SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. Using >900 genomes from common pathogens, we show SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment. Here we have demonstrated the use of SRST2 for microbial genome surveillance in a variety of public health and hospital settings. In the face of rising threats of antimicrobial resistance and emerging virulence amongst bacterial pathogens, SRST2 represents a powerful tool for rapidly extracting clinically useful information from raw WGS data. Source code is available from http://katholt.github.io/srst2/.

[1]  Maria Victoria Schneider,et al.  Live Genomics for Pathogen Monitoring in Public Health , 2014, Pathogens.

[2]  Nicholas J Loman,et al.  High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. , 2010, Current opinion in microbiology.

[3]  G. Smith,et al.  Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. , 2013, JAMA internal medicine.

[4]  Ole Lund,et al.  In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing , 2014, Antimicrobial Agents and Chemotherapy.

[5]  N. Loman,et al.  High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity , 2012, Nature Reviews Microbiology.

[6]  G. Dougan,et al.  Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology , 2012, PLoS pathogens.

[7]  Justin Zobel,et al.  Short read sequence typing (SRST): multi-locus sequence types from short reads , 2012, BMC Genomics.

[8]  J. R. Johnson,et al.  Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data , 2013, The Journal of antimicrobial chemotherapy.

[9]  Julian Parkhill,et al.  A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic , 2013, Genome research.

[10]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[11]  M. Schatz,et al.  Algorithms Gage: a Critical Evaluation of Genome Assemblies and Assembly Material Supplemental , 2008 .

[12]  B. Spratt,et al.  How Clonal Is Staphylococcus aureus? , 2003, Journal of bacteriology.

[13]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[14]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[15]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[16]  J. Corander,et al.  Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus , 2012, Genome Biology.

[17]  N. Fittipaldi,et al.  Deriving Group A Streptococcus Typing Information from Short-Read Whole-Genome Sequencing Data , 2014, Journal of Clinical Microbiology.

[18]  K. Jolley,et al.  Automated extraction of typing information for bacterial pathogens from whole genome sequence data: Neisseria meningitidis as an exemplar. , 2013, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[19]  Paolo Piazza,et al.  Microevolutionary analysis of Clostridium difficile genomes to investigate transmission , 2012, Genome Biology.

[20]  Torsten Seemann,et al.  A sustained hospital outbreak of vancomycin-resistant Enterococcus faecium bacteremia due to emergence of vanB E. faecium sequence type 203. , 2010, The Journal of infectious diseases.

[21]  S. Peacock,et al.  Rapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory--pipe dream or reality? , 2012, The Journal of antimicrobial chemotherapy.

[22]  Daniel J. Wilson,et al.  A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance , 2012, BMJ Open.

[23]  D. Posada,et al.  Coalescent Simulation of Intracodon Recombination , 2010, Genetics.

[24]  J. Rolain,et al.  ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes , 2013, Antimicrobial Agents and Chemotherapy.

[25]  Sergey Koren,et al.  Automated ensemble assembly and validation of microbial genomes , 2014, BMC Bioinformatics.

[26]  T. Seemann,et al.  Outbreak Investigation Using High-Throughput Genome Sequencing within a Diagnostic Microbiology Laboratory , 2013, Journal of Clinical Microbiology.

[27]  X. Didelot,et al.  Whole genome sequencing in the prevention and control of Staphylococcus aureus infection , 2012, Journal of Hospital Infection.

[28]  Timothy D Read,et al.  Bacterial population genomics and infectious disease diagnostics. , 2010, Trends in biotechnology.

[29]  D. W. Kim,et al.  Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe , 2012, Nature Genetics.

[30]  Junhua Li,et al.  Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. , 2011, The New England journal of medicine.

[31]  Ole Lund,et al.  Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria , 2012, Journal of Clinical Microbiology.

[32]  J. Burton,et al.  Rapid Pneumococcal Evolution in Response to Clinical Interventions , 2011, Science.

[33]  A. Friedrich,et al.  Overview of molecular typing methods for outbreak detection and epidemiological surveillance. , 2013, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[34]  Paul D. R. Johnson,et al.  Enterococcal vanB resistance locus in anaerobic bacteria in human faeces , 2001, The Lancet.

[35]  S. Brisse,et al.  A New Perspective on Listeria monocytogenes Evolution , 2008, PLoS pathogens.

[36]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[37]  S. Rasmussen,et al.  Identification of acquired antimicrobial resistance genes , 2012, The Journal of antimicrobial chemotherapy.

[38]  Lior Pachter,et al.  Identification and correction of systematic error in high-throughput sequence data , 2011, BMC Bioinformatics.

[39]  A. Carattoli,et al.  Identification of plasmids by PCR-based replicon typing. , 2005, Journal of microbiological methods.

[40]  Keith A. Jolley,et al.  Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing , 2013, Journal of Clinical Microbiology.

[41]  Torsten Seemann,et al.  Genomic Insights to Control the Emergence of Vancomycin-Resistant Enterococci , 2013, mBio.

[42]  M. Maiden.  Multilocus sequence typing of bacteria. , 2006, Annual review of microbiology.

[43]  Daniel J. Wilson,et al.  Transforming clinical microbiology with bacterial genome sequencing , 2012, Nature Reviews Genetics.

[44]  M. Gilmour,et al.  Public Health Genomics and the New Molecular Epidemiology of Bacterial Pathogens , 2013, Public Health Genomics.

[45]  C. Bertelli,et al.  Rapid bacterial genome sequencing: methods and applications in clinical microbiology. , 2013, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[46]  Julian Parkhill,et al.  Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study , 2013, The Lancet. Infectious Diseases.