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

Sarah L. Baines; Anders Gonçalves da Silva; Glen P. Carter; Amy Jennison; Irani Rathnayake; Rikki M. Graham; Vitali Sintchenko; Qinning Wang; Rebecca J. Rockett; Verlaine J. Timms; Elena Martinez; Susan Ballard; Takehiro Tomita; Nicole Isles; Kristy A. Horan; William Pitchers; Timothy P. Stinear; Deborah A. Williamson; Benjamin P. Howden; Torsten Seemann; Communicable Diseases Genomics Network (CDGN)

doi:10.1099/mgen.0.000471

Volume 6, Issue 12

Research Article

Open Access

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

Sarah L. Baines¹, Anders Gonçalves da Silva², Glen P. Carter¹, Amy Jennison³, Irani Rathnayake³, Rikki M. Graham³, Vitali Sintchenko^4,5, Qinning Wang⁴, Rebecca J. Rockett^4,5, Verlaine J. Timms^4,5, Elena Martinez⁴, Susan Ballard², Takehiro Tomita², Nicole Isles², Kristy A. Horan², William Pitchers², Timothy P. Stinear¹, Deborah A. Williamson^1,2, Benjamin P. Howden^1,2, Torsten Seemann^1,2 and Communicable Diseases Genomics Network (CDGN)
View Affiliations Hide Affiliations

Affiliations: ¹ Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia ² Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia ³ Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia ⁴ Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia ⁵ Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
*Correspondence: Sarah L. Baines, [email protected] *Correspondence: Torsten Seemann, [email protected]
Published: 12 November 2020 https://doi.org/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.

Received: 19/08/2020
Accepted: 21/10/2020
Published Online: 12/11/2020

Keyword(s): genomics , public health microbiology and reference genomes

This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000471

2020-11-12

2024-04-19

Full text loading...

/deliver/fulltext/mgen/6/12/mgen000471.html?itemId=/content/journal/mgen/10.1099/mgen.0.000471&mimeType=html&fmt=ahah

References

Allard MW. The future of whole-genome sequencing for public health and the clinic. J Clin Microbiol 2016; 54:1946–1948 [View Article][PubMed]
[Google Scholar]
Arnold C. Public Health England Initiative for Infectious Disease Genomics 2014
[Google Scholar]
Brown EW, Gonzalez-Escalona N, Stones R, Timme R, Allard MW. The rise of genomics and the promise of whole genome sequencing for understanding microbial foodborne pathogens. In Gurtler J, Doyle M, Kornacki J. (editors) Foodborne Pathogens Food Microbiology and Food Saftey Cham: Springer; 2017 pp 333–351
[Google Scholar]
Kwong JC, McCallum N, Sintchenko V, Howden BP. Whole genome sequencing in clinical and public health microbiology. Pathology 2015; 47:199–210 [View Article][PubMed]
[Google Scholar]
Gardy J, Loman NJ, Rambaut A. Real-time digital pathogen surveillance - the time is now. Genome Biol 2015; 16:155 [View Article][PubMed]
[Google Scholar]
Kwong JC, Lane CR, Romanes F, Gonçalves da Silva A, Easton M et al. Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak. PeerJ 2018; 6:e4210 [View Article][PubMed]
[Google Scholar]
Gonçalves da Silva A, Baines SL, Carter GP, Heffernan H, French NP et al. A phylogenomic framework for assessing the global emergence and evolution of clonal complex 398 methicillin-resistant Staphylococcus aureus . Microb Genom 2017; 3:e000105 [View Article][PubMed]
[Google Scholar]
Gwinn M, MacCannell D, Armstrong GL. Next-Generation sequencing of infectious pathogens. JAMA 2019; 321:893–894 [View Article][PubMed]
[Google Scholar]
Luheshi L, Raza S, Moorthie S, Hall A, Blackburn L. Pathogen Genomics into Practice PHG Foundation; 2015
[Google Scholar]
Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I et al. Pulsenet international: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. Euro Surveill. 2017; 22: [View Article][PubMed]
[Google Scholar]
Williamson DA, Kirk MD, Sintchenko V, Howden BP. The importance of public health genomics for ensuring health security for Australia. Med J Aust 2019; 210:e291295–297 [View Article][PubMed]
[Google Scholar]
Weimer BC. 100K pathogen genome Project. Genome Announc 2017; 5: [View Article]
[Google Scholar]
Arnott A, Wang Q, Bachmann N, Sadsad R, Biswas C et al. Multidrug-resistant Salmonella enterica 4,[5],12:i:- sequence Type 34, New South Wales, Australia, 2016-2017. Emerg Infect Dis 2018; 24:751–753 [View Article][PubMed]
[Google Scholar]
Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E. Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol Biol Evol 2014; 31:1077–1088 [View Article][PubMed]
[Google Scholar]
Edwards DJ, Holt KE. Beginner's guide to comparative bacterial genome analysis using next-generation sequence data. Microb Inform Exp 2013; 3:2 [View Article][PubMed]
[Google Scholar]
Olson ND, Lund SP, Colman RE, Foster JT, Sahl JW et al. Best practices for evaluating single nucleotide variant calling methods for microbial genomics. Front Genet 2015; 6:235 [View Article][PubMed]
[Google Scholar]
Baines SL, Holt KE, Schultz MB, Seemann T, Howden BO et al. Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus . mBio 2015; 6:e00080 [View Article][PubMed]
[Google Scholar]
Carter GP, Buultjens AH, Ballard SA, Baines SL, Tomita T et al. Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium . J Antimicrob Chemother 2016; 71:3367–3371 [View Article][PubMed]
[Google Scholar]
Gymoese P, Sørensen G, Litrup E, Olsen JE, Nielsen EM et al. Investigation of outbreaks of Salmonella enterica serovar Typhimurium and Its monophasic variants using whole-genome sequencing, Denmark. Emerg Infect Dis 2017; 23:1631–1639 [View Article][PubMed]
[Google Scholar]
Graham RMA, Hiley L, Rathnayake IU, Jennison AV. Comparative genomics identifies distinct lineages of S. enteritidis from Queensland, Australia. PLoS One 2018; 13:e0191042 [View Article][PubMed]
[Google Scholar]
Rockett RJ, Oftadeh S, Bachmann NL, Timms VJ, Kong F et al. Genome-wide analysis of Streptococcus pneumoniae serogroup 19 in the decade after the introduction of pneumococcal conjugate vaccines in Australia. Sci Rep 2018; 8:16969 [View Article][PubMed]
[Google Scholar]
Timms VJ, Rockett R, Bachmann NL, Martinez E, Wang Q et al. Genome sequencing links persistent outbreak of legionellosis in Sydney (New South Wales, Australia) to an emerging clone of Legionella pneumophila sequence Type 211. Appl Environ Microbiol 2018; 84: [View Article][PubMed]
[Google Scholar]
Ingle DJ, Gonçalves da Silva A, Valcanis M, Ballard SA, Seemann T et al. Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia. Microb Genom 2019; 5: [View Article][PubMed]
[Google Scholar]
Saltykova A, Wuyts V, Mattheus W, Bertrand S, Roosens NHC et al. Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i. PLoS One 2018; 13:e0192504 [View Article][PubMed]
[Google Scholar]
Kwong JC, Mercoulia K, Tomita T, Easton M, Li HY et al. Prospective whole-genome sequencing enhances national surveillance of Listeria monocytogenes . J Clin Microbiol 2016; 54:333–342 [View Article][PubMed]
[Google Scholar]
McNerney R, Clark TG, Campino S, Rodrigues C, Dolinger D et al. Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action. Int J Infect Dis 2017; 56:130–135 [View Article][PubMed]
[Google Scholar]
Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014; 15:R46 [View Article][PubMed]
[Google Scholar]
Pettengill EA, Pettengill JB, Binet R. Phylogenetic analyses of Shigella and enteroinvasive Escherichia coli for the identification of molecular epidemiological markers: whole-genome comparative analysis does not support distinct genera designation. Front Microbiol 2015; 6:1573 [View Article][PubMed]
[Google Scholar]
Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article][PubMed]
[Google Scholar]
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article][PubMed]
[Google Scholar]
Chin CS, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article][PubMed]
[Google Scholar]
Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article][PubMed]
[Google Scholar]
Wick RR, Holt KE. Benchmarking of long-read assemblers for prokaryote whole genome sequencing. F1000Res 2019; 8:2138 [View Article][PubMed]
[Google Scholar]
Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010; 5:e11147 [View Article][PubMed]
[Google Scholar]
Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 2018; 3:124 [View Article][PubMed]
[Google Scholar]
Epping L, van Tonder AJ, Gladstone RA. The global pneumococcal sequencing C, Bentley SD, et al. SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data. Microb Genom 2018; 4:
[Google Scholar]
Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VPJ et al. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PLoS One 2016; 11:e0147101 [View Article][PubMed]
[Google Scholar]
Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 2014; 6:90 [View Article][PubMed]
[Google Scholar]

http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000471

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

M Gen 6, e000471 (2020); https://doi.org/10.1099/mgen.0.000471

/content/journal/mgen/10.1099/mgen.0.000471

Data & Media loading...

Supplements

Volume 6, Issue 12

Research Article

Open Access

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

Abstract

Supplementary material 1

Most read this month

Most cited Most Cited RSS feed

ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification

MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Completing bacterial genome assemblies with multiplex MinION sequencing

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping

Identification of Klebsiella capsule synthesis loci from whole genome data

Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

The diversity of Klebsiella pneumoniae surface polysaccharides