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

BMC Bioinformatics

Matthew VN O’Sullivan¹  Vitali Sintchenko¹  Gwendolyn L Gilbert¹ 

[1] Centre for Infectious Diseases and Microbiology and Sydney Institute for Emerging Infections and Biosecurity, University of Sydney, Westmead Hospital, Hawkesbury Road, Westmead, NSW 2145, Australia

关键词: Streptococcus pneumoniae;    Staphylococcus aureus;    Cryptococcus;    MRSA;    Microbial typing;    Software;    Binary typing;    MVLA;    Multilocus sequence typing;    Comparative genomics;   

Others  :  1087887
DOI  :  10.1186/1471-2105-14-148

 received in 2012-06-22, accepted in 2013-04-30,  发布年份 2013

【 摘 要 】

Background

High-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.

Results

AuSeTTS 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 webcite) 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.

Conclusions

Computerised 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 webcite.

【 授权许可】

   
2013 O’Sullivan et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

【 参考文献 】

• [1]Joseph SJ, Read TD: Bacterial population genomics and infectious disease diagnostics. Trends Biotechnol 2010, 28:611-618.
• [2]Chan JZ, Pallen MJ, Oppenheim B, Constantinidou C: Genome sequencing in clinical microbiology. Nat Biotechnol 2012, 30:1068-1071.
• [3]Köser CU, Holden MTG, Ellington MJ, Cartwright EJP, Brown NM, Ogilvy-Stuart AL, Hsu LY, Chewapreecha C, Croucher NJ, Harris SR: Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. New England J Med 2012, 366:2267-2275.
• [4]Stefani S, Chung DR, Lindsay JA, Friedrich AW, Kearns AM, Westh H, Mackenzie FM: Meticillin-resistant Staphylococcus aureus (MRSA): global epidemiology and harmonisation of typing methods. Int J Antimicrobial Agents 2012, 39:273-282.
• [5]Struelens MJ: Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. Clin Microbiol Infect 1996, 2:2-11.
• [6]Robertson GA, Thiruvenkataswamy V, Shilling H, Price EP, Huygens F, Henskens FA, Giffard PM: Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases. J Med Microbiol 2004, 53:35-45.
• [7]Price E, Inman-Bamber J, Thiruvenkataswamy V, Huygens F, Giffard P: Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants. BMC Bioinformatics 2007, 8:278. BioMed Central Full Text
• [8]Hunter PR, Gaston MA: Numerical index of the discriminatory ability of typing systems: an application of Simpson’s index of diversity. J Clin Microbiol 1988, 26:2465-2466.
• [9]Grundmann H, Hori S, Tanner G: Determining confidence intervals when measuring genetic diversity and the discriminatory abilities of typing methods for microorganisms. J Clin Microbiol 2001, 39:4190-4192.
• [10]Simpson EH: Measurement of diversity. Nature 1949, 163:688.
• [11]Carrico JA, Silva-Costa C, Melo-Cristino J, Pinto FR, De Lencastre H, Almeida JS, Ramirez M: Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant streptococcus pyogenes. J Clin Microbiol 2006, 44:2524-2532.
• [12]Severiano A, Pinto FR, Ramirez M, Carriço JA: Adjusted wallace coefficient as a measure of congruence between typing methods. J Clin Microbiol 2011, 49:3997-4000.
• [13]Pinto FR, Melo-Cristino J, Ramirez MR: A confidence interval for the wallace coefficient of concordance and Its application to microbial typing methods. PLoS One 2008, 3:e3696.
• [14]Severiano A, Carriço JA, Robinson DA, Ramirez M, Pinto FR: Evaluation of jackknife and bootstrap for defining confidence intervals for pairwise agreement measures. PLoS One 2011, 6:e19539.
• [15]Comparing Partitions. http://darwin.phyloviz.net/ComparingPartitions webcite
• [16]Cai L, Kong F, Wang Q, Wang H, Xiao M, Sintchenko V, Gilbert GL: A new multiplex PCR-based reverse line-blot hybridization (mPCR/RLB) assay for rapid staphylococcal cassette chromosome mec (SCCmec) typing. J Med Microbiol 2009, 58:1045-1057.
• [17]Cai Y, Kong F, Wang Q, Tong Z, Sintchenko V, Zeng X, Gilbert GL: Comparison of single and multilocus sequence typing and toxin gene profiling for characterisation of methicillin resistant Staphylococcus aureus (MRSA). J Med Microbiol 2007, 45:3302-3308.
• [18]O’Sullivan MV, Kong F, Sintchenko V, Gilbert GL: 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. J Clin Microbiol 2010, 48:2741-2748.
• [19]Koeck J-L, Njanpop-Lafourcade B-M, Cade S, Varon E, Sangare L, Valjevac S, Vergnaud G, Pourcel C: Evaluation and selection of tandem repeat loci for Streptococcus pneumoniae MLVA strain typing. BMC Microbiol 2005, 5:66. BioMed Central Full Text
• [20]Fraser JA, Giles SS, Wenink EC, Geunes-Boyer SG, Wright JR, Diezmann S, Allen A, Stajich JE, Dietrich FS, Perfect JR, Heitman J: Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak. Nature 2005, 437:1360-1364.
• [21]Litvintseva AP, Thakur R, Vilgalys R, Mitchell TG: Multilocus sequence typing reveals three genetic subpopulations of cryptococcus neoformans var. grubii (Serotype A): including a unique population in Botswana. Genetics 2006, 172:2223-2238.
• [22]O’Sullivan MV, Zhou F, Sintchenko V, Kong F, Gilbert GL: Multiplex PCR and reverse line blot hybridization assay (mPCR/RLB). J Vis Exp 2011, 54:e2781.
• [23]Kong F, Gilbert GL: Multiplex PCR-based reverse line blot hybridization assay (mPCR/RLB)–a practical epidemiological and diagnostic tool. Nat Protoc 2006, 1:2668-2680.
• [24]Enright MC, Day NPJ, Davies CE, Peacock SJ, Spratt BG: Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of staphylococcus aureus. J Med Microbiol 2000, 38:1008-1015.
• [25]Huygens F, Inman-Bamber J, Nimmo GR, Munckhof W, Schooneveldt J, Harrison B, McMahon JA, Giffard PM: Staphylococcus aureus genotyping using novel real-time PCR formats. J Med Microbiol 2006, 44:3712-3719.
• [26]O’Sullivan MVN, Zhou F, Sintchenko V, Gilbert GL: Prospective genotyping of hospital-acquired MRSA using a novel, highly discriminatory binary typing system. J Med Microbiol 2012, 50:3513-3519.
• [27]Meyer W, Aanensen DM, Boekhout T, Cogliati M, Diaz MR, Esposto MC, Fisher M, Gilgado F, Hagen F, Kaocharoen S: Consensus multi-locus sequence typing scheme for Cryptococcus neoformans and Cryptococcus gattii. Med Mycol 2009, 47:561-570.