CiteULike | Further Information

• {"link"=>{"url"=>"http://www.citeulike.org/user/emaynard/article/3276694"}, "post_time"=>"2011-03-10 02:03:46", "tag"=>["e_coli", "food_safety"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pone.0001159"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/18174909"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=18174909"}], "username"=>"emaynard", "article_id"=>"3276694"}

Mendeley | Further Information

{"title"=>"Incidence and tracking of escherichia coli O157:H7 in a major produce production region in California", "type"=>"journal", "authors"=>[{"first_name"=>"Michael", "last_name"=>"Cooley", "scopus_author_id"=>"7004535834"}, {"first_name"=>"Diana", "last_name"=>"Carychao", "scopus_author_id"=>"23059672400"}, {"first_name"=>"Leta", "last_name"=>"Crawford-Miksza", "scopus_author_id"=>"6602509166"}, {"first_name"=>"Michele T.", "last_name"=>"Jay", "scopus_author_id"=>"7102176236"}, {"first_name"=>"Carol", "last_name"=>"Myers", "scopus_author_id"=>"36795434500"}, {"first_name"=>"Christopher", "last_name"=>"Rose", "scopus_author_id"=>"36813239100"}, {"first_name"=>"Christine", "last_name"=>"Keys", "scopus_author_id"=>"8081350200"}, {"first_name"=>"Jeff", "last_name"=>"Farrar", "scopus_author_id"=>"7103292670"}, {"first_name"=>"Robert E.", "last_name"=>"Mandrell", "scopus_author_id"=>"7006646680"}], "year"=>2007, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"37049010237", "doi"=>"10.1371/journal.pone.0001159", "pui"=>"351637970", "pmid"=>"18174909", "scopus"=>"2-s2.0-37049010237", "issn"=>"19326203", "isbn"=>"5325420000450"}, "id"=>"9d769608-52f9-3835-8fb7-0faf8fd00c67", "abstract"=>"Fresh vegetables have become associated with outbreaks caused by Escherichia coli O157:H7 (EcO157). Between 1995-2006, 22 produce outbreaks were documented in the United States, with nearly half traced to lettuce or spinach grown in California. Outbreaks between 2002 and 2006 induced investigations of possible sources of pre-harvest contamination on implicated farms in the Salinas and San Juan valleys of California, and a survey of the Salinas watershed. EcO157 was isolated at least once from 15 of 22 different watershed sites over a 19 month period. The incidence of EcO157 increased significantly when heavy rain caused an increased flow rate in the rivers. Approximately 1000 EcO157 isolates obtained from cultures of>100 individual samples were typed using Multi-Locus Variable-number-tandem-repeat Analysis (MLVA) to assist in identifying potential fate and transport of EcO157 in this region. A subset of these environmental isolates were typed by Pulse Field Gel Electrophoresis (PFGE) in order to make comparisons with human clinical isolates associated with outbreak and sporadic illness. Recurrence of identical and closely related EcO157 strains from specific locations in the Salinas and San Juan valleys suggests that transport of the pathogen is usually restricted. In a preliminary study, EcO157 was detected in water at multiple locations in a low-flow creek only within 135 meters of a point source. However, possible transport up to 32 km was detected during periods of higher water flow associated with flooding. During the 2006 baby spinach outbreak investigation, transport was also detected where water was unlikely to be involved. These results indicate that contamination of the environment is a dynamic process involving multiple sources and methods of transport. Intensive studies of the sources, incidence, fate and transport of EcO157 near produce production are required to determine the mechanisms of pre-harvest contamination and potential risks for human illness.", "link"=>"http://www.mendeley.com/research/incidence-tracking-escherichia-coli-o157h7-major-produce-production-region-california", "reader_count"=>85, "reader_count_by_academic_status"=>{"Unspecified"=>7, "Professor > Associate Professor"=>13, "Researcher"=>17, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>2, "Student > Master"=>13, "Other"=>6, "Student > Bachelor"=>6, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>7, "Professor > Associate Professor"=>13, "Researcher"=>17, "Student > Doctoral Student"=>3, "Student > Ph. D. 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• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/f9381cc0-5a7f-4695-985f-aa741cec349b", "title"=>"Important", "body"=>"Well written but lacked organisation.", "isRemoved"=>false, "created"=>"2007-11-14T09:25:09Z", "lastModified"=>"2007-11-14T09:25:09Z", "creator"=>{"userId"=>"157937"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0001159", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2007-11-14T09:25:09Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/c921cdf7-ae82-4934-bfd6-292e039834ea", "title"=>"incorrect change during revision", "body"=>"leafy green vegetable", "highlightedText"=>"''produce''\nhttp://plosone.org/article/info:doi/10.1371/journal.pone.0001159#article1.front1.article-meta1.abstract1.p1", "isRemoved"=>false, "created"=>"2007-11-14T15:51:03Z", "lastModified"=>"2007-11-14T15:51:03Z", "creator"=>{"userId"=>"9445"}, "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0001159", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2007-11-14T15:51:03Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/ea55e3ce-a5f3-455c-92c7-30aef0e0d474", "title"=>"Referee Comments: Referee 3 (Benedicte Lafay)", "body"=>"Reviewer 3's Review (Benedicte Lafay)\n\n-----\n\nThe manuscript presents data obtained in the course of several investigations dealing with Escherichia coli O157:H7 occurrence in the environment. E. coli O157:H7 is responsible for severe foodborne pathologies in humans and it is thus of importance to understand its ecology in order to assess the epidemiological risk associated with environmental contamination. \n\nWhereas a lot of work has obviously been involved in producing the results, the manuscript unfortunately fails in providing a coherent story. Most critically, little effort seems to have been put into organizing the various data and relevant facts, analyzing them together as well as in a general context, and providing a (hypo)synthesis. \n\nIt actually looks as though the paper was built from the compilation of separate reports, each dealing with a different aspect of the study, and that the only trace of an attempt at presenting them into a larger story is that results and partial conclusions are scrambled in and scattered across all parts of the manuscript (and at times repeated). The reader is then left to extract and organize the relevant data -and to imagine those missing- to be able to comprehend: \n\n- what the aim of the paper really was : investigating the epidemiological risk associated to in-field contamination, survival and spread of E. coli O157:H7, in contrast to what the title and abstract suggest and what is stated at the end of the introduction (they appear essentially to correspond to the molecular typing part of the study) ; \n\n- how the survey was conceived and conducted : a paragraph describing the sampling strategy and a map presenting the locations of all -including the farms/ranches- sampled sites are critically missing. A different presentation of the results (for example, the organisation of Table S1 according to the spatial and temporal sampling source, the use of histogrammes, the removal of Figure 1 which is not cited in the text) may be considered ; \n\n- what the conclusions may be and how they compare to what is already know on the subject. As reported here, the whole story cannot be made out without a major imagination and data processing (and rewriting) effort from the reader. \nIt is thus unfortunately currently difficult to grasp the real impact of the study. \n\nPossibly because of this, the manuscript is overly long. A more concise and focused presentation would most likely contribute better to emphasize the major findings. \n\nAnother concern is that at least some of the results have been published elsewhere (although apparently mostly in the form of administrative reports, e.g., references 9 and 41, but see also the citation on page 32).\n\n-----\n\nN.B. These are the general comments made by the reviewer when reviewing this paper in light of which the manuscript was revised. Specific points addressed during revision of the paper are not shown.\n", "isRemoved"=>false, "created"=>"2007-11-22T09:47:31Z", "lastModified"=>"2007-11-22T09:47:31Z", "creator"=>{"userId"=>"80539"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0001159", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>3, "mostRecentActivity"=>"2007-12-05T20:07:52Z", "replies"=>[{"type"=>"REPLY", "parentID"=>20719, "annotationUri"=>"info:doi/10.1371/reply/dcf85d6f-3096-48e0-9932-7920809f5c57", "title"=>"RE: Referee Comments: Referee 3 (Benedicte Lafay)", "body"=>"I find it more than a little unusual that reviewer comment are posted, especially since these comments were made prior to extensive revision of the manuscript. The tiny comment by N.B. at the bottom is grossly insufficient.", "isRemoved"=>false, "created"=>"2007-11-28T20:36:57Z", "lastModified"=>"2007-11-28T20:36:57Z", "creator"=>{"userId"=>"169863"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0001159", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>2, "mostRecentActivity"=>"2007-12-05T20:07:52Z", "replies"=>[{"type"=>"REPLY", "parentID"=>35527, "annotationUri"=>"info:doi/10.1371/reply/ede7b926-834c-4a32-aaf5-84c540c92bbe", "title"=>"RE: RE: Referee Comments: Referee 3 (Benedicte Lafay)", "body"=>"I agree with \"mcooley\" on this particular point.\r\n\r\nIf reviewer's comments are included into the discussion board, it seems obvious that reviewers responses should be added as well. By doing so, we could clearly track the major changes added in the revised version of the manuscript.\r\n\r\nNicolas Corradi", "isRemoved"=>false, "created"=>"2007-12-05T19:39:55Z", "lastModified"=>"2007-12-05T19:39:55Z", "creator"=>{"userId"=>"127179"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0001159", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2007-12-05T20:07:52Z", "replies"=>[{"type"=>"REPLY", "parentID"=>35577, "annotationUri"=>"info:doi/10.1371/reply/6f7bb924-8b97-4b79-95ac-0cec92e34fd3", "title"=>"RE: RE: RE: Referee Comments: Referee 3 (Benedicte Lafay)", "body"=>"EDIT: it seems obvious that author's responses should be added as well", "isRemoved"=>false, "created"=>"2007-12-05T20:07:52Z", "lastModified"=>"2007-12-05T20:07:52Z", "creator"=>{"userId"=>"127179"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0001159", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2007-12-05T20:07:52Z", "replies"=>[]}]}]}]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/3cf1e2eb-e279-4b30-94b6-a82e55a36fe8", "title"=>"Citation update", "body"=>"Jay M, Cooley M, Carychao D, Wiscomb GW, Sweitzer RA, Crawford-Miksza L, Farrar JA, Lau DK, O’Connell J, Millington A, Asmundson RV, Atwill ER, and Mandrell RE. 2007. Escherichia coli O157:H7 in feral swine near spinach fields and cattle, central California coast. Emerging Infectious Diseases. 13:1908-1911.", "highlightedText"=>"''Jay MT, Cooley MB, Carychao D, Wiscomb GW, Sweitzer RA, et al. (2007) Escherichia coli O157:H7 in feral swine near spinach fields and cattle, central California coast''\nhttp://plosone.org/article/info:doi/10.1371/journal.pone.0001159#article1.body1.sec2.sec2.p1", "isRemoved"=>false, "created"=>"2007-11-27T00:07:58Z", "lastModified"=>"2007-11-27T00:07:58Z", "creator"=>{"userId"=>"9445"}, "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0001159", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2007-11-27T00:07:58Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/6a1f1047-dbb2-4d71-b793-70dfc7dd97e3", "title"=>"Citation update", "body"=>"Jay M, Cooley M, Carychao D, Wiscomb GW, Sweitzer RA, Crawford-Miksza L, Farrar JA, Lau DK, O’Connell J, Millington A, Asmundson RV, Atwill ER, and Mandrell RE. 2007. Escherichia coli O157:H7 in feral swine near spinach fields and cattle, central California coast. Emerging Infectious Diseases. 13:1908-1911.", "highlightedText"=>"''Jay MT, Cooley MB, Carychao D, Wiscomb GW, Sweitzer RA, et al. (2007) Escherichia coli O157:H7 in feral swine near spinach fields and cattle, central California coast, Emerg. Infect. Dis. (Accepted for publication)''\nhttp://plosone.org/article/info:doi/10.1371/journal.pone.0001159#article1.body1.sec4.sec3.p6", "isRemoved"=>false, "created"=>"2007-11-27T00:08:51Z", "lastModified"=>"2007-11-27T00:08:51Z", "creator"=>{"userId"=>"9445"}, "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0001159", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2007-11-27T00:08:51Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/a83cb19d-b515-4036-9a05-70f02f5d9f83", "title"=>"Referee Comments: Referee 2 (Brian D Wade)", "body"=>"Reviewer 2's Review\n\n-----\n\nThe manuscript submitted by Cooley et al. for publication in PLoS ONE entitled, \"Molecular typing of Escherichia coli O157:H7 isolated from a major produce production region and human strains causing outbreak and sporadic illness\", compares the efficacy of two molecular genotyping techniques, PFGE and MLVA, to differentiate subpopulations of Escherichia coli O157:H7 (\"EcO157\"). Food safety scientists employ these two techniques to determine relatedness among subpopulations of food-borne pathogens. Currently, they use PFGE more often than MLVA for such purposes, due primarily to the availability of a database of pathogen PFGE profiles which they can query for matches with ones of their environmental and clinical isolates. Here, the authors isolated EcO157 subpopulations from various types of samples collected from agricultural regions implicated in previous leafy green vegetable-borne EcO157 outbreaks. They then utilized PFGE and MLVA to genotypically profile these environmental isolates and human clinical EcO157 isolates cultivated by others during various food-borne EcO157 outbreaks. The authors used these profiles to compare the two techniques and to examine the relatedness of subpopulations isolated from different locales and from the same locales sampled during different months of the year. The latter was done in an attempt to identify some potential environmental factors underlying the aforementioned leafy green vegetable-borne EcO157 outbreaks and to narrow the possible sources of these outbreaks. The authors conclude, as have others in previous publications, that MLVA is an effective technique for genotyping environmental and clinical isolates of EcO157. Regarding the discriminatory power of each technique, they report that MLVA profiles generally permitted them to better discriminate isolates than did PFGE ones. The ability of MLVA to discern closely related EcO157 isolates has also been documented by others in previous publications. This apparent advantage of MLVA over PFGE when genotyping EcO157 isolates should be noted by the food safety community. The use of these techniques by the authors also aided them in narrowing the possible sources of the aforementioned leafy green vegetable-borne EcO157 outbreaks to certain farm/ranch sites. They also conclude that such outbreaks are dynamic and complex processes involving temporal and spatial aspects yet to be fully understood. Results presented by the authors here will likely appeal to food safety scientists and perhaps to professionals in other public health fields. As stated by the authors, MLVA \"is being evaluated by [the] CDC as a potential next generation typing system\". \n\nBelow are methodological suggestions and an idea for possible future work, they are not intended for inclusion in the manuscript reviewed here: \n\nThe following are methodological suggestions for the authors regarding two parts of their isolation procedure, that, if implemented, could potentially surmount the specific problems and limitations they mention. First, concerning the growth of non-EcO157 microbes on the selective plates (page 26, line 1), consider including tellurite and novobiocin in the TSB during the enrichment step, as this may reduce the number of non-target microbes on the these plates. Second, regarding the preclusion of determining the concentration of EcO157 in water samples due to the enrichment step (page 26, line 22), consider passing the samples through a 0.2 micron filter to collect the cells, resuspend them in a greatly reduced volume, and then plate portions of this concentrate directly onto the selective plates. Chemical (e.g., addition of a nonionic detergent such as Tween 80) and/or physical (e.g., brief sonication) treatment of the samples before filtering them may aid in detaching cells adhering to sediments. Alternatively, Neogen Corporation (www.neogen.com) offers an EcO157-specific kit (ISO-GRID) which essentially does this (Payne and Kroll, 1991, Trends in Food Science and Technology 2: 315-319), and probably more easily and rapidly than the just described method. This procedure may eliminate the need to enrich the dilute water samples and thus allow the authors to determine the concentration of EcO157 in the water samples. For a review of methods for separating bacteria from food matrices, of which the authors could possibly adapt to their sample types, see Stevens and Jaykus (2004, Critical Reviews in Microbiology 30: 7-24). \n\nThe following is an idea for possible future work. If the authors have not already done so, perhaps they may consider PCR amplifying directly from the environmental samples (whole community DNA extracts), if frozen portions of them still exist, the EcO157 virulence genes that they amplified from the environmental isolates (rfbE, fliC, stx1, stx2, eae, hly). There is at least one pitfall to doing this, most of these genes can be found in other strains of E. coli and thus are not unique to EcO157, so PCR products from environmental samples will likely contain some non-EcO157 amplicons. To overcome this, they may consider using the recently developed E. coli O157:H7-specific RQ3 primer set (Lin and Lin, 2007, Molecular and Cellular Probes 21: 182-189). Another possible primer set is RJD3/SF6 (Perelle et al., 2002, Journal of Applied Microbiology 93: 250-260). If the authors amplify these genes (former) and/or regions (latter two) from clinical isolates, environmental isolates, and directly from the environmental samples, phylogenetic comparisons of alleles from the former two may clarify relationships among the isolates, while analyses of the latter may further elucidate the temporal and spatial dynamics of EcO157 subpopulations in the environment, perhaps enhancing traceback investigations. Analyses of gene alleles comprising the PCR products from the environmental samples could include fingerprinting techniques such as Denaturing Gradient Gel Electrophoresis (DGGE), and subsequent sequencing of the separated alleles, and other allele separating and sequencing methods such as clone library construction. If the PCR products of the virulence genes they used to screen environmental isolates or the DNA extracts from these isolates still exist, part of what has just been outlined, multigene phylogenetic comparisons between the environmental isolates and clinical isolates, could be done with little further effort. The MLVA and PFGE derived relationships the authors established among the EcO157 isolates could serve as a guide to confine the proposed analyses. Doing so may afford the authors even better phylogenetic resolution of their isolates than MLVA profiles provided, a need they mention on page 30, line 19 and again on page 31, line 7. \n\n-----\n", "isRemoved"=>false, "created"=>"2007-11-30T18:12:22Z", "lastModified"=>"2007-11-30T18:12:22Z", "creator"=>{"userId"=>"80539"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0001159", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2007-11-30T18:12:22Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/c71a402e-7a83-4f6b-98ec-b4d96b0255ca", "title"=>"Corrected URL for CA surface water data from USGS", "body"=>"http://waterdata.usgs.gov/ca/nwis/sw", "highlightedText"=>"''http://waterdata/usgs.gov/ca''\nhttp://plosone.org/article/info:doi/10.1371/journal.pone.0001159#article1.body1.sec2.sec8.p1", "isRemoved"=>false, "created"=>"2008-01-09T05:56:20Z", "lastModified"=>"2008-01-09T05:56:20Z", "creator"=>{"userId"=>"9445"}, "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0001159", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2008-01-09T05:56:20Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/5f1b4aad-ed15-42dd-a5f5-412a0e4989ae", "title"=>"F/R C information", "body"=>"Multiple strains of EcO157 were isolated from four soil samples obtained near cattle fecal samples at F/R C, as noted in the CDHS-FDA report of the spinach outbreak investigation (see reference 9). Of the 8 strains isolated and selected for further study, all were identical, or highly related, to one another by MLVA (3 different MLVA types); PFGE profiles were unrelated to the outbreak strains. ", "highlightedText"=>"''.''\nhttp://plosone.org/article/info:doi/10.1371/journal.pone.0001159#article1.body1.sec3.sec3.p1", "isRemoved"=>false, "created"=>"2008-01-09T06:22:23Z", "lastModified"=>"2008-01-09T06:22:23Z", "creator"=>{"userId"=>"9445"}, "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0001159", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2008-01-09T06:22:23Z", "replies"=>[]}

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• {"month"=>"3", "year"=>"2016", "pdf_views"=>"6", "xml_views"=>"2", "html_views"=>"82"}
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• {"month"=>"5", "year"=>"2016", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"42"}
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• {"month"=>"9", "year"=>"2016", "pdf_views"=>"23", "xml_views"=>"0", "html_views"=>"60"}
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• {"month"=>"3", "year"=>"2021", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"36"}
• {"month"=>"4", "year"=>"2021", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"10"}

Figshare

• {"files"=>["https://ndownloader.figshare.com/files/942212"], "description"=>"<p>Blue lines on the map are waterways.</p>", "links"=>[], "tags"=>["salinas", "san", "juan", "valleys", "positions", "implicated", "traceback", "investigations", "spinach", "outbreak"], "article_id"=>612601, "categories"=>["Microbiology"], "users"=>["Michael Cooley", "Diana Carychao", "Leta Crawford-Miksza", "Michele T. Jay", "Carol Myers", "Christopher Rose", "Christine Keys", "Jeff Farrar", "Robert E. Mandrell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001159.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_Salinas_and_San_Juan_valleys_showing_the_positions_A_8211_D_of_F_Rs_implicated_in_the_traceback_investigations_associated_with_the_baby_spinach_outbreak_2006_/612601", "title"=>"Map of Salinas and San Juan valleys showing the positions (A–D) of F/Rs implicated in the traceback investigations associated with the baby spinach outbreak 2006.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-14 00:43:21"}
• {"files"=>["https://ndownloader.figshare.com/files/942920"], "description"=>"a<p>See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone.0001159.s001\" target=\"_blank\">Table S1</a> for MLVA data and source information.</p>b<p><i>XbaI</i> profile in PulseNet database (last checked Dec, 2006) matching designated strain. <i>Xba</i>I patterns EXHX01.3535, EXHX01.3536, EXHX01.3537 were new to the PulseNet database at the time of submission.</p>c<p>Frequency of this <i>XbaI</i> profile in PulseNet database.</p>d<p><i>BlnI</i> profile in PulseNet database (last checked Dec, 2006) matching designated strain. <i>Bln</i>I patterns EXHA26.1395, EXHA26.1411, EXHA26.1412 are new to the PulseNet database.</p>e<p>Clusters of illnesses identified from PFGE profiles submitted to PulseNet as <i>XbaI</i> profile, or both <i>XbaI</i> and <i>BlnI</i> profiles. Designation is by state (2 letter abbreviation):month-2 digit year; Multi, multiple states.</p>f<p>RM5038 and RM5037 were isolated from the same sample of feces; MLVAs 15 and 16 differ by one TR only in locus 4.</p>g<p><i>XbaI</i>-<i>BlnI</i> profile EXHX01.0047-EXHA26.0015 represents>6% of the PulseNet database (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone-0001159-t002\" target=\"_blank\">Table 2</a>).</p>h<p>One band difference between the profile for this strain and the <i>BlnI</i> PulseNet profile designated.</p>I<p>Major MLVA type for human clinical strains associated with the spinach outbreak.</p>", "links"=>[], "tags"=>["mlva", "types", "strains", "pfge"], "article_id"=>613314, "categories"=>["Microbiology"], "users"=>["Michael Cooley", "Diana Carychao", "Leta Crawford-Miksza", "Michele T. Jay", "Carol Myers", "Christopher Rose", "Christine Keys", "Jeff Farrar", "Robert E. Mandrell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001159.t001", "stats"=>{"downloads"=>6, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_MLVA_types_of_Ec_O157_environmental_strains_with_PFGE_profile_designations_/613314", "title"=>"Comparison of MLVA types of <i>Ec</i>O157 environmental strains with PFGE profile designations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-11-14 00:55:14"}
• {"files"=>["https://ndownloader.figshare.com/files/942603"], "description"=>"<p>The size of the circles indicate relative number of isolates of each MLVA type (numbers in the circles) recovered from the environment. Those MLVA types shown with the smallest circles were isolated only once. Letters A–H indicate clusters (colored regions) in which types differ at only 1 of the 10 MLVA loci from a neighbor.</p>", "links"=>[], "tags"=>["phylogenetic", "relationships", "92", "mlva"], "article_id"=>613007, "categories"=>["Microbiology"], "users"=>["Michael Cooley", "Diana Carychao", "Leta Crawford-Miksza", "Michele T. Jay", "Carol Myers", "Christopher Rose", "Christine Keys", "Jeff Farrar", "Robert E. Mandrell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001159.g007", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_comparison_of_the_phylogenetic_relationships_among_92_MLVA_types_/613007", "title"=>"A comparison of the phylogenetic relationships among 92 MLVA types.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-14 00:50:07"}
• {"files"=>["https://ndownloader.figshare.com/files/941964"], "description"=>"<p>Linear regression R² values are indicated. EcO157 incidence is calculated as the fraction of the number of positive samples compared to the total samples obtained. The flow rate was obtained from data from the USGS sampling station #11152600 located at position D (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone-0001159-g001\" target=\"_blank\">Figure 1</a>). EcO157 incidence and generic <i>E. coli</i> concentration were determined with duplicate samples.</p>", "links"=>[], "tags"=>["generic", "incidence", "eco157", "gabilan", "creek"], "article_id"=>612366, "categories"=>["Microbiology"], "users"=>["Michael Cooley", "Diana Carychao", "Leta Crawford-Miksza", "Michele T. Jay", "Carol Myers", "Christopher Rose", "Christine Keys", "Jeff Farrar", "Robert E. Mandrell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001159.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_of_water_flow_the_concentration_of_generic_E_coli_and_the_incidence_of_EcO157_in_the_Gabilan_Creek_Salinas_CA_/612366", "title"=>"Correlation of water flow, the concentration of generic <i>E. coli</i>, and the incidence of EcO157 in the Gabilan Creek (Salinas, CA).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-14 00:39:26"}
• {"files"=>["https://ndownloader.figshare.com/files/941797"], "description"=>"<p>Farm A is marked as a black dot. The circle marked with “X” is coded by positions numbered clockwise 1 to 23 and representing the sampling dates show in the list below the circle. The approximate rainfall in cm for the 5 days prior to sampling is shown in the list. Dates indicated in red text indicate at least one EcO157 strain was isolated on that date. Circles on the map designated “A” through “V” correspond to the locations where samples were obtained; these are also listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone.0001159.s001\" target=\"_blank\">Table S1</a>. <u>Open</u> circles within the “Location circle” designate that no sample was obtained on that date; <u>blue</u> circles designate that a sample was obtained, but no EcO157 strain was isolated; and <u>red</u> circles designate that a sample was obtained, and at least one strain of EcO157 was isolated.</p>", "links"=>[], "tags"=>["ca"], "article_id"=>612203, "categories"=>["Microbiology"], "users"=>["Michael Cooley", "Diana Carychao", "Leta Crawford-Miksza", "Michele T. Jay", "Carol Myers", "Christopher Rose", "Christine Keys", "Jeff Farrar", "Robert E. Mandrell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001159.g001", "stats"=>{"downloads"=>3, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_Salinas_CA_region_showing_sample_locations_/612203", "title"=>"Map of Salinas, CA region showing sample locations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-14 00:36:43"}
• {"files"=>["https://ndownloader.figshare.com/files/942486"], "description"=>"<p>The change in stream elevation is indicated as a function of the distance from a corral with cattle. Sampling positions are indicated by: ⧫; different MLVA types isolated from each location are indicated. The inset shows a phylogenetic tree designating the relationship among the MLVA types isolated in this study (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone-0001159-g007\" target=\"_blank\">Figure 7</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone.0001159.s001\" target=\"_blank\">Table S1</a> for more detail).</p>", "links"=>[], "tags"=>["persistence", "eco157", "elevated"], "article_id"=>612892, "categories"=>["Microbiology"], "users"=>["Michael Cooley", "Diana Carychao", "Leta Crawford-Miksza", "Michele T. Jay", "Carol Myers", "Christopher Rose", "Christine Keys", "Jeff Farrar", "Robert E. Mandrell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001159.g006", "stats"=>{"downloads"=>5, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_persistence_and_transport_of_EcO157_in_a_stream_in_an_elevated_area_near_a_point_source_/612892", "title"=>"The persistence and transport of EcO157 in a stream in an elevated area near a point source.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-14 00:48:12"}
• {"files"=>["https://ndownloader.figshare.com/files/942843"], "description"=>"<p>Taxa are designated as RMXXXX (##), where RMXXXX is the isolate name and ## is an arbitrary number assigned to that MLVA type [refer to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone.0001159.s001\" target=\"_blank\">Table S1</a>]. Taxa in red type are identical MLVA types differentiated by PFGE. Colored clusters (labeled B–H) are similar to labeled MLVA clusters in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone-0001159-g007\" target=\"_blank\">Figure 7</a>.</p>", "links"=>[], "tags"=>["isolates", "pfge"], "article_id"=>613241, "categories"=>["Microbiology"], "users"=>["Michael Cooley", "Diana Carychao", "Leta Crawford-Miksza", "Michele T. Jay", "Carol Myers", "Christopher Rose", "Christine Keys", "Jeff Farrar", "Robert E. Mandrell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001159.g008", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dendrogram_of_selected_isolates_from_PFGE_data_/613241", "title"=>"Dendrogram of selected isolates from PFGE data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-14 00:54:01"}
• {"files"=>["https://ndownloader.figshare.com/files/942961"], "description"=>"a<p>PulseNet patterns designated as described previously <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone.0001159-Ribot1\" target=\"_blank\">[35]</a>.</p>b<p>Source of isolate (state).</p>c<p>The number of TR are listed in the order noted in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone.0001159.s001\" target=\"_blank\">Table S1</a>.</p>d<p>Data for strains designated VA_01-577 and F7410 are from a previous study comparing PFGE and MLVA data <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone.0001159-HyytiaTrees1\" target=\"_blank\">[39]</a>. X, not determined for these two strains.</p>", "links"=>[], "tags"=>["differences", "strains", "pulsenet", "pfge"], "article_id"=>613349, "categories"=>["Microbiology"], "users"=>["Michael Cooley", "Diana Carychao", "Leta Crawford-Miksza", "Michele T. Jay", "Carol Myers", "Christopher Rose", "Christine Keys", "Jeff Farrar", "Robert E. Mandrell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001159.t002", "stats"=>{"downloads"=>6, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MLVA_differences_between_strains_of_the_common_PulseNet_PFGE_profile_EXHX01_0047_EXHA26_0015_a_/613349", "title"=>"MLVA differences between strains of the common PulseNet PFGE profile, EXHX01.0047-EXHA26.0015^a.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-11-14 00:55:49"}
• {"files"=>["https://ndownloader.figshare.com/files/463854"], "description"=>"<div><p>Fresh vegetables have become associated with outbreaks caused by <em>Escherichia coli</em> O157:H7 (EcO157). Between 1995–2006, 22 produce outbreaks were documented in the United States, with nearly half traced to lettuce or spinach grown in California. Outbreaks between 2002 and 2006 induced investigations of possible sources of pre-harvest contamination on implicated farms in the Salinas and San Juan valleys of California, and a survey of the Salinas watershed. EcO157 was isolated at least once from 15 of 22 different watershed sites over a 19 month period. The incidence of EcO157 increased significantly when heavy rain caused an increased flow rate in the rivers. Approximately 1000 EcO157 isolates obtained from cultures of>100 individual samples were typed using <u>M</u>ulti-<u>L</u>ocus <u>V</u>ariable-number-tandem-repeat <u>A</u>nalysis (MLVA) to assist in identifying potential fate and transport of EcO157 in this region. A subset of these environmental isolates were typed by Pulse Field Gel Electrophoresis (PFGE) in order to make comparisons with human clinical isolates associated with outbreak and sporadic illness. Recurrence of identical and closely related EcO157 strains from specific locations in the Salinas and San Juan valleys suggests that transport of the pathogen is usually restricted. In a preliminary study, EcO157 was detected in water at multiple locations in a low-flow creek only within 135 meters of a point source. However, possible transport up to 32 km was detected during periods of higher water flow associated with flooding. During the 2006 baby spinach outbreak investigation, transport was also detected where water was unlikely to be involved. These results indicate that contamination of the environment is a dynamic process involving multiple sources and methods of transport. Intensive studies of the sources, incidence, fate and transport of EcO157 near produce production are required to determine the mechanisms of pre-harvest contamination and potential risks for human illness.</p></div>", "links"=>[], "tags"=>["incidence", "tracking", "california"], "article_id"=>151428, "categories"=>["Microbiology"], "users"=>["Michael Cooley", "Diana Carychao", "Leta Crawford-Miksza", "Michele T. Jay", "Carol Myers", "Christopher Rose", "Christine Keys", "Jeff Farrar", "Robert E. Mandrell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001159", "stats"=>{"downloads"=>11, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Incidence_and_Tracking_of_Escherichia_coli_O157_H7_in_a_Major_Produce_Production_Region_in_California/151428", "title"=>"Incidence and Tracking of <em>Escherichia coli</em> O157:H7 in a Major Produce Production Region in California", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-11-14 00:23:48"}
• {"files"=>["https://ndownloader.figshare.com/files/942080"], "description"=>"<p>Sample locations refer to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone-0001159-g001\" target=\"_blank\">Figure 1</a>. Red and black dots indicate isolation or non-isolation of EcO157 for the corresponding duplicate water samples, respectively.</p>", "links"=>[], "tags"=>["generic", "salinas"], "article_id"=>612481, "categories"=>["Microbiology"], "users"=>["Michael Cooley", "Diana Carychao", "Leta Crawford-Miksza", "Michele T. Jay", "Carol Myers", "Christopher Rose", "Christine Keys", "Jeff Farrar", "Robert E. Mandrell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001159.g003", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concentration_of_generic_E_coli_in_the_Salinas_watershed_/612481", "title"=>"Concentration of generic <i>E. coli</i> in the Salinas watershed.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-14 00:41:21"}
• {"files"=>["https://ndownloader.figshare.com/files/942398"], "description"=>"<p>Location designations refer to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001159#pone-0001159-g001\" target=\"_blank\">Figure 1</a> and are separated by horizontal lines in (A) to indicate separate waterways. Black and red dots indicate isolation of the MLVA type at the indicated location or date. Red dots indicate that differences were detected between that isolate and the other isolates of that MLVA type by PFGE.</p>", "links"=>[], "tags"=>["types", "compared", "salinas", "watershed"], "article_id"=>612799, "categories"=>["Microbiology"], "users"=>["Michael Cooley", "Diana Carychao", "Leta Crawford-Miksza", "Michele T. Jay", "Carol Myers", "Christopher Rose", "Christine Keys", "Jeff Farrar", "Robert E. Mandrell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001159.g005", "stats"=>{"downloads"=>10, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MLVA_types_compared_to_A_Salinas_watershed_location_or_B_sample_date_/612799", "title"=>"MLVA types compared to (A) Salinas watershed location or (B) sample date.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-11-14 00:46:39"}

PMC Usage Stats | Further Information

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• {"unique-ip"=>"21", "full-text"=>"27", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
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• {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}
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• {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"12"}
• {"unique-ip"=>"14", "full-text"=>"19", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2021", "month"=>"1"}
• {"unique-ip"=>"8", "full-text"=>"14", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2021", "month"=>"2"}

Relative Metric

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F1000Prime