title: Genomic Epidemiology and Management of Salmonella in Island Ecosystems Used for Takahe Conservation.
abstract: Translocation and isolation of threatened wildlife in new environments may have unforeseen consequences on pathogen transmission and evolution in host populations. Disease threats associated with intensive conservation management of wildlife remain speculative without gaining an understanding of pathogen dynamics in meta-populations and how location attributes may determine pathogen prevalence. We determined the prevalence and population structure of an opportunistic pathogen, Salmonella, in geographically isolated translocated sub-populations of an endangered New Zealand flightless bird, the takahe (Porphyrio hochstetteri). Out of the nine sub-populations tested, Salmonella was only isolated from takahe living on one private island. The apparent prevalence of Salmonella in takahe on the private island was 32% (95% CI 13-57%), with two serotypes, Salmonella Mississippi and Salmonella houtenae 40:gt-, identified. Epidemiological investigation of reservoirs on the private island and another island occupied by takahe identified environmental and reptile sources of S. Mississippi and S. houtenae 40:gt- on the private island. Single nucleotide polymorphism analysis of core genomes revealed low-level diversity among isolates belonging to the same serotype and little differentiation according to host and environmental source. The pattern observed may be representative of transmission between sympatric hosts and environmental sources, the presence of a common unsampled source, and/or evidence of a recent introduction into the ecosystem. This study highlights how genomic epidemiology can be used to ascertain and understand disease dynamics to inform the management of disease threats in endangered wildlife populations.
authors.affiliation: Allan Wilson Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand. zlgrange@ucdavis.edu.|mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand. zlgrange@ucdavis.edu.|Wildbase, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand. zlgrange@ucdavis.edu.|One Health Institute, University of California Davis, Davis, CA, USA. zlgrange@ucdavis.edu.
authors.forename: Zoë L
authors.initials: ZL
authors.lastname: Grange
authors.affiliation: Allan Wilson Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.|mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Biggs
authors.affiliation: Allan Wilson Centre, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
authors.forename: Shanna P
authors.initials: SP
authors.lastname: Rose
authors.affiliation: Allan Wilson Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.|Wildbase, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
authors.forename: Brett D
authors.initials: BD
authors.lastname: Gartrell
authors.affiliation: Allan Wilson Centre, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
authors.forename: Nicola J
authors.initials: NJ
authors.lastname: Nelson
authors.affiliation: Allan Wilson Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.|mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
authors.forename: Nigel P
authors.initials: NP
authors.lastname: French
mesh_terms: D000818:Animals; D001715:Bird Diseases / Q000453:epidemiology* / Q000382:microbiology / Q000635:transmission; D001717:Birds; D003247:Conservation of Natural Resources; D004197:Disease Reservoirs / Q000382:microbiology*; D009520:New Zealand; D020641:Polymorphism, Single Nucleotide; D015995:Prevalence; D012475:Salmonella / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012481:Salmonella Infections, Animal / Q000453:epidemiology* / Q000382:microbiology / Q000635:transmission
keywords: Disease ecology; New Zealand; Porphyrio hochstetteri; Translocation; Whole genome sequencing