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Multilocus Sequence analysis of Escherichia isolates from pristine and
contaminated rivers in Mexico reveals contrasting population structures and the
presence of cryptic lineages.
Pablo Rodriguez Bucheli Torres Torija, Jazmín Ramos Madrigal, Pablo Vinuesa Fleischmann. Centro
de Ciencias Genómicas UNAM campus Cuernavaca, prodriguez@lcg.unam.mx
Multilocus sequence analyses (MLSA) have recently revealed 5 cryptic lineages in the genus
Escherichia (clades I-V). Little is known about their environmental distribution. We present a MLSA of
Escherichia strains recovered from Mexican water bodies with contrasting levels of residual
contamination. Isolates were recovered from the Apatlaco (highly contaminated with sewage water)
and Tembembe (almost pristine) rivers in Morelos, Mexico.
A total of 56 isolates were subjected to MLST using Achtman's scheme, a maximum likelihood
phylogeny based on a concatenated alignment of the 7 loci strains revealed the presence of 13 novel
clade-II isolates in our collection. Only two isolates from this clade were previously reported. The
remaining isolates grouped within the E.coli-Shigella spp. Among those, the majority showed novel
alleles and hence novel STs.
The strong genetic differentiation between the E. coli populations from both rivers was formally
confirmed by Hudson's KSt test of genetic differentiation. Based on Clermont's 2000 typing method,
the strains were grouped within phylogroups A, B1, B2 and D, the first being dominant in the highly
polluted river (Apatlaco) compared to the pristine river isolates (Tembembe) which are in their majority
grouped in B2. We used STRUCTURE under the admixure model with linkage to detect population
subdivision within the E. coli-Shigella spp. clade. The agreement with Clermont's phylogroups was
perfect, as confirmed by the Evanno test. We used a coalescent approach as implemented in
ClonalFrame to estimate the population recombination/mutation rate (r/m) for the Apatlaco (mean of
1.353; CI: 0.588-2.694) and the Tembembe population (r/m mean = 2.385; CI: 0.944-4.916).
Tembembe population was found to be in demographic equilibrium (p=0.152) while the Apatlaco had a
clear signal of growth (p=0.003).
This work reveals that a large diversity of Escherichia and E. coli remains to be discovered among
environmental strains in subtropical and tropical regions.