zoonotic pathogen of clinical and veterinary significance, with over 2500 serovars. In previous work we compared two serovars displaying host associations inferred from isolation statistics. Here, to validate genome sequence data and to expand on the role of environmental metabolite constitution in host range determination we use a phenotypic microarray approach to assess the ability of these serovars to metabolise ~500 substrates at 25°C with oxygen (aerobic conditions) to represent the ex vivo environment and at 37°C with and without oxygen (aerobic/anaerobic conditions) to represent the in vivo environment. A total of 26 substrates elicited a significant difference in the rate of metabolism of which only one, D-galactonic acid-g-lactone, could be explained by the presence (S. Mbandaka) or the absence (S. Derby) of metabolic genes. We find that S. Mbandaka respires more efficiently at ambient temperatures and under aerobic conditions on 18 substrates including: glucosominic acid, saccharic acid, trehalose, fumaric acid, maltotriose, N-acetyl-D-glucosamine, N-acetyl-beta-D-mannosamine, fucose, L-serine and dihydroxy-acetone; whereas S. Derby is more metabolically competent anaerobically at 37°C for dipeptides, glutamine-glutamine, alanine-lysine, asparagine-glutamine and nitrogen sources glycine and nitrite. We conclude that the specific phenotype cannot be reliably predicted from the presence of metabolic genes directly relating to the metabolic pathways under study.
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Detection of Salmonella enterica in Magellanic penguins (Spheniscus magellanicus) of Chilean Patagonia: evidences of inter-species transmission. Epidemiol Infect 2014; 143:1187-93. [PMID: 25148565 DOI: 10.1017/s0950268814002052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Patagonia in southern South America is among the few world regions where direct human impact is still limited but progressively increasing, mainly represented by tourism, farming, fishing and mining activities. The sanitary condition of Patagonian wildlife is unknown, in spite of being critical for the assessment of anthropogenic effects there. The aim of this study was the characterization of Salmonella enterica strains isolated from wild colonies of Magellanic penguins (Spheniscus magellanicus) located in Magdalena Island and Otway Sound, in Chilean Patagonia. Eight isolates of Salmonella were found, belonging to Agona and Enteritidis serotypes, with an infection rate of 0·38%. Resistance to ampicillin, cefotaxime, ceftiofur and tetracycline antimicrobials were detected, and some of these strains showed genotypic similarity with Salmonella strains isolated from humans and gulls, suggesting inter-species transmission cycles and strengthening the role of penguins as sanitary sentinels in the Patagonian ecosystem.
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RNA sequencing reveals differences between the global transcriptomes of Salmonella enterica serovar enteritidis strains with high and low pathogenicities. Appl Environ Microbiol 2013; 80:896-906. [PMID: 24271167 DOI: 10.1128/aem.02740-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serovar Enteritidis is one of the important causes of bacterial food-borne gastroenteritis worldwide. Field strains of S. Enteritidis are relatively genetically homogeneous; however, they show extensive phenotypic diversity and differences in virulence potential. RNA sequencing (RNA-Seq) was used to characterize differences in the global transcriptome between several genetically similar but phenotypically diverse poultry-associated field strains of S. Enteritidis grown in laboratory medium at avian body temperature (42°C). These S. Enteritidis strains were previously characterized as high-pathogenicity (HP; n = 3) and low-pathogenicity (LP; n = 3) strains based on both in vitro and in vivo virulence assays. Using the negative binomial distribution-based statistical tools edgeR and DESeq, 252 genes were identified as differentially expressed in LP strains compared with their expression in the HP strains (P < 0.05). A majority of genes (235, or 93.2%) showed significantly reduced expression, whereas a few genes (17, or 6.8%) showed increased expression in all LP strains compared with HP strains. LP strains showed a unique transcriptional profile that is characterized by significantly reduced expression of several transcriptional regulators and reduced expression of genes involved in virulence (e.g., Salmonella pathogenicity island 1 [SPI-1], SPI-5, and fimbrial and motility genes) and protection against osmotic, oxidative, and other stresses, such as iron-limiting conditions commonly encountered within the host. Several functionally uncharacterized genes also showed reduced expression. This study provides a first concise view of the global transcriptional differences between field strains of S. Enteritidis with various levels of pathogenicity, providing the basis for future functional characterization of several genes with potential roles in virulence or stress regulation of S. Enteritidis.
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17
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Fresno M, Barrera V, Gornall V, Lillo P, Paredes N, Abalos P, Fernández A, Retamal P. Identification of diverse Salmonella serotypes, virulotypes, and antimicrobial resistance phenotypes in waterfowl from Chile. Vector Borne Zoonotic Dis 2013; 13:884-7. [PMID: 24107205 DOI: 10.1089/vbz.2013.1408] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Salmonella enterica is a pathogen with a wide host-range that presents great concern in developed and developing countries. To determine and characterize Salmonella strains found in Chile's waterfowl, we sampled 758 birds along 2000 km of the Chilean coast. In this sample, 46 isolates from 10 serotypes were detected, several with multidrug resistance phenotypes and different combinations of virulence-associated genes (virulotypes). These results suggest that Salmonella infection in waterfowl in Chile could have impacts on public and animal health.
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Affiliation(s)
- Marcela Fresno
- 1 Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile , Santiago, Chile
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18
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Evangelopoulou G, Kritas S, Govaris A, Burriel AR. Animal salmonelloses: a brief review of “host adaptation and host specificity” of Salmonella spp. Vet World 2013. [DOI: 10.14202/vetworld.2013.703-708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Guard J, Morales CA, Fedorka-Cray P, Gast RK. Single nucleotide polymorphisms that differentiate two subpopulations of Salmonella enteritidis within phage type. BMC Res Notes 2011; 4:369. [PMID: 21942987 PMCID: PMC3220660 DOI: 10.1186/1756-0500-4-369] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 09/26/2011] [Indexed: 11/16/2022] Open
Abstract
Background Salmonella Enteritidis is currently the world's leading cause of salmonellosis, in part because of its ability to contaminate the internal contents of eggs. Previous analyses have shown that it is an exceptionally clonal serotype, which nonetheless generates considerable phenotypic heterogeneity. Due to its clonality, whole genome analysis is required to find genetic determinants that contribute to strain heterogeneity of Salmonella Enteritidis. Comparative whole genome mutational mapping of two PT13a strains that varied in the ability to contaminate eggs and to form biofilm was achieved using a high-density tiling platform with primers designed from a PT4 reference genome. Confirmatory Sanger sequencing was used on each putative SNP identified by mutational mapping to confirm its presence and location as compared to the reference sequence. High coverage pyrosequencing was used as a supporting technology to review results. Results A total of 250 confirmed SNPs were detected that differentiated the PT13a strains. From these 250 SNPS, 247 were in the chromosome and 3 were in the large virulence plasmid. SNPs ranged from single base pair substitutions to a deletion of 215 bp. A total of 15 SNPs (3 in egg-contaminating PT13a 21046 and 12 in biofilm forming PT13a 21027) altered coding sequences of 16 genes. Pyrosequencing of the two PT13a subpopulations detected 8.9% fewer SNPs than were detected by high-density tiling. Deletions and ribosomal gene differences were classes of SNPs not efficiently detected by pyrosequencing. Conclusions These results increase knowledge of evolutionary trends within Salmonella enterica that impact the safety of the food supply. Results may also facilitate designing 2nd generation vaccines, because gene targets were identified that differentiate subpopulations with variant phenotypes. High-throughput genome sequencing platforms should be assessed for the ability to detect classes of SNPs equivalently, because each platform has different advantages and limits of detection.
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Affiliation(s)
- Jean Guard
- Agricultural Research Service (ARS), U, S, Department of Agriculture (USDA), 950 College Station Road, Athens, GA, 30605, USA.
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20
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Atterbury RJ, Hobley L, Till R, Lambert C, Capeness MJ, Lerner TR, Fenton AK, Barrow P, Sockett RE. Effects of orally administered Bdellovibrio bacteriovorus on the well-being and Salmonella colonization of young chicks. Appl Environ Microbiol 2011; 77:5794-803. [PMID: 21705523 PMCID: PMC3165243 DOI: 10.1128/aem.00426-11] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 06/14/2011] [Indexed: 11/20/2022] Open
Abstract
Bdellovibrio bacteriovorus is a bacterium which preys upon and kills Gram-negative bacteria, including the zoonotic pathogens Escherichia coli and Salmonella. Bdellovibrio has potential as a biocontrol agent, but no reports of it being tested in living animals have been published, and no data on whether Bdellovibrio might spread between animals are available. In this study, we tried to fill this knowledge gap, using B. bacteriovorus HD100 doses in poultry with a normal gut microbiota or predosed with a colonizing Salmonella strain. In both cases, Bdellovibrio was dosed orally along with antacids. After dosing non-Salmonella-infected birds with Bdellovibrio, we measured the health and well-being of the birds and any changes in their gut pathology and culturable microbiota, finding that although a Bdellovibrio dose at 2 days of age altered the overall diversity of the natural gut microbiota in 28-day-old birds, there were no adverse effects on their growth and well-being. Drinking water and fecal matter from the pens in which the birds were housed as groups showed no contamination by Bdellovibrio after dosing. Predatory Bdellovibrio orally administered to birds that had been predosed with a gut-colonizing Salmonella enterica serovar Enteritidis phage type 4 strain (an important zoonotic pathogen) significantly reduced Salmonella numbers in bird gut cecal contents and reduced abnormal cecal morphology, indicating reduced cecal inflammation, compared to the ceca of the untreated controls or a nonpredatory ΔpilA strain, suggesting that these effects were due to predatory action. This work is a first step to applying Bdellovibrio therapeutically for other animal, and possibly human, infections.
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Affiliation(s)
- Robert J. Atterbury
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Laura Hobley
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Robert Till
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Carey Lambert
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Michael J. Capeness
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Thomas R. Lerner
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Andrew K. Fenton
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Paul Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - R. Elizabeth Sockett
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
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Knudsen GM, Sommer HM, Sørensen ND, Olsen JE, Aabo S. Survival of Salmonella on cuts of beef carcasses subjected to dry aging. J Appl Microbiol 2011; 111:848-54. [PMID: 21714838 DOI: 10.1111/j.1365-2672.2011.05094.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS The aim of this study was to determine the survival of 15 different strains of Salmonella of selected serotypes during prolonged cold storage of beef. METHODS AND RESULTS Fifteen strains of eight different serotypes of Salmonella were spiked onto fresh cuts beef portions, and the survival was followed during storage in a laboratory cooling system. Over a 14-day period, all strains were reduced significantly in numbers; however, strains of Salmonella Typhimurium DT104 and Salmonella Enteritidis PT4 and PT8 survived significantly longer than strains of the serovars Dublin, Derby, Infantis and Newport. For five selected strains, the observations were verified in a pilot plant cooling facility mimicking industrial cooling. No significant differences in reduction were found between the two cooling methods. CONCLUSIONS A significant reduction in Salmonella can be obtained by dry aging of beef during cold storage but the survival is strain dependent. SIGNIFICANCE AND IMPACT OF THE STUDY From a hygienic point of view, cold storage of unpacked beef, which is still performed in small slaughterhouses, is a good alternative to vacuum packaging.
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Affiliation(s)
- G M Knudsen
- National Food Institute, Technical University of Denmark, Søborg, Denmark
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22
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In vitro and in vivo pathogenicity of Salmonella enteritidis clinical strains isolated from North America. Arch Microbiol 2011; 193:811-21. [DOI: 10.1007/s00203-011-0719-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 05/18/2011] [Accepted: 05/19/2011] [Indexed: 02/01/2023]
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Shah DH, Zhou X, Addwebi T, Davis MA, Orfe L, Call DR, Guard J, Besser TE. Cell invasion of poultry-associated Salmonella enterica serovar Enteritidis isolates is associated with pathogenicity, motility and proteins secreted by the type III secretion system. MICROBIOLOGY-SGM 2011; 157:1428-1445. [PMID: 21292746 DOI: 10.1099/mic.0.044461-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Salmonella enterica serovar Enteritidis (S. Enteritidis) is a major cause of food-borne gastroenteritis in humans worldwide. Poultry and poultry products are considered the major vehicles of transmission to humans. Using cell invasiveness as a surrogate marker for pathogenicity, we tested the invasiveness of 53 poultry-associated isolates of S. Enteritidis in a well-differentiated intestinal epithelial cell model (Caco-2). The method allowed classification of the isolates into low (n = 7), medium (n = 18) and high (n = 30) invasiveness categories. Cell invasiveness of the isolates did not correlate with the presence of the virulence-associated gene spvB or the ability of the isolates to form biofilms. Testing of representative isolates with high and low invasiveness in a mouse model revealed that the former were more invasive in vivo and caused more and earlier mortalities, whereas the latter were significantly less invasive in vivo, causing few or no mortalities. Further characterization of representative isolates with low and high invasiveness showed that most of the isolates with low invasiveness had impaired motility and impaired secretion of either flagella-associated proteins (FlgK, FljB and FlgL) or type III secretion system (TTSS)-secreted proteins (SipA and SipD) encoded on Salmonella pathogenicity island-1. In addition, isolates with low invasiveness had impaired ability to invade and/or survive within chicken macrophages. These data suggest that not all isolates of S. Enteritidis recovered from poultry may be equally pathogenic, and that the pathogenicity of S. Enteritidis isolates is associated, in part, with both motility and secretion of TTSS effector proteins.
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Affiliation(s)
- Devendra H Shah
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA
| | - Xiaohui Zhou
- WSU-Zoonoses Unit, Washington State University, Pullman, WA 99164, USA.,Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA
| | - Tarek Addwebi
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA
| | - Margaret A Davis
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA
| | - Lisa Orfe
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA
| | - Douglas R Call
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA
| | - Jean Guard
- Egg Quality and Safety Research Unit, Agriculture Research Service, United States Department of Agriculture, Athens, GA 30605, USA
| | - Thomas E Besser
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA
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Optical genetic mapping defines regions of chromosomal variation in serovars of S. enterica subsp. enterica of concern for human and animal health. Epidemiol Infect 2010; 139:1065-74. [PMID: 20860874 DOI: 10.1017/s0950268810002086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Infections involving Salmonella enterica subsp. enterica serovars have serious animal and human health implications; causing gastroenteritis in humans and clinical symptoms, such as diarrhoea and abortion, in livestock. In this study an optical genetic mapping technique was used to screen 20 field isolate strains from four serovars implicated in disease outbreaks. The technique was able to distinguish between the serovars and the available sequenced strains and group them in agreement with similar data from microarrays and PFGE. The optical maps revealed variation in genome maps associated with antimicrobial resistance and prophage content in S. Typhimurium, and separated the S. Newport strains into two clear geographical lineages defined by the presence of prophage sequences. The technique was also able to detect novel insertions that may have had effects on the central metabolism of some strains. Overall optical mapping allowed a greater level of differentiation of genomic content and spatial information than more traditional typing methods.
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Comparison of genotypes of Salmonella enterica serovar Enteritidis phage type 30 and 9c strains isolated during three outbreaks associated with raw almonds. Appl Environ Microbiol 2010; 76:3723-31. [PMID: 20363782 DOI: 10.1128/aem.03053-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In 2000 to 2001, 2003 to 2004, and 2005 to 2006, three outbreaks of Salmonella enterica serovar Enteritidis were linked with the consumption of raw almonds. The S. Enteritidis strains from these outbreaks had rare phage types (PT), PT30 and PT9c. Clinical and environmental S. Enteritidis strains were subjected to pulsed-field gel electrophoresis (PFGE), multilocus variable-number tandem repeat analysis (MLVA), and DNA microarray-based comparative genomic indexing (CGI) to evaluate their genetic relatedness. All three methods differentiated these S. Enteritidis strains in a manner that correlated with PT. The CGI analysis confirmed that the majority of the differences between the S. Enteritidis PT9c and PT30 strains corresponded to bacteriophage-related genes present in the sequenced genomes of S. Enteritidis PT4 and S. enterica serovar Typhimurium LT2. However, PFGE, MLVA, and CGI failed to discriminate between S. Enteritidis PT30 strains related to outbreaks from unrelated clinical strains or between strains separated by up to 5 years. However, metabolic fingerprinting demonstrated that S. Enteritidis PT4, PT8, PT13a, and clinical PT30 strains metabolized L-aspartic acid, L-glutamic acid, L-proline, L-alanine, and D-alanine amino acids more efficiently than S. Enteritidis PT30 strains isolated from orchards. These data indicate that S. Enteritidis PT9c and 30 strains are highly related genetically and that PT30 orchard strains differ from clinical PT30 strains metabolically, possibly due to fitness adaptations.
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Wu G, Abuoun M, Hackl E, La Ragione RM, Fookes M, Fenner J, Pan Z, Wenzl P, Anjum MF, Woodward MJ. Epidemic multidrug-resistant (MDR-AmpC) Salmonella enterica serovar Newport strains contain three phage regions and a MDR resistance plasmid. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:228-235. [PMID: 23766073 DOI: 10.1111/j.1758-2229.2009.00095.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Multidrug-resistant (MDR-AmpC) Salmonella enterica serovar Newport has caused serious disease in animals and humans in North America, whereas in the UK S. enterica serovar Newport is not associated with severe disease and usually sensitive to antibiotics; MDR S. Newport (not AmpC) strains have only been isolated from poultry. We found that UK poultry strains belonged to MLST type ST166 and were distinct from cattle isolates for being able to utilize D-tagotose and when compared by pulsed-field gel electrophoresis (PFGE), comparative genomic hybridization (CGH) and diversity arrays technology (DArT). Cattle strains belonged to the ST45 complex differing from ST166 at all seven loci. PFGE showed that 19 out of 27 cattle isolates were more than 85% similar to each other and some UK and US strains were indistinguishable. Both CGH and DArT identified genes (including phage-related ones) that were uniquely present in the US isolates and two such genes identified by DArT showed sequence similarities with the pertussis-like (artAB) toxin. This work demonstrates that MDR-AmpC S. Newport from the USA are genetically closely related to pan-susceptible strains from the UK, but contained three extra phage regions and a MDR plasmid.
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Affiliation(s)
- Guanghui Wu
- Department for Food and Environmental Safety, Veterinary Laboratories Agency (VLA)-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT13 3NB, UK. AIT Austrian Institute of Technology GmbH, Bioresources Unit, 2444 Seibersdorf, Austria. The Pathogen Genetics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Diversity Arrays Technology Pty Ltd, Yarralumla, Canberra, ACT 2600, Australia
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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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