Journal Article

Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises

Neimanis, Aleksija, Eriksson, Jenny, Sandholt, Arnar K. S., Söderlund, Robert, Roos, Anna

2021

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Adaptation / Analysis / Bacterial infections / Bacterial pneumonia / bycatch / cetaceans / cgMLST / clones / coasts / death / Dolphins & porpoises / Epidemiology / Fulica / gastrointestinal system / gene ontology / General Veterinary / Genes / genome / Genomes / Genomics / Harbors / Health aspects / host bias / hosts / Immunology / Infections / Infectious diseases / Life Sciences / lungs / Machine learning / Man and the environment / Marine mammals / Medicine / Medicine & Public Health / Microbiology / Naturmiljö och människan / Pangenome analysis / Parasites / pathogenicity / Phocoena phocoena / Pneumonia / Porpoises / Research Article / Salmonella / Salmonella enterica / salmonellosis / sequence analysis / serotypes / veterinary medicine / Veterinary Medicine/Veterinary Science / Virology / Whole genome sequencing