Whole-Genome Sequencing of Bacterial Isolate

Genomic DNA extraction, library preparation, and whole-genome sequencing on a NextSeq 500 platform (Illumina, Inc.), using 2 × 150-bp chemistry, was performed as previously described (24 (link)). One isolate (designated NZ-SC16875) underwent genomic DNA extraction with the GenElute bacterial genomic DNA kit (Sigma-Aldrich), followed by sequencing on the RSII (Pacific Biosciences) with P6-C4 chemistry according to the 20-kb template preparation using the BluePippin size selection system protocol (Pacific Biosciences). Sequences were initially analyzed using the Nullarbor pipeline (T. Seeman; https://github.com/tseemann/nullarbor). Phage regions were detected using Phaster (25 (link)). Maximum likelihood trees were inferred using IQ-TREE (26 (link)). Recombination was detected using Gubbins (version 2.2.0-1) (27 (link)), and population structure was investigated using hierarchical Bayesian analysis with hierBAPS (28 (link)). Additional information on bioinformatic analyses is provided in the Supplemental Methods.

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Carter G.P., Ussher J.E., Da Silva A.G., Baines S.L., Heffernan H., Riley T.V., Broadbent R., van der Linden A., Lee J., Monk I.R., Stinear T.P., Howden B.P, & Williamson D.A. (2018). Genomic Analysis of Multiresistant Staphylococcus capitis Associated with Neonatal Sepsis. Antimicrobial Agents and Chemotherapy, 62(11), e00898-18.

Publication 2018

NextSeq 500 platform GenElute bacterial genomic DNA kit RSII BluePippin size selection system protocol

Bacterial dna Genomic Library Phage Recombination Tree

Corresponding Organization :

Other organizations : Peter Doherty Institute, University of Melbourne, University of Otago, Southern Community Laboratories (New Zealand), Institute of Environmental Science and Research, Pathwest Laboratory Medicine

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Variable analysis

independent variables

Genomic DNA extraction method (GenElute bacterial genomic DNA kit)
Sequencing platform (NextSeq 500 and RSII)
Sequencing chemistry (2 × 150-bp and P6-C4)

dependent variables

Genomic sequences of the bacterial isolate NZ-SC16875

control variables

Library preparation and whole-genome sequencing protocol as previously described (24)
Bioinformatic analysis tools (Nullarbor pipeline, Phaster, IQ-TREE, Gubbins, hierBAPS)

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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