publication . Article . 2018

Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites

Tara N. Furstenau; Jill H. Cocking; Jason W. Sahl; Viacheslav Y. Fofanov;
Open Access English
  • Published: 01 Jun 2018 Journal: BMC Bioinformatics, volume 19 (eissn: 1471-2105, Copyright policy)
  • Publisher: BioMed Central
Abstract
Abstract Background Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by targeting housekeeping genes that provide resolution down to the family, genera, and sometimes species level. Unfortunately, this level of resolution is not sufficient in many applications where strain-level identification of bacteria is required (biodefense, forensics, clinical diagnostics, and outbreak investigations). Adding more genomic targets will increase the resolution, but the challenge is identifying the appropriate targets. VaS...
Subjects
free text keywords: Software, Targeted PCR Amplicon sequencing, Bacterial strain typing, Single nucleotide polymorphisms, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5, Biochemistry, Applied Mathematics, Molecular Biology, Structural Biology, Computer Science Applications
65 references, page 1 of 5

1 Brzuszkiewicz E, Thürmer A, Schuldes J, Leimbach A, Liesegang H, Meyer F, et al. Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC). Arch Microbiol. 2011; 193(12):883–91. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219860/.

2 Deng X, den Bakker HC, Hendriksen RS. Genomic Epidemiology: Whole-Genome-Sequencing Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens. Annu Rev Food Sci Technol. 2016; 7(1):353–74. PMID: 26772415 Available from: 10.1146/annurev-food-041715-033259.

3 Pires dos Santos T, Damborg P, Moodley A, Guardabassi L. Systematic Review on Global Epidemiology of Methicillin-Resistant Staphylococcus pseudintermedius: Inference of Population Structure from Multilocus Sequence Typing Data. Front Microbiol. 2016; 7:1599. Available from: https://www.frontiersin.org/article/10.3389/fmicb.2016.01599.

Rasko, D, Worsham, P, Abshire, T, Stanley, S, Bannan, J, Wilson, M. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proc Natl Acad Sci U S A. 2011; 108: 5027-32 [OpenAIRE] [PubMed] [DOI]

5 Schmedes SE, Sajantila A, Budowle B. Expansion of Microbial Forensics. J Clin Microbiol. 2016; 54(8):1964–74. Available from: http://jcm.asm.org/content/54/8/1964.abstract.

6 Yang R, Keim P. Microbial forensics: A powerful tool for pursuing bioterrorism perpetrators and the need for an international database. J Bioterr Biodef. 2012; S3:007. 10.4172/2157-2526.S3-007.

7 Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, et al. Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics. Genome Biol Evol. 2011; 01(3):1312–23. Available from: 10.1093/gbe/evr106.

8 Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, et al. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010; 01(7):111–8. Available from: 10.1038/nmeth.1419.

9 Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991; 173:697–703. Available from: http://jb.asm.org/content/173/2/697.abstract.

10 Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, et al. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci. 1998; 95(6):3140–5. Available from: http://www.pnas.org/content/95/6/3140.

11 Boers SA, van der Reijden WA, Jansen R. High-Throughput Multilocus Sequence Typing: Bringing Molecular Typing to the Next Level. PLoS ONE. 2012; 7(7):1–8. Available from: 10.1371/journal.pone.003 9630.

12 Fournier P, Dubourg G, Raoult D. Clinical detection and characterization of bacterial pathogens in the genomics era. Genome Med. 2014; 6(11):114. Available from: 10.1186/s13073-014-0114-2.

13 Bartual SG, Seifert H, Hippler C, Luzon MAD, Wisplinghoff H, Rodríguez-Valera F. Development of a Multilocus Sequence Typing Scheme for Characterization of Clinical Isolates of Acinetobacter baumannii. J Clin Microbiol. 2005; 43(9):4382–90. Available from: http://jcm.asm.org/content/43/9/4382.abstract.

14 Blanchard AM, Jolley KA, Maiden MCJ, Coffey TJ, Maboni G, Staley CE, et al. The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for Dichelobacter nodosus. Front Microbiol. 2018; 9:551. Available from: https://www.frontiersin.org/article/10.3389/fmicb.2018.00551.

15 Boonsilp S, Thaipadungpanit J, Amornchai P, Wuthiekanun V, Bailey MS, Holden MTG, et al. A Single Multilocus Sequence Typing (MLST) Scheme for Seven Pathogenic Leptospira Species. PLoS Negl Trop Dis. 2013; 7(1):1–10. Available from: 10.1371/journal.pntd.0001954.

65 references, page 1 of 5
Abstract
Abstract Background Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by targeting housekeeping genes that provide resolution down to the family, genera, and sometimes species level. Unfortunately, this level of resolution is not sufficient in many applications where strain-level identification of bacteria is required (biodefense, forensics, clinical diagnostics, and outbreak investigations). Adding more genomic targets will increase the resolution, but the challenge is identifying the appropriate targets. VaS...
Subjects
free text keywords: Software, Targeted PCR Amplicon sequencing, Bacterial strain typing, Single nucleotide polymorphisms, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5, Biochemistry, Applied Mathematics, Molecular Biology, Structural Biology, Computer Science Applications
65 references, page 1 of 5

1 Brzuszkiewicz E, Thürmer A, Schuldes J, Leimbach A, Liesegang H, Meyer F, et al. Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC). Arch Microbiol. 2011; 193(12):883–91. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219860/.

2 Deng X, den Bakker HC, Hendriksen RS. Genomic Epidemiology: Whole-Genome-Sequencing Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens. Annu Rev Food Sci Technol. 2016; 7(1):353–74. PMID: 26772415 Available from: 10.1146/annurev-food-041715-033259.

3 Pires dos Santos T, Damborg P, Moodley A, Guardabassi L. Systematic Review on Global Epidemiology of Methicillin-Resistant Staphylococcus pseudintermedius: Inference of Population Structure from Multilocus Sequence Typing Data. Front Microbiol. 2016; 7:1599. Available from: https://www.frontiersin.org/article/10.3389/fmicb.2016.01599.

Rasko, D, Worsham, P, Abshire, T, Stanley, S, Bannan, J, Wilson, M. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proc Natl Acad Sci U S A. 2011; 108: 5027-32 [OpenAIRE] [PubMed] [DOI]

5 Schmedes SE, Sajantila A, Budowle B. Expansion of Microbial Forensics. J Clin Microbiol. 2016; 54(8):1964–74. Available from: http://jcm.asm.org/content/54/8/1964.abstract.

6 Yang R, Keim P. Microbial forensics: A powerful tool for pursuing bioterrorism perpetrators and the need for an international database. J Bioterr Biodef. 2012; S3:007. 10.4172/2157-2526.S3-007.

7 Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, et al. Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics. Genome Biol Evol. 2011; 01(3):1312–23. Available from: 10.1093/gbe/evr106.

8 Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, et al. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010; 01(7):111–8. Available from: 10.1038/nmeth.1419.

9 Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991; 173:697–703. Available from: http://jb.asm.org/content/173/2/697.abstract.

10 Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, et al. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci. 1998; 95(6):3140–5. Available from: http://www.pnas.org/content/95/6/3140.

11 Boers SA, van der Reijden WA, Jansen R. High-Throughput Multilocus Sequence Typing: Bringing Molecular Typing to the Next Level. PLoS ONE. 2012; 7(7):1–8. Available from: 10.1371/journal.pone.003 9630.

12 Fournier P, Dubourg G, Raoult D. Clinical detection and characterization of bacterial pathogens in the genomics era. Genome Med. 2014; 6(11):114. Available from: 10.1186/s13073-014-0114-2.

13 Bartual SG, Seifert H, Hippler C, Luzon MAD, Wisplinghoff H, Rodríguez-Valera F. Development of a Multilocus Sequence Typing Scheme for Characterization of Clinical Isolates of Acinetobacter baumannii. J Clin Microbiol. 2005; 43(9):4382–90. Available from: http://jcm.asm.org/content/43/9/4382.abstract.

14 Blanchard AM, Jolley KA, Maiden MCJ, Coffey TJ, Maboni G, Staley CE, et al. The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for Dichelobacter nodosus. Front Microbiol. 2018; 9:551. Available from: https://www.frontiersin.org/article/10.3389/fmicb.2018.00551.

15 Boonsilp S, Thaipadungpanit J, Amornchai P, Wuthiekanun V, Bailey MS, Holden MTG, et al. A Single Multilocus Sequence Typing (MLST) Scheme for Seven Pathogenic Leptospira Species. PLoS Negl Trop Dis. 2013; 7(1):1–10. Available from: 10.1371/journal.pntd.0001954.

65 references, page 1 of 5
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