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.
Highlights
The harbour porpoise (Phocoena phocoena) is a species of small cetaceans that inhabit coastal waters of the northern hemisphere
Necropsy findings associated with Salmonella infection The first Salmonella isolate in the present study (17VLT002652) was recovered from a porpoise found stranded in Varberg municipality (N 57°7.1′, E 12°11.5′) on the Swedish west coast in July 2017
Phylogenetic analysis based on core genome multi-locus sequence typing (cgMLST) indicated that the Swedish isolates most closely matched 17 “Fulica-like” or “Fulicalike rough” ST416 or ST417 isolates in Enterobase, of which 16 were from harbour porpoises in Scotland and 1 was from Scotland but lacked metadata
Summary
The harbour porpoise (Phocoena phocoena) is a species of small cetaceans that inhabit coastal waters of the northern hemisphere. While it is abundant in the North Atlantic and the North Pacific, the Baltic Sea and Black Sea populations are critically endangered [1]. Because of their near-shore habitat, harbour porpoises are vulnerable to anthropogenic environmental disturbance. In a study of 98 stranded porpoises collected from 2008 to 2019, infectious disease was the second most common cause of death (17%) after bycatch and probable bycatch (25%).
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