Recombination Blurs Phylogenetic Groups Routine Assignment in Escherichia coli: Setting the Record Straight

Abstract

The characterization of population structures plays a main role for understanding outbreaks and the dynamics of bacterial spreading. In Escherichia coli, the widely used combination of multiplex-PCR scheme together with goeBURST has some limitations. The purpose of this study is to show that the combination of different phylogenetic approaches based on concatenated sequences of MLST genes results in a more precise assignment of E. coli phylogenetic groups, complete understanding of population structure and reconstruction of ancestral clones. A collection of 80 Escherichia coli strains of different origins was analyzed following the Clermont and Doumith's multiplex-PCR schemes. Doumith's multiplex-PCR showed only 1.7% of misassignment, whereas Clermont's-2000 protocol reached 14.0%, although the discrepancies reached 30% and 38.7% respectively when recombinant C, F and E phylogroups were considered. Therefore, correct phylogroup attribution is highly variable and depends on the clonal composition of the sample. As far as population structure of these E. coli strains, including 48 E. coli genomes from GenBank, goeBURST provides a quite dispersed population structure; whereas NeighborNet approach reveals a complex population structure. MLST-based eBURST can infer different founder genotypes, for instance ST23/ST88 could be detected as the founder genotypes for STC23; however, phylogenetic reconstructions might suggest ST410 as the ancestor clone and several evolutionary trajectories with different founders. To improve our routine understanding of E. coli molecular epidemiology, we propose a strategy based on three successive steps; first, to discriminate three main groups A/B1/C, D/F/E and B2 following Doumith's protocol; second, visualization of population structure based on MLST genes according to goeBURST, using NeighborNet to establish more complex relationships among STs; and third, to perform, a cost-free characterization of evolutionary trajectories in variants emerging along the clonal expansion using parsimony methods of phylogenetic analysis.

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

“…Recombinant sequences have been known for a long time to strongly distort phylogenies because they merge independent evolutionary histories into a single lineage. Recombination erodes the phylogenetic signal and misleads classic treeing algorithms, which assume a single underlying history (Didelot and Maiden, 2010;Martin, 2009;Pease and Hahn, 2013;Posada and Crandall, 2002;Schierup and Hein, 2000;Turrientes et al, 2014). Hence, the first filtering step in the pipeline is the detection of putative recombinant sequences using the very fast, sensitive and robust phi(w) statistic (Bruen et al, 2005).…”

Extra-intestinal pathogenic Escherichia coli (ExPEC): Disease, carriage and clones

“…An updated multiplex PCR method was more recently devised by Doumith et al (19). An independent study by Turrientes et al subsequently compared both methods against a multi-locus sequence typing standard and demonstrated superiority of Doumith's method with regards to accuracy of phylogroup assignment (20).…”

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates collected from diseased food-producing animals in the GERM-Vet monitoring program 2008–2014

“…In order to maintain the comparability of the results obtained during the years 2008-2014, we decided not to replace the multiplex-PCR scheme used by the novel multiplex-PCR scheme of Clermont et al (2013). Moreover, the assignment of the phylogroups obtained with the protocol of Doumith et al (2012) already showed a better correlation to the MLST types than the protocol of Clermont et al (2013) and, therefore, has been also recommended as the protocol of choice for the phylotyping (Turrientes et al, 2014).…”