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Burkholderia pseudomallei genome plasticity associated with genomic island variation.
BMC Genomics. 2008 Apr 25; 9:190.BG

Abstract

BACKGROUND

Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulence potential. The genome contains genomic island (GI) regions that encode a broad array of functions. Although there is some evidence for the variable distribution of genomic islands in B. pseudomallei isolates, little is known about the extent of variation between related strains or their association with disease or environmental survival.

RESULTS

Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with micro-evolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates) was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9), to 76% for a metabolic island (GI 16). The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p > 0.05 for all five islands). The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3). The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p = 0.27). The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing); these were ST 70 (n = 15 isolates), ST 54 (n = 11), and ST 167 (n = 9). The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained from the environment and from patients with melioidosis in order to examine the role of genomic islands in virulence and clinical associations. There was no reproducible association between the individual or cumulative presence of five GIs and a range of clinical features in 103 patients with melioidosis.

CONCLUSION

Horizontal gene transfer of mobile genetic elements can rapidly alter the gene repertoire of B. pseudomallei. This study confirms the utility of a range of approaches in defining the presence and significance of genomic variation in natural populations of B. pseudomallei.

Authors+Show Affiliations

Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. jay@tropmedres.ac <jay@tropmedres.ac>No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

18439288

Citation

Tumapa, Sarinna, et al. "Burkholderia Pseudomallei Genome Plasticity Associated With Genomic Island Variation." BMC Genomics, vol. 9, 2008, p. 190.
Tumapa S, Holden MT, Vesaratchavest M, et al. Burkholderia pseudomallei genome plasticity associated with genomic island variation. BMC Genomics. 2008;9:190.
Tumapa, S., Holden, M. T., Vesaratchavest, M., Wuthiekanun, V., Limmathurotsakul, D., Chierakul, W., Feil, E. J., Currie, B. J., Day, N. P., Nierman, W. C., & Peacock, S. J. (2008). Burkholderia pseudomallei genome plasticity associated with genomic island variation. BMC Genomics, 9, 190. https://doi.org/10.1186/1471-2164-9-190
Tumapa S, et al. Burkholderia Pseudomallei Genome Plasticity Associated With Genomic Island Variation. BMC Genomics. 2008 Apr 25;9:190. PubMed PMID: 18439288.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Burkholderia pseudomallei genome plasticity associated with genomic island variation. AU - Tumapa,Sarinna, AU - Holden,Matthew T G, AU - Vesaratchavest,Mongkol, AU - Wuthiekanun,Vanaporn, AU - Limmathurotsakul,Direk, AU - Chierakul,Wirongrong, AU - Feil,Edward J, AU - Currie,Bart J, AU - Day,Nicholas P J, AU - Nierman,William C, AU - Peacock,Sharon J, Y1 - 2008/04/25/ PY - 2007/10/01/received PY - 2008/04/25/accepted PY - 2008/4/29/pubmed PY - 2008/7/1/medline PY - 2008/4/29/entrez SP - 190 EP - 190 JF - BMC genomics JO - BMC Genomics VL - 9 N2 - BACKGROUND: Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulence potential. The genome contains genomic island (GI) regions that encode a broad array of functions. Although there is some evidence for the variable distribution of genomic islands in B. pseudomallei isolates, little is known about the extent of variation between related strains or their association with disease or environmental survival. RESULTS: Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with micro-evolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates) was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9), to 76% for a metabolic island (GI 16). The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p > 0.05 for all five islands). The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3). The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p = 0.27). The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing); these were ST 70 (n = 15 isolates), ST 54 (n = 11), and ST 167 (n = 9). The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained from the environment and from patients with melioidosis in order to examine the role of genomic islands in virulence and clinical associations. There was no reproducible association between the individual or cumulative presence of five GIs and a range of clinical features in 103 patients with melioidosis. CONCLUSION: Horizontal gene transfer of mobile genetic elements can rapidly alter the gene repertoire of B. pseudomallei. This study confirms the utility of a range of approaches in defining the presence and significance of genomic variation in natural populations of B. pseudomallei. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/18439288/Burkholderia_pseudomallei_genome_plasticity_associated_with_genomic_island_variation_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-190 DB - PRIME DP - Unbound Medicine ER -