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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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Survival of six E. coli O157 and non-O157 strains grouped together on a normalized scale showed that E. coli O103:H2 survived the longest in all the soils, followed by E. coli O26:H21. Gray nodes are as explained in Figure 3. The distance metric and filters are as shown in Figure 1.
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Figure 4: Survival of six E. coli O157 and non-O157 strains grouped together on a normalized scale showed that E. coli O103:H2 survived the longest in all the soils, followed by E. coli O26:H21. Gray nodes are as explained in Figure 3. The distance metric and filters are as shown in Figure 1.

Mentions: Survival of non-O157 in soils was longer that E. coli O157:H7 except E. coli O91.H21. It was found that two non-O157 strains, E. coli O26:H21 and E. coli O103:H2 survived much longer that E. coli O91:H21. The three non-O157 strains survived significantly longer (E. coli O91.H21: 4.12E–06, O26:H21:0.079, and 0103: 2.84E–06) in soils from the Salinas Valley region than in soils from the Yuma and Imperial Valleys (Table 2). There were no differences of survival between organic and conventionally managed soils with the non-O157 strains. In the current study no isogenic strains (with and without stx) were used. When the six E. coli O157 and non-O157 strains were grouped together on the same scale it was shown that E. coli O103:H2 survived the longest in all the soils, followed by E. coli O26:H21 (Figure 4).


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)

Survival of six E. coli O157 and non-O157 strains grouped together on a normalized scale showed that E. coli O103:H2 survived the longest in all the soils, followed by E. coli O26:H21. Gray nodes are as explained in Figure 3. The distance metric and filters are as shown in Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4155871&req=5

Figure 4: Survival of six E. coli O157 and non-O157 strains grouped together on a normalized scale showed that E. coli O103:H2 survived the longest in all the soils, followed by E. coli O26:H21. Gray nodes are as explained in Figure 3. The distance metric and filters are as shown in Figure 1.
Mentions: Survival of non-O157 in soils was longer that E. coli O157:H7 except E. coli O91.H21. It was found that two non-O157 strains, E. coli O26:H21 and E. coli O103:H2 survived much longer that E. coli O91:H21. The three non-O157 strains survived significantly longer (E. coli O91.H21: 4.12E–06, O26:H21:0.079, and 0103: 2.84E–06) in soils from the Salinas Valley region than in soils from the Yuma and Imperial Valleys (Table 2). There were no differences of survival between organic and conventionally managed soils with the non-O157 strains. In the current study no isogenic strains (with and without stx) were used. When the six E. coli O157 and non-O157 strains were grouped together on the same scale it was shown that E. coli O103:H2 survived the longest in all the soils, followed by E. coli O26:H21 (Figure 4).

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