Avian Mycobacteriosis: Whole-Genome Sequence Analysis for Transmission Source Identification
American Association of Zoo Veterinarians Conference 2014
Josephine Braun1, Dr med vet; Wayne Pfeiffer2, PhD; Carmel Witte1, MS; Bruce Rideout1, DVM, PhD, DACVP
1San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA; 2San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA


Avian mycobacteriosis is a troubling disease facing bird collections and conservation programs around the world and has led to euthanasia of exposed but clinically healthy suspects in the past. There is growing evidence on the importance of the environment in transmission.1,2 The hypothesis of this study is that whole-genome sequence variation between infected birds will help reveal the importance of an environmental route of infection rather than bird-to-bird transmission. From 2001 through 2013, mycobacteria from 33 birds of various species from San Diego Zoo diagnosed with mycobacteriosis at necropsy were successfully isolated. These birds were divided into 11 groups including at least two individuals sharing a spatial and temporal period based on their movement history between enclosures. Whole-genome sequencing of each isolate and alignment against reference genomes in the NCBI databases enabled higher resolution isolate differentiation than previous DNA fingerprinting methods. A phylogenetic tree was inferred based on the number of single nucleotide variants between the isolates. The phylogenetic tree showed that 20 of the Mycobacterium avium samples group into three closely related clusters. Seven other M. avium isolates are distant from these clusters. The remaining isolates are other species, including M. fortuitum and M. intracellulare. In conclusion, the avian mycobacterial isolates show strain diversity. Mutation rate experiments will enable assessment of the significance of the relatively few variants between some isolates within a cluster. Preliminary interpretation suggests the infections were acquired independently from the environment.


Thank you to the Ellen Browning Scripps Foundation for funding, to Jennifer Burchell for technical support, and to the National Science Foundation for computer time at the San Diego Supercomputer Center.

Literature Cited

1.  Schrenzel M, Nicolas M, Witte C, Papendick R, Tucker T, Keener L, Sutherland-Smith M, Lamberski N, Orndorff D, Heckard D, Witman P, Mace M, Rimlinger D, Reed S, Rideout B. Molecular epidemiology of Mycobacterium avium subsp. avium and Mycobacterium intracellulare in captive birds. Vet Microbiol. 2008;126:122–131.

2.  Witte CL, Hungerford L, Papendick R, Stalis I, Rideout BA. Investigation of factors predicting disease among zoo birds exposed to avian mycobacteriosis. J Am Vet Med Assoc. 2010;236:211–218.


Speaker Information
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Josephine Braun, Dr med vet
San Diego Zoo Institute for Conservation Research
San Diego Zoo Global
Escondido, CA, USA

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