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Topological data analysis of Escherichia coli O157:H7 and non-O157 survival in soils.

Ibekwe AM, Ma J, Crowley DE, Yang CH, Johnson AM, Petrossian TC, Lum PY - Front Cell Infect Microbiol (2014)

Bottom Line: Network analysis showed that Shiga toxin negative strain E. coli O157:H7 4554 survived significantly longer in comparison to E. coli O157:H7 EDL 933, while the survival time of E. coli O157:NM was comparable to that of E. coli O157:H7 EDL 933 in all of the tested soils.Two non-O157 strains, E. coli O26:H11 and E. coli O103:H2 survived much longer than E. coli O91:H21 and the three strains of E. coli O157.We show that there are complex interactions between E. coli strain survival, microbial community structures, and soil parameters.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Research Service-US Salinity Laboratory, United States Department of Agriculture Riverside, CA, USA.

ABSTRACT
Shiga toxin-producing E. coli O157:H7 and non-O157 have been implicated in many foodborne illnesses caused by the consumption of contaminated fresh produce. However, data on their persistence in soils are limited due to the complexity in datasets generated from different environmental variables and bacterial taxa. There is a continuing need to distinguish the various environmental variables and different bacterial groups to understand the relationships among these factors and the pathogen survival. Using an approach called Topological Data Analysis (TDA); we reconstructed the relationship structure of E. coli O157 and non-O157 survival in 32 soils (16 organic and 16 conventionally managed soils) from California (CA) and Arizona (AZ) with a multi-resolution output. In our study, we took a community approach based on total soil microbiome to study community level survival and examining the network of the community as a whole and the relationship between its topology and biological processes. TDA produces a geometric representation of complex data sets. Network analysis showed that Shiga toxin negative strain E. coli O157:H7 4554 survived significantly longer in comparison to E. coli O157:H7 EDL 933, while the survival time of E. coli O157:NM was comparable to that of E. coli O157:H7 EDL 933 in all of the tested soils. Two non-O157 strains, E. coli O26:H11 and E. coli O103:H2 survived much longer than E. coli O91:H21 and the three strains of E. coli O157. We show that there are complex interactions between E. coli strain survival, microbial community structures, and soil parameters.

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Topological network data analysis of survival of E. coli O157:H7 and non-O157:H7 across the sub-networks identified in Figure 1A. Survival of E. coli O157:H7 EDL933, E. coli O157:NM, and E. coli O157 strain 4554 (stx-) and shown in (A–C). Survival of non-O157 strains, E. coli O26:H21, E. coli O103:H2, and E. coli O91:H21are shown in (D–F). Gray nodes represent missing ttd (d) measurements for E. coli O157:NM, E. coli O157 strain 4554, E. coli O26:H21, E. coli O103:H2, and E. coli O91:H21. The distance metric and filters are as shown in Figure 1.
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Figure 3: Topological network data analysis of survival of E. coli O157:H7 and non-O157:H7 across the sub-networks identified in Figure 1A. Survival of E. coli O157:H7 EDL933, E. coli O157:NM, and E. coli O157 strain 4554 (stx-) and shown in (A–C). Survival of non-O157 strains, E. coli O26:H21, E. coli O103:H2, and E. coli O91:H21are shown in (D–F). Gray nodes represent missing ttd (d) measurements for E. coli O157:NM, E. coli O157 strain 4554, E. coli O26:H21, E. coli O103:H2, and E. coli O91:H21. The distance metric and filters are as shown in Figure 1.

Mentions: Next, we investigated survival of different E. coli strains in these different soil sub-networks. The network remains the same but we can now probe the network to see if any survival variables show any significant trends between these sub-networks. To do this we colored the same network by the length of survival of E. coli O157:H7 EDL933, E. coli O157:NM, and E. coli O157 strain 4554 (stx-) across the topological network to observe if differences exist in the soil networks. The shortest survival time (ttd) was observed for E. coli O157:H7 EDL933 (13.8–32.6 days) while the longest was observed for E. coli O157NM (20.6–56.0 days) and E. coli O157:H7 strain 4554 as intermediate at 21.1–45.0 days (Figures 3A–C). Figure 3 is colored by survival time of the indicated strain for all the soils. We also performed statistical test on the survival times and show that the survival time of E. coli O157:H7 EDL933 was significantly longer in soils from the Salinas Valley area (8.18E–05), whereas the survival time of E. coli O157:NM and the stx- E. coli O157:H7 strain 4554 were not significantly different in soils from the Salinas Valley area (0.0995 and 0.4823, respectively) and in soils from the Yuma and Imperial Valley region (Table 2). Furthermore, the coloring pattern indicates no differences in survival (ttd) between organic and conventional soils from Imperial Valley and Salinas. Survival time was much shorter in the organic soil than the conventional soils with E. coli O157:NM. This can be observed by the deep blue color (Figure 3B).


Topological data analysis of Escherichia coli O157:H7 and non-O157 survival in soils.

Ibekwe AM, Ma J, Crowley DE, Yang CH, Johnson AM, Petrossian TC, Lum PY - Front Cell Infect Microbiol (2014)

Topological network data analysis of survival of E. coli O157:H7 and non-O157:H7 across the sub-networks identified in Figure 1A. Survival of E. coli O157:H7 EDL933, E. coli O157:NM, and E. coli O157 strain 4554 (stx-) and shown in (A–C). Survival of non-O157 strains, E. coli O26:H21, E. coli O103:H2, and E. coli O91:H21are shown in (D–F). Gray nodes represent missing ttd (d) measurements for E. coli O157:NM, E. coli O157 strain 4554, E. coli O26:H21, E. coli O103:H2, and E. coli O91:H21. The distance metric and filters are as shown in Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
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Figure 3: Topological network data analysis of survival of E. coli O157:H7 and non-O157:H7 across the sub-networks identified in Figure 1A. Survival of E. coli O157:H7 EDL933, E. coli O157:NM, and E. coli O157 strain 4554 (stx-) and shown in (A–C). Survival of non-O157 strains, E. coli O26:H21, E. coli O103:H2, and E. coli O91:H21are shown in (D–F). Gray nodes represent missing ttd (d) measurements for E. coli O157:NM, E. coli O157 strain 4554, E. coli O26:H21, E. coli O103:H2, and E. coli O91:H21. The distance metric and filters are as shown in Figure 1.
Mentions: Next, we investigated survival of different E. coli strains in these different soil sub-networks. The network remains the same but we can now probe the network to see if any survival variables show any significant trends between these sub-networks. To do this we colored the same network by the length of survival of E. coli O157:H7 EDL933, E. coli O157:NM, and E. coli O157 strain 4554 (stx-) across the topological network to observe if differences exist in the soil networks. The shortest survival time (ttd) was observed for E. coli O157:H7 EDL933 (13.8–32.6 days) while the longest was observed for E. coli O157NM (20.6–56.0 days) and E. coli O157:H7 strain 4554 as intermediate at 21.1–45.0 days (Figures 3A–C). Figure 3 is colored by survival time of the indicated strain for all the soils. We also performed statistical test on the survival times and show that the survival time of E. coli O157:H7 EDL933 was significantly longer in soils from the Salinas Valley area (8.18E–05), whereas the survival time of E. coli O157:NM and the stx- E. coli O157:H7 strain 4554 were not significantly different in soils from the Salinas Valley area (0.0995 and 0.4823, respectively) and in soils from the Yuma and Imperial Valley region (Table 2). Furthermore, the coloring pattern indicates no differences in survival (ttd) between organic and conventional soils from Imperial Valley and Salinas. Survival time was much shorter in the organic soil than the conventional soils with E. coli O157:NM. This can be observed by the deep blue color (Figure 3B).

Bottom Line: Network analysis showed that Shiga toxin negative strain E. coli O157:H7 4554 survived significantly longer in comparison to E. coli O157:H7 EDL 933, while the survival time of E. coli O157:NM was comparable to that of E. coli O157:H7 EDL 933 in all of the tested soils.Two non-O157 strains, E. coli O26:H11 and E. coli O103:H2 survived much longer than E. coli O91:H21 and the three strains of E. coli O157.We show that there are complex interactions between E. coli strain survival, microbial community structures, and soil parameters.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Research Service-US Salinity Laboratory, United States Department of Agriculture Riverside, CA, USA.

ABSTRACT
Shiga toxin-producing E. coli O157:H7 and non-O157 have been implicated in many foodborne illnesses caused by the consumption of contaminated fresh produce. However, data on their persistence in soils are limited due to the complexity in datasets generated from different environmental variables and bacterial taxa. There is a continuing need to distinguish the various environmental variables and different bacterial groups to understand the relationships among these factors and the pathogen survival. Using an approach called Topological Data Analysis (TDA); we reconstructed the relationship structure of E. coli O157 and non-O157 survival in 32 soils (16 organic and 16 conventionally managed soils) from California (CA) and Arizona (AZ) with a multi-resolution output. In our study, we took a community approach based on total soil microbiome to study community level survival and examining the network of the community as a whole and the relationship between its topology and biological processes. TDA produces a geometric representation of complex data sets. Network analysis showed that Shiga toxin negative strain E. coli O157:H7 4554 survived significantly longer in comparison to E. coli O157:H7 EDL 933, while the survival time of E. coli O157:NM was comparable to that of E. coli O157:H7 EDL 933 in all of the tested soils. Two non-O157 strains, E. coli O26:H11 and E. coli O103:H2 survived much longer than E. coli O91:H21 and the three strains of E. coli O157. We show that there are complex interactions between E. coli strain survival, microbial community structures, and soil parameters.

Show MeSH
Related in: MedlinePlus