Browsing by Author "Scott P"

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Preparing for the next pandemic: insights from Aotearoa New Zealand's Covid-19 response
(Elsevier Ltd, 2025-03-18) French NP; Maxwell H; Baker MG; Callaghan F; Dyet K; Geoghegan JL; Hayman DTS; Huang QS; Kvalsvig A; Russell E; Scott P; Thompson TP; Plank MJ
In 2020 Aotearoa New Zealand, like many other countries, faced the coronavirus pandemic armed with an influenza-based pandemic plan. The country adapted rapidly to mount a highly strategic and effective elimination response to the SARS-CoV-2 pandemic. However, implementation was hampered by gaps in pandemic preparedness. These gaps undermined effectiveness of the response and exacerbated inequitable impacts of both Covid-19 disease and control measures. Our review examines the Covid-19 response, reflecting on strengths, limitations and implications for pandemic planning. We identify three key areas for improvement: 1) development of a systematised procedure for risk assessment of a new pandemic pathogen; 2) investment in essential capabilities during inter-pandemic periods; and 3) building equity into all stages of the response. We present a typology of potential pathogens and scenarios and describe the evidence assessment process and core capabilities required for countries to respond fluidly, equitably, and effectively to a rapidly emerging pandemic threat.
Whole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school
(Springer Nature Limited, 2021-10-13) Scott P; Zhang J; Anderson T; Priest PC; Chambers S; Smith H; Murdoch DR; French N; Biggs PJ
Epidemiological studies of communicable diseases increasingly use large whole-genome sequencing (WGS) datasets to explore the transmission of pathogens. It is important to obtain an initial overview of datasets and identify closely related isolates, but this can be challenging with large numbers of isolates and imperfect sequencing. We used an ad hoc whole-genome multi locus sequence typing method to summarise data from a longitudinal study of Staphylococcus aureus in a primary school in New Zealand. Each pair of isolates was compared and the number of genes where alleles differed between isolates was tallied to produce a matrix of "allelic differences". We plotted histograms of the number of allelic differences between isolates for: all isolate pairs; pairs of isolates from different individuals; and pairs of isolates from the same individual. 340 sequenced isolates were included, and the ad hoc shared genome contained 445 genes. There were between 0 and 420 allelic differences between isolate pairs and the majority of pairs had more than 260 allelic differences. We found many genetically closely related S. aureus isolates from single individuals and a smaller number of closely-related isolates from separate individuals. Multiple S. aureus isolates from the same individual were usually very closely related or identical over the ad hoc shared genome. Siblings carried genetically similar, but not identical isolates. An ad hoc shared genome approach to WGS analysis can accommodate imperfect sequencing of the included isolates, and can provide insights into relationships between isolates in epidemiological studies with large WGS datasets containing diverse isolates.
Zoonotic transmission of asymptomatic carriage Staphylococcus aureus on dairy farms in Canterbury, New Zealand.
(Microbiology Society, 2024-12-04) Straub C; Taylor W; French NP; Murdoch DR; Priest P; Anderson T; Scott P
Zoonotic pathogen transmission is of growing concern globally, with agricultural intensification facilitating interactions between humans, livestock and wild animals. Staphylococcus aureus is a major human pathogen, but it also causes mastitis in dairy cattle, leading to an economic burden on the dairy industry. Here, we investigated transmission within and between cattle and humans, including potential zoonotic transmission of S. aureus isolated from cattle and humans from three dairy farms and an associated primary school in New Zealand. Nasal swabs (N=170) were taken from healthy humans. Inguinal and combined nasal/inguinal swabs were taken from healthy cattle (N=1163). Whole-genome sequencing was performed for 96 S. aureus isolates (44 human and 52 cattle). Multilocus sequence typing and assessments of antimicrobial resistance and virulence were carried out. Potential within- and across-species transmission events were determined based on single nucleotide polymorphisms (SNPs). Thirteen potential transmission clusters were detected, with 12 clusters restricted to within-species and one potential zoonotic transmission cluster (ST5). Potential transmission among cattle was mostly limited to single age groups, likely because different age groups are managed separately on farms. While the prevalence of antimicrobial resistance (AMR) was low among both bovine and human isolates, the discovery of an extended-spectrum beta-lactamase gene (bla TEM-116) in a bovine isolate was concerning. This study provides evidence around frequency and patterns of potential transmission of S. aureus on dairy farms and highlights the AMR and virulence profile of asymptomatic carriage S. aureus isolates.