PMC

The branch lengths are proportional to the number of variable nucleotides.

The branch lengths are proportional to the number of variable nucleotides. All of the isolates from Manhiça cluster together and are most closely related to isolates from India, Nepal, Kenya, Haiti and Bangladesh. Other isolates from Mozambique and Kenya are more distantly related.

Only variable nucleotides 80 to 120 are shown. Each row contains sequence from a single isolate. Two examples in which two loci with alleles occur in all four possible combinations are identified by boxes around the four chromosomes. These examples are consistent with recombination events.

Splitstree allows for parallel changes whether they are derived by recurrent mutation or by recombination. The branch lengths are proportional to the number of nucleotide changes. The figure reveals extensive parallel changes (the parallelograms). The parallel lines of a parallelogram indicate potential recombination. Of note the isolates from 2008, those of 2009 and those of 2010 are in separate regions of the diagram and each has potential parallelograms in the diagrams. The lines extending to a single isolate represent the mutational variation. The smaller font indicates the isolate names. The four digit red numbers are the years in which different isolates were collected. The letter R identifies isolates found in the river. CC2 indicates those isolates found in MLVA CC2. The four isolates from 2008, the two isolates from 2009 and four of the five isolates from 2010 cluster with their contemporaries.

Each box with five numbers represents a genotype; each connecting line, an allelic change at a single locus. The solid boxes are around genotypes found in both the river and in patients, dotted boxes are for genotypes found only in patients and dashed boxes for genotypes found only in river isolates (R). The numbers outside the boxes indicate the year or years isolates with that genotype were found. There are twenty genotypes in CC1, two genotypes in CC2 and four singleton genotypes unrelated to any other genotypes using eBURST. An alternative analysis using Network revealed the following differences: i) a connection in eBURST, but not in Network, was represented by a dotted line (single locus change), ii) a connection in Network, but not in eBURST, by a dashed line (single locus change), iii) in Network, but not in eBURST, CC2 is connected to CC1, we have represented this by a dot and dashed line (representing changes at two loci), finally, iv) in Network, but not in eBURST, all three singleton genotypes are connected to the founder genotype regardless of whether the singleton genotype differs at three or four loci from the founder.