Browsing by Author "Greening SS"

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    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.
  • Thumbnail Image
    Item
    The Genetic Relatedness and Antimicrobial Resistance Patterns of Mastitis-Causing Staphylococcus aureus Strains Isolated from New Zealand Dairy Cattle
    (MDPI (Basel, Switzerland), 2021-11-22) Greening SS; Zhang J; Midwinter AC; Wilkinson DA; McDougall S; Gates MC; French NP; Butaye P
    Staphylococcus aureus is one of the leading causes of bovine mastitis worldwide and is a common indication for use of antimicrobials on dairy farms. This study aims to investigate the association between on-farm antimicrobial usage and the antimicrobial resistance (AMR) profiles of mastitis-causing S. aureus. Whole-genome sequencing was performed on 57 S. aureus isolates derived from cows with either clinical or subclinical mastitis from 17 dairy herds in New Zealand. The genetic relatedness between isolates was examined using the core single nucleotide polymorphism alignment whilst AMR and virulence genes were identified in-silico. The association between gene presence-absence and sequence type (ST), antimicrobial susceptibility and dry cow therapy treatment was investigated using Scoary. Altogether, eight STs were identified with 61.4% (35/57) belonging to ST-1. Furthermore, 14 AMR-associated genes and 76 virulence-associated genes were identified, with little genetic diversity between isolates belonging to the same ST. Several genes including merR1 which is thought to play a role in ciprofloxacin-resistance were found to be significantly overrepresented in isolates sampled from herds using ampicillin/cloxacillin dry cow therapy. Overall, the presence of resistance genes remains low and current antimicrobial usage patterns do not appear to be driving AMR in S. aureus associated with bovine mastitis.
  • Thumbnail Image
    Item
    Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand’s commercial poultry network
    (Elsevier B.V, 2021-12) Greening SS; Zhang J; Midwinter AC; Wilkinson DA; Fayaz A; Williamson DA; Anderson MJ; Gates MC; French NP
    Understanding the relative contribution of different between-farm transmission pathways is essential in guiding recommendations for mitigating disease spread. This study investigated the association between contact pathways linking poultry farms in New Zealand and the genetic relatedness of antimicrobial resistant Campylobacter jejuni Sequence Type 6964 (ST-6964), with the aim of identifying the most likely contact pathways that contributed to its rapid spread across the industry. Whole-genome sequencing was performed on 167C. jejuni ST-6964 isolates sampled from across 30 New Zealand commercial poultry enterprises. The genetic relatedness between isolates was determined using whole genome multilocus sequence typing (wgMLST). Permutational multivariate analysis of variance and distance-based linear models were used to explore the strength of the relationship between pairwise genetic associations among the C. jejuni isolates and each of several pairwise distance matrices, indicating either the geographical distance between farms or the network distance of transportation vehicles. Overall, a significant association was found between the pairwise genetic relatedness of the C. jejuni isolates and the parent company, the road distance and the network distance of transporting feed vehicles. This result suggests that the transportation of feed within the commercial poultry industry as well as other local contacts between flocks, such as the movements of personnel, may have played a significant role in the spread of C. jejuni. However, further information on the historical contact patterns between farms is needed to fully characterise the risk of these pathways and to understand how they could be targeted to reduce the spread of C. jejuni.