Power of Minim typing to identify and discriminate <i>K. pneumoniae</i> STs of particular significance.

<p>*SLV = single locus variant, DLV = double locus variant, TLV = triple locus variant, QLV = quadruple locus variant.</p

Discriminatory power from different combinations of markers, calculated against all STs (863 STs, <i>D</i> = 1).

<p>Discriminatory power from different combinations of markers, calculated against all STs (863 STs, <i>D</i> = 1).</p

Examples of melting curves for each target region

<p>. For some target regions not all melting curves were represented among the isolates analysed in this study, therefore not all theoretically possible curves are depicted in the figure. <b>A</b>) Target region <i>infB</i>729, showing two (12, 13) of two predicted melting curves. <b>B</b>) Target region <i>mdh</i>1197, showing two (9, 10) of three predicted melting curves. <b>C</b>) Target region <i>pho</i>E2013, showing four (18, 19, 20, 21) of four predicted melting curves. <b>D</b>) Target region <i>rpoB</i>2227, showing six (41, 42 43, 44, 45, 46) of seven predicted melting curves. <b>E</b>) Target region <i>tonB</i>2693, showing three (39, 40, 41) of seven predicted melting curves. <b>F</b>) Target region <i>tonB</i>2886, showing three (54, 55, 56) of eight predicted melting curves.</p

Indices of association for combinations of MLST alleles with and without <i>tonB</i>, and measurements of diversity conferred by individual loci indicate that <i>tonB</i> is highly diverse and likely subjected to horizontal gene transfer.

<p>Indices of association for combinations of MLST alleles with and without <i>tonB</i>, and measurements of diversity conferred by individual loci indicate that <i>tonB</i> is highly diverse and likely subjected to horizontal gene transfer.</p

Numbers and percentages of successful PCR amplifications from 113 <i>C</i>. <i>trachomatis</i> positive clinical specimens.

<p>Numbers and percentages of successful PCR amplifications from 113 <i>C</i>. <i>trachomatis</i> positive clinical specimens.</p

Control isolates used during development of <i>Ct</i>GEM typing.

<p>Control isolates used during development of <i>Ct</i>GEM typing.</p

Relationship between rg1 and HRMA alleles alone and in combination, and <i>C</i>. <i>trachomatis</i> phylogeny.

<p>The phylogenetic tree is based on genome-wide orthologous SNPs and adapted from Andersson et al (2). HRMA alleles and <i>Ct</i>GEM types are indicated with colours.</p

<i>Ct</i>GEM types defined by 559 genomes.

<p><i>Ct</i>GEM types defined by 559 genomes.</p

Descriptions of the <i>Ct</i>GEM types, and the numbers and frequencies of the types in sets of genomes/clinical specimens.

<p>Descriptions of the <i>Ct</i>GEM types, and the numbers and frequencies of the types in sets of genomes/clinical specimens.</p

HRMA analysis of the <i>ompA</i> fragment (ofr).

<p>(A) Sequence alignment of the known haplotypes of ofr showing the primer sequences (grey shading). (B) HRMA curves showing the resolution of the genotypes. A detailed guide for the HRMA is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195454#pone.0195454.s002" target="_blank">S2 File</a> in the supplemental material.</p