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...
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Springer Science and Business Media LLC
2021
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Online Access: | http://dx.doi.org/10.1186/s13567-021-01001-0 https://link.springer.com/content/pdf/10.1186/s13567-021-01001-0.pdf https://link.springer.com/article/10.1186/s13567-021-01001-0/fulltext.html |
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crspringernat:10.1186/s13567-021-01001-0 2023-05-15T17:59:14+02:00 Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises Sandholt, Arnar K. S. Neimanis, Aleksija Roos, Anna Eriksson, Jenny Söderlund, Robert The Swedish Agency for Marine and Water Management The Swedish Environmental Protection Agency 2021 http://dx.doi.org/10.1186/s13567-021-01001-0 https://link.springer.com/content/pdf/10.1186/s13567-021-01001-0.pdf https://link.springer.com/article/10.1186/s13567-021-01001-0/fulltext.html en eng Springer Science and Business Media LLC https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Veterinary Research volume 52, issue 1 ISSN 1297-9716 General Veterinary journal-article 2021 crspringernat https://doi.org/10.1186/s13567-021-01001-0 2022-01-04T15:12:28Z 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 Springer Nature (via Crossref) Veterinary Research 52 1 |
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Springer Nature (via Crossref) |
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crspringernat |
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English |
topic |
General Veterinary |
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General Veterinary Sandholt, Arnar K. S. Neimanis, Aleksija Roos, Anna Eriksson, Jenny Söderlund, Robert Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises |
topic_facet |
General Veterinary |
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. |
author2 |
The Swedish Agency for Marine and Water Management The Swedish Environmental Protection Agency |
format |
Article in Journal/Newspaper |
author |
Sandholt, Arnar K. S. Neimanis, Aleksija Roos, Anna Eriksson, Jenny Söderlund, Robert |
author_facet |
Sandholt, Arnar K. S. Neimanis, Aleksija Roos, Anna Eriksson, Jenny Söderlund, Robert |
author_sort |
Sandholt, Arnar K. S. |
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 |
Springer Science and Business Media LLC |
publishDate |
2021 |
url |
http://dx.doi.org/10.1186/s13567-021-01001-0 https://link.springer.com/content/pdf/10.1186/s13567-021-01001-0.pdf https://link.springer.com/article/10.1186/s13567-021-01001-0/fulltext.html |
genre |
Phocoena phocoena |
genre_facet |
Phocoena phocoena |
op_source |
Veterinary Research volume 52, issue 1 ISSN 1297-9716 |
op_rights |
https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1186/s13567-021-01001-0 |
container_title |
Veterinary Research |
container_volume |
52 |
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1 |
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1766168001661370368 |