Whole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school

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dc.citation.issue1
dc.citation.volume11
dc.contributor.authorScott P
dc.contributor.authorZhang J
dc.contributor.authorAnderson T
dc.contributor.authorPriest PC
dc.contributor.authorChambers S
dc.contributor.authorSmith H
dc.contributor.authorMurdoch DR
dc.contributor.authorFrench N
dc.contributor.authorBiggs PJ
dc.coverage.spatialEngland
dc.date.accessioned2024-01-08T22:57:15Z
dc.date.accessioned2024-07-25T06:33:09Z
dc.date.available2021-10-13
dc.date.available2024-01-08T22:57:15Z
dc.date.available2024-07-25T06:33:09Z
dc.date.issued2021-10-13
dc.description.abstractEpidemiological 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.
dc.description.confidentialfalse
dc.format.pagination20328-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/34645857
dc.identifier.citationScott P, Zhang J, Anderson T, Priest PC, Chambers S, Smith H, Murdoch DR, French N, Biggs PJ. (2021). Whole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school.. Sci Rep. 11. 1. (pp. 20328-).
dc.identifier.doi10.1038/s41598-021-99080-8
dc.identifier.eissn2045-2322
dc.identifier.elements-typejournal-article
dc.identifier.issn2045-2322
dc.identifier.numberARTN 20328
dc.identifier.pii10.1038/s41598-021-99080-8
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/70399
dc.languageeng
dc.publisherSpringer Nature Limited
dc.publisher.urihttps://www.nature.com/articles/s41598-021-99080-8
dc.relation.isPartOfSci Rep
dc.rights(c) The author/sen
dc.rights.licenseCC BY 4.0en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectAlleles
dc.subjectBacteremia
dc.subjectChild
dc.subjectComputational Biology
dc.subjectFemale
dc.subjectGenetic Variation
dc.subjectGenome
dc.subjectGenome, Bacterial
dc.subjectHumans
dc.subjectLongitudinal Studies
dc.subjectMale
dc.subjectMethicillin-Resistant Staphylococcus aureus
dc.subjectMultilocus Sequence Typing
dc.subjectNew Zealand
dc.subjectSchools
dc.subjectStaphylococcal Infections
dc.subjectStaphylococcus aureus
dc.subjectStudents
dc.subjectWhole Genome Sequencing
dc.titleWhole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school
dc.typeJournal article
pubs.elements-id448987
pubs.organisational-groupOther
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