Journal Articles

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    20 years later: unravelling the genomic success of New Zealand’s home-grown AK3 community-associated methicillin-resistant Staphylococcus aureus
    (Microbiology Society, 2025-07-25) White RT; Bakker S; Bloomfield M; Burton M; Elvy J; Eustace A; French NP; Grant J; Greening SS; Grinberg A; Harland C; Hutton S; Karkaba A; Martin J; Matthews B; Miller H; Straub C; Tarring C; Taylor WT; Ussher J; Velasco C; Voss EM; Dyet K
    Methicillin-resistant Staphylococcus aureus (MRSA) represents a significant public health challenge. In New Zealand, the community-associated MRSA sequence type (ST)5, carrying the staphylococcal cassette chromosome mec (SCCmec) type IV genetic element (which confers methicillin resistance), has been predominant since its detection in 2005. Known informally as the AK3 strain, it also exhibits resistance to fusidic acid. Here, we investigated the genomic evolution of the AK3 strain by analysing 397 genomes, comprising 361 MRSA and 36 closely related methicillin-susceptible S. aureus (MSSA) genomes, including 285 recently sequenced isolates from New Zealand spanning 2020 (n=30), 2021 (n=77), 2022 (n=88), 2023 (n=73) and 2024 (n=17). Phylogenetic analysis revealed that the AK3 strain evolved through stepwise acquisition of mobile genetic elements, with an MSSA ancestor likely introduced to New Zealand in the late 1970s. The lineage first acquired a SaPITokyo12571-like pathogenicity island, which contains the staphylococcal enterotoxin C bovine variant (sec-bov) and an enterotoxin-like protein (sel), between 1984 and 1991. This was followed by the integration of SCCmec type IV and adjacent fusidic acid resistance operon between 1997 and 2000. This timing coincides with increased community fusidic acid use in New Zealand. The AK3 strain then diversified into three major clades, spreading throughout New Zealand and Australia, with sporadic detection in European countries and Samoa. Our findings demonstrate how the sequential acquisition of mobile genetic elements, combined with antibiotic selection pressure, likely contributed to the successful emergence of AK3 and its spread in the South Pacific region.
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    Bovine viral diarrhoea viruses from New Zealand belong predominantly to the BVDV-1a genotype.
    (Taylor and Francis Group, 2024-03-01) Dunowska M; Lal R; Dissanayake SD; Bond SD; Burrows E; Moffat J; Howe L
    AIM: To determine which genotypes of bovine viral diarrhoea virus (BVDV) circulate among cattle in New Zealand. METHODS: Samples comprised BVDV-1-positive sera sourced from submissions to veterinary diagnostic laboratories in 2019 (n = 25), 2020 (n = 59) and 2022 (n = 74) from both beef and dairy herds, as well as archival BVDV-1 isolates (n = 5). Fragments of the 5' untranslated region (5' UTR) and glycoprotein E2 coding sequence of the BVDV genome were amplified and sequenced. The sequences were aligned to each other and to international BVDV-1 sequences to determine their similarities and phylogenetic relationships. The 5' UTR sequences were also used to create genetic haplotype networks to determine if they were correlated with selected traits (location, type of farm, and year of collection). RESULTS: The 5' UTR sequences from New Zealand BVDV were closely related to each other, with pairwise identities between 89% and 100%. All clustered together and were designated as BVDV-1a (n = 144) or BVDV-1c (n = 5). There was no evidence of a correlation between the 5' UTR sequence and the geographical origin within the country, year of collection or the type of farm. Partial E2 sequences from New Zealand BVDV (n = 76) showed 74-100% identity to each other and clustered in two main groups. The subtype assignment based on the E2 sequence was the same as based on the 5' UTR analysis. This is the first comprehensive analysis of genomic variability of contemporary New Zealand BVDV based on the analysis of the non-coding (5' UTR) and coding (E2) sequences. CONCLUSIONS AND CLINICAL RELEVANCE: Knowledge of the diversity of the viruses circulating in the country is a prerequisite for the development of effective control strategies, including a selection of suitable vaccines. The data presented suggest that New Zealand BVDV are relatively homogeneous, which should facilitate eradication efforts including selection or development of the most suitable vaccines.