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Mohsen JJ, Mohsen MG, Jiang K, Landajuela A, Quinto L, Isaacs FJ, Karatekin E, Slavoff SA. Cellular function of the GndA small open reading frame-encoded polypeptide during heat shock. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.29.601336. [PMID: 38979229 PMCID: PMC11230408 DOI: 10.1101/2024.06.29.601336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Over the past 15 years, hundreds of previously undiscovered bacterial small open reading frame (sORF)-encoded polypeptides (SEPs) of fewer than fifty amino acids have been identified, and biological functions have been ascribed to an increasing number of SEPs from intergenic regions and small RNAs. However, despite numbering in the dozens in Escherichia coli, and hundreds to thousands in humans, same-strand nested sORFs that overlap protein coding genes in alternative reading frames remain understudied. In order to provide insight into this enigmatic class of unannotated genes, we characterized GndA, a 36-amino acid, heat shock-regulated SEP encoded within the +2 reading frame of the gnd gene in E. coli K-12 MG1655. We show that GndA pulls down components of respiratory complex I (RCI) and is required for proper localization of a RCI subunit during heat shock. At high temperature GndA deletion (ΔGndA) cells exhibit perturbations in cell growth, NADH+/NAD ratio, and expression of a number of genes including several associated with oxidative stress. These findings suggest that GndA may function in maintenance of homeostasis during heat shock. Characterization of GndA therefore supports the nascent but growing consensus that functional, overlapping genes occur in genomes from viruses to humans.
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Affiliation(s)
- Jessica J. Mohsen
- Department of Chemistry, Yale University, New Haven, CT 06511
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516
| | - Michael G. Mohsen
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06511
| | - Kevin Jiang
- Department of Chemistry, Yale University, New Haven, CT 06511
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516
| | - Ane Landajuela
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06510
- Nanobiology Institute, Yale University, West Haven, CT 06516
| | - Laura Quinto
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
- Systems Biology Institute, Yale University, West Haven, CT 06516
| | - Farren J. Isaacs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
- Systems Biology Institute, Yale University, West Haven, CT 06516
| | - Erdem Karatekin
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06510
- Nanobiology Institute, Yale University, West Haven, CT 06516
- Wu Tsai Institute, Yale University, New Haven, CT 06511
- Université de Paris, Saints-Pères Paris Institute for the Neurosciences (SPPIN), Centre National de la Recherche Scientifique (CNRS), 75006 Paris, France
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06511
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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Moinet M, Rogers L, Biggs P, Marshall J, Muirhead R, Devane M, Stott R, Cookson A. High-resolution genomic analysis to investigate the impact of the invasive brushtail possum (Trichosurus vulpecula) and other wildlife on microbial water quality assessments. PLoS One 2024; 19:e0295529. [PMID: 38236841 PMCID: PMC10796070 DOI: 10.1371/journal.pone.0295529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/21/2023] [Indexed: 01/22/2024] Open
Abstract
Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been thoroughly studied as a source of fecal contamination in freshwater. To investigate their potential role, Escherichia spp. isolates (n = 420) were recovered from possum gut contents and feces and were compared to those from water, soil, sediment, and periphyton samples, and from birds and other introduced mammals collected within the Mākirikiri Reserve, Dannevirke. Isolates were characterized using E. coli-specific real-time PCR targeting the uidA gene, Sanger sequencing of a partial gnd PCR product to generate a gnd sequence type (gST), and for 101 isolates, whole genome sequencing. Escherichia populations from 106 animal and environmental sample enrichments were analyzed using gnd metabarcoding. The alpha diversity of Escherichia gSTs was significantly lower in possums and animals compared with aquatic environmental samples, and some gSTs were shared between sample types, e.g., gST535 (in 85% of samples) and gST258 (71%). Forty percent of isolates gnd-typed and 75% of reads obtained by metabarcoding had gSTs shared between possums, other animals, and the environment. Core-genome single nucleotide polymorphism (SNP) analysis showed limited variation between several animal and environmental isolates (<10 SNPs). Our data show at an unprecedented scale that Escherichia clones are shared between possums, other wildlife, water, and the wider environment. These findings support the potential role of possums as contributors to fecal contamination in Aotearoa/New Zealand freshwater. Our study deepens the current knowledge of Escherichia populations in under-sampled wildlife. It presents a successful application of high-resolution genomic methods for fecal source tracking, thereby broadening the analytical toolbox available to water quality managers. Phylogenetic analysis of isolates and profiling of Escherichia populations provided useful information on the source(s) of fecal contamination and suggest that comprehensive invasive species management strategies may assist in restoring not only ecosystem health but also water health where microbial water quality is compromised.
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Affiliation(s)
- Marie Moinet
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
| | - Lynn Rogers
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
| | - Patrick Biggs
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Jonathan Marshall
- School of Mathematical and Computational Sciences, Massey University, Palmerston North, New Zealand
| | | | - Megan Devane
- Institute of Environmental Science and Research Ltd. (ESR), Christchurch, New Zealand
| | - Rebecca Stott
- National Institute of Water and Atmospheric Research (NIWA), Hamilton, New Zealand
| | - Adrian Cookson
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
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Manage DP, Lauzon J, Pilarski LM, Pilarski PM, McMullen LM. Comparison of a Miniaturized Cassette PCR System with a Commercially Available Platform for Detecting Escherichia coli in Beef Carcass Swabs. MICROMACHINES 2021; 12:mi12080959. [PMID: 34442581 PMCID: PMC8398369 DOI: 10.3390/mi12080959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/07/2021] [Accepted: 08/08/2021] [Indexed: 12/05/2022]
Abstract
Detection sensitivity of cassette PCR was compared with a commercial BAX® PCR system for detection of eae and stx genes in Escherichia coli from 806 beef carcass swabs. Cassette PCR detects multiple genetic markers on multiple samples using PCR and melt curve analysis. Conventional PCR served as a gold standard. Overall, for positive and negative concordance, cassette PCR was 98.6% concordant with conventional PCR, and BAX PCR was 65.4% concordant. Of 806 beef carcass swabs, 339 by cassette PCR and 84 by BAX PCR harbored eae + stx+E. coli. For BAX PCR reactions, 84% of eae+ swabs, 79% of stx+ swabs, and 86% of eae + stx+ swabs were also detected by cassette PCR. For cassette PCR reactions, 457 swabs were eae+ with only 117 scored as eae+ using BAX PCR for 26% positive concordance. For stx primers, cassette PCR scored 480 samples as stx+ but only 215 samples were stx+ by BAX PCR, giving 45% positive concordance. Importantly, cassette PCR scored 339 swabs as harboring eae + stx+ E. coli, but BAX PCR detected only 71 positives giving only 21% positive concordance, with many false negatives. Cassette PCR is a highly sensitive method for detection of STEC genes in E. coli found in carcass swabs.
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Affiliation(s)
- Dammika P. Manage
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Ag/For Centre, Edmonton, AB T6G 2P5, Canada; (D.P.M.); (J.L.)
| | - Jana Lauzon
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Ag/For Centre, Edmonton, AB T6G 2P5, Canada; (D.P.M.); (J.L.)
| | - Linda M. Pilarski
- Department of Oncology, University of Alberta and Cross Cancer Institute, 11560 University Ave, Edmonton, AB T6G 1Z2, Canada;
| | - Patrick M. Pilarski
- 5-005 Katz Group Centre for Pharmacy and Health Research, Department of Medicine, Division of Physical Medicine & Rehabilitation, University of Alberta, Edmonton, AB T6G 2E1, Canada;
| | - Lynn M. McMullen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Ag/For Centre, Edmonton, AB T6G 2P5, Canada; (D.P.M.); (J.L.)
- Correspondence:
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Rosario AILS, Castro VS, Santos LF, Lisboa RC, Vallim DC, Silva MCA, Figueiredo EES, Conte-Junior CA, Costa MP. Shiga toxin-producing Escherichia coli isolated from pasteurized dairy products from Bahia, Brazil. J Dairy Sci 2021; 104:6535-6547. [PMID: 33741165 DOI: 10.3168/jds.2020-19511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 01/28/2021] [Indexed: 11/19/2022]
Abstract
The presence of pathogenic Shiga toxin-producing Escherichia coli (STEC) in dairy products represents a public health concern because of its ability to produce the toxins Stx1 and Stx2, which cause intestinal diseases. Monitoring the stages of milk production and checking dairy products for contamination are crucial steps to ensure dairy safety. This study aimed to report the occurrence of thermotolerant coliforms, E. coli, and STEC strains in pasteurized dairy products and to evaluate the antibiotic resistance profiles, serotypes, and characterizations of the STEC isolates by pulsed-field gel electrophoresis. We obtained a total of 138 pasteurized dairy products from 15 processing plants in Bahia, Brazil, to examine coliforms, E. coli, and STEC strains. We found that 43% of samples (59/138) contained thermotolerant coliforms, and 30% (42/138) did not comply with Brazilian regulations. Overall, 6% (9/138) were positive for E. coli and 4% (5/138) were positive for STEC. We recovered 9 STEC isolates from pasteurized cream (2/9), Minas Padrão cheese (2/9), Minas Frescal cheese (4/9), and ricotta (1/9). All isolates were stx2-positive, and 2 were eae-positive. All isolates were negative for the "big 6" STEC serogroups, belonging instead to serotypes ONT:HNT, ONT:H12, O148:H-, OR:H40, OR:HNT, and O148:HNT. Pulsed-field gel electrophoresis revealed 100% genetic similarity among 3 isolates from 2 different samples produced in the same production facility, which may suggest cross-contamination. As well, we found isolates that were 98% similar but in samples produced in different production facilities, suggesting a mutual source of contamination or a circulating strain. Two STEC strains exhibited resistance to streptomycin. Although the isolates presented a low resistance profile and no strain belonged to the "big 6" pathogenic group, the circulation of stx2-positive STEC strains in ready-to-eat products highlights the importance of epidemiological surveillance inside the Brazilian dairy chain.
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Affiliation(s)
- Anisio I L S Rosario
- Graduate Program in Food Science (PGAli), Faculty of Pharmacy, Federal University of Bahia (UFBA), Salvador, BA, 40170-115, Brazil; Laboratório de Inspeção e Tecnologia de Leite e Derivados (LAITLACTEOS), Federal University of Bahia (UFBA), Salvador, BA, 40170-110, Brazil; Center for Food Analysis (NAL), Technological Development Support, Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil
| | - Vinicius S Castro
- Center for Food Analysis (NAL), Technological Development Support, Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil; Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-909, Brazil
| | - Luis F Santos
- Núcleo de Doenças Entéricas e Infecções por Patógenos Especiais, Adolfo Lutz Institute, São Paulo, SP, 01246-902, Brazil
| | - Rodrigo C Lisboa
- Laboratório de Zoonoses Bacterianas, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, 21040-900, Brazil
| | - Deyse C Vallim
- Laboratório de Zoonoses Bacterianas, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, 21040-900, Brazil
| | - Maurício C A Silva
- Laboratório de Inspeção e Tecnologia de Carnes e Derivados (LABCARNE), Federal University of Bahia (UFBA), Salvador, BA, 40170-110, Brazil
| | - Eduardo E S Figueiredo
- Laboratório de Microbiologia Molecular de Alimentos, Federal University of Mato Grosso (UFMT), Cuiabá, MT, 78060-900, Brazil
| | - Carlos A Conte-Junior
- Center for Food Analysis (NAL), Technological Development Support, Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil; Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-909, Brazil; Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-909, Brazil; Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói, RJ, 24230-340, Brazil; Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, 21040-900, Brazil; Graduate Program in Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-909, Brazil
| | - Marion P Costa
- Graduate Program in Food Science (PGAli), Faculty of Pharmacy, Federal University of Bahia (UFBA), Salvador, BA, 40170-115, Brazil; Laboratório de Inspeção e Tecnologia de Leite e Derivados (LAITLACTEOS), Federal University of Bahia (UFBA), Salvador, BA, 40170-110, Brazil.
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Smith AM, Tau NP, Kalule BJ, Nicol MP, McCulloch M, Jacobs CA, McCarthy KM, Ismail A, Allam M, Kleynhans J. Shiga toxin-producing Escherichia coli O26:H11 associated with a cluster of haemolytic uraemic syndrome cases in South Africa, 2017. Access Microbiol 2019; 1:e000061. [PMID: 32974561 PMCID: PMC7472548 DOI: 10.1099/acmi.0.000061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/22/2019] [Indexed: 01/17/2023] Open
Abstract
INTRODUCTION Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens that may cause diarrhoeal outbreaks and occasionally are associated with haemolytic-uraemic syndrome (HUS). We report on STEC O26:H11 associated with a cluster of four HUS cases in South Africa in 2017. METHODOLOGY All case-patients were female and aged 5 years and under. Standard microbiological tests were performed for culture and identification of STEC from specimens (human stool and food samples). Further analysis of genomic DNA extracted from bacterial cultures and specimens included PCR for specific virulence genes, whole-genome sequencing and shotgun metagenomic sequencing. RESULTS For 2/4 cases, stool specimens revealed STEC O26:H11 containing eae, stx2a and stx2b virulence genes. All food samples were found to be negative for STEC. No epidemiological links could be established between the HUS cases. Dried meat products were the leading food item suspected to be the vehicle of transmission for these cases, as 3/4 case-patients reported they had eaten this. However, testing of dried meat products could not confirm this. CONCLUSION Since STEC infection does not always lead to severe symptoms, it is possible that many more cases were associated with this cluster and largely went unrecognized.
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Affiliation(s)
- Anthony M. Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nomsa P. Tau
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Bosco J. Kalule
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P. Nicol
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Mignon McCulloch
- Red Cross Children’s Hospital, University of Cape Town, Cape Town, South Africa
| | - Charlene A. Jacobs
- Communicable Disease Control, Department of Health, Cape Town, South Africa
| | - Kerrigan M. McCarthy
- Division of Public Health Surveillance and Response, NICD, NHLS, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, NICD, NHLS, Johannesburg, South Africa
| | - Mushal Allam
- Sequencing Core Facility, NICD, NHLS, Johannesburg, South Africa
| | - Jackie Kleynhans
- South African Field Epidemiology Training Programme, NICD, NHLS, Johannesburg, South Africa
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Triplett OA, Xuan J, Foley S, Nayak R, Tolleson WH. Immunomagnetic Capture of Big Six Shiga Toxin-Producing Escherichia coli Strains in Apple Juice with Detection by Multiplex Real-Time PCR Eliminates Interference from the Food Matrix. J Food Prot 2019; 82:1512-1523. [PMID: 31414899 DOI: 10.4315/0362-028x.jfp-19-134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Having reliable methods for detecting Shiga toxin-producing Escherichia coli (STEC) in foods is an important food safety goal. The majority of STEC outbreaks have involved either the O157:H7 serotype or one of six non-O157 serogroups, O26, O45, O103, O111, O121, and O145, termed "The Big Six." We have compared detection by PCR of the Shiga toxin genes stx1a and stx2a from STEC bacteria isolated from unclarified apple juice by simple centrifugation with the use of an immunocapture technique to minimize contaminants (such as pectin and polyphenols that may copurify with DNA) that may interfere with DNA amplification efficiencies and limit sensitivity. An internal control for successful immunocapture, DNA extraction, and PCR amplification was generated by introducing the pmRaspberry plasmid into an stx null strain, yielding an E. coli O45 pmRaspberry derivative that can be added to food samples directly. Using serial dilutions of a representative Big Six STEC in apple juice, our immunocapture method resulted in a 50% probability of detection value of 3.34, 2.25, and 4.25 CFU for detection by multiplex real-time PCR, growth on solid agar, and multiplex endpoint PCR, respectively. The time to result was 6.5 h, 9.5 h, and 1.5 days for immunocapture of Big Six STECs and detection by multiplex real-time PCR, endpoint PCR, and growth on solid agar, respectively. A set of 52 Big Six STEC isolates and 30 non-Big Six STEC strains was used to establish the inclusivity and exclusivity of the method. Finally, the ability to detect Big Six STEC contamination reliably was confirmed at 4.5 and 45 CFU/25-mL portions of refrigerated apple juice.
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Affiliation(s)
- Odbert A Triplett
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
| | - Jiekun Xuan
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
| | - Steven Foley
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
| | - Rajesh Nayak
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
| | - William H Tolleson
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
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Manage DP, Lauzon J, Jones CM, Ward PJ, Pilarski LM, Pilarski PM, McMullen LM. Detection of pathogenic Escherichia coli on potentially contaminated beef carcasses using cassette PCR and conventional PCR. BMC Microbiol 2019; 19:175. [PMID: 31362696 PMCID: PMC6668150 DOI: 10.1186/s12866-019-1541-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 07/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over a one year period, swabs of 820 beef carcasses were tested for the presence of Shiga toxin-producing Escherichia coli by performing Polymerase Chain Reaction (PCR) in a novel technology termed "cassette PCR", in comparison to conventional liquid PCR. Cassette PCR is inexpensive and ready-to-use. The operator need only add the sample and press "go". Cassette PCR can simultaneously test multiple samples for multiple targets. Carcass swab samples were first tested for the presence of STEC genes (O157, eae, stx1 and stx2). Samples were considered to be pathogenic if positive for eae plus stx1 and/or stx2. For samples scored as pathogenic, further testing screened for 6 additional high frequency O-antigens (O26, O45, O103, O111, O121, and O145). RESULTS Of the 820 samples, 41% were pathogenic and 30% were O157 positive. Of these, 19% of samples were positive for O157 and carried potentially pathogenic E. coli (eae plus stx1 and/or stx2). Of all samples identified as carrying pathogenic E. coli, 18.9, 38.8, 41.4, 0, 36.1, and 4.1% respectively were positive for O26, O45, O103, O111, O121, and O145. To validate cassette PCR testing, conventional PCR using STEC primers was performed on each of the 820 samples. Only 148 of 3280 cassette PCR tests were discordant with conventional PCR results. However, further fractional testing showed that 110 of these 148 PCRs reflected low numbers of E. coli in the enrichment broth and could be explained as due to Poisson limiting dilution of the template, affecting both cassette PCR and conventional PCR. Of the remaining 38 discordant tests, 27 initial capillary PCRs and 10 initial conventional tests were nominally discordant between cassette and conventional PCR, perhaps reflecting human/technical error on both sides of the comparison. CONCLUSIONS Contaminated beef carcass swabs were often complex, likely harboring more than one strain of pathogenic E. coli. Cassette PCR had 98.8% concordance with parallel conventional PCR for detection of STEC genes. This indicates that cassette PCR is highly reliable for detecting multiple pathogens in beef carcass swabs from processing plants.
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Affiliation(s)
- Dammika P Manage
- Department of Oncology, University of Alberta and Cross Cancer Institute, 11560 University Ave, Edmonton, AB, T6G 1Z2, Canada
| | - Jana Lauzon
- Department of Oncology, University of Alberta and Cross Cancer Institute, 11560 University Ave, Edmonton, AB, T6G 1Z2, Canada
| | - Christina M Jones
- Department of Oncology, University of Alberta and Cross Cancer Institute, 11560 University Ave, Edmonton, AB, T6G 1Z2, Canada
| | - Patrick J Ward
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Linda M Pilarski
- Department of Oncology, University of Alberta and Cross Cancer Institute, 11560 University Ave, Edmonton, AB, T6G 1Z2, Canada
| | - Patrick M Pilarski
- Division of Physical Medicine & Rehabilitation, Department of Medicine, University of Alberta, 5-005 Katz Group Centre for Pharmacy and Health Research, Edmonton, AB, T6G 2E1, Canada
| | - Lynn M McMullen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.
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Forghani F, den Bakker M, Futral AN, Diez-Gonzalez F. Long-Term Survival and Thermal Death Kinetics of Enterohemorrhagic Escherichia coli Serogroups O26, O103, O111, and O157 in Wheat Flour. Appl Environ Microbiol 2018; 84:e00283-18. [PMID: 29678913 PMCID: PMC6007106 DOI: 10.1128/aem.00283-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/12/2018] [Indexed: 11/20/2022] Open
Abstract
Wheat flour has been associated with outbreaks of enterohemorrhagic Escherichia coli (EHEC), but little is known on EHEC's survival during storage and thermal processing. The objective of this study was to determine long-term viability and thermal inactivation kinetics of EHEC serogroups O26, O103, O111, and O157. Wheat flour samples were inoculated with a cocktail of five strains of a single serogroup and stored at 23 and 35°C. Inoculated samples were heated at 55, 60, 65, and 70°C. Viability was determined by plate counting. Decimal reduction time (D) and first decimal reduction time (δ) values were calculated with log-linear and Weibull models, respectively. At 23°C, EHEC counts declined gradually for 84 days and samples tested positive from 84 to 280 days. The thermal resistance (D and δ) values ranged from 7.5 to 8.2 and 3.1 to 5.3 days, respectively, but there were no significant differences among serogroups (P ≤ 0.05). At 35°C, no EHEC was quantifiable by day 7 and no positive samples were detected after 49 days. Heating at 55 and 65°C resulted in δ-value ranges of 15.6 to 39.7 min and 3.0 to 3.9 min, respectively, with no significant difference among serogroups either. Z values were 12.6, 6.7, 10.2, and 13.4°C for O26, O103, O111, and O157, respectively. Thermal death kinetics of EHEC in flour were better described using the Weibull model. Survival and inactivation rates of four serogroups were remarkably similar. These findings indicated that all EHEC serovars tested remained viable for at least 9 months at room temperature and survived for up to 60 min at 70°C in wheat flour.IMPORTANCE Enterohemorrhagic Escherichia coli (EHEC) and Salmonella have recently caused several gastroenteritis outbreaks and recalls of wheat flour. Because EHEC can cause illness with very low doses and there is very scarce information regarding their ability to survive storage and heating in flour, the present study was undertaken to assess the long-term survival of EHEC serogroups O26, O103, O111, and O157 in flour. These findings are relevant, as we report that EHEC can survive for more than 9 months in wheat flour during storage. In addition, results obtained suggest that thermal inactivation at 65°C for 30 min or 2 months of storage at 35°C may be feasible strategies to mitigate the risk of most EHEC serovars in wheat flour.
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Affiliation(s)
- Fereidoun Forghani
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| | - Meghan den Bakker
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| | - Alexandra N Futral
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| | - Francisco Diez-Gonzalez
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
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Genome Sequence for Shiga Toxin-Producing Escherichia coli O26:H11, Associated with a Cluster of Hemolytic-Uremic Syndrome Cases in South Africa, 2017. GENOME ANNOUNCEMENTS 2017; 5:5/38/e00989-17. [PMID: 28935743 PMCID: PMC5609422 DOI: 10.1128/genomea.00989-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) strains are primarily foodborne pathogens that may cause diarrheal outbreaks and are associated with severe complications, specifically hemolytic-uremic syndrome (HUS). We report here genome sequence data for STEC O26:H11, which is associated with a cluster of cases of HUS, a rarely described syndrome in South Africa.
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Cookson AL, Biggs PJ, Marshall JC, Reynolds A, Collis RM, French NP, Brightwell G. Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure. Sci Rep 2017; 7:841. [PMID: 28404985 PMCID: PMC5429811 DOI: 10.1038/s41598-017-00890-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/16/2017] [Indexed: 01/09/2023] Open
Abstract
Current culture methods to investigate changes in Escherichia coli community structure are often slow and laborious. Genes such as gnd (6-phosphogluconate dehydrogenase) have a highly variable nucleotide sequence and may provide a target for E. coli microbiome analysis using culture-independent methods. Metabarcoded PCR primers were used to generate separate libraries from calf faecal samples for high throughput sequencing. Although a total of 348 separate gnd sequence types (gSTs) were identified, 188 were likely to be due to sequencing errors. Of the remaining 160 gSTs, 92 did not match those in a database of 319 separate gnd sequences. ‘Animal’ was the main determinant of E. coli diversity with limited impact of sample type or DNA extraction method on intra-host E. coli community variation from faeces and recto-anal mucosal swab samples. This culture-independent study has addressed the difficulties of quantifying bacterial intra-species diversity and revealed that, whilst individual animals may harbour >50 separate E. coli strains, communities are dominated by <10 strains alongside a large pool of subdominant strains present at low abundances. This method will be useful for characterising the diversity and population structure of E. coli in experimental studies designed to assess the impact of interventions on the gut microbiome.
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Affiliation(s)
- Adrian L Cookson
- AgResearch Limited, Hopkirk Research Institute, Palmerston North, New Zealand. .,mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand.
| | - Patrick J Biggs
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand.,Massey Genome Service, New Zealand Genomics Limited, Massey University, Palmerston North, New Zealand
| | - Jonathan C Marshall
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand.,Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Angela Reynolds
- AgResearch Limited, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Rose M Collis
- AgResearch Limited, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Nigel P French
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Gale Brightwell
- AgResearch Limited, Hopkirk Research Institute, Palmerston North, New Zealand
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