Microbial Ecology

, Volume 74, Issue 3, pp 735–744 | Cite as

Genomic Epidemiology and Management of Salmonella in Island Ecosystems Used for Takahe Conservation

  • Zoë L. GrangeEmail author
  • Patrick J. Biggs
  • Shanna P. Rose
  • Brett D. Gartrell
  • Nicola J. Nelson
  • Nigel P. French
Host Microbe Interactions


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.


Disease ecology New Zealand Whole genome sequencing Porphyrio hochstetteri Translocation 



This study was funded by the Allan Wilson Centre as part of the PhD study of Dr. Grange and MSc of S. Rose. We would like to thank Ngai Tahu for their support of this research, T. Burns for field assistance, A. Reynolds for laboratory support, and Dr. Howe for guidance.

Supporting Information

A map of pitfall locations on Maud Island (Appendix S1), the number of lizards captured and sampled (Appendix S2), the list of Salmonella genomes used for 51 gene ribosomal multi-locus sequence comparison (Appendix S3), SNP information for Salmonella Mississippi (Appendix S4) and S. houtenae 40:gt- (Appendix S5) study isolates, and the alignment of rMLST gene sequences (Appendix S6) are available online. The authors are solely responsible for the content and functionality of these materials. Queries (other than absence of the material) should be directed to the corresponding author.

Compliance with Ethical Standards

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted. Reptile capture and sampling was conducted according to a Victoria University of Wellington animal ethics permit 2012R33 and the New Zealand Department of Conservation research permit 37543-FAU. Takahe samples were collected under a Massey University animal ethics permit MUAEC Protocol 11/95. This article does not contain any studies with human participants performed by any of the authors. This study was funded by the Allan Wilson Centre.

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

248_2017_959_MOESM1_ESM.phylip (2.7 mb)
ESM 1 (PHYLIP 2750 kb)


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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Zoë L. Grange
    • 1
    • 2
    • 3
    • 4
    Email author
  • Patrick J. Biggs
    • 1
    • 2
  • Shanna P. Rose
    • 5
  • Brett D. Gartrell
    • 1
    • 3
  • Nicola J. Nelson
    • 5
  • Nigel P. French
    • 1
    • 2
  1. 1.Allan Wilson Centre, Institute of Veterinary, Animal and Biomedical SciencesMassey UniversityPalmerston NorthNew Zealand
  2. 2.mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical SciencesMassey UniversityPalmerston NorthNew Zealand
  3. 3.Wildbase, Institute of Veterinary, Animal and Biomedical SciencesMassey UniversityPalmerston NorthNew Zealand
  4. 4.One Health InstituteUniversity of California DavisDavisUSA
  5. 5.Allan Wilson Centre, School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand

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