Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises
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 al...
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ftdoajarticles:oai:doaj.org/article:850b3863cd074893965b183d9e603341 2023-05-15T17:59:14+02:00 Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises Arnar K. S. Sandholt Aleksija Neimanis Anna Roos Jenny Eriksson Robert Söderlund 2021-10-01T00:00:00Z https://doi.org/10.1186/s13567-021-01001-0 https://doaj.org/article/850b3863cd074893965b183d9e603341 EN eng BMC https://doi.org/10.1186/s13567-021-01001-0 https://doaj.org/toc/1297-9716 doi:10.1186/s13567-021-01001-0 1297-9716 https://doaj.org/article/850b3863cd074893965b183d9e603341 Veterinary Research, Vol 52, Iss 1, Pp 1-11 (2021) Pangenome analysis cgMLST salmonellosis marine mammals cetaceans host bias Veterinary medicine SF600-1100 article 2021 ftdoajarticles https://doi.org/10.1186/s13567-021-01001-0 2022-12-31T15:22:25Z 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. Article in Journal/Newspaper Phocoena phocoena Directory of Open Access Journals: DOAJ Articles Veterinary Research 52 1 |
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Directory of Open Access Journals: DOAJ Articles |
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English |
topic |
Pangenome analysis cgMLST salmonellosis marine mammals cetaceans host bias Veterinary medicine SF600-1100 |
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Pangenome analysis cgMLST salmonellosis marine mammals cetaceans host bias Veterinary medicine SF600-1100 Arnar K. S. Sandholt Aleksija Neimanis Anna Roos Jenny Eriksson Robert Söderlund Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises |
topic_facet |
Pangenome analysis cgMLST salmonellosis marine mammals cetaceans host bias Veterinary medicine SF600-1100 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Arnar K. S. Sandholt Aleksija Neimanis Anna Roos Jenny Eriksson Robert Söderlund |
author_facet |
Arnar K. S. Sandholt Aleksija Neimanis Anna Roos Jenny Eriksson Robert Söderlund |
author_sort |
Arnar K. S. Sandholt |
title |
Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises |
title_short |
Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises |
title_full |
Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises |
title_fullStr |
Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises |
title_full_unstemmed |
Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises |
title_sort |
genomic signatures of host adaptation in group b salmonella enterica st416/st417 from harbour porpoises |
publisher |
BMC |
publishDate |
2021 |
url |
https://doi.org/10.1186/s13567-021-01001-0 https://doaj.org/article/850b3863cd074893965b183d9e603341 |
genre |
Phocoena phocoena |
genre_facet |
Phocoena phocoena |
op_source |
Veterinary Research, Vol 52, Iss 1, Pp 1-11 (2021) |
op_relation |
https://doi.org/10.1186/s13567-021-01001-0 https://doaj.org/toc/1297-9716 doi:10.1186/s13567-021-01001-0 1297-9716 https://doaj.org/article/850b3863cd074893965b183d9e603341 |
op_doi |
https://doi.org/10.1186/s13567-021-01001-0 |
container_title |
Veterinary Research |
container_volume |
52 |
container_issue |
1 |
_version_ |
1766167999822168064 |