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Sandholt AKS, Neimanis A, Roos A, Eriksson J, Söderlund R. Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises. Vet Res 2021; 52:134. [PMID: 34674747 PMCID: PMC8529817 DOI: 10.1186/s13567-021-01001-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 09/21/2021] [Indexed: 11/21/2022] Open
Abstract
A type of monophasic group B Salmonella enterica with the antigenic formula 4,12:a:- (“Fulica-like”) has been described as associated with harbour porpoises (Phocoena phocoena), most frequently recovered from lung samples. In the present study, lung tissue samples from 47 porpoises found along the Swedish coast or as bycatch in fishing nets were analysed, two of which were positive for S. enterica. Pneumonia due to the infection was considered the likely cause of death for one of the two animals. The recovered isolates were whole genome sequenced and found to belong to sequence type (ST) 416 and to be closely related to ST416/ST417 porpoise isolates from UK waters as determined by core-genome MLST. Serovars Bispebjerg, Fulica and Abortusequi were identified as distantly related to the porpoise isolates, but no close relatives from other host species were found. All ST416/417 isolates had extensive loss of function mutations in key Salmonella pathogenicity islands, but carried accessory genetic elements associated with extraintestinal infection such as iron uptake systems. Gene ontology and pathway analysis revealed reduced secondary metabolic capabilities and loss of function in terms of signalling and response to environmental cues, consistent with adaptation for the extraintestinal niche. A classification system based on machine learning identified ST416/417 as more invasive than classical gastrointestinal serovars. Genome analysis results are thus consistent with ST416/417 as a host-adapted and extraintestinal clonal population of S. enterica, which while found in porpoises without associated pathology can also cause severe opportunistic infections.
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Affiliation(s)
- Arnar K S Sandholt
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Aleksija Neimanis
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden
| | - Anna Roos
- Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Stockholm, Sweden
| | - Jenny Eriksson
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Robert Söderlund
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden.
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Key FM, Posth C, Esquivel-Gomez LR, Hübler R, Spyrou MA, Neumann GU, Furtwängler A, Sabin S, Burri M, Wissgott A, Lankapalli AK, Vågene ÅJ, Meyer M, Nagel S, Tukhbatova R, Khokhlov A, Chizhevsky A, Hansen S, Belinsky AB, Kalmykov A, Kantorovich AR, Maslov VE, Stockhammer PW, Vai S, Zavattaro M, Riga A, Caramelli D, Skeates R, Beckett J, Gradoli MG, Steuri N, Hafner A, Ramstein M, Siebke I, Lösch S, Erdal YS, Alikhan NF, Zhou Z, Achtman M, Bos K, Reinhold S, Haak W, Kühnert D, Herbig A, Krause J. Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nat Ecol Evol 2020; 4:324-333. [PMID: 32094538 PMCID: PMC7186082 DOI: 10.1038/s41559-020-1106-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/08/2020] [Indexed: 11/13/2022]
Abstract
It has been hypothesized that the Neolithic transition towards an
agricultural and pastoralist economy facilitated the emergence of human adapted
pathogens. Here, we recovered eight Salmonella enterica subsp.
enterica genomes from human skeletons of transitional
foragers, pastoralists, and agro-pastoralists in western Eurasia that were up to
6,500 years old. Despite the high genetic diversity of S.
enterica all ancient bacterial genomes clustered in a single
previously uncharacterized branch that contains S. enterica
adapted to multiple mammalian species. All ancient bacterial genomes from
prehistoric (agro-)pastoralists fall within a part of this branch that also
includes the human-specific S. enterica Paratyphi C,
illustrating the evolution of a human pathogen over a period of five thousand
years. Bacterial genomic comparisons suggest that the earlier ancient strains
were not host specific, differed in pathogenic potential, and experienced
convergent pseudogenization that accompanied their downstream host adaptation.
These observations support the concept that the emergence of human adapted
S. enterica is linked to human cultural
transformations.
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Affiliation(s)
- Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Luis R Esquivel-Gomez
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tuebingen, Tuebingen, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Marta Burri
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Aditya Kumar Lankapalli
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Åshild J Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rezeda Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russian Federation
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Samara, Russian Federation
| | - Andrey Chizhevsky
- Institute of Archaeology named after A.Kh. Khalikov of the Academy of Sciences of the Republic of Tatarstan, Kazan, Russian Federation
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | | | - Alexey Kalmykov
- 'Nasledie' Cultural Heritage Unit, Stavropol, Russian Federation
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, Munich, Germany
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Monica Zavattaro
- Museum of Anthropology and Ethnology, Museum System of the University of Florence, Florence, Italy
| | - Alessandro Riga
- Department of Biology, University of Florence, Florence, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy
| | - Robin Skeates
- Department of Archaeology, Durham University, Durham, UK
| | | | | | - Noah Steuri
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Albert Hafner
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | | | - Inga Siebke
- Department of Physical Anthropology Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Sandra Lösch
- Department of Physical Anthropology Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | | | | | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
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Sannö A, Jacobson M, Sterner S, Thisted-Lambertz S, Aspán A. The development of a screening protocol for Salmonella spp. and enteropathogenic Yersinia spp. in samples from wild boar (Sus scrofa) also generating MLVA-data for Y. enterocolitica and Y. pseudotuberculosis. J Microbiol Methods 2018; 150:32-38. [PMID: 29792943 DOI: 10.1016/j.mimet.2018.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 02/02/2023]
Abstract
Salmonellosis and yersiniosis are notifiable human diseases that are commonly associated with contaminated food. Domestic pigs as well as wild boars and other wild-life have been identified as reservoirs of these bacteria. Methods for cultivation and molecular epidemiological investigations of Salmonella spp. are well established, however, cultivation of enteropathogenic Yersinia spp. is time- consuming and the commonly used method for molecular epidemiological investigations, pulsed-field gel electrophoresis, lack in discriminatory power. The aim of this study was to develop and evaluate a screening protocol well suited for wildlife samples and other highly contaminated samples. The method is based on PCR-screening followed by Multiple Loci Variant number tandem repeat Analysis (MLVA) on enrichment broth to obtain molecular epidemiological data for enteropathogenic Yersinia spp. without the need for pure isolates. The performance of the protocol was evaluated using wild boar samples (n=354) including tonsils, faeces and lymph nodes from 90 Swedish wild boars. The new protocol performed as well as or better than the established ISO-standards for detection and cultivation of Y. enterocolitica and Salmonella spp., however for cultivation of Y. pseudotuberculosis, further development is needed. The selection for motility seems beneficial for the enrichment of Salmonella spp. and Y. enterocolitica. Further, the selective enrichment prior to PCR-analysis eliminates inhibitory factors present in the original sample. In total, ten isolates of Y. enterocolitica of various bio-serotypes were obtained, and the MLVA-profile of these isolates were consistent with the profiles from the corresponding enrichment broth. Further, 22 isolates of Salmonella spp. comprising six different serovars were obtained with S. Fulica, S. Hadar and a monophasic S. Typhimurium being the most common. In conclusion, the presented screening protocol offers a rapid and efficient way to obtain prevalence data from a large sample set as well as MLVA-data within a short time frame. These results can hence improve the knowledge on the epidemiology and distribution of these pathogens and their importance to public health.
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Affiliation(s)
- Axel Sannö
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Magdalena Jacobson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Sandra Sterner
- School of Health Sciences, Örebro University, Örebro, Sweden.
| | | | - Anna Aspán
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden; Department of Microbiology, National Veterinary Institute, Uppsala, Sweden.
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