Complete microbial genomes for public health in Australia and the Southwest Pacific

Sarah L Baines,Qinning Wang,Glen P Carter,Takehiro Tomita,Irani Rathnayake,Vitali Sintchenko,Timothy P Stinear,Torsten Seemann,Verlaine J Timms,Anders Gonçalves Da Silva,William Pitchers,Nicole Isles,Benjamin P Howden ,Amy V Jennison ,Rebecca Rockett ,Susan Ballard ,Rikki Graham ,Kristy Horan ,Elena Martínez ,Deborah A Williamson

doi:10.1099/mgen.0.000471

Abstract

Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific; enriching the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health microbiology laboratories. In this first step, we present 26 complete high-quality bacterial genomes. Additionally, we describe here a framework for reconstructing complete microbial genomes and highlight some of the challenges and considerations for accurate and reproducible genome reconstruction.

Highlights

Whole-g enome sequence (WGS) data are a critical tool in public health microbiology [1,2,3,4]
The appeal of WGS data comes from the promise of a single workflow to process all microbial pathogens, and the provision of portable data that promote deeper integration of surveillance and investigation efforts across jurisdictions
To further support public health activities, we provide a detailed framework for bacterial genome reconstruction, using a combination of short- and long-read sequence data generated from different platforms

Summary

Introduction

Whole-g enome sequence (WGS) data are a critical tool in public health microbiology [1,2,3,4]. The appeal of WGS data comes from the promise of a single workflow to process all microbial pathogens, and the provision of portable data that promote deeper integration of surveillance and investigation efforts across jurisdictions This promise is leading to a concerted effort to move microbial public health to a primarily genome-b ased workflow in numerous countries [8,9,10], including Australia [11]. Essential to the success of this transition to a genomics workflow is the need to develop catalogues of high-quality complete reference genomes of microbial pathogens [12]

Methods

Results

Conclusion