Spatiotemporal Analysis of Microbiological Contamination in New York State Produce Fields following Extensive Flooding from Hurricane Irene, August 2011

Abstract

Although flooding introduces microbiological, chemical, and physical hazards onto croplands, few data are available on the spatial extent, patterns, and development of contamination over time postflooding. To address this paucity of information, we conducted a spatially explicit study of Escherichia coli and Salmonella contamination prevalence and genetic diversity in produce fields after the catastrophic flooding that occurred in New England during 2011. Although no significant differences were detected between the two participating farms, both random forest and logistic regression revealed changes in the spatial pattern of E. coli contamination in drag swab samples over time. Analyses also indicated that E. coli detection was associated with changes in farm management to remediate the land after flooding. In particular, E. coli was widespread in drag swab samples at 21 days postflooding, but the spatial pattern changed by 238 days postflooding such that E. coli was then most prevalent in close proximity to surface water features. The combined results of several population genetics analyses indicated that over time postflooding E. coli populations on the farms (i) changed in composition and (ii) declined overall. Salmonella was primarily detected in surface water features, but some Salmonella strains were isolated from soil and drag swab samples at 21 and 44 days postflooding. Although postflood contamination and land management responses should always be evaluated in the context of each unique farm landscape, our results provide quantitative data on the general patterns of contamination after flooding and support the practice of establishing buffer zones between flood-contaminated cropland and harvestable crops in produce fields.

Landscape-Scale Factors Affecting the Prevalence of Escherichia coli in Surface Soil Include Land Cover Type, Edge Interactions, and Soil pH

“…Two other studies found a prevalence of 48% in croplands located in or near riparian areas (P.W. Bergholz, unpublished data) and a prevalence of 65% at 248 days after natural flooding in other New York State farms (24).…”

“…Reports of the prevalence of E. coli in soils of pastures and forests compared to cropland are not entirely new (44,45), though they have been sparse and focused on isolated single-use land areas (3,11,23,24,40). Here, we report a contemporary analysis of E. coli from 1,428 samples collected in an agricultural landscape totaling 585,589 ha.…”

“…We did not describe a comparable set of fecal isolates during this study. Although it is indisputable that fecal deposition is frequent in some soils and that movement of some wild animal hosts among sites is rapid at spatial scales of 10 1 to 10 3 meters, this soil isolate collection can be especially useful to detect adaptation to soil environments, because (i) death of unfit E. coli genotypes after deposition is rapid, especially when soil communities are unperturbed (35)(36)(37); (ii) as a result of this rapid death, even sevengene multilocus sequence typing (MLST) has been capable of detecting geneenvironment interactions in other studies of E. coli in the environment in the absence of fecal isolates obtained simultaneously (11,12,24); (iii) fecal communities in wild animals fluctuate over time, and deposition by wild animals imposes an easily detectable spatial structure on E. coli in soil only at the scale of 10 2 m (11, 23); and thus, (iv) the best means of detecting the selective effect of the soil environment is to examine soil isolates in a study that comports with a landscape genomics analytical framework in which movements can be taken into account when seeking to detect environmental selection (38,39).…”

“…Numerous survival experiments have shown that commensal and pathogenic E. coli strains can persist in soil for months (20)(21)(22)(23). Some studies have shown that E. coli is genetically structured by selection in the soil environment (11,23,24). Indeed, the host-soil-water cycle presents one mechanism by which E. coli can reach new hosts, because some E. coli strains will then be mobilized in overland or groundwater flow, leading to redeposition into new soil environments or entry into surface water, where they can transfer to hosts directly or via food (25)(26)(27)(28)(29).…”

Contamination of Fresh Produce by Microbial Indicators on Farms and in Packing Facilities: Elucidation of Environmental Routes

“…Ultimately, there are no comprehensive prospective studies directly linking microbial contamination of fresh produce to that of hands, soil, water, or surfaces in the natural setting of the agricultural production environment. This may be due to logistical constraints in setting up a matched study design (6,17), resource constraints in acquiring large sample sizes (18), application of the appropriate statistical analyses to account for multivariable factors affecting microbial contamination (6,(19)(20)(21), and data variability from diverse microbial distributions on produce and environmental samples (22)(23)(24). Because of the low rate of detection of pathogen contamination (25)(26)(27)(28), populations of microbial-indicator organisms, including organisms that indicate filth (coliforms) and/or fecal contamination (Escherichia coli, Enterococcus spp., and somatic coliphage), can be monitored (reviewed in references 29 to 31).…”