Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere

Andrea R. Ottesen, Antonio Gonzalez, Rebecca Bell, Caroline Arce, Steven Rideout, Marc Allard, Peter Evans, Errol Strain, Steven Musser, Rob Knight, Eric Wayne Brown, James B. Pettengill

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

The ability to detect a specific organism from a complex environment is vitally important to many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles of foodborne outbreaks due to strains of Salmonella but few studies have ever recovered Salmonella from a tomato phyllosphere environment. Precision of culturing techniques that target agents associated with outbreaks depend on numerous factors. One important factor to better understand is which species co-enrich during enrichment procedures and how microbial dynamics may impede or enhance detection of target pathogens. We used a shotgun sequence approach to describe taxa associated with samples pre-enrichment and throughout the enrichment steps of the Bacteriological Analytical Manual's (BAM) protocol for detection of Salmonella from environmental tomato samples. Recent work has shown that during efforts to enrich Salmonella (Proteobacteria) from tomato field samples, Firmicute genera are also co-enriched and at least one co-enriching Firmicute genus (Paenibacillus sp.) can inhibit and even kills strains of Salmonella. Here we provide a baseline description of microflora that co-culture during detection efforts and the utility of a bioinformatic approach to detect specific taxa from metagenomic sequence data. We observed that uncultured samples clustered together with distinct taxonomic profiles relative to the three cultured treatments (Universal Pre-enrichment broth (UPB), Tetrathionate (TT), and Rappaport-Vassiliadis (RV)). There was little consistency among samples exposed to the same culturing medias, suggesting significant microbial differences in starting matrices or stochasticity associated with enrichment processes. Interestingly, Paenibacillus sp. (Salmonella inhibitor) was significantly enriched from uncultured to cultured (UPB) samples. Also of interest was the sequence based identification of a number of sequences as Salmonella despite indication by all media, that samples were culture negative for Salmonella. Our results substantiate the nascent utility of metagenomic methods to improve both biological and bioinformatic pathogen detection methods.

Original languageEnglish (US)
Article numbere73079
JournalPloS one
Volume8
Issue number9
DOIs
StatePublished - Sep 9 2013

Fingerprint

phyllosphere
Salmonella
Lycopersicon esculentum
tomatoes
microorganisms
Paenibacillus
Metagenomics
sampling
Pathogens
Bioinformatics
Computational Biology
methodology
bioinformatics
Disease Outbreaks
microbial detection
Food safety
Proteobacteria
health foods
Food Safety
Firearms

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Ottesen, A. R., Gonzalez, A., Bell, R., Arce, C., Rideout, S., Allard, M., ... Pettengill, J. B. (2013). Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere. PloS one, 8(9), [e73079]. https://doi.org/10.1371/journal.pone.0073079
Ottesen, Andrea R. ; Gonzalez, Antonio ; Bell, Rebecca ; Arce, Caroline ; Rideout, Steven ; Allard, Marc ; Evans, Peter ; Strain, Errol ; Musser, Steven ; Knight, Rob ; Brown, Eric Wayne ; Pettengill, James B. / Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere. In: PloS one. 2013 ; Vol. 8, No. 9.
@article{062b24380f2748fc80cc355580ae89df,
title = "Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere",
abstract = "The ability to detect a specific organism from a complex environment is vitally important to many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles of foodborne outbreaks due to strains of Salmonella but few studies have ever recovered Salmonella from a tomato phyllosphere environment. Precision of culturing techniques that target agents associated with outbreaks depend on numerous factors. One important factor to better understand is which species co-enrich during enrichment procedures and how microbial dynamics may impede or enhance detection of target pathogens. We used a shotgun sequence approach to describe taxa associated with samples pre-enrichment and throughout the enrichment steps of the Bacteriological Analytical Manual's (BAM) protocol for detection of Salmonella from environmental tomato samples. Recent work has shown that during efforts to enrich Salmonella (Proteobacteria) from tomato field samples, Firmicute genera are also co-enriched and at least one co-enriching Firmicute genus (Paenibacillus sp.) can inhibit and even kills strains of Salmonella. Here we provide a baseline description of microflora that co-culture during detection efforts and the utility of a bioinformatic approach to detect specific taxa from metagenomic sequence data. We observed that uncultured samples clustered together with distinct taxonomic profiles relative to the three cultured treatments (Universal Pre-enrichment broth (UPB), Tetrathionate (TT), and Rappaport-Vassiliadis (RV)). There was little consistency among samples exposed to the same culturing medias, suggesting significant microbial differences in starting matrices or stochasticity associated with enrichment processes. Interestingly, Paenibacillus sp. (Salmonella inhibitor) was significantly enriched from uncultured to cultured (UPB) samples. Also of interest was the sequence based identification of a number of sequences as Salmonella despite indication by all media, that samples were culture negative for Salmonella. Our results substantiate the nascent utility of metagenomic methods to improve both biological and bioinformatic pathogen detection methods.",
author = "Ottesen, {Andrea R.} and Antonio Gonzalez and Rebecca Bell and Caroline Arce and Steven Rideout and Marc Allard and Peter Evans and Errol Strain and Steven Musser and Rob Knight and Brown, {Eric Wayne} and Pettengill, {James B.}",
year = "2013",
month = "9",
day = "9",
doi = "10.1371/journal.pone.0073079",
language = "English (US)",
volume = "8",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "9",

}

Ottesen, AR, Gonzalez, A, Bell, R, Arce, C, Rideout, S, Allard, M, Evans, P, Strain, E, Musser, S, Knight, R, Brown, EW & Pettengill, JB 2013, 'Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere', PloS one, vol. 8, no. 9, e73079. https://doi.org/10.1371/journal.pone.0073079

Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere. / Ottesen, Andrea R.; Gonzalez, Antonio; Bell, Rebecca; Arce, Caroline; Rideout, Steven; Allard, Marc; Evans, Peter; Strain, Errol; Musser, Steven; Knight, Rob; Brown, Eric Wayne; Pettengill, James B.

In: PloS one, Vol. 8, No. 9, e73079, 09.09.2013.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere

AU - Ottesen, Andrea R.

AU - Gonzalez, Antonio

AU - Bell, Rebecca

AU - Arce, Caroline

AU - Rideout, Steven

AU - Allard, Marc

AU - Evans, Peter

AU - Strain, Errol

AU - Musser, Steven

AU - Knight, Rob

AU - Brown, Eric Wayne

AU - Pettengill, James B.

PY - 2013/9/9

Y1 - 2013/9/9

N2 - The ability to detect a specific organism from a complex environment is vitally important to many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles of foodborne outbreaks due to strains of Salmonella but few studies have ever recovered Salmonella from a tomato phyllosphere environment. Precision of culturing techniques that target agents associated with outbreaks depend on numerous factors. One important factor to better understand is which species co-enrich during enrichment procedures and how microbial dynamics may impede or enhance detection of target pathogens. We used a shotgun sequence approach to describe taxa associated with samples pre-enrichment and throughout the enrichment steps of the Bacteriological Analytical Manual's (BAM) protocol for detection of Salmonella from environmental tomato samples. Recent work has shown that during efforts to enrich Salmonella (Proteobacteria) from tomato field samples, Firmicute genera are also co-enriched and at least one co-enriching Firmicute genus (Paenibacillus sp.) can inhibit and even kills strains of Salmonella. Here we provide a baseline description of microflora that co-culture during detection efforts and the utility of a bioinformatic approach to detect specific taxa from metagenomic sequence data. We observed that uncultured samples clustered together with distinct taxonomic profiles relative to the three cultured treatments (Universal Pre-enrichment broth (UPB), Tetrathionate (TT), and Rappaport-Vassiliadis (RV)). There was little consistency among samples exposed to the same culturing medias, suggesting significant microbial differences in starting matrices or stochasticity associated with enrichment processes. Interestingly, Paenibacillus sp. (Salmonella inhibitor) was significantly enriched from uncultured to cultured (UPB) samples. Also of interest was the sequence based identification of a number of sequences as Salmonella despite indication by all media, that samples were culture negative for Salmonella. Our results substantiate the nascent utility of metagenomic methods to improve both biological and bioinformatic pathogen detection methods.

AB - The ability to detect a specific organism from a complex environment is vitally important to many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles of foodborne outbreaks due to strains of Salmonella but few studies have ever recovered Salmonella from a tomato phyllosphere environment. Precision of culturing techniques that target agents associated with outbreaks depend on numerous factors. One important factor to better understand is which species co-enrich during enrichment procedures and how microbial dynamics may impede or enhance detection of target pathogens. We used a shotgun sequence approach to describe taxa associated with samples pre-enrichment and throughout the enrichment steps of the Bacteriological Analytical Manual's (BAM) protocol for detection of Salmonella from environmental tomato samples. Recent work has shown that during efforts to enrich Salmonella (Proteobacteria) from tomato field samples, Firmicute genera are also co-enriched and at least one co-enriching Firmicute genus (Paenibacillus sp.) can inhibit and even kills strains of Salmonella. Here we provide a baseline description of microflora that co-culture during detection efforts and the utility of a bioinformatic approach to detect specific taxa from metagenomic sequence data. We observed that uncultured samples clustered together with distinct taxonomic profiles relative to the three cultured treatments (Universal Pre-enrichment broth (UPB), Tetrathionate (TT), and Rappaport-Vassiliadis (RV)). There was little consistency among samples exposed to the same culturing medias, suggesting significant microbial differences in starting matrices or stochasticity associated with enrichment processes. Interestingly, Paenibacillus sp. (Salmonella inhibitor) was significantly enriched from uncultured to cultured (UPB) samples. Also of interest was the sequence based identification of a number of sequences as Salmonella despite indication by all media, that samples were culture negative for Salmonella. Our results substantiate the nascent utility of metagenomic methods to improve both biological and bioinformatic pathogen detection methods.

UR - http://www.scopus.com/inward/record.url?scp=84883629306&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84883629306&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0073079

DO - 10.1371/journal.pone.0073079

M3 - Article

C2 - 24039862

AN - SCOPUS:84883629306

VL - 8

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 9

M1 - e73079

ER -