Ough the data in Fig. 1 shows that MPEC originate from a

Ough the data in Fig. 1 shows that MPEC originate from a wide spectrum of lineages within buy EPZ004777 phylogroup A, we noted that many strains appeared clustered onto closely neighbouring branches. Our hypothesis is that only certain strains of E. coli are capable of eliciting bovine mastitis. We reasoned we could test this hypothesis by asking whether all lineages of phylogroup A E. coli were equally likely to be observed in cases of mastitis. To do this, we elaborated a much more comprehensive maximum likelihood phylogenetic tree for the 533 phylogroup A isolates, using the nucleotide sequence of 520 non-recombining core phylogroup A genes, and investigated the positions of the MPEC genomes within this tree (Fig. 2A). For clarity of presentation, bootstrap values have been removed. A tree with bootstrap values is included as Additional Figure S1. This refined tree reflected our earlier observation that many MPEC have close neighbours within the tree that are also MPEC, as well as revealing that many MPEC are not epidemiologically related by country. To investigate this statistically, we reasoned that any such distinction between MPEC and the wider phylogroup A population should be reflected in the tendency for MPEC isolates to be more closely related to each other than would a random selection of phylogroup A E. coli. To test this, we sampled sixty-six random phylogroup A genomes from the population over 100,000 replications and, for each AZD3759MedChemExpress AZD3759 sample, calculated the average phylogenetic distance observed between the genomes within the sample. This distribution of average distances is shown as a density plot in Fig. 2(B). Next, we compared the actual average distance observed between the MPEC isolates with this null distribution (shown as a red vertical line in Fig. 2B), and calculated the p value of how likely this distance is to have been caused by chance alone by using the number of randomised samples which exhibited average distance as small or smaller than that observed between MPEC divided by the number of replications. These data show that it is incredibly unlikely (p = 0.00015) that an average distance as small as that observed between MPEC could be generated by random positioning of MPEC within phylogroup A. Overall, these analyses point to significant reduction in phylogenetic diversity of MPEC strains within phylogroup A compared with what may be expected if these strains were randomly positioned within the phylogroup A population structure. It is possible that this analysis could have been affected by biases imposed by the uneven sampling of E. coli targeted for genome sequencing, many of which originate from humans in countriesScientific RepoRts | 6:30115 | DOI: 10.1038/srepwww.nature.com/scientificreports/Figure 1. Position of 66 mastitis-associated E. coli isolates within phylogroup A. A maximum likelihood tree constructed from the concatenated sequence of 159 core E. coli genes elaborates the known population structure of E. coli. Using this tree, we positioned the 66 MPEC isolate within phylogroup A (grey bars). Branches are coloured according to phylogroup: (A) blue; (B1), green; (B2), red; (C) magenta; (D) brown; (E) cyan; F purple; Shigella; gold. Shigella genomes which fall into other phylogroups are not coloured.such as the USA, Bangladesh or Tanzania (see Additional Table 1 for stain information). However, our analysis of the diversity within phylogroup A as represented by the sequenced population (see Additional Figure S2) indic.Ough the data in Fig. 1 shows that MPEC originate from a wide spectrum of lineages within phylogroup A, we noted that many strains appeared clustered onto closely neighbouring branches. Our hypothesis is that only certain strains of E. coli are capable of eliciting bovine mastitis. We reasoned we could test this hypothesis by asking whether all lineages of phylogroup A E. coli were equally likely to be observed in cases of mastitis. To do this, we elaborated a much more comprehensive maximum likelihood phylogenetic tree for the 533 phylogroup A isolates, using the nucleotide sequence of 520 non-recombining core phylogroup A genes, and investigated the positions of the MPEC genomes within this tree (Fig. 2A). For clarity of presentation, bootstrap values have been removed. A tree with bootstrap values is included as Additional Figure S1. This refined tree reflected our earlier observation that many MPEC have close neighbours within the tree that are also MPEC, as well as revealing that many MPEC are not epidemiologically related by country. To investigate this statistically, we reasoned that any such distinction between MPEC and the wider phylogroup A population should be reflected in the tendency for MPEC isolates to be more closely related to each other than would a random selection of phylogroup A E. coli. To test this, we sampled sixty-six random phylogroup A genomes from the population over 100,000 replications and, for each sample, calculated the average phylogenetic distance observed between the genomes within the sample. This distribution of average distances is shown as a density plot in Fig. 2(B). Next, we compared the actual average distance observed between the MPEC isolates with this null distribution (shown as a red vertical line in Fig. 2B), and calculated the p value of how likely this distance is to have been caused by chance alone by using the number of randomised samples which exhibited average distance as small or smaller than that observed between MPEC divided by the number of replications. These data show that it is incredibly unlikely (p = 0.00015) that an average distance as small as that observed between MPEC could be generated by random positioning of MPEC within phylogroup A. Overall, these analyses point to significant reduction in phylogenetic diversity of MPEC strains within phylogroup A compared with what may be expected if these strains were randomly positioned within the phylogroup A population structure. It is possible that this analysis could have been affected by biases imposed by the uneven sampling of E. coli targeted for genome sequencing, many of which originate from humans in countriesScientific RepoRts | 6:30115 | DOI: 10.1038/srepwww.nature.com/scientificreports/Figure 1. Position of 66 mastitis-associated E. coli isolates within phylogroup A. A maximum likelihood tree constructed from the concatenated sequence of 159 core E. coli genes elaborates the known population structure of E. coli. Using this tree, we positioned the 66 MPEC isolate within phylogroup A (grey bars). Branches are coloured according to phylogroup: (A) blue; (B1), green; (B2), red; (C) magenta; (D) brown; (E) cyan; F purple; Shigella; gold. Shigella genomes which fall into other phylogroups are not coloured.such as the USA, Bangladesh or Tanzania (see Additional Table 1 for stain information). However, our analysis of the diversity within phylogroup A as represented by the sequenced population (see Additional Figure S2) indic.