Are these patterns unique to the Central Coast or reflective of broader environmental microbiome dynamics?
The patterns observed in this study are likely not unique to the Central Coast. Similar differences in soil microbiomes associated with land use and production practices have been reported in other studies. In addition, environmental factors such as soil temperature and moisture are known to influence soil microbiome composition across a range of agricultural systems and geographic regions.
Can you elaborate on the dates where you isolated STEC or non-STEC strains? The SNP distances are very close. Where they from the same year or across multiple years?
These data are currently being analyzed with plans to publish a manuscript in 2027 or 2028. Some of these data will be presented as a poster at the 2026 annual meeting of the International Association of Food Protection (IAFP). The abstract will be available then.
Kase, J. A., A. Kataoka, X. Wei, A.-L. Moyne, R. F. Bond, J. Wolny, J. R. Guzman, P. Aminabadi, S. R. Leonard, R. L. Bell, M. Jay-Russell, L. J. Harris, and E. R. Atwill. 2026. Pathogenic Shiga toxin-producing Escherichia coli distribution and transmission pathways in California's Central Coastal leafy greens growing region: A longitudinal environmental survey. (Abstract #T4-10) Technical Presentation. Tuesday, July 28, 2026. Annual IAFP meeting 2026, New Orleans, LA, July 26-29.
Given that isolates move around in the ecosystem, how should growers react if a WGS associated with an outbreak is found on farm? Can FDA still use this to link outbreaks?
This question is difficult to answer without further knowledge of the operational status and conditions of the farm and where, when, why and how the hypothetical outbreak-associated isolate was determined. The answer would also depend on the outbreak in question. This question may be best addressed within FDA’s broader outbreak-investigation framework. In general, FDA and public health agencies use whole genome sequencing (WGS) together with epidemiology, traceback, and other environmental and product information during outbreak investigations. A close genomic match between isolates can help investigators evaluate whether illnesses may be related to a common source, but WGS results are not typically interpreted in isolation.
One important finding from this study is that highly related STEC strains may be detected across different environmental matrices, locations, and time periods. These observations highlight the complexity of interpreting environmental WGS matches and reinforce the importance of considering genomic data within the broader epidemiologic and environmental context of an outbreak investigation.
How do stress factors from seasonality influence gene transfer?
This study was not designed to evaluate the effects of seasonal stress factors on gene transfer, so no conclusions can be drawn regarding that relationship from these data.
In the vineyard-produce site, did you also test for mitochondrial DNA in the STEC negative samples?
Yes. For all soil samples from either wine-grape vineyards or produce fields that were included in the subset of samples subjected to metagenomic sequencing, the analysis included mitochondrial DNA identification, regardless of STEC status.
Is both E. coli O157 and nonO157 STEC pathogenic to humans? Have we investigated if non-O157 STEC is causing health problems? Are they becoming pathogenic?
Both E. coli O157 and non-O157 STEC can cause illness in humans. Disease severity can vary depending on the strain and the individual infected, ranging from mild gastrointestinal illness to severe disease, including bloody diarrhea and hemolytic uremic syndrome (HUS). While E. coli O157 is historically the most recognized STEC associated with severe outbreaks, some non-O157 STEC strains can also cause serious human illness.
Is there a reason to examine microbiomes of enriched samples?
Yes. In many environmental samples, E. coli is present at very low relative abundance compared to other microorganisms, making detection difficult in unenriched, culture-independent samples. Enrichment increases the relative abundance of E. coli, improving the ability to detect STEC-associated targets such as Shiga toxin genes and to further characterize the E. coli population associated with STEC-positive samples.
Was previous BSAAO use, or field crop history considered for differences in metagenomic analysis? Was the history of BSAAO application noted for soil transects?
To our knowledge, untreated BSAAO was never used in the produce farms that were included in the study. Treated BSAAO, if present, was sampled on participating produce farms, vineyard and compost sites. The history of treated BSAAO use was not recorded for soil transects.
What is the potential for a non-O157 to, thru gene transfer, become a O157 in the future via biofilms?
Biofilm formation and potential gene transfer were not specifically studied as part of this study.
What is the significance of non O157 STEC that was “more common” in region? Is that any different from what would be expected to as “background?”
A wide diversity of non-O157 STEC was identified in this study, with nearly 70 different serotypes recovered. Some serotypes of recognized public health significance, such as O26:H11, were isolated repeatedly from multiple sample matrices, while many others were detected only once. It is not clear why certain serotypes were more commonly detected than others, although factors such as strain fitness may contribute.
What percent of STEC were EHEC?
We do not yet know the percentage of STEC isolates that meet the criteria for EHEC classification, as additional characterization and analysis are still in progress.
What specific characteristics in the sample are you looking for further analysis using metagenomics?
Further metagenomic analyses will focus on differences in microbiome composition and diversity among samples, as well as potential associations between microbiome profiles and environmental or weather-related factors.
Which factors most likely affected the finding that REPHEX02 receded? Given that REPHEX02 hasn’t been detected for more than 6 years, what mechanisms might explain its apparent disappearance, and have comparable strain-level dynamics been observed in other environments?
We do not know why REPHEX02 was not detected. One important consideration is sampling limitation: although the study included over 6,000 samples collected across more than 7,000 square miles over 5 years, it remains possible that the strain persisted at low prevalence below our detection capacity or in unsampled reservoirs. While it was a different strain of STEC O157:H7, we did observe fluctuations of dominant strains within one cattle ranch, but the exact drivers of such strain-level dynamics are not fully established.
You found 12 O157 strains, but how many times were O157 positives in samples found?
There were a total of 83 samples that tested positive for E. coli O157 across the different sample matrices.
You spoke of STEC strains A, B, C and D. Might these be mutations of each other? When you detect same strains a year later, how many SNP differences are there? Basically, how much does it evolve?
We evaluated the genetic relatedness of isolates using single nucleotide polymorphism (SNP) analysis. The strains labeled A, B, C, and D differed from one another by more than 70 SNPs, indicating they were genetically distinct strains rather than recent mutations of each other. In contrast, isolates grouped within the same strain were typically separated by fewer than 25 SNPs, with most differing by fewer than 15 SNPs.