Browsing by Author "Uddstrom L"

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    Avian Influenza Virus Surveillance Across New Zealand and Its Subantarctic Islands Detects H1N9 in Migratory Shorebirds, but Not 2.3.4.4b HPAI H5N1
    (John Wiley and Sons Ltd, 2025-04) Waller SJ; Wierenga JR; Heremia L; Darnley JA; de Vries I; Dubrulle J; Robinson Z; Miller AK; Niebuhr CN; Melville DS; Schuckard R; Battley PF; Wille M; Alai B; Cole R; Cooper J; Ellenberg U; Elliott G; Faulkner J; Fischer JH; Fyfe J; Hay L; Houston D; Keys BC; Long J; Long R; Mattern T; McGovern H; McNutt L; Moore P; Neil O; Osborne J; Pagé A-S; Parker KA; Perry M; Philp B; Reid J; Rexer-Huber K; Russell JC; Sagar R; Ruru TT; Thompson T; Thomson L; Tinnemans J; Uddstrom L; Waipoua TA; Walker K; Whitehead E; Wickes C; Young MJ; McInnes K; Winter D; Geoghegan JL
    Highly pathogenic avian influenza (HPAI) virus subtype H5N1 has never been detected in New Zealand. The potential impact of this virus on New Zealand's wild birds would be catastrophic. To expand our knowledge of avian influenza viruses across New Zealand, we sampled wild aquatic birds from New Zealand, its outer islands and its subantarctic territories. Metatranscriptomic analysis of 700 individuals spanning 33 species revealed no detection of H5N1 during the annual 2023–2024 migration. A single detection of H1N9 in red knots (Calidris canutus) was noted. This study provides a baseline for expanding avian influenza virus monitoring in New Zealand.
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    Evidence for a Role of Extraintestinal Pathogenic Escherichia coli, Enterococcus faecalis and Streptococcus gallolyticus in the Aetiology of Exudative Cloacitis in the Critically Endangered Kākāpō (Strigops habroptilus)
    (John Wiley and Sons Ltd, 2025-04-19) French RK; Waller SJ; Wierenga JR; Grimwood RM; Hodgkinson-Bean J; Digby A; Uddstrom L; Eason D; Kākāpō Recovery Team; Argilla LS; Biggs PJ; Cookson A; French NP; Geoghegan JL
    The kākāpō is a critically endangered flightless parrot which suffers from exudative cloacitis, a debilitating disease resulting in inflammation of the vent margin or cloaca. Despite this disease emerging over 20 years ago, the cause of exudative cloacitis remains elusive. We used total RNA sequencing and metatranscriptomic analysis to characterise the infectome of lesions and cloacal swabs from nine kākāpō affected with exudative cloacitis, and compared this to cloacal swabs from 45 non-diseased kākāpō. We identified three bacterial species—Streptococcus gallolyticus, Enterococcus faecalis and Escherichia coli—as significantly more abundant in diseased kākāpō compared to healthy individuals. The genetic diversity observed in both S. gallolyticus and E. faecalis among diseased kākāpō suggests that these bacteria originate from exogenous sources rather than from kākāpō-to-kākāpō transmission. The presence of extraintestinal pathogenic E. coli (ExPEC)-associated virulence factors in the diseased kākāpō population suggests that E. coli may play a critical role in disease progression by facilitating iron acquisition and causing DNA damage in host cells, possibly in association with E. faecalis. No avian viral, fungal nor other parasitic species were identified. These results, combined with the consistent presence of one E. coli gnd sequence type across multiple diseased birds, suggest that this species may be the primary cause of exudative cloacitis. These findings shed light on possible causative agents of exudative cloacitis, and offer insights into the interplay of microbial factors influencing the disease.
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    Influence of management practice on the microbiota of a critically endangered species: a longitudinal study of kākāpō chick faeces and associated nest litter
    (BioMed Central, Ltd., 2022-09-30) West AG; Digby A; Lear G; Armstrong D; Armstrong-James D; Bromley M; Buckley E; Chatterton J; Cox MP; Cramer RA; Crane J; Dearden PK; Eason D; Fisher MC; Gago S; Gartrell B; Gemmell NJ; Glare TR; Guhlin J; Howard J; Lacap-Bugler D; Le Lec M; Lin XX; Lofgren L; Mackay J; Meis J; Morelli KA; Perrott J; Petterson M; Quinones-Mateu M; Rhodes J; Roberts J; Stajich J; Taylor MW; Tebbutt SJ; Truter-Meyer A; Uddstrom L; Urban L; van Rhijn N; Vercoe D; Vesely E; Weir BS; Winter DJ; Yeung J
    Background: The critically endangered kākāpō is a flightless, nocturnal parrot endemic to Aotearoa New Zealand. Recent efforts to describe the gastrointestinal microbial community of this threatened herbivore revealed a low-diversity microbiota that is often dominated by Escherichia-Shigella bacteria. Given the importance of associated microbial communities to animal health, and increasing appreciation of their potential relevance to threatened species conservation, we sought to better understand the development of this unusual gut microbiota profile. To this end, we conducted a longitudinal analysis of faecal material collected from kākāpō chicks during the 2019 breeding season, in addition to associated nest litter material. Results: Using an experimental approach rarely seen in studies of threatened species microbiota, we evaluated the impact of a regular conservation practice on the developing kākāpō microbiota, namely the removal of faecal material from nests. Artificially removing chick faeces from nests had negligible impact on bacterial community diversity for either chicks or nests (p > 0.05). However, the gut microbiota did change significantly over time as chick age increased (p < 0.01), with an increasing relative abundance of Escherichia-Shigella coli over the study period and similar observations for the associated nest litter microbiota (p < 0.01). Supplementary feeding substantially altered gut bacterial diversity of kākāpō chicks (p < 0.01), characterised by a significant increase in Lactobacillus bacteria. Conclusions: Overall, chick age and hand rearing conditions had the most marked impact on faecal bacterial communities. Similarly, the surrounding nest litter microbiota changed significantly over time since a kākāpō chick was first placed in the nest, though we found no evidence that removal of faecal material influenced the bacterial communities of either litter or faecal samples. Taken together, these observations will inform ongoing conservation and management of this most enigmatic of bird species.