Show simple item record

dc.contributor.authorPfeiffer, Wayne
dc.contributor.authorBraun, Josephine
dc.contributor.authorBurchell, Jennifer
dc.contributor.authorWitte, Carmel L.
dc.contributor.authorRideout, Bruce
dc.date.accessioned2020-05-27T22:44:08Z
dc.date.available2020-05-27T22:44:08Z
dc.date.issued2017
dc.identifier1932-6203
dc.identifier.doi10.1371/journal.pone.0173464
dc.identifier.urihttp://hdl.handle.net/20.500.12634/257
dc.description.abstractMethods Mycobacteria isolated from more than 100 birds diagnosed with avian mycobacteriosis at the San Diego Zoo and its Safari Park were cultured postmortem and had their whole genomes sequenced. Computational workflows were developed and applied to identify the mycobacterial species in each DNA sample, to find single-nucleotide polymorphisms (SNPs) between samples of the same species, to further differentiate SNPs between as many as three different genotypes within a single sample, and to identify which samples are closely clustered genomically. Results Nine species of mycobacteria were found in 123 samples from 105 birds. The most common species were Mycobacterium avium and Mycobacterium genavense, which were in 49 and 48 birds, respectively. Most birds contained only a single mycobacterial species, but two birds contained a mixture of two species. The M. avium samples represent diverse strains of M. avium avium and M. avium hominissuis, with many pairs of samples differing by hundreds or thousands of SNPs across their common genome. By contrast, the M. genavense samples are much closer genomically; samples from 46 of 48 birds differ from each other by less than 110 SNPs. Some birds contained two, three, or even four genotypes of the same bacterial species. Such infections were found in 4 of 49 birds (8%) with M. avium and in 11 of 48 birds (23%) with M. genavense. Most were mixed infections, in which the bird was infected by multiple mycobacterial strains, but three infections with two genotypes differing by ≤ 10 SNPs were likely the result of within-host evolution. The samples from 31 birds with M. avium can be grouped into nine clusters within which any sample is ≤ 12 SNPs from at least one other sample in the cluster. Similarly, the samples from 40 birds with M. genavense can be grouped into ten such clusters. Information about these genomic clusters is being used in an ongoing, companion study of mycobacterial transmission to help inform management of bird collections.
dc.language.isoen
dc.relation.urlhttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0173464
dc.rights© 2017 Pfeiffer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectGENOMICS
dc.subjectSAN DIEGO ZOO
dc.subjectWILDLIFE MANAGEMENT
dc.subjectBIRDS
dc.subjectAVIARY BIRDS
dc.subjectEXPERIMENTAL METHODS
dc.titleWhole-genome analysis of mycobacteria from birds at the San Diego Zoo
dc.typeArticle
dc.source.journaltitlePLOS ONE
dc.source.volume12
dc.source.issue3
dc.source.beginpagee0173464
dcterms.dateAccepted2017
refterms.dateFOA2020-05-27T22:44:08Z
html.description.abstractMethods Mycobacteria isolated from more than 100 birds diagnosed with avian mycobacteriosis at the San Diego Zoo and its Safari Park were cultured postmortem and had their whole genomes sequenced. Computational workflows were developed and applied to identify the mycobacterial species in each DNA sample, to find single-nucleotide polymorphisms (SNPs) between samples of the same species, to further differentiate SNPs between as many as three different genotypes within a single sample, and to identify which samples are closely clustered genomically. Results Nine species of mycobacteria were found in 123 samples from 105 birds. The most common species were Mycobacterium avium and Mycobacterium genavense, which were in 49 and 48 birds, respectively. Most birds contained only a single mycobacterial species, but two birds contained a mixture of two species. The M. avium samples represent diverse strains of M. avium avium and M. avium hominissuis, with many pairs of samples differing by hundreds or thousands of SNPs across their common genome. By contrast, the M. genavense samples are much closer genomically; samples from 46 of 48 birds differ from each other by less than 110 SNPs. Some birds contained two, three, or even four genotypes of the same bacterial species. Such infections were found in 4 of 49 birds (8%) with M. avium and in 11 of 48 birds (23%) with M. genavense. Most were mixed infections, in which the bird was infected by multiple mycobacterial strains, but three infections with two genotypes differing by ≤ 10 SNPs were likely the result of within-host evolution. The samples from 31 birds with M. avium can be grouped into nine clusters within which any sample is ≤ 12 SNPs from at least one other sample in the cluster. Similarly, the samples from 40 birds with M. genavense can be grouped into ten such clusters. Information about these genomic clusters is being used in an ongoing, companion study of mycobacterial transmission to help inform management of bird collections.


Files in this item

Thumbnail
Name:
Pfeiffer_2017_PLOSOne.pdf
Size:
1.355Mb
Format:
PDF
Thumbnail
Name:
Pfeiffer_2017_PLOSOne_s001.xlsx
Size:
10.28Kb
Format:
Microsoft Excel 2007
Thumbnail
Name:
Pfeiffer_2017_PLOSOne_S1File.xlsx
Size:
10.28Kb
Format:
Microsoft Excel 2007
Thumbnail
Name:
Pfeiffer_2017_PLOSOne_s004.ppt
Size:
172Kb
Format:
Microsoft PowerPoint
Thumbnail
Name:
Pfeiffer_2017_PLOSOnes_002.xlsx
Size:
126.8Kb
Format:
Microsoft Excel 2007
Thumbnail
Name:
Pfeiffer_2017_PLOSOne_s003.xlsx
Size:
305.8Kb
Format:
Microsoft Excel 2007

This item appears in the following Collection(s)

  • Conservation Science Publications
    Works by SDZWA's Conservation Scientists and co-authors. Includes books, book sections, articles and conference publications and presentations.

Show simple item record

© 2017 Pfeiffer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Except where otherwise noted, this item's license is described as © 2017 Pfeiffer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.