Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination

<p>Abstract</p> <p>Background</p> <p><it>Escherichia coli </it>strains are commonly found in the gut microflora of warm-blooded animals. These strains can be assigned to one of the four main phylogenetic groups, A, B1, B2 and D, which can be divided into seven subgroups (A₀, A₁, B1, B2₂, B2₃, D₁and D₂), according to the combination of the three genetic markers <it>chuA</it>, <it>yjaA </it>and DNA fragment TspE4.C2. Distinct studies have demonstrated that these phylo-groups differ in the presence of virulence factors, ecological niches and life-history. Therefore, the aim of this work was to analyze the distribution of these <it>E. coli </it>phylo-groups in 94 human strains, 13 chicken strains, 50 cow strains, 16 goat strains, 39 pig strains and 29 sheep strains and to verify the potential of this analysis to investigate the source of fecal contamination.</p> <p>Results</p> <p>The results indicated that the distribution of phylogenetic groups, subgroups and genetic markers is non-random in the hosts analyzed. Strains from group B1 were present in all hosts analyzed but were more prevalent in cow, goat and sheep samples. Subgroup B2₃was only found in human samples. The diversity and the similarity indexes have indicated a similarity between the <it>E. coli </it>population structure of human and pig samples and among cow, goat and sheep samples. Correspondence analysis using contingence tables of subgroups, groups and genetic markers frequencies allowed the visualization of the differences among animal samples and the identification of the animal source of an external validation set. The classifier tools Binary logistic regression and Partial least square -- discriminant analysis, using the genetic markers profile of the strains, differentiated the herbivorous from the omnivorous strains, with an average error rate of 17%.</p> <p>Conclusions</p> <p>This is the first work, as far as we are aware, that identifies the major source of fecal contamination of a pool of strains instead of a unique strain. We concluded that the analysis of the <it>E. coli </it>population structure can be useful as a supplementary bacterial source tracking tool.</p

Reproductive capacity of VDPV2 isolate 44624 and Sabin 2 strain at different temperatures (RCT marker).

<p>The RCT value is defined as the difference between the log 10 virus titer of the viral stock measured at the optimal temperature 36,5°C and supraoptimal temperature 40°C. The values are expressed as log 10 TCID50 / 0,1ml. Virus were considered thermosensitive if the ΔRCT value was greater or equal to 2, and thermo resistant when RCT value was inferior to 2.00.</p

Molecular and Phenotypic Characterization of a Highly Evolved Type 2 Vaccine-Derived Poliovirus Isolated from Seawater in Brazil, 2014

<div><p>A type 2 vaccine-derived poliovirus (VDPV), differing from the Sabin 2 strain at 8.6% (78/903) of VP1 nucleotide positions, was isolated from seawater collected from a seaport in São Paulo State, Brazil. The P1/capsid region is related to the Sabin 2 strain, but sequences within the 5'-untranslated region and downstream of the P1 region were derived from recombination with other members of Human Enterovirus Species C (HEV-C). The two known attenuating mutations had reverted to wild-type (A481G in the 5'-UTR and Ile143Thr in VP1). The VDPV isolate had lost the temperature sensitive phenotype and had accumulated amino acid substitutions in neutralizing antigenic (NAg) sites 3a and 3b. The date of the initiating OPV dose, estimated from the number of synonymous substitutions in the capsid region, was approximately 8.5 years before seawater sampling, a finding consistent with a long time of virus replication and possible transmission among several individuals. Although no closely related type 2 VDPVs were detected in Brazil or elsewhere, this VDPV was found in an area with a mobile population, where conditions may favor both viral infection and spread. Environmental surveillance serves as an important tool for sensitive and early detection of circulating poliovirus in the final stages of global polio eradication.</p></div

Amino acid substitutions in the capsid protomer of isolate 44624.

<p>VP1, VP2, VP3 and VP4 are represented as a 3-dimensional structured protomer. The image was generated using the software Swiss-PdbViewer [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152251#pone.0152251.ref024" target="_blank">24</a>], based on X-ray crystallographic analysis of type 2 poliovirus strain Lansing (Protein Data Bank accession number 1EAH.pdb) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152251#pone.0152251.ref023" target="_blank">23</a>]. Colour codes: Substitutions at known antigenic sites, brown. Substitutions elsewhere, pink. The BC-loop of VP1 is not visible in this model.</p

Alignment of amino acids residues of neutralizing antigenic (NAg) sites for Sabin 2 (GenBank accession number AY184220) and isolate 44624.

<p>Amino acid positions are numbered according to Sabin 2 NAg1 (VP1 88–106), NAg2 (VP2 163–169; VP2 268–270; VP1 220–225), NAg3a (VP3 54–61; VP3 70–74; VP1 286–291) and NA3b (VP2 71–73; VP3 75–79).</p