Next-generation sequencing technologies and their application to the study and control of bacterial infections.

BACKGROUND With the efficiency and the decreasing cost of next-generation sequencing, the technology is being rapidly introduced into clinical and public health laboratory practice. AIMS The historical background and principles of first-, second- and third-generation sequencing are described, as are the characteristics of the most commonly used sequencing instruments. SOURCES Peer-reviewed literature, white papers and meeting reports. CONTENT AND IMPLICATIONS Next-generation sequencing is a technology that could potentially replace many traditional microbiological workflows, providing clinicians and public health specialists with more actionable information than hitherto achievable. Examples of the clinical and public health uses of the technology are provided. The challenge of comparability of different sequencing platforms is discussed. Finally, the future directions of the technology integrating it with laboratory management and public health surveillance systems, and moving it towards performing sequencing directly from the clinical specimen (metagenomics), could lead to yet another fundamental transformation of clinical diagnostics and public health surveillance.

[1]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Keith A. Jolley,et al.  A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter , 2014, PloS one.

[3]  Ole Lund,et al.  Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli , 2014, Journal of Clinical Microbiology.

[4]  I. Van Walle,et al.  PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance , 2017, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[5]  Ole Lund,et al.  Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. , 2013, The Journal of antimicrobial chemotherapy.

[6]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[7]  V. Vaillant,et al.  Outbreak of Shiga toxin-producing Escherichia coli O104:H4 associated with organic fenugreek sprouts, France, June 2011. , 2012, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[8]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[9]  J. Rothberg,et al.  Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology , 2011, PloS one.

[10]  G. Weinstock,et al.  High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. , 2010, The Journal of hospital infection.

[11]  Lawrence G. Wayne,et al.  International Committee on Systematic Bacteriology announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. , 1988, The Journal of applied bacteriology.

[12]  Francesca Giordano,et al.  Oxford Nanopore MinION Sequencing and Genome Assembly , 2016, Genom. Proteom. Bioinform..

[13]  David Stoddart,et al.  Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore , 2009, Proceedings of the National Academy of Sciences.

[14]  A. Friedrich,et al.  Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae , 2016, Journal of Clinical Microbiology.

[15]  L. May,et al.  Better Tests, Better Care: Improved Diagnostics for Infectious Diseases , 2013, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[16]  J. Rothberg,et al.  Semiconductor Sequencing for Life , 2011 .

[17]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[18]  S. Brisse,et al.  Real-Time Whole-Genome Sequencing for Surveillance of Listeria monocytogenes, France , 2017, Emerging infectious diseases.

[19]  Ole Lund,et al.  A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance , 2016, PloS one.

[20]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[21]  Jenny Shu,et al.  Efficient and accurate whole genome assembly and methylome profiling of E. coli , 2013, BMC Genomics.

[22]  Eduardo P C Rocha,et al.  Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes , 2016, Nature Microbiology.

[23]  Julian Parkhill,et al.  Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks , 2013 .

[24]  Yi Chen,et al.  Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation. , 2016, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[25]  Frank M. Aarestrup,et al.  Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data , 2015, Journal of Clinical Microbiology.

[26]  Ole Lund,et al.  PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data , 2013, PloS one.

[27]  Kin-Fan Au,et al.  PacBio Sequencing and Its Applications , 2015, Genom. Proteom. Bioinform..

[28]  P. Vandamme,et al.  DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. , 2007, International journal of systematic and evolutionary microbiology.

[29]  M. Achtman,et al.  Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[30]  O. Lund,et al.  Correction: PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data , 2013, PLoS ONE.

[31]  A. T. Vincent,et al.  Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money. , 2017, Journal of microbiological methods.

[32]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[33]  Evan S Snitkin,et al.  Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing , 2012, Science Translational Medicine.

[34]  J. T. Dunnen,et al.  Next generation sequencing technology: Advances and applications. , 2014, Biochimica et biophysica acta.

[35]  R. Rosselló-Móra,et al.  Shifting the genomic gold standard for the prokaryotic species definition , 2009, Proceedings of the National Academy of Sciences.

[36]  Mette Voldby Larsen,et al.  Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences , 2014, Bacteriophage.

[37]  H. Swerdlow,et al.  A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers , 2012, BMC Genomics.

[38]  Julian Parkhill,et al.  Evolution of MRSA During Hospital Transmission and Intercontinental Spread , 2010, Science.

[39]  Whole-Genome Sequencing Is Taking over Foodborne Disease Surveillance: Public health microbiology is undergoing its biggest change in a generation, replacing traditional methods with whole-genome sequencing , 2016 .

[40]  C. Thermes,et al.  Ten years of next-generation sequencing technology. , 2014, Trends in genetics : TIG.

[41]  A. Kasarskis,et al.  A window into third-generation sequencing. , 2010, Human molecular genetics.

[42]  Gary Van Domselaar,et al.  A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens , 2017, Front. Microbiol..

[43]  J. Tappero,et al.  Cholera surveillance during the Haiti epidemic--the first 2 years. , 2013, The New England journal of medicine.

[44]  E. Lander.  Initial impact of the sequencing of the human genome , 2011, Nature.

[45]  C. Beard,et al.  Whole genome multilocus sequence typing as an epidemiologic tool for Yersinia pestis. , 2016, Diagnostic microbiology and infectious disease.

[46]  N. Loman,et al.  A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.

[47]  Donald J. Sharp,et al.  An Economic Evaluation of PulseNet: A Network for Foodborne Disease Surveillance. , 2016, American journal of preventive medicine.

[48]  David A. Matthews,et al.  Real-time, portable genome sequencing for Ebola surveillance , 2016, Nature.