Phylogenetic group and virulence profile classification in Escherichia coli from distinct isolation sources in Mexico

Authors: AGUIRRE-SANCHEZ, JOSE - Center For Research In Food And Development (CIAD); VALDEZ-TORRES, JOSE - Center For Research In Food And Development (CIAD); CASTRO DEL CAMPO, NOHEMI - Center For Research In Food And Development (CIAD); MARTINEZ-URTAZA, JAIME - Autonomous University Of Barcelona; CASTRO DEL CAMPO, NOHELIA - Center For Research In Food And Development (CIAD); Lee, Bertram; Quinones, Beatriz; CHAIDEZ-QUIROZ, CRISTOBAL - Center For Research In Food And Development (CIAD)

Submitted to: Infection, Genetics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2022
Publication Date: 11/1/2022
Citation: Aguirre-Sanchez, J.R., Valdez-Torres, J.B., Castro del Campo, N., Martinez-Urtaza, J., Castro del Campo, N., Lee, B.G., Quinones, B., Chaidez-Quiroz, C. 2022. Phylogenetic group and virulence profile classification in Escherichia coli from distinct isolation sources in Mexico. Infection, Genetics and Evolution. 106. Article 105380. https://doi.org/10.1016/j.meegid.2022.105380.
DOI: https://doi.org/10.1016/j.meegid.2022.105380

Interpretive Summary: Escherichia coli is a bacterium that resides in the gastrointestinal tract of warm-blooded animals. Several strains of E. coli are responsible for a broad range of enteric human diseases like diarrhea, colitis, dysentery, and hemolytic uremic syndrome. Techniques for differentiating E. coli strains, causing disease in humans, have relied on the identification of housekeeping genes and virulence gene profiles. To better address the epidemiological importance of E. coli, a new classification into phylogenetic groups (phylogroups) has been recently developed based on the presence of specific gene targets. As high-resolution sequencing continues to be implemented, phylogroup classification has been expanded. The accumulation of E. coli sequenced genomes, readily available on public databases, has allowed to improve the study of E. coli population structure, and the genome information has also enabled an investigation of the composition and diversity of virulence factors in E. coli strains from different sources. The classification of E. coli strains, based on phylogroup designations, has identified a relationship to different niches and lifestyles. To develop better epidemiological tools in geographical locations with high enteric disease, the present study analyzed the distribution and prevalence of hundreds of E. coli strains with distinct phylogenetic groups and virulence profiles, recovered from environmental, clinical, animal and food sources in Mexico. The findings from this study is providing fundamental information on the relationships of E. coli phylogroup classification with virulence profiles and isolation sources. Additionally, the results from this study will improve our understanding of population structure for E. coli strains and will enable the development of better tools for source tracking.

Technical Abstract: Escherichia coli is a leading cause of human enteric diseases worldwide. The rapid and accurate causal agent identification to a particular source represents a crucial step in the establishment of safety and health measures in the affected human populations and would provide insights into the relationship of traits that may contribute for pathogen persistence in a particular reservoir. The objective of the present study was to analyze the distribution and prevalence of over two hundred E. coli strains from different isolation sources in Mexico by conducting a correspondence analysis using qualitative variables to explore associations within categories. The results indicated that E. coli isolates, recovered from distinct sources in Mexico, were classified into phylogroups B1 (35.8%), A (27.8%), and D (12.3%) and were clustered to particular clades according to the predicted phylogroups. The results from correspondence analysis showed that E. coli populations from distinct sources in Mexico, belonging to different phylogroups, were not dispersed randomly and were associated with a particular isolation source. Phylogroup A was strongly associated with human sources. Additionally, phylogroups D and B1 were also related to human sources. Phylogroup B2 was associated with herbivorous and omnivorous mammals like cattle and pigs. Moreover, the B1 phylogenetic group showed a significant relationship with food sources. Common virulence genes in the examined E. coli strains, assigned to all phylogroups, were identified as essential markers for survival and invasion in the host. Although virulence profiles varied among the phylogroups, E. coli strains belonging to phylogroup D were found to be associated with human source and contained the largest virulence gene repertoire conferring a persistence in the host. In summary, these findings provide fundamental information for a better characterization of pathogenic E. coli, recovered from distinct isolation sources in Mexico, and would assist in the development of better tools for identifying potential transmission routes of contamination.