The Process of Scour Surrounding Objects Freely Settling on the Seabed on the Effect of Typhoon Based on Drambuie Model

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchive

Seasonal Transfer and Net Accumulation of Suspended Sediment in the Yellow and East China Seas

Sediment Transport and Morphodynamic

Development of a Hierarchical Variable-Number Tandem Repeat Typing Scheme for <i>Mycobacterium tuberculosis</i> in China

<div><p>Molecular typing based on variable-number tandem repeats (VNTR) analysis is a promising tool for identifying transmission of <i>Mycobacterium tuberculosis</i>. However, the currently proposed 15- and 24-locus VNTR sets (VNTR-15/24) only have limited resolution and contain too many loci for large-scale typing in high burden countries. To develop an optimal typing scheme in China, we evaluated the resolution and robustness of 25 VNTR loci, using population-based collections of 1362 clinical isolates from six provinces across the country. The resolution of most loci showed considerable variations among regions. By calculating the average resolution of all possible combinations of 20 robust loci, we identified an optimal locus set with a minimum of 9 loci (VNTR-9) that could achieve comparable resolution of the standard VNTR-15. The VNTR-9 had consistently high resolutions in all six regions, and it was highly concordant with VNTR-15 for defining both clustered and unique genotypes. Furthermore, VNTR-9 was phylogenetically informative for classifying lineages/sublineages of <i>M. tuberculosis</i>. Three hypervariable loci (HV-3), VNTR 3232, VNTR 3820 and VNTR 4120, were proved important for further differentiating unrelated clustered strains based on VNTR-9. We propose the optimized VNTR-9 as first-line method and the HV-3 as second-line method for molecular typing of <i>M. tuberculosis</i> in China and surrounding countries. The development of hierarchical VNTR typing methods that can achieve high resolution with a small number of loci could be suitable for molecular epidemiology study in other high burden countries.</p></div

Discriminatory powers of VNTR-9 and VNTR-15 among six field sites and their concordance for defining clustered and unique strains.

<p>Discriminatory powers of VNTR-9 and VNTR-15 among six field sites and their concordance for defining clustered and unique strains.</p

Distribution of single- (S), double- (D), or triple-locus variations (TLV) in 20 robust VNTR loci.

<p>Variation events were detected according to the minimal spanning trees of <i>M. tuberculosis</i> strains in each field site.</p

Concordance between different locus set for defining <i>M. tuberculosis</i> lineages/sublineages.

<p>Minimal spanning trees (MST) of 1167 strains based on all 20 robust VNTR loci (<b>A</b>), the standard VNTR-15 (<b>B</b>), or the optimized VNTR-9 (<b>C</b>). Clonal complexes were shaded in different colors. Circles in each MST indicated Beijing strains and three major clonal complexes of Non-Beijing strains.</p

The optimal VNTR combinations at different locus number and their average discriminatory powers in all strains or genetic subpopulations of <i>M. tuberculosis</i> form six field sites.

a<p>VNTR loci were numbered according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089726#pone-0089726-t001" target="_blank">Table 1</a>; the combination in bold indicates the optimal 9-locus VNTR set.</p

The homogeneity of “modern” Beijing strains and the differentiation of cross-regional clusters by hypervariable loci.

<p>(<b>A</b>) Minimal spanning tree (MST) of 678 “modern” Beijing strains based on 17 loci from VNTR-9 and VNTR-15; (<b>B</b>) The geographical designations for strains of the major VNTR genotype A and B, and their single-locus variants; (<b>C</b>) The MSTs of strains that belong to genotype A and B based on three hypervariable loci (QUB-3232, VNTR 3820, VNTR 4120). Black arrows indicate clusters.</p

The average discriminatory powers of 25 VNTR loci in six field sites and their resolutions in genetic subpopulations of <i>M. tuberculosis</i>.

a<p>value in bold and underline indicates high discriminatory power (HGI>0.6); value in underline indicates intermediate discriminatory power (0.3≤HGI≤0.6).</p

The discriminatory powers of 25 VNTR loci in strains from six field sites.

<p>Two dotted lines indicated the thresholds for defining high (HGI>0.6), intermediate (0.3≤HGI≤0.6) and low (HGI<0.3) discriminatory powers. The mean value and standard deviations for each locus were indicated.</p