Whole genome sequencing in clinical and public health microbiology

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Abstract

SummaryGenomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology.

The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology.

Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories.

As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future.

Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure.

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Most cited references 45

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Performance comparison of benchtop high-throughput sequencing platforms.

Nicholas Loman, Raju V. Misra, Timothy Dallman … (2012)

Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Each instrument can generate data required for a draft bacterial genome sequence in days, making them attractive for identifying and characterizing pathogens in the clinical setting. We compared the performance of these instruments by sequencing an isolate of Escherichia coli O104:H4, which caused an outbreak of food poisoning in Germany in 2011. The MiSeq had the highest throughput per run (1.6 Gb/run, 60 Mb/h) and lowest error rates. The 454 GS Junior generated the longest reads (up to 600 bases) and most contiguous assemblies but had the lowest throughput (70 Mb/run, 9 Mb/h). Run in 100-bp mode, the Ion Torrent PGM had the highest throughput (80–100 Mb/h). Unlike the MiSeq, the Ion Torrent PGM and 454 GS Junior both produced homopolymer-associated indel errors (1.5 and 0.38 errors per 100 bases, respectively).

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Comparison of Next-Generation Sequencing Systems

Lin Liu, Yinhu Li, Siliang Li … (2012)

With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.

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Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

E Kirkness, C Bult, A Kerlavage … (1995)

An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism.

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Author and article information

Journal

Journal ID (nlm-ta): Pathology

Journal ID (iso-abbrev): Pathology

Journal ID (publisher-id): PTHY

Title: Pathology

Publisher: Lippincott Williams & Wilkins

ISSN (Print): 0031-3025

ISSN (Electronic): 1465-3931

Publication date (Print): April 2015

Publication date (Electronic): 13 March 2015

Volume: 47

Issue: 3

Pages: 199-210

Affiliations

[1 ]Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, the University of Melbourne, at the Doherty Institute for Infection and Immunity, Melbourne, Vic

[2 ]Department of Infectious Diseases, Austin Health, Heidelberg, Vic

[3 ]Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW

[4 ]Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, NSW

[5 ]Department of Microbiology, Monash University, Clayton, Vic, Australia

Author notes

Address for correspondence: Professor Benjamin Howden, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, the University of Melbourne, The Doherty Institute for Infection amd Immunity, 792 Elizabeth Street, Melbourne, Vic 3000, Australia. E-mail: bhowden@ 123456unimelb.edu.au

Article

DOI: 10.1097/PAT.0000000000000235

PMC ID: 4389090

PubMed ID: 25730631

SO-VID: 964f854c-9836-4d4b-a8aa-eefef1db5ea8

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This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License, where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially. http://creativecommons.org/licenses/by-nc-nd/4.0

History

Date received : 11 December 2014

Date revision received : 5 January 2015

Date accepted : 22 January 2015

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Keywords: clinical microbiology,genomics,public health microbiology,sequencing,wgs,whole genome sequencing

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Keywords: clinical microbiology, genomics, public health microbiology, sequencing, wgs, whole genome sequencing

Whole genome sequencing in clinical and public health microbiology

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Most cited references 45

Performance comparison of benchtop high-throughput sequencing platforms.

Comparison of Next-Generation Sequencing Systems

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

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