Flowchart describing the steps of the molecular analysis.

<p>Methods used to detect and to identify <i>Leptospira</i> species and genotypes from samples collected in French Polynesia are detailed. Seven-loci MLST was attempted only for a selected subgroup of the animal and human samples successfully amplified on <i>secY</i> locus using MLST scheme #1.</p

<i>Leptospira</i> detection and identification by host species.

<p>The prevalence of renal infection by <i>Leptospira</i> in farm pigs and rodents is based on RT-qPCR detection results. Infecting <i>Leptospira</i> species were determined by PCR, targeting either <i>secY</i>, <i>rrs</i> (16S) or <i>LipL32</i> gene in positive samples. The number of successful amplification for <i>secY</i> is provided. Based on the observed diversity within the <i>secY</i> gene, MLST amplifications were attempted on a subset of positive samples; the number of successful complete MLST on seven (or six) loci is given.</p

Geographic localization of piggeries and rat sampling sites on Tahiti Island.

<p>The pig kidneys tested for <i>Leptospira</i> infection originated from 17 herds representing 16 farms. Rats were trapped at 12 sampling sites, including five farms from which pig kidneys originated.</p

Maximum-likelihood phylogenetic tree (model TN93+I; 1,000 replicates) inferred from <i>LipL32</i> gene (229-bp sequence).

<p>Clinical and animal samples from Tahiti are shown in light blue, clinical samples from other islands in French Polynesia (FP) in dark blue; referred to using identifiers accompanied by the host name. Corresponding GenBank accession numbers are reported in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005676#pntd.0005676.s005" target="_blank">S5 Table</a>. Published sequences included in the phylogeny are shown in black using the identified <i>Leptospira</i> species followed by GenBank accession numbers, the host species and the country of origin. The major genetic groups are highlighted with grey boxes (numbered 1 to 3). Bootstrap values higher than 70% are indicated by a dark circle. Black silhouettes represent host groups from FP (i.e. human, dog, pig or rat).</p