Software for selecting the most informative sets of genomic loci for multi-target microbial typing

BackgroundHigh-throughput sequencing can identify numerous potential genomic targets for microbial strain typing, but identification of the most informative combinations requires the use of computational screening tools. This paper describes novel software - Automated Selection of Typing Target Subsets (AuSeTTS) - that allows intelligent selection of optimal targets for pathogen strain typing. The objective of this software is to maximise both discriminatory power, using Simpson’s index of diversity (D), and concordance with existing typing methods, using the adjusted Wallace coefficient (AW). The program interrogates molecular typing results for panels of isolates, based on large target sets, and iteratively examines each target, one-by-one, to determine the most informative subset.ResultsAuSeTTS was evaluated using three target sets: 51 binary targets (13 toxin genes, 16 phage-related loci and 22 SCCmec elements), used for multilocus typing of 153 methicillin-resistant Staphylococcus aureus (MRSA) isolates; 17 MLVA loci in 502 Streptococcus pneumoniae isolates from the MLVA database (http://www.mlva.eu) and 12 MLST loci for 98 Cryptococcus spp. isolates.The maximum D for MRSA, 0.984, was achieved with a subset of 20 targets and a D value of 0.954 with 7 targets. Twelve targets predicted MLST with a maximum AW of 0.9994. All 17 S. pneumoniae MLVA targets were required to achieve maximum D of 0.997, but 4 targets reached D of 0.990. Twelve targets predicted pneumococcal serotype with a maximum AW of 0.899 and 9 predicted MLST with maximum AW of 0.963. Eight of the 12 MLST loci were sufficient to achieve the maximum D of 0.963 for Cryptococcus spp.ConclusionsComputerised analysis with AuSeTTS allows rapid selection of the most discriminatory targets for incorporation into typing schemes. Output of the program is presented in both tabular and graphical formats and the software is available for free download from http://www.cidmpublichealth.org/pages/ausetts.html.

[1]  T. G. Mitchell,et al.  Consensus multi-locus sequence typing scheme for Cryptococcus neoformans and Cryptococcus gattii. , 2009, Medical mycology.

[2]  G. Vergnaud,et al.  Evaluation and selection of tandem repeat loci for Streptococcus pneumoniae MLVA strain typing , 2005, BMC Microbiology.

[3]  J A Carriço,et al.  Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant Streptococcus pyogenes , 2006, Journal of Clinical Microbiology.

[4]  W. Bossert,et al.  The Measurement of Diversity , 2001 .

[5]  BMC Bioinformatics , 2005 .

[6]  Gregor Tanner,et al.  Determining Confidence Intervals When Measuring Genetic Diversity and the Discriminatory Abilities of Typing Methods for Microorganisms , 2001, Journal of Clinical Microbiology.

[7]  M. Ramirez,et al.  A Confidence Interval for the Wallace Coefficient of Concordance and Its Application to Microbial Typing Methods , 2008, PloS one.

[8]  B. Spratt,et al.  Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. , 2000, Journal of clinical microbiology.

[9]  Venugopal Thiruvenkataswamy,et al.  Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases. , 2004, Journal of medical microbiology.

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

[11]  P. Hunter,et al.  Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity , 1988, Journal of clinical microbiology.

[12]  F. Kong,et al.  Multiplex PCR-based reverse line blot hybridization assay (mPCR/RLB)—a practical epidemiological and diagnostic tool , 2006, Nature Protocols.

[13]  Prospective Genotyping of Hospital-Acquired Methicillin-Resistant Staphylococcus aureus Isolates by Use of a Novel, Highly Discriminatory Binary Typing System , 2012, Journal of Clinical Microbiology.

[14]  M. Struelens.  Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. , 1996, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[15]  V. Sintchenko,et al.  A new multiplex PCR-based reverse line-blot hybridization (mPCR/RLB) assay for rapid staphylococcal cassette chromosome mec (SCCmec) typing. , 2009, Journal of medical microbiology.

[16]  Julian Parkhill,et al.  Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. , 2012, The New England journal of medicine.

[17]  T. G. Mitchell,et al.  Multilocus Sequence Typing Reveals Three Genetic Subpopulations of Cryptococcus neoformans var. grubii (Serotype A), Including a Unique Population in Botswana , 2006, Genetics.

[18]  João A. Carriço,et al.  Evaluation of Jackknife and Bootstrap for Defining Confidence Intervals for Pairwise Agreement Measures , 2011, PloS one.

[19]  Chrystala Constantinidou,et al.  Genome sequencing in clinical microbiology , 2012, Nature Biotechnology.

[20]  J. Heitman,et al.  Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak , 2005, Nature.

[21]  P. Giffard,et al.  Staphylococcus aureus Genotyping Using Novel Real-Time PCR Formats , 2006, Journal of Clinical Microbiology.

[22]  V. Sintchenko,et al.  Comparison of Single- and Multilocus Sequence Typing and Toxin Gene Profiling for Characterization of Methicillin-Resistant Staphylococcus aureus , 2007, Journal of Clinical Microbiology.

[23]  A. Friedrich,et al.  Meticillin-resistant Staphylococcus aureus (MRSA): global epidemiology and harmonisation of typing methods. , 2012, International journal of antimicrobial agents.

[24]  V. Sintchenko,et al.  Rapid Identification of Methicillin-Resistant Staphylococcus aureus Transmission in Hospitals by Use of Phage-Derived Open Reading Frame Typing Enhanced by Multiplex PCR and Reverse Line Blot Assay , 2010, Journal of Clinical Microbiology.

[25]  Erin P. Price,et al.  Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants , 2007, BMC Bioinformatics.

[26]  V. Sintchenko,et al.  Multiplex PCR and Reverse Line Blot Hybridization Assay (mPCR/RLB) , 2011, Journal of visualized experiments : JoVE.

[27]  João André Carriço,et al.  Adjusted Wallace Coefficient as a Measure of Congruence between Typing Methods , 2011, Journal of Clinical Microbiology.