Cargando…

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

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 recove...

Descripción completa

Detalles Bibliográficos
Autores principales: Ottesen, Andrea R., Gonzalez, Antonio, Bell, Rebecca, Arce, Caroline, Rideout, Steven, Allard, Marc, Evans, Peter, Strain, Errol, Musser, Steven, Knight, Rob, Brown, Eric, Pettengill, James B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767688/
https://www.ncbi.nlm.nih.gov/pubmed/24039862
http://dx.doi.org/10.1371/journal.pone.0073079
_version_ 1782283689898541056
author Ottesen, Andrea R.
Gonzalez, Antonio
Bell, Rebecca
Arce, Caroline
Rideout, Steven
Allard, Marc
Evans, Peter
Strain, Errol
Musser, Steven
Knight, Rob
Brown, Eric
Pettengill, James B.
author_facet Ottesen, Andrea R.
Gonzalez, Antonio
Bell, Rebecca
Arce, Caroline
Rideout, Steven
Allard, Marc
Evans, Peter
Strain, Errol
Musser, Steven
Knight, Rob
Brown, Eric
Pettengill, James B.
author_sort Ottesen, Andrea R.
collection PubMed
description 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.
format Online
Article
Text
id pubmed-3767688
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-37676882013-09-13 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 Pettengill, James B. PLoS One Research Article 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. Public Library of Science 2013-09-09 /pmc/articles/PMC3767688/ /pubmed/24039862 http://dx.doi.org/10.1371/journal.pone.0073079 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
spellingShingle Research Article
Ottesen, Andrea R.
Gonzalez, Antonio
Bell, Rebecca
Arce, Caroline
Rideout, Steven
Allard, Marc
Evans, Peter
Strain, Errol
Musser, Steven
Knight, Rob
Brown, Eric
Pettengill, James B.
Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere
title Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere
title_full Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere
title_fullStr Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere
title_full_unstemmed Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere
title_short Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere
title_sort co-enriching microflora associated with culture based methods to detect salmonella from tomato phyllosphere
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767688/
https://www.ncbi.nlm.nih.gov/pubmed/24039862
http://dx.doi.org/10.1371/journal.pone.0073079
work_keys_str_mv AT ottesenandrear coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere
AT gonzalezantonio coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere
AT bellrebecca coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere
AT arcecaroline coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere
AT rideoutsteven coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere
AT allardmarc coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere
AT evanspeter coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere
AT strainerrol coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere
AT mussersteven coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere
AT knightrob coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere
AT browneric coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere
AT pettengilljamesb coenrichingmicrofloraassociatedwithculturebasedmethodstodetectsalmonellafromtomatophyllosphere