publication . Article . 2016

The effects of signal erosion and core genome reduction on the identification of diagnostic markers

Sahl, Jason W.; Vazquez, Adam J.; Hall, Carina M.; Busch, Joseph D.; Tuanyok, Apichai; Mayo, Mark; Schupp, James M.; Lummis, Madeline; Pearson, Talima; Shippy, Kenzie; ...
Open Access English
  • Published: 01 Sep 2016 Journal: mBio, volume 7, issue 5 (issn: 2150-7511, eissn: 2150-7511, Copyright policy)
  • Publisher: American Society for Microbiology
Abstract
Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives.A comparative analysis of 1,130 Burkholderia genomes identified unique markers for many named species, including the human pathogens B. pseudomallei and B....
Subjects
free text keywords: Research Article, Microbiology, QR1-502
42 references, page 1 of 3

1.Driebe EM, Sahl JW, Roe C, Bowers JR, Schupp JM, Gillece JD, Kelley E, Price LB, Pearson TR, Hepp CM, Brzoska PM, Cummings CA, Furtado MR, Andersen PS, Stegger M, Engelthaler DM, Keim PS 2015 Using whole genome analysis to examine recombination across diverse sequence types of Staphylococcus aureus. PLoS One 10:e0130955. doi:10.1371/journal.pone.0130955.26161978 [OpenAIRE] [PubMed] [DOI]

2.Sahl JW, Morris CR, Emberger J, Fraser CM, Ochieng JB, Juma J, Fields B, Breiman RF, Gilmour M, Nataro JP, Rasko DA 2015 Defining the phylogenomics of Shigella species: a pathway to diagnostics. J Clin Microbiol 53:951–960. doi:10.1128/JCM.03527-14.25588655 [OpenAIRE] [PubMed] [DOI]

3.Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J 2008 The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190:6881–6893. doi:10.1128/JB.00619-08.18676672 [OpenAIRE] [PubMed] [DOI]

4.Califf KJ, Keim P, Wagner DM, Sahl JW 2015 Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics. Microb Genom 1(4):000028. doi:10.1099/mgen.0.000028. [OpenAIRE] [DOI]

5.Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E, Achtman M 2010 Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet 42:1140–1143. doi:10.1038/ng.705.21037571 [OpenAIRE] [PubMed] [DOI]

6.Spring-Pearson SM, Stone JK, Doyle A, Allender CJ, Okinaka RT, Mayo M, Broomall SM, Hill JM, Karavis MA, Hubbard KS, Insalaco JM, McNew LA, Rosenzweig CN, Gibbons HS, Currie BJ, Wagner DM, Keim P, Tuanyok A 2015 Pangenome analysis of Burkholderia pseudomallei: genome evolution preserves gene order despite high recombination rates. PLoS One 10:e0140274. doi:10.1371/journal.pone.0140274.26484663 [OpenAIRE] [PubMed] [DOI]

7.Coenye T, Vandamme P 2003 Diversity and significance of Burkholderia species occupying diverse ecological niches. Environ Microbiol 5:719–729. doi:10.1046/j.1462-2920.2003.00471.x.12919407 [PubMed] [DOI]

8.Wiersinga WJ, Currie BJ, Peacock SJ 2012 Melioidosis. N Engl J Med 367:1035–1044. doi:10.1056/NEJMra1204699.22970946 [OpenAIRE] [PubMed] [DOI]

9.Losada L, Ronning CM, DeShazer D, Woods D, Fedorova N, Kim HS, Shabalina SA, Pearson TR, Brinkac L, Tan P, Nandi T, Crabtree J, Badger J, Beckstrom-Sternberg S, Saqib M, Schutzer SE, Keim P, Nierman WC 2010 Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biol Evol 2:102–116. doi:10.1093/gbe/evq003.20333227 [OpenAIRE] [PubMed] [DOI]

10.Gee JE, Allender CJ, Tuanyok A, Elrod MG, Hoffmaster AR 2014 Burkholderia pseudomallei type G in Western Hemisphere. Emerg Infect Dis 20:682–684. doi:10.3201/eid2004.130960.24655932 [OpenAIRE] [PubMed] [DOI]

11.Ho CC, Lau CC, Martelli P, Chan SY, Tse CW, Wu AK, Yuen KY, Lau SK, Woo PC 2011 Novel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: a proof-of-concept study. J Clin Microbiol 49:814–821. doi:10.1128/JCM.01702-10.21177905 [OpenAIRE] [PubMed] [DOI]

12.De Smet B, Mayo M, Peeters C, Zlosnik JE, Spilker T, Hird TJ, LiPuma JJ, Kidd TJ, Kaestli M, Ginther JL, Wagner DM, Keim P, Bell SC, Jacobs JA, Currie BJ, Vandamme P 2015 Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources. Int J Syst Evol Microbiol 65:2265–2271 doi:10.1099/ijs.0.000251.25872960 [PubMed] [DOI]

13.Payne GW, Vandamme P, Morgan SH, Lipuma JJ, Coenye T, Weightman AJ, Jones TH, Mahenthiralingam E 2005 Development of a recA gene-based identification approach for the entire Burkholderia genus. Appl Environ Microbiol 71:3917–3927. doi:10.1128/AEM.71.7.3917-3927.2005.16000805 [OpenAIRE] [PubMed] [DOI]

14.Ginther JL, Mayo M, Warrington SD, Kaestli M, Mullins T, Wagner DM, Currie BJ, Tuanyok A, Keim P 2015 Identification of Burkholderia pseudomallei near-neighbor species in the Northern Territory of Australia. PLoS Negl Trop Dis 9:e0003892. doi:10.1371/journal.pntd.0003892.26121041 [OpenAIRE] [PubMed] [DOI]

15.Baldwin A, Mahenthiralingam E, Thickett KM, Honeybourne D, Maiden MC, Govan JR, Speert DP, Lipuma JJ, Vandamme P, Dowson CG 2005 Multilocus sequence typing scheme that provides both species and strain differentiation for the Burkholderia cepacia complex. J Clin Microbiol 43:4665–4673. doi:10.1128/JCM.43.9.4665-4673.2005.16145124 [OpenAIRE] [PubMed] [DOI]

42 references, page 1 of 3
Abstract
Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives.A comparative analysis of 1,130 Burkholderia genomes identified unique markers for many named species, including the human pathogens B. pseudomallei and B....
Subjects
free text keywords: Research Article, Microbiology, QR1-502
42 references, page 1 of 3

1.Driebe EM, Sahl JW, Roe C, Bowers JR, Schupp JM, Gillece JD, Kelley E, Price LB, Pearson TR, Hepp CM, Brzoska PM, Cummings CA, Furtado MR, Andersen PS, Stegger M, Engelthaler DM, Keim PS 2015 Using whole genome analysis to examine recombination across diverse sequence types of Staphylococcus aureus. PLoS One 10:e0130955. doi:10.1371/journal.pone.0130955.26161978 [OpenAIRE] [PubMed] [DOI]

2.Sahl JW, Morris CR, Emberger J, Fraser CM, Ochieng JB, Juma J, Fields B, Breiman RF, Gilmour M, Nataro JP, Rasko DA 2015 Defining the phylogenomics of Shigella species: a pathway to diagnostics. J Clin Microbiol 53:951–960. doi:10.1128/JCM.03527-14.25588655 [OpenAIRE] [PubMed] [DOI]

3.Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J 2008 The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190:6881–6893. doi:10.1128/JB.00619-08.18676672 [OpenAIRE] [PubMed] [DOI]

4.Califf KJ, Keim P, Wagner DM, Sahl JW 2015 Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics. Microb Genom 1(4):000028. doi:10.1099/mgen.0.000028. [OpenAIRE] [DOI]

5.Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E, Achtman M 2010 Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet 42:1140–1143. doi:10.1038/ng.705.21037571 [OpenAIRE] [PubMed] [DOI]

6.Spring-Pearson SM, Stone JK, Doyle A, Allender CJ, Okinaka RT, Mayo M, Broomall SM, Hill JM, Karavis MA, Hubbard KS, Insalaco JM, McNew LA, Rosenzweig CN, Gibbons HS, Currie BJ, Wagner DM, Keim P, Tuanyok A 2015 Pangenome analysis of Burkholderia pseudomallei: genome evolution preserves gene order despite high recombination rates. PLoS One 10:e0140274. doi:10.1371/journal.pone.0140274.26484663 [OpenAIRE] [PubMed] [DOI]

7.Coenye T, Vandamme P 2003 Diversity and significance of Burkholderia species occupying diverse ecological niches. Environ Microbiol 5:719–729. doi:10.1046/j.1462-2920.2003.00471.x.12919407 [PubMed] [DOI]

8.Wiersinga WJ, Currie BJ, Peacock SJ 2012 Melioidosis. N Engl J Med 367:1035–1044. doi:10.1056/NEJMra1204699.22970946 [OpenAIRE] [PubMed] [DOI]

9.Losada L, Ronning CM, DeShazer D, Woods D, Fedorova N, Kim HS, Shabalina SA, Pearson TR, Brinkac L, Tan P, Nandi T, Crabtree J, Badger J, Beckstrom-Sternberg S, Saqib M, Schutzer SE, Keim P, Nierman WC 2010 Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biol Evol 2:102–116. doi:10.1093/gbe/evq003.20333227 [OpenAIRE] [PubMed] [DOI]

10.Gee JE, Allender CJ, Tuanyok A, Elrod MG, Hoffmaster AR 2014 Burkholderia pseudomallei type G in Western Hemisphere. Emerg Infect Dis 20:682–684. doi:10.3201/eid2004.130960.24655932 [OpenAIRE] [PubMed] [DOI]

11.Ho CC, Lau CC, Martelli P, Chan SY, Tse CW, Wu AK, Yuen KY, Lau SK, Woo PC 2011 Novel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: a proof-of-concept study. J Clin Microbiol 49:814–821. doi:10.1128/JCM.01702-10.21177905 [OpenAIRE] [PubMed] [DOI]

12.De Smet B, Mayo M, Peeters C, Zlosnik JE, Spilker T, Hird TJ, LiPuma JJ, Kidd TJ, Kaestli M, Ginther JL, Wagner DM, Keim P, Bell SC, Jacobs JA, Currie BJ, Vandamme P 2015 Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources. Int J Syst Evol Microbiol 65:2265–2271 doi:10.1099/ijs.0.000251.25872960 [PubMed] [DOI]

13.Payne GW, Vandamme P, Morgan SH, Lipuma JJ, Coenye T, Weightman AJ, Jones TH, Mahenthiralingam E 2005 Development of a recA gene-based identification approach for the entire Burkholderia genus. Appl Environ Microbiol 71:3917–3927. doi:10.1128/AEM.71.7.3917-3927.2005.16000805 [OpenAIRE] [PubMed] [DOI]

14.Ginther JL, Mayo M, Warrington SD, Kaestli M, Mullins T, Wagner DM, Currie BJ, Tuanyok A, Keim P 2015 Identification of Burkholderia pseudomallei near-neighbor species in the Northern Territory of Australia. PLoS Negl Trop Dis 9:e0003892. doi:10.1371/journal.pntd.0003892.26121041 [OpenAIRE] [PubMed] [DOI]

15.Baldwin A, Mahenthiralingam E, Thickett KM, Honeybourne D, Maiden MC, Govan JR, Speert DP, Lipuma JJ, Vandamme P, Dowson CG 2005 Multilocus sequence typing scheme that provides both species and strain differentiation for the Burkholderia cepacia complex. J Clin Microbiol 43:4665–4673. doi:10.1128/JCM.43.9.4665-4673.2005.16145124 [OpenAIRE] [PubMed] [DOI]

42 references, page 1 of 3
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publication . Article . 2016

The effects of signal erosion and core genome reduction on the identification of diagnostic markers

Sahl, Jason W.; Vazquez, Adam J.; Hall, Carina M.; Busch, Joseph D.; Tuanyok, Apichai; Mayo, Mark; Schupp, James M.; Lummis, Madeline; Pearson, Talima; Shippy, Kenzie; ...