CoChat
Sign Up
Cited by 21Antifungal resistance and susceptibilityPlant Pathogens and Fungal DiseasesFungal Infections and Studies

A single fungal strain was the unexpected cause of a mass aspergillosis outbreak in the world’s largest and only flightless parrot

Open access
Winter, David J., Weir, Bevan S., Glare, Travis, Rhodes, Johanna, Perrott, John, Fisher, Matthew C., Stajich, Jason E., Digby, Andrew +2 more·2022·iScience
DOI 10.1016/j.isci.2022.105470PMC PMC9668684
Open this paper in CoChat — free accountOpen PDF

Abstract

Kākāpō are a critically endangered species of parrots restricted to a few islands off the coast of New Zealand. Kākāpō are very closely monitored, especially during nesting seasons. In 2019, during a highly successful nesting season, an outbreak of aspergillosis affected 21 individuals and led to the deaths of 9, leaving a population of only 211 kākāpō. In monitoring this outbreak, cultures of aspergillus were grown, and genome sequenced. These sequences demonstrate that, very unusually for an aspergillus outbreak, a single strain of aspergillus caused the outbreak. This strain was found on two islands, but only one had an outbreak of aspergillosis; indicating that the strain was necessary, but not sufficient, to cause disease. Our analysis provides an understanding of the 2019 outbreak and provides potential ways to manage such events in the future.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.isci.2022.105470

Cites

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

No references could be resolved yet.

Research works printed but not linked: 35

  1. [1]Bergner L.M. Dussex N. Jamieson I.G. Robertson B.C. European colonization, not polynesianarrival, impacted population size and genetic diversity in the critically endangered New Zealand kākāpō J. Hered. 107 2016 593 602 10.1093/jhered/esw065 27694405 · DOI
  2. [2]Dussex N. van der Valk T. Morales H.E. Wheat C.W. Díez-del-Molino D. von Seth J. Foster Y. Kutschera V.E. Guschanski K. Rhie A. Population genomics of the critically endangered kākāpō Cell Genomics 2021 100002 10.1016/j.xgen.2021.100002 PMC9903828 36777713 · DOI · Paper page
  3. [3]Dussex N. Von Seth J. Robertson B.C. Dalén L. Full mitogenomes in the critically endangered kākāpō reveal major post-glacial and anthropogenic effects on neutral genetic diversity Genes 9 2018 220 10.3390/genes9040220 PMC5924562 29671759 · DOI
  4. [7]Gartrell B.D. Alley M.R. Mack H. Donald J. McInnes K. Jansen P. Erysipelas in the critically endangered kakapo (Strigops habroptilus) Avian Pathol. 34 2005 383 387 10.1080/03079450500268583 16236568 · DOI
  5. [9]White D.J. Hall R.J. Jakob-Hoff R. Wang J. Jackson B. Tompkins D.M. Exudative cloacitis in the kakapo (Strigops habroptilus) potentially linked to Escherichia coli infection N. Z. Vet. J. 63 2015 167 170 10.1080/00480169.2014.960905 25186371 · DOI
  6. [12]Denning D.W. Invasive aspergillosis Clin. Infect. Dis. 26 1998 781 803 quiz 804–5 9564455
  7. [13]Latgé J.-P. Aspergillus fumigatus and aspergillosis Clin. Microbiol. Rev. 12 1999 310 350 10194462 PMC88920
  8. [14]Tell L.A. Aspergillosis in mammals and birds: impact on veterinary medicine Med. Mycol. 43 2005 S71 S73 10.1080/13693780400020089 16110795 · DOI
  9. [15]Tell L.A. Burco J.D. Woods L. Clemons K.V. Aspergillosis in birds and mammals: considerations for veterinary medicine Gupta A. Singh N.P. Recent Developments in Fungal Diseases of Laboratory Animals Fungal Biology 2019 Springer International Publishing 49 72 10.1007/978-3-030-18586-2_4 · DOI
  10. [16]Beernaert L.A. Pasmans F. Van Waeyenberghe L. Haesebrouck F. Martel A. Aspergillus infections in birds: a review Avian Pathol. 39 2010 325 331 10.1080/03079457.2010.506210 20954008 · DOI
  11. [17]Cork S.C. Alley M.R. Johnstone A.C. Stockdale P.H.G. Aspergillosis and other causesofmortalityin the stitchbird in New Zealand J. Wildl. Dis. 35 1999 481 486 10.7589/0090-3558-35.3.481 10479082 · DOI
  12. [18]Glare T.R. Gartrell B.D. Brookes J.J. Perrott J.K. Isolation and identification of Aspergillus spp. from Brown kiwi (apteryx mantelli) nocturnal houses in New Zealand Avian Dis. 58 2013 16 24 10.1637/10589-061013-Reg.1 24758108 · DOI
  13. [19]Perrott J.K. Armstrong D.P. Aspergillus fumigatus densities in relation to forest succession and edge effects: implications for wildlife health in modified environments EcoHealth 8 2011 290 300 10.1007/s10393-011-0716-8 22076057 · DOI
  14. [20]Drees K.P. Lorch J.M. Puechmaille S.J. Parise K.L. Wibbelt G. Hoyt J.R. Sun K. Jargalsaikhan A. Dalannast M. Palmer J.M. Phylogenetics of a fungal invasion: origins and widespread dispersal of white-nose syndrome mBio 2017 10.1128/mBio.01941-17 PMC5727414 29233897 · DOI
  15. [21]O’Hanlon S.J. Rieux A. Farrer R.A. Rosa G.M. Waldman B. Bataille A. Kosch T.A. Murray K.A. Brankovics B. Fumagalli M. Recent Asian origin of chytrid fungi causing global amphibian declines Science 360 2018 621 627 10.1126/science.aar1965 29748278 PMC6311102 · DOI
  16. [23]Rhodes J. Abdolrasouli A. Dunne K. Sewell T.R. Zhang Y. Ballard E. Brackin A.P. van Rhijn N. Chown H. Tsitsopoulou A. Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment Nat. Microbiol. 7 2022 663 674 10.1038/s41564-022-01091-2 35469019 PMC9064804 · DOI
  17. [24]Kowalski C.H. Beattie S.R. Fuller K.K. McGurk E.A. Tang Y.-W. Hohl T.M. Obar J.J. CramerJr R.A. Heterogeneity among isolates reveals that fitness in low oxygen correlates with Aspergillus fumigatus virulence mBio 2016 10.1128/mBio.01515-16 PMC5040115 27651366 · DOI · Paper page
  18. [25]Mondon P. De Champs C. Donadille A. Ambroise-Thomas P. Grillot R. Variation in virulence of Aspergillus fumigatus strains in a murine model of invasive pulmonary aspergillosis J. Med. Microbiol. 45 1996 186 191 10.1099/00222615-45-3-186 8810945 · DOI
  19. [26]Askew D.S. Aspergillus fumigatus: virulence genes in a street-smart mold Curr.Opin.Microbiol. 11 2008 331 337 10.1016/j.mib.2008.05.009 18579432 PMC2559812 · DOI
  20. [27]Mitsuguchi H. Seshime Y. Fujii I. Shibuya M. Ebizuka Y. Kushiro T. Biosynthesis of steroidal antibiotic fusidanes: functional analysis of oxidosqualene cyclase and subsequent tailoring enzymes from Aspergillus fumigatus J. Am. Chem. Soc. 131 2009 6402 6411 10.1021/ja8095976 19415934 · DOI
  21. [28]Lofgren L.A. Lorch J.M. Cramer R.A. Blehert D.S. Berlowski-Zier B.M. Winzeler M.E. Gutierrez-Perez C. Kordana N.E. Stajich J.E. Avian-associated Aspergillus fumigatus displays broad phylogenetic distribution, no evidence for host specificity, and multiple genotypes within epizootic events G3 12 2022 jkac075 35377435 PMC9073692
  22. [29]Jones M.P. Orosz S.E. The diagnosis of aspergillosis in birds Seminars in Avian and Exotic Pet Medicine 2000 Elsevier 52 58
  23. [31]Abdolrasouli A. Rhodes J. Beale M.A. Hagen F. Rogers T.R. Chowdhary A. Meis J.F. Armstrong-James D. Fisher M.C. Genomic context of azole resistance mutations in Aspergillus fumigatus determined using whole-genome sequencing mBio 6 2015 e00536 10.1128/mBio.00536-15 26037120 PMC4453006 · DOI
  24. [32]Nierman W.C. Pain A. Anderson M.J. Wortman J.R. Kim H.S. Arroyo J. Berriman M. Abe K. Archer D.B. Bermejo C. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus Nature 438 2005 1151 1156 10.1038/nature04332 16372009 · DOI · Paper page
  25. [33]Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM ArXiv 2013
  26. [34]McKenna A. Hanna M. Banks E. Sivachenko A. Cibulskis K. Kernytsky A. Garimella K. Altshuler D. Gabriel S. Daly M. DePristo M.A. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Genome Res. 20 2010 1297 1303 10.1101/gr.107524.110 20644199 PMC2928508 · DOI · Paper page
  27. [35]Yates A.D. Allen J. Amode R.M. Azov A.G. Barba M. Becerra A. Bhai J. Campbell L.I. Carbajo Martinez M. Chakiachvili M. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates Nucleic Acids Res. 50 2022 D996 D1003 10.1093/nar/gkab1007 34791415 PMC8728113 · DOI
  28. [36]McLaren W. Gil L. Hunt S.E. Riat H.S. Ritchie G.R.S. Thormann A. Flicek P. Cunningham F. The Ensembl variant effect predictor Genome Biol. 17 2016 122 10.1186/s13059-016-0974-4 27268795 PMC4893825 · DOI · Paper page
  29. [37]Danecek P. Auton A. Abecasis G. Albers C.A. Banks E. DePristo M.A. Handsaker R.E. Lunter G. Marth G.T. Sherry S.T. The variant call format and VCFtools Bioinformatics 27 2011 2156 2158 10.1093/bioinformatics/btr330 21653522 PMC3137218 · DOI
  30. [39]Knaus B.J. Grünwald N.J. vcfr: a package to manipulate and visualize variant call format data in R Mol. Ecol. Resour. 17 2017 44 53 10.1111/1755-0998.12549 27401132 · DOI
  31. [40]Jombart T. adegenet: a R package for the multivariate analysis of genetic markers Bioinformatics 24 2008 1403 1405 10.1093/bioinformatics/btn129 18397895 · DOI
  32. [41]Kamvar Z.N. Tabima J.F. Grünwald N.J. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction PeerJ 2 2014 e281 10.7717/peerj.281 24688859 PMC3961149 · DOI
  33. [42]Bankevich A. Nurk S. Antipov D. Gurevich A.A. Dvorkin M. Kulikov A.S. Lesin V.M. Nikolenko S.I. Pham S. Prjibelski A.D. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing J. Comput. Biol. 19 2012 455 477 10.1089/cmb.2012.0021 22506599 PMC3342519 · DOI
  34. [43]Gurevich A. Saveliev V. Vyahhi N. Tesler G. QUAST: quality assessment tool for genome assemblies Bioinformatics 29 2013 1072 1075 10.1093/bioinformatics/btt086 23422339 PMC3624806 · DOI · Paper page
  35. [44]Slater G.S.C. Birney E. Automated generation of heuristics for biological sequence comparison BMC Bioinformatics 6 2005 31 10.1186/1471-2105-6-31 15713233 PMC553969 · DOI

Cited by

Sorted by citations

Authors
Winter, D. J., Weir, B. S., Glare, T., Rhodes, J., Perrott, J., Fisher, M. C., Stajich, J. E., Digby, A., Dearden, P. K., & Cox, M. P.
Affiliations
  • Massey University (NZ)
  • Manaaki Whenua – Landcare Research (NZ)
  • Lincoln University (NZ)
  • Imperial College London (GB)
  • Auckland University of Technology (NZ)
  • University of California, Riverside (US)
  • Department of Conservation (NZ)
  • University of Otago (NZ)
Corresponding author
Dearden, Peter K.
ORCID
Venue
iScience
Publisher
Elsevier BV
Published
2022-12
Volume
25
Issue
12
Pages
105470
ISSN
2589-0042 (ISSN-L)
DOI
10.1016/j.isci.2022.105470
PMC
PMC9668684
OpenAlex
W4308153469
Cited by
21
References
0
Citations by year
2026: 5 · 2025: 4 · 2024: 7 · 2023: 5
FWCI
1.96
Type
journal article
Language
en
Open access
Licence
Locations
  • iScience (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Tuwhera (Auckland University of Technology) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
  • University of Birmingham Research Portal (University of Birmingham) (submittedVersion, other-oa)
  • Lincoln University Research Archive (Lincoln University) (submittedVersion, cc-by)
  • Spiral (Imperial College London) (submittedVersion, other-oa)
Funders
  • University of Manchester
  • California Department of Conservation
  • University of Auckland
  • Auckland University of Technology, New Zealand
  • Massey University
  • University of Otago
  • Ministry of Business, Innovation and Employment
  • Audrey and Theodor Geisel School of Medicine at Dartmouth
  • University of British Columbia
  • Imperial College London
Topics
  • Health Sciences › Medicine › Infectious Diseases › Antifungal resistance and susceptibility
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Plant Pathogens and Fungal Diseases
  • Health Sciences › Medicine › Epidemiology › Fungal Infections and Studies
Keywords
aspergillosis, kakapo, Aspergillus, fungal outbreak, critically endangered species, avian fungal disease, epidemic control

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review