Table 1.
Admission clinical characteristics of Leptospira spp. culture positive patients.
Fig 1.
The majority of Laos strains belong to the clonal group 272 of L. interrogans sg Autumnalis.
A. Maximum-likelihood phylogeny based on the variable sites of the cgMLST scheme consisting of 545 core genes showing the distribution of species, cgMLST clonal groups, and serogroups circulating in Laos during 2006–2017 (n = 75, S1 Table). The samples were divided into 43 cgMLST clonal groups belonging to 12 different serogroups; white color indicates that the serogroup is unknown or undetermined. Bootstrap values are shown with the size of circles in the middle of branches, bootstraps lower than 80 are not shown. Species and serogroups are given by the color codes (from inner to outer circles) and cgMLST clonal groups as numbers. B: Muller diagram showing distribution of clonal groups in Laos during 2006–2017. The most prevalent clonal group, CG272, is indicated. The bar chart is showing the number of samples sequenced in each year. The population dynamic of genotypes was produced in R using the MullerPlot package [54].
Fig 2.
Prevalence of the ST34-like strains in Laos and neighbouring countries.
Phylogenetic relatedness of pathogenic Leptospira strains (n = 258) circulating in Southeast Asia. Maximum-likelihood phylogeny based on 994 SNVs found in 3,113 bp-long concatenated sequences of glmU, pntA, sucA, tpiA, pfkB, mreA and caiB loci characterized by MLST1 [30] together with the samples analyzed in this study. Isolates belonging to the ST34 (CG272) are highlighted in red. Metadata associated with the isolates not listed in S1 Table are provided in S2 Table. The base layer of the map is from outline-world-map.com.
Fig 3.
Genome features of L. interrogans sg Autumnalis strain id779.
A. Circular maps and genome features of the three replicons of L. interrogans sg Autumnalis strain id779. B. Heatmap showing absence/presence of plasmid genes of L. interrogans sg Autumnalis strain id779 in other Laos strains. The strains were ordered according to the phylogenetic tree shown in Fig 1A. The heatmap was obtained by doing a TBLASTN analysis of the sequences of the plasmid against the genomic sequences of the strains. A gene was considered to be present if the hit had an e-value greater than 1e-10 and 50% similarity. The light green represents sequences with a similarity percentage between 50% and 79%, while the dark green represents sequences with a similarity percentage of 80% to 100%. Color bar on the left corresponds to: red, L. interrogans; blue, L. weilii, green, L. borgpetersenii; yellow: L. kirschneri.
Fig 4.
Distribution in functional categories of the predicted CDSs (%).
Each dot represents the value for a specific genome after normalizing by its predicted total number of proteins. The genome-specific values of the L. interrogans CG272 strains and L. interrogans non- CG272 strains are presented. The genome of L. interrogans sg Autumnalis strain id779 is represented as a red dot. Only functional categories showing significant difference between the different groups are shown (*** P < 0.001, **** P < 0.0001).
Fig 5.
The Leptospira ST34-like strains have limited genetic variation.
A: ML phylogeny based on whole genome sequences of L. interrogans. Bootstrap values are shown with the size of circles in the middle of the branches, bootstraps lower than 70 are not shown. Clade and serogroup names are given by the color codes (from inner to outer strips). White color indicates that the information was not available. B: Matrix showing absence or presence of 5,543 genes found in the pangenome of L. interrogans strains. Clade names are given by the color codes.