Investigating the cause of disease in kākāpō
Kākāpō. Image - Bethany Jackson
Diseases of endangered wildlife pose critical threats to their survival. However, often very little is known about the causes and even the history of wildlife diseases. This is exactly the situation for critically endangered kākāpō suffering from exudative cloacitis.
The kākāpō is a flightless night parrot endemic to New Zealand. Considered to be almost extinct by the mid-1970s due to the impact of introduced mammalian predators, intensive efforts to recover the species on predator-free offshore islands are now underway. The Kākāpō Recovery program (http://kakaporecovery.org.nz/) is considered to be one of the most intensive recovery programs worldwide and includes exhaustive monitoring, supplementary feeding, artificial incubation and hand-rearing, regular health checks and predator control.
Since 2002, cloacitis (inflammation of the cloaca) has been confirmed in nine individuals, and suspected in a further two, with infected tissue frequently becoming ulcerated and exudative with associated heavy bacterial growth. With such symptoms potentially resulting in either infertility or mortality, and a current total population of just 126 birds, there is a critical need to understand the cause(s) of cloacitis in kākāpō to guide both treatment and preventive management.
To help find the cause of the disease, Daniel White and colleagues at Landcare Research teamed up with Richard Hall and colleagues at Environmental Science and Research Ltd (ESR) to do de novo metagenomics on samples from kākāpō. De novo metagenomics is the linchpin of the newly emerging field of pathogen discovery. It works by generating millions of DNA or cDNA sequence ‘reads’ from biomedical samples, such as faeces or cloacal swabs, followed by aligning all these reads against sequence databases to identify which taxa are present (Fig. 1). This work relies heavily on Landcare Research’s pre-existing collaboration with the National eScience Infrastructure (NeSI) for computing power. As such, de novo metagenomics performed on faeces has the potential to generate an unbiased representation of all organisms present in the digestive tract of infected birds, importantly including viruses.
Comparing the taxa in an infected bird (named Rakiura) both before and after treatment with antibiotics with those in a pool of eight healthy individuals (Fig. 2) has yielded identification of a possible cause of the disease. In contrast to the healthy kākāpō tested, a bacteriophage TL-2011b, or something closely related, was found in Rakiura. Bacteriophages are essentially viruses that infect bacteria, and the host E. coli strain of this phage is known to be associated with serious foodborne disease in humans. Veterinary studies were not able to identify this E. coli strain as a potential cause of cloacitis in kākāpō because it couldn’t be distinguished from other E. coli strains that are components of healthy kākāpō gut microflora.
This exciting result needed confirmation and the team has now developed a diagnostic PCR assay for the TL-2011b-like bacteriophage, which has provided strong support for its presence in Rakiura. The next step is to try and replicate the finding in another kākāpō. This relies on getting a faecal sample from another infected bird, which thankfully are in short supply. However, in March another bird started to show signs of the disease and, working closely with the New Zealand Centre for Conservation Medicine and the Department of Conservation, samples have been taken and are currently at the Ecogene Laboratory at Landcare Research, Tamaki. The team is now processing samples to try to replicate a positive result with the newly developed PCR assay. The presence of this phage in a second cloacitis case would strengthen evidence for its cause, making it possible to put in place better tailored treatment for the disease, and importantly preventive measures to reduce its incidence.
This work is funded by the New Zealand Ministry for Business, Innovation and Employment and the Department of Conservation.
Fig. 1 De novo metagenomics.
Fig. 2 A summary of the number of viral phage cDNA sequences present in pre-treated Rakiura, post-treated Rakiura and a pool of healthy birds.
