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Zhao Z, Marotta F, Wu M. Thanos: An R Package for the Gene-Centric Analysis of Functional Potential in Metagenomic Samples. Microorganisms 2024; 12:1264. [PMID: 39065033 PMCID: PMC11278725 DOI: 10.3390/microorganisms12071264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
As the amount of metagenomic sequencing continues to increase, there is a growing need for tools that help biologists make sense of the data. Specifically, researchers are often interested in the potential of a microbial community to carry out a metabolic reaction, but this analysis requires knitting together multiple software tools into a complex pipeline. Thanos offers a user-friendly R package designed for the pathway-centric analysis and visualization of the functions encoded within metagenomic samples. It allows researchers to go beyond taxonomic profiles and find out, quantitatively, which pathways are prevalent in an environment, as well as comparing different environments in terms of their functional potential. The analysis is based on the sequencing depth of the genes of interest, either in the metagenome-assembled genomes (MAGs) or in the assembled reads (contigs), using a normalization strategy that enables comparison across samples. The package can import the data from multiple formats and offers functions for the visualization of the results as bar plots of the functional profile, box plots of compare functions across samples, and annotated pathway graphs. By streamlining the analysis of the functional potential encoded in microbial communities, Thanos can enable impactful discoveries in all the fields touched by metagenomics, from human health to the environmental sciences.
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Affiliation(s)
- Zhe Zhao
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;
| | - Federico Marotta
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
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2
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Hematian A, Goudarzi H, Ghalavand Z, Goudarzi M, Shafieian M, Hashemi A, Ghafourian S. The relationship between phoH and colistin-heteroresistant in clinical isolates of Acinetobacter baumannii. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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3
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Sheikh SW, Ali A, Ahsan A, Shakoor S, Shang F, Xue T. Insights into Emergence of Antibiotic Resistance in Acid-Adapted Enterohaemorrhagic Escherichia coli. Antibiotics (Basel) 2021; 10:522. [PMID: 34063307 PMCID: PMC8147483 DOI: 10.3390/antibiotics10050522] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of multidrug-resistant pathogens presents a global challenge for treating and preventing disease spread through zoonotic transmission. The water and foodborne Enterohaemorrhagic Escherichia coli (EHEC) are capable of causing intestinal and systemic diseases. The root cause of the emergence of these strains is their metabolic adaptation to environmental stressors, especially acidic pH. Acid treatment is desired to kill pathogens, but the protective mechanisms employed by EHECs cross-protect against antimicrobial peptides and thus facilitate opportunities for survival and pathogenesis. In this review, we have discussed the correlation between acid tolerance and antibiotic resistance, highlighting the identification of novel targets for potential production of antimicrobial therapeutics. We have also summarized the molecular mechanisms used by acid-adapted EHECs, such as the two-component response systems mediating structural modifications, competitive inhibition, and efflux activation that facilitate cross-protection against antimicrobial compounds. Moving beyond the descriptive studies, this review highlights low pH stress as an emerging player in the development of cross-protection against antimicrobial agents. We have also described potential gene targets for innovative therapeutic approaches to overcome the risk of multidrug-resistant diseases in healthcare and industry.
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Affiliation(s)
- Salma Waheed Sheikh
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
| | - Ahmad Ali
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China;
| | - Asma Ahsan
- Faculty of Life Sciences, University of Central Punjab, Lahore 54000, Punjab, Pakistan;
| | - Sidra Shakoor
- Station de Neucfchateau, CIRAD, 97130 Sainte-Marie, Capesterre Belle Eau, Guadeloupe, France;
| | - Fei Shang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
| | - Ting Xue
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
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4
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Yu L, Zhang S, Xu Y, Mi X, Xing T, Li J, Zhang L, Gao F, Jiang Y. Acid resistance of E. coli O157:H7 and O26:H11 exposure to lactic acid revealed by transcriptomic analysis. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Shawki A, Ramirez R, Spalinger MR, Ruegger PM, Sayoc-Becerra A, Santos AN, Chatterjee P, Canale V, Mitchell JD, Macbeth JC, Gries CM, Tremblay ML, Hsiao A, Borneman J, McCole DF. The autoimmune susceptibility gene, PTPN2, restricts expansion of a novel mouse adherent-invasive E. coli. Gut Microbes 2020; 11:1547-1566. [PMID: 32586195 PMCID: PMC7524159 DOI: 10.1080/19490976.2020.1775538] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/30/2020] [Accepted: 05/18/2020] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) pathogenesis involves significant contributions from genetic and environmental factors. Loss-of-function single-nucleotide polymorphisms (SNPs) in the protein tyrosine phosphatase non-receptor type 2 (PTPN2) gene increase IBD risk and are associated with altered microbiome population dynamics in IBD. Expansion of intestinal pathobionts, such as adherent-invasive E. coli (AIEC), is strongly implicated in IBD pathogenesis as AIEC increases pro-inflammatory cytokine production and alters tight junction protein regulation - suggesting a potential mechanism of pathogen-induced barrier dysfunction and inflammation. We aimed to determine if PTPN2 deficiency alters intestinal microbiome composition to promote expansion of specific bacteria with pathogenic properties. In mice constitutively lacking Ptpn2, we identified increased abundance of a novel mouse AIEC (mAIEC) that showed similar adherence and invasion of intestinal epithelial cells, but greater survival in macrophages, to the IBD-associated AIEC, LF82. Furthermore, mAIEC caused disease when administered to mice lacking segmented-filamentous bacteria (SFB), and in germ-free mice but only when reconstituted with a microbiome, thus supporting its classification as a pathobiont, not a pathogen. Moreover, mAIEC infection increased the severity of, and prevented recovery from, induced colitis. Although mAIEC genome sequence analysis showed >90% similarity to LF82, mAIEC contained putative virulence genes with >50% difference in gene/protein identities from LF82 indicating potentially distinct genetic features of mAIEC. We show for the first time that an IBD susceptibility gene, PTPN2, modulates the gut microbiome to protect against a novel pathobiont. This study generates new insights into gene-environment-microbiome interactions in IBD and identifies a new model to study AIEC-host interactions.
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Affiliation(s)
- Ali Shawki
- Division of Biomedical Sciences, University of California Riverside, Riverside, California, USA
| | - Rocio Ramirez
- Division of Biomedical Sciences, University of California Riverside, Riverside, California, USA
| | - Marianne R. Spalinger
- Division of Biomedical Sciences, University of California Riverside, Riverside, California, USA
| | - Paul M. Ruegger
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - Anica Sayoc-Becerra
- Division of Biomedical Sciences, University of California Riverside, Riverside, California, USA
| | - Alina N. Santos
- Division of Biomedical Sciences, University of California Riverside, Riverside, California, USA
| | - Pritha Chatterjee
- Division of Biomedical Sciences, University of California Riverside, Riverside, California, USA
| | - Vinicius Canale
- Division of Biomedical Sciences, University of California Riverside, Riverside, California, USA
| | - Jonathan D. Mitchell
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - John C. Macbeth
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - Casey M. Gries
- Division of Biomedical Sciences, University of California Riverside, Riverside, California, USA
| | | | - Ansel Hsiao
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - James Borneman
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - Declan F. McCole
- Division of Biomedical Sciences, University of California Riverside, Riverside, California, USA
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6
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Dos Santos Rosario AIL, da Silva Mutz Y, Castro VS, da Silva MCA, Conte-Junior CA, da Costa MP. Everybody loves cheese: crosslink between persistence and virulence of Shiga-toxin Escherichia coli. Crit Rev Food Sci Nutr 2020; 61:1877-1899. [PMID: 32519880 DOI: 10.1080/10408398.2020.1767033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
General cheese manufacturing involves high temperatures, fermentation and ripening steps that function as hurdles to microbial growth. On the other hand, the application of several different formulations and manufacturing techniques may create a bacterial protective environment. In cheese, the persistent behavior of Shiga toxin-producing Escherichia coli (STEC) relies on complex mechanisms that enable bacteria to respond to stressful conditions found in cheese matrix. In this review, we discuss how STEC manages to survive to high and low temperatures, hyperosmotic conditions, exposure to weak organic acids, and pH decreasing related to cheese manufacturing, the cheese matrix itself and storage. Moreover, we discuss how these stress responses interact with each other by enhancing adaptation and consequently, the persistence of STEC in cheese. Further, we show how virulence genes eae and tir are affected by stress response mechanisms, increasing either cell adherence or virulence factors production, which leads to a selection of more resistant and virulent pathogens in the cheese industry, leading to a public health issue.
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Affiliation(s)
- Anisio Iuri Lima Dos Santos Rosario
- Postgraduate Program in Food Science, Faculty of Pharmacy, Universidade Federal da Bahia, Salvador, Brazil.,Department of Preventive Veterinary Medicine and Animal Production, School of Veterinary Medicine and Zootechnics of Veterinary, Universidade Federal da Bahia, Salvador, Brazil
| | - Yhan da Silva Mutz
- Postgraduate Program in Food Science, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói, Brazil
| | - Vinícius Silva Castro
- Postgraduate Program in Food Science, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maurício Costa Alves da Silva
- Department of Preventive Veterinary Medicine and Animal Production, School of Veterinary Medicine and Zootechnics of Veterinary, Universidade Federal da Bahia, Salvador, Brazil
| | - Carlos Adam Conte-Junior
- Postgraduate Program in Food Science, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói, Brazil.,National Institute for Health Quality Control, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Marion Pereira da Costa
- Postgraduate Program in Food Science, Faculty of Pharmacy, Universidade Federal da Bahia, Salvador, Brazil.,Department of Preventive Veterinary Medicine and Animal Production, School of Veterinary Medicine and Zootechnics of Veterinary, Universidade Federal da Bahia, Salvador, Brazil
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7
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Yu L, Ji S, Yu J, Fu W, Zhang L, Li J, Gao F, Jiang Y. Effects of lactic acid stress with lactic acid adaptation on the survival and expression of virulence‐related genes inEscherichia coliO157:H7. J Food Saf 2019. [DOI: 10.1111/jfs.12701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Lanlin Yu
- College of Animal Science and TechnologyNanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Animal Origin Food Production and Safety GuaranteeNanjing Agricultural University Nanjing China
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety ControlNanjing Agricultural University Nanjing China
| | - Saisai Ji
- School of Food Science and Pharmaceutical EngineeringNanjing Normal University Nanjing China
| | - Jinlong Yu
- School of Food Science and Pharmaceutical EngineeringNanjing Normal University Nanjing China
| | - Wenjing Fu
- School of Food Science and Pharmaceutical EngineeringNanjing Normal University Nanjing China
| | - Lin Zhang
- College of Animal Science and TechnologyNanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Animal Origin Food Production and Safety GuaranteeNanjing Agricultural University Nanjing China
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety ControlNanjing Agricultural University Nanjing China
| | - Jiaolong Li
- College of Animal Science and TechnologyNanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Animal Origin Food Production and Safety GuaranteeNanjing Agricultural University Nanjing China
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety ControlNanjing Agricultural University Nanjing China
| | - Feng Gao
- College of Animal Science and TechnologyNanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Animal Origin Food Production and Safety GuaranteeNanjing Agricultural University Nanjing China
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety ControlNanjing Agricultural University Nanjing China
| | - Yun Jiang
- School of Food Science and Pharmaceutical EngineeringNanjing Normal University Nanjing China
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8
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Kovács JK, Felső P, Horváth G, Schmidt J, Dorn Á, Ábrahám H, Cox A, Márk L, Emődy L, Kovács T, Schneider G. Stress Response and Virulence Potential Modulating Effect of Peppermint Essential Oil in Campylobacter jejuni. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2971741. [PMID: 30719441 PMCID: PMC6335803 DOI: 10.1155/2019/2971741] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/14/2018] [Indexed: 12/12/2022]
Abstract
Campylobacter jejuni is one of the most common food-borne bacteria that causes gastrointestinal symptoms. In the present study we have investigated the molecular basis of the anti-Campylobacter effect of peppermint essential oil (PEO), one of the oldest EO used to treat gastrointestinal diseases. Transcriptomic, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and proteomic, two-dimensional polyacryl amid gel electrophoresis (2D-PAGE) methods have revealed that, in the presence of a sublethal concentration of PEO, the expression of several virulence-associated genes was decreased (cheY 0.84x; flhB 0.79x; flgE 0.205x; cadF 0.08x; wlaB 0.89x; porA 0.25x; cbf2 4.3x) while impaired motility was revealed with a functional analysis. Scanning electron micrographs of the exposed cells showed that, unlike in the presence of other stresses, the originally curved C. jejuni cells straightened upon PEO exposure. Gaining insight into the molecular background of this stress response, we have revealed that in the presence of PEO C. jejuni dominantly exerts a general stress response that elevates the expression of general stress genes like dnaK, groEL, groES (10.41x, 3.63x, and 4.77x). The most important genes dps, sodB, and katA involved in oxidative stress responses showed however moderate transcriptional elevations (1,58x, 1,55x, and 1,85x).
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Affiliation(s)
- J. K. Kovács
- Department of Medical Microbiology and Immunology, University of Pécs Medical School, Hungary
| | - P. Felső
- Department of Medical Microbiology and Immunology, University of Pécs Medical School, Hungary
| | - Gy. Horváth
- Department of Pharmacognosy, University of Pécs Medical School, Hungary
| | - J. Schmidt
- Department of Biochemistry and Medical Chemistry, University of Pécs Medical School, Hungary
| | - Á. Dorn
- Department of Medical Microbiology and Immunology, University of Pécs Medical School, Hungary
| | - H. Ábrahám
- Department of Medical Biology and Central Electron Microscope Laboratory, University of Pécs Medical School, Hungary
| | - A. Cox
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - L. Márk
- Department of Biochemistry and Medical Chemistry, University of Pécs Medical School, Hungary
| | - L. Emődy
- Department of Medical Microbiology and Immunology, University of Pécs Medical School, Hungary
- Veterinary Medical Research Institute, Hungarian Academy of Sciences, Budapest, Hungary
| | - T. Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gy. Schneider
- Department of Medical Microbiology and Immunology, University of Pécs Medical School, Hungary
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9
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Ferreira M, Stella A, Freitas-Filho E, Silva T, Nascimento K, Pinto J, Dias M, Moreira C. Distribution of the stx1 and stx2 genes in Escherichia coli isolated from milk cattle according to season, age, and production scale in southwestern region of Goiás, Brazil. ARQ BRAS MED VET ZOO 2018. [DOI: 10.1590/1678-4162-9861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
ABSTRACT This study determined the distribution of stx1 and stx2 genes in Escherichia coli isolated from dairy herds with regard to animal age, season, and farm production-scale, and analyzed the phylogenetic distribution of the groups A, B1, B2, and D of 276 isolates of bovine feces Shiga toxin-producing E. coli (STEC). The stx1 profile was the most common, detected in 20.4% (202/990) of the isolates, followed by stx2 (4.54%, 45/990) and stx1+stx2 (2.92%, 29/990). The stx1 gene was detected more frequently in calves than in adult animals. In the dry season (winter), the presence of stx1+stx2 profile in cattle feces was higher than in the rainy season (summer), while no significant changes were observed between seasons for the stx1 and stx2 profiles. The most predominant phylogenetic groups in adult animals were B1, A, and D, while groups A and B1 prevailed in calves. Our data highlight the importance of identifying STEC reservoirs, since 7.5% of the tested isolates were positive for stx2, the main profile responsible for the hemolytic-uremic syndrome (HUS). Moreover, these microorganisms are adapted to survive even in hostile environments and can contaminate the food production chain, posing a significant risk to consumers of animal products.
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Affiliation(s)
- M.R.A. Ferreira
- Universidade Federal de Goiás, Brazil; Universidade Federal de Pelotas, Brazil
| | | | - E.G. Freitas-Filho
- Universidade Federal de Goiás, Brazil; Universidade de São Paulo, Brazil
| | | | - K.A. Nascimento
- Universidade Federal de Goiás, Brazil; Universidade Estadual Paulista “Júlio de Mesquita Filho”, Brazil
| | | | - M. Dias
- Universidade Federal de Goiás, Brazil
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10
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Andjelković U, Šrajer Gajdošik M, Gašo-Sokač D, Martinović T, Josić D. Foodomics and Food Safety: Where We Are. Food Technol Biotechnol 2017; 55:290-307. [PMID: 29089845 PMCID: PMC5654429 DOI: 10.17113/ftb.55.03.17.5044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 05/31/2017] [Indexed: 12/21/2022] Open
Abstract
The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling.
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Affiliation(s)
- Uroš Andjelković
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, RS-11000 Belgrade, Serbia
| | - Martina Šrajer Gajdošik
- Department of Chemistry, J. J. Strossmayer University of Osijek, Cara Hadrijana 8/A, HR-31000 Osijek, Croatia
| | - Dajana Gašo-Sokač
- Faculty of Food Technology, J. J. Strossmayer University of Osijek, Franje Kuhača 20, HR-31000 Osijek, Croatia
| | - Tamara Martinović
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
| | - Djuro Josić
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Warren Alpert Medical School, Brown University, 222 Richmond St, Providence, RI 02903, USA
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11
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Development of an HTS system to identify natural chemicals that specifically inhibit Escherichia coli O157:H7 adhesion to host cells. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Li H, Gänzle M. Some Like It Hot: Heat Resistance of Escherichia coli in Food. Front Microbiol 2016; 7:1763. [PMID: 27857712 PMCID: PMC5093140 DOI: 10.3389/fmicb.2016.01763] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/20/2016] [Indexed: 11/13/2022] Open
Abstract
Heat treatment and cooking are common interventions for reducing the numbers of vegetative cells and eliminating pathogenic microorganisms in food. Current cooking method requires the internal temperature of beef patties to reach 71°C. However, some pathogenic Escherichia coli such as the beef isolate E. coli AW 1.7 are extremely heat resistant, questioning its inactivation by current heat interventions in beef processing. To optimize the conditions of heat treatment for effective decontaminations of pathogenic E. coli strains, sufficient estimations, and explanations are necessary on mechanisms of heat resistance of target strains. The heat resistance of E. coli depends on the variability of strains and properties of food formulations including salt and water activity. Heat induces alterations of E. coli cells including membrane, cytoplasm, ribosome and DNA, particularly on proteins including protein misfolding and aggregations. Resistant systems of E. coli act against these alterations, mainly through gene regulations of heat response including EvgA, heat shock proteins, σE and σS, to re-fold of misfolded proteins, and achieve antagonism to heat stress. Heat resistance can also be increased by expression of key proteins of membrane and stabilization of membrane fluidity. In addition to the contributions of the outer membrane porin NmpC and overcome of osmotic stress from compatible solutes, the new identified genomic island locus of heat resistant performs a critical role to these highly heat resistant strains. This review aims to provide an overview of current knowledge on heat resistance of E. coli, to better understand its related mechanisms and explore more effective applications of heat interventions in food industry.
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Affiliation(s)
- Hui Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, EdmontonAB, Canada
| | - Michael Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, EdmontonAB, Canada
- College of Bioengineering and Food Science, Hubei University of TechnologyHubei, China
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13
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Kennedy NM, Mukherjee N, Banerjee P. Escherichia coli O157:H7 Cells Exposed to Lettuce Leaf Lysate in Refrigerated Conditions Exhibit Differential Expression of Selected Virulence and Adhesion-Related Genes with Altered Mammalian Cell Adherence. J Food Prot 2016; 79:1259-65. [PMID: 27357048 DOI: 10.4315/0362-028x.jfp-15-504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Contamination by and persistence of pathogenic bacteria in ready-to-eat produce have emerged as significant food safety and public health concerns. Viable produceborne pathogens cope with several stresses (e.g., temperature fluctuations and lowtemperature storage) during production and storage of the commodities. In this study, we investigated the impact of transient cold shock on Escherichia coli O157:H7 (EcO157) cells in a produce matrix (romaine lettuce leaf lysate). EcO157 cells were exposed to 25°C for 1 h, 4°C for 1 h, and 4°C for 10 min in lettuce lysate. The expression of selected genes coding for virulence, stress response, and heat and cold shock proteins was quantified by real-time quantitative reverse transcription PCR assay. Treated EcO157 cells adhered to MAC-T mammalian cells were enumerated by in vitro bioassay. Expression of the Shiga toxin 1 gene (stx1a) was upregulated significantly (P < 0.05) upon cold shock treatments, but virulence genes related to EcO157 attachment (eaeA, lpfA, and hcpA) were down-regulated. Two key members of the cold shock regulon, cold shock protein (cspA) and gyrA, were significantly induced (P < 0.05) at the refrigeration temperature (4°C). Significant upregulation of an SOS response gene, recA, was also observed. E. coli heat shock regulon member grpE was induced, but a universal stress protein (uspA) was downregulated at the refrigeration temperatures in lettuce lysate. The adhesion assay revealed a temperature-dependent reduction in the attachment of cold-shocked EcO157 cells. The results of the current study indicate a reduction in the attachment of cold-shocked EcO157 to epithelial cells and higher levels of Shiga toxin gene expression at the molecular level.
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Affiliation(s)
- Nicole M Kennedy
- Department of Food and Animal Sciences, Alabama A&M University, Huntsville, Alabama 35762, USA
| | - Nabanita Mukherjee
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, Tennessee 38152, USA
| | - Pratik Banerjee
- Department of Food and Animal Sciences, Alabama A&M University, Huntsville, Alabama 35762, USA; Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, Tennessee 38152, USA.
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14
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Nagar V, Bandekar JR, Shashidhar R. Expression of virulence and stress response genes in Aeromonas hydrophila under various stress conditions. J Basic Microbiol 2016; 56:1132-1137. [PMID: 27163835 DOI: 10.1002/jobm.201600107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/19/2016] [Indexed: 11/10/2022]
Abstract
Aeromonas hydrophila has emerged as an important human pathogen as it causes gastroenteritis and extra-intestinal infections. Information regarding the influence of environmental stresses on gene expression profile of A. hydrophila is lacking. The impact of nutrient replenishment, nutrient deprivation, acid stress, and cold shock on housekeeping, general stress-response, and virulence genes was studied using quantitative real-time PCR in two A. hydrophila strains, CECT 839T , and A331. These sub-lethal stresses invoked significant changes in the expression of these genes in a strain-dependent manner. Overall, nutrient replenishment and deprivation significantly induced the expression of housekeeping (rpoD), general stress regulators (uspA and rpoS), and virulence (aer) genes, indicating their importance in regulating the survival and virulence of A. hydrophila under these stress conditions. rpoS gene was significantly induced under cold shock; whereas, acid stress significantly induced the expression of uspA gene. This is the first study to investigate the effect of environmental parameters on the expression of stress-response and virulence genes in A. hydrophila strains.
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Affiliation(s)
- Vandan Nagar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India.
| | - Jayant R Bandekar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
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Influence of Low-Shear Modeled Microgravity on Heat Resistance, Membrane Fatty Acid Composition, and Heat Stress-Related Gene Expression in Escherichia coli O157:H7 ATCC 35150, ATCC 43889, ATCC 43890, and ATCC 43895. Appl Environ Microbiol 2016; 82:2893-2901. [PMID: 26944847 DOI: 10.1128/aem.00050-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/01/2016] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED We previously showed that modeled microgravity conditions alter the physiological characteristics of Escherichia coli O157:H7. To examine how microgravity conditions affect bacterial heat stress responses, D values, membrane fatty acid composition, and heat stress-related gene expression (clpB, dnaK, grpE, groES, htpG, htpX, ibpB, and rpoH), E. coli O157:H7 ATCC 35150, ATCC 43889, ATCC 43890, and ATCC 43895 were cultured under two different conditions: low-shear modeled microgravity (LSMMG, an analog of spaceflight conditions) and normal gravity (NG, Earth-like conditions). When 24-h cultures were heated to 55°C, cells cultured under LSMMG conditions showed reduced survival compared with cells cultured under NG conditions at all time points (P < 0.05). D values of all tested strains were lower after LSMMG culture than after NG culture. Fourteen of 37 fatty acids examined were present in the bacterial membrane: nine saturated fatty acids (SFA) and five unsaturated fatty acids (USFA). The USFA/SFA ratio, a measure of membrane fluidity, was higher under LSMMG conditions than under NG conditions. Compared with control cells grown under NG conditions, cells cultured under LSMMG conditions showed downregulation of eight heat stress-related genes (average, -1.9- to -3.7-fold). The results of this study indicate that in a simulated space environment, heat resistance of E. coli O157:H7 decreased, and this might be due to the synergistic effects of the increases in membrane fluidity and downregulated relevant heat stress genes. IMPORTANCE Microgravity is a major factor that represents the environmental conditions in space. Since infectious diseases are difficult to deal with in a space environment, comprehensive studies on the behavior of pathogenic bacteria under microgravity conditions are warranted. This study reports the changes in heat stress resistance of E. coli O157:H7, the severe foodborne pathogen, under conditions that mimic microgravity. The results provide scientific clues for further understanding of the bacterial response under the simulated microgravity conditions. It will contribute not only to the improvement of scientific knowledge in the academic fields but also ultimately to the development of a prevention strategy for bacterial disease in the space environment.
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Kim JC, Oh E, Kim J, Jeon B. Regulation of oxidative stress resistance in Campylobacter jejuni, a microaerophilic foodborne pathogen. Front Microbiol 2015; 6:751. [PMID: 26284041 PMCID: PMC4518328 DOI: 10.3389/fmicb.2015.00751] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/08/2015] [Indexed: 12/31/2022] Open
Abstract
Campylobacter jejuni is one of the leading bacterial causes of human gastroenteritis. Due to the increasing rates of human campylobacteriosis, C. jejuni is considered as a serious public health concern worldwide. C. jejuni is a microaerophilic, fastidious bacterium. C. jejuni must overcome a wide range of stress conditions during foodborne transmission to humans, such as food preservation and processing conditions, and even in infection of the gastrointestinal tracts of humans. Particularly, this microaerophilic foodborne pathogen must survive in the atmospheric conditions prior to the initiation of infection. C. jejuni possesses unique regulatory mechanisms for oxidative stress resistance. Lacking OxyR and SoxRS that are highly conserved in other Gram-negative foodborne pathogens, C. jejuni modulates the expression of genes involved in oxidative stress resistance mainly via the peroxide resistance regulator and Campylobacter oxidative stress regulator. Based on recent findings of ours and others, in this review, we described how C. jejuni regulates the expression of oxidative stress defense.
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Affiliation(s)
| | | | | | - Byeonghwa Jeon
- School of Public Health, University of Alberta, EdmontonAB, Canada
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17
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De Biase D, Lund PA. The Escherichia coli Acid Stress Response and Its Significance for Pathogenesis. ADVANCES IN APPLIED MICROBIOLOGY 2015; 92:49-88. [PMID: 26003933 DOI: 10.1016/bs.aambs.2015.03.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Escherichia coli has a remarkable ability to survive low pH and possesses a number of different genetic systems that enable it to do this. These may be expressed constitutively, typically in stationary phase, or induced by growth under a variety of conditions. The activities of these systems have been implicated in the ability of E. coli to pass the acidic barrier of the stomach and to become established in the gastrointestinal tract, something causing serious infections. However, much of the work characterizing these systems has been done on standard laboratory strains of E. coli and under conditions which do not closely resemble those found in the human gut. Here we review what is known about acid resistance in E. coli as a model laboratory organism and in the context of its lifestyle as an inhabitant-sometimes an unwelcome one-of the human gut.
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18
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Kjeldsen TSB, Overgaard M, Nielsen SS, Bortolaia V, Jelsbak L, Sommer M, Guardabassi L, Olsen JE. CTX-M-1 β-lactamase expression in Escherichia coli is dependent on cefotaxime concentration, growth phase and gene location. J Antimicrob Chemother 2014; 70:62-70. [DOI: 10.1093/jac/dku332] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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King T, Kocharunchitt C, Gobius K, Bowman JP, Ross T. Global genome response of Escherichia coli O157∶H7 Sakai during dynamic changes in growth kinetics induced by an abrupt temperature downshift. PLoS One 2014; 9:e99627. [PMID: 24926786 PMCID: PMC4057180 DOI: 10.1371/journal.pone.0099627] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 05/17/2014] [Indexed: 11/23/2022] Open
Abstract
Escherichia coli O157∶H7 is a mesophilic food-borne pathogen. We investigated the growth kinetics of E. coli O157∶H7 Sakai during an abrupt temperature downshift from 35°C to either 20°C, 17°C, 14°C or 10°C; as well as the molecular mechanisms enabling growth after cold stress upon an abrupt downshift from 35°C to 14°C in an integrated transcriptomic and proteomic analysis. All downshifts caused a lag period of growth before growth resumed at a rate typical of the post-shift temperature. Lag and generation time increased with the magnitude of the shift or with the final temperature, while relative lag time displayed little variation across the test range. Analysis of time-dependent molecular changes revealed, in keeping with a decreased growth rate at lower temperature, repression of genes and proteins involved in DNA replication, protein synthesis and carbohydrate catabolism. Consistent with cold-induced remodelling of the bacterial cell envelope, alterations occurred in the expression of genes and proteins involved in transport and binding. The RpoS regulon exhibited sustained induction confirming its importance in adaptation and growth at 14°C. The RpoE regulon was transiently induced, indicating a potential role for this extracytoplasmic stress response system in the early phase of low temperature adaptation during lag phase. Interestingly, genes previously reported to be amongst the most highly up-regulated under oxidative stress were consistently down-regulated. This comprehensive analysis provides insight into the molecular mechanisms operating during adaptation of E. coli to growth at low temperature and is relevant to its physiological state during chilling in foods, such as carcasses.
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Affiliation(s)
- Thea King
- Commonwealth Scientific and Industrial Research Organisation, Animal, Food and Health Sciences, North Ryde, New South Wales, Australia
- * E-mail:
| | - Chawalit Kocharunchitt
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Kari Gobius
- Commonwealth Scientific and Industrial Research Organisation, Animal, Food and Health Sciences, Werribee, Victoria, Australia
| | - John P. Bowman
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Tom Ross
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
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Mondani L, Roupioz Y, Delannoy S, Fach P, Livache T. Simultaneous enrichment and optical detection of low levels of stressed Escherichia coli
O157:H7 in food matrices. J Appl Microbiol 2014; 117:537-46. [DOI: 10.1111/jam.12522] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 11/29/2022]
Affiliation(s)
- L. Mondani
- SPrAM; UMR 5819 CEA/CNRS/UJF-Grenoble 1; Institute for Nanosciences & Cryogeny; Grenoble France
| | - Y. Roupioz
- SPrAM; UMR 5819 CEA/CNRS/UJF-Grenoble 1; Institute for Nanosciences & Cryogeny; Grenoble France
| | - S. Delannoy
- French Agency for Food, Environmental and Occupational Health and Safety (ANSES); Food Safety Laboratory; Maisons-Alfort France
| | - P. Fach
- French Agency for Food, Environmental and Occupational Health and Safety (ANSES); Food Safety Laboratory; Maisons-Alfort France
| | - T. Livache
- SPrAM; UMR 5819 CEA/CNRS/UJF-Grenoble 1; Institute for Nanosciences & Cryogeny; Grenoble France
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21
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Choi S, Kim Y, Oh S, Oh S, Chun T, Kim S. Inhibitory effect of skatole (3-methylindole) on enterohemorrhagic Escherichia coli
O157:H7 ATCC 43894 biofilm formation mediated by elevated endogenous oxidative stress. Lett Appl Microbiol 2014; 58:454-61. [DOI: 10.1111/lam.12212] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 12/05/2013] [Accepted: 12/20/2013] [Indexed: 12/23/2022]
Affiliation(s)
- S.H. Choi
- Division of Food Bioscience and Technology; Korea University; Seoul Korea
| | - Y. Kim
- BK21 Plus Graduate Program; Department of Animal Science and Institute of Rare Earth for Biological Application; Chonbuk National University; Jeonju Korea
| | - S. Oh
- BK21 Plus Graduate Program; Department of Animal Science and Institute of Rare Earth for Biological Application; Chonbuk National University; Jeonju Korea
| | - S. Oh
- Division of Animal Science; Institute of Agricultural Science and Technology; Chonnam National University; Gwangju Korea
| | - T. Chun
- Division of Biotechnology; School of Life Sciences and Biotechnology; Korea University; Seoul Korea
| | - S.H. Kim
- Division of Food Bioscience and Technology; Korea University; Seoul Korea
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22
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Lee YJ, van Nostrand JD, Tu Q, Lu Z, Cheng L, Yuan T, Deng Y, Carter MQ, He Z, Wu L, Yang F, Xu J, Zhou J. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME JOURNAL 2013; 7:1974-84. [PMID: 23765101 DOI: 10.1038/ismej.2013.88] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/10/2013] [Accepted: 04/20/2013] [Indexed: 12/21/2022]
Abstract
Pathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. As many pathogens can survive and proliferate in the environment, it is important to understand their population dynamics and pathogenic potential in the environment. To assess pathogenic potential in diverse habitats, we developed a functional gene array, the PathoChip, constructed with key virulence genes related to major virulence factors, such as adherence, colonization, motility, invasion, toxin, immune evasion and iron uptake. A total of 3715 best probes were selected from 13 virulence factors, covering 7417 coding sequences from 1397 microbial species (2336 strains). The specificity of the PathoChip was computationally verified, and approximately 98% of the probes provided specificity at or below the species level, proving its excellent capability for the detection of target sequences with high discrimination power. We applied this array to community samples from soil, seawater and human saliva to assess the occurrence of virulence genes in natural environments. Both the abundance and diversity of virulence genes increased in stressed conditions compared with their corresponding controls, indicating a possible increase in abundance of pathogenic bacteria under environmental perturbations such as warming or oil spills. Statistical analyses showed that microbial communities harboring virulence genes were responsive to environmental perturbations, which drove changes in abundance and distribution of virulence genes. The PathoChip provides a useful tool to identify virulence genes in microbial populations, examine the dynamics of virulence genes in response to environmental perturbations and determine the pathogenic potential of microbial communities.
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Affiliation(s)
- Yong-Jin Lee
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
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23
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Sample preparation and further proteomic investigation of the inhibitory activity of pyridinium oximes to Gram-positive and Gram-negative food pathogens. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.11.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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24
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Elhadidy M, Mohammed M. Shiga toxin-producing Escherichia coli
from raw milk cheese in Egypt: prevalence, molecular characterization and survival to stress conditions. Lett Appl Microbiol 2012; 56:120-7. [DOI: 10.1111/lam.12023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 10/18/2012] [Accepted: 10/26/2012] [Indexed: 11/26/2022]
Affiliation(s)
- M. Elhadidy
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine; Mansoura University; Mansoura Egypt
| | - M.A. Mohammed
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine; Mansoura University; Mansoura Egypt
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25
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Bui XT, Qvortrup K, Wolff A, Bang DD, Creuzenet C. Effect of environmental stress factors on the uptake and survival of Campylobacter jejuni in Acanthamoeba castellanii. BMC Microbiol 2012; 12:232. [PMID: 23051891 PMCID: PMC3538707 DOI: 10.1186/1471-2180-12-232] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 10/03/2012] [Indexed: 11/22/2022] Open
Abstract
Background Campylobacter jejuni is a major cause of bacterial food-borne illness in Europe and North America. The mechanisms allowing survival in the environment and transmission to new hosts are not well understood. Environmental free-living protozoa may facilitate both processes. Pre-exposure to heat, starvation, oxidative or osmotic stresses encountered in the environment may affect the subsequent interaction of C. jejuni with free-living protozoa. To test this hypothesis, we examined the impact of environmental stress on expression of virulence-associated genes (ciaB, dnaJ, and htrA) of C. jejuni and on its uptake by and intracellular survival within Acanthamoeba castellanii. Results Heat, starvation and osmotic stress reduced the survival of C. jejuni significantly, whereas oxidative stress had no effect. Quantitative RT-PCR experiments showed that the transcription of virulence genes was slightly up-regulated under heat and oxidative stresses but down-regulated under starvation and osmotic stresses, the htrA gene showing the largest down-regulation in response to osmotic stress. Pre-exposure of bacteria to low nutrient or osmotic stress reduced bacterial uptake by amoeba, but no effect of heat or oxidative stress was observed. Finally, C. jejuni rapidly lost viability within amoeba cells and pre-exposure to oxidative stress had no significant effect on intracellular survival. However, the numbers of intracellular bacteria recovered 5 h post-gentamicin treatment were lower with starved, heat treated or osmotically stressed bacteria than with control bacteria. Also, while ~1.5 × 103 colony forming unit/ml internalized bacteria could typically be recovered 24 h post-gentamicin treatment with control bacteria, no starved, heat treated or osmotically stressed bacteria could be recovered at this time point. Overall, pre-exposure of C. jejuni to environmental stresses did not promote intracellular survival in A. castellanii. Conclusions Together, these findings suggest that the stress response in C. jejuni and its interaction with A. castellanii are complex and multifactorial, but that pre-exposure to various stresses does not prime C. jejuni for survival within A. castellanii.
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Affiliation(s)
- Xuan Thanh Bui
- National Veterinary Institute, Technical University of Denmark, Aarhus NDK-8200, Denmark
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26
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Effects of subinhibitory concentrations of menthol on adaptation, morphological, and gene expression changes in enterohemorrhagic Escherichia coli. Appl Environ Microbiol 2012; 78:5361-7. [PMID: 22635999 DOI: 10.1128/aem.00894-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Menthol (C(10)H(20)O) possesses antibacterial activity; nevertheless, bacterial adaptation to this compound has never been studied. Here we report that precultivation of enterohemorrhagic Escherichia coli (EHEC) strains in increasing subinhibitory (SI) concentrations of menthol significantly elevates (4- to 16-fold) their resistance to menthol. Concomitant morphological alterations included the appearance of mucoid colonies and reduced biofilm production. Scanning electron microscopy (SEM) examination revealed suppressed curli formation in menthol-adapted cells. Expression of the gene cpsB10 (encoding one of the enzymes responsible for colanic acid production) was elevated in response to SI concentrations of menthol in a laboratory E. coli strain, whereas expression in an rcsC null mutant was reduced, implicating a partial role for the Rcs phosphorelay system in mediating the menthol signal. Adaptation to menthol also reduced expression of the locus of enterocyte effacement-encoded regulator (Ler). This reduction, together with reduced curli and biofilm formation and elevated mucoidity, suggests a general reduction in bacterial virulence following adaptation to menthol. Our results thus suggest menthol as a potential lead in the recently emerging alternative strategy of targeting bacterial virulence factors to develop new types of anti-infective agents.
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27
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Importance of RNA stabilization: evaluation of ansB, ggt, and rpoA transcripts in microaerophilic Campylobacter jejuni 81-176. Arch Microbiol 2012; 194:803-8. [DOI: 10.1007/s00203-012-0820-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/10/2012] [Accepted: 04/27/2012] [Indexed: 11/29/2022]
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Guernec A, Robichaud-Rincon P, Saucier L. Physiological adaptation of Escherichia coli after transfer onto refrigerated ground meat and other solid matrices: a molecular approach. Food Microbiol 2012; 32:63-71. [PMID: 22850375 DOI: 10.1016/j.fm.2012.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 04/11/2012] [Accepted: 04/17/2012] [Indexed: 10/28/2022]
Abstract
Bacteria on meat are subjected to specific living conditions that differ drastically from typical laboratory procedures in synthetic media. This study was undertaken to determine the behavior of bacteria when transferred from a rich-liquid medium to solid matrices, as is the case during microbial process validation. Escherichia coli cultured in Brain-Heart Infusion (BHI) broth to different growth phases were inoculated in ground beef (GB) and stored at 5°C for 12 days or spread onto BHI agar and cooked meat medium (CMM), and incubated at 37°C for several hours. We monitored cell densities and the expression of σ factors and genes under their control over time. The initial growth phase of the inoculum influenced growth resumption after transfer onto BHI agar and CMM. Whatever the solid matrix, bacteria adapted to their new environment and did not perceive stress immediately after inoculation. During this period, the σ(E) and σ(H) regulons were not activated and rpoD mRNA levels adjusted quickly. The rpoS and gadA mRNA levels did not increase after inoculation on solid surfaces and displayed normal growth-dependent modifications. After transfer onto GB, dnaK and groEL gene expression was affected more by the low temperature than by the composition of a meat environment.
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Affiliation(s)
- Anthony Guernec
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Pavillon Paul Comtois, Université Laval, Québec G1K 7P4, Canada
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Impact of hydroxyl- and superoxide anion-based oxidative stress on logarithmic and stationary phase Escherichia coli O157:H7 stress and virulence gene expression. Food Microbiol 2012; 29:141-7. [DOI: 10.1016/j.fm.2011.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 09/18/2011] [Accepted: 09/21/2011] [Indexed: 11/20/2022]
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30
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Slanec T, Schmidt H. Specific expression of adherence-related genes in Escherichia coli O157:H7 strain EDL933 after heat treatment in ground beef. J Food Prot 2011; 74:1434-40. [PMID: 21902911 DOI: 10.4315/0362-028x.jfp-11-018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this study, the expression of particular stress- and virulence-associated genes of Escherichia coli O157:H7 strain EDL933 in ground beef was investigated using real-time PCR. Specific gene expression in the food matrix was found in combination with heat treatment. In contrast to a treatment at 37°C, treatment at 48°C for 10 min resulted in increased expression of the genes eae, hcpA, iha, lpfA, and toxB. Adherence to human intestinal HT-29 cells was enhanced in bacterial cells inoculated and heat treated in ground beef. The expression of gadE, which encodes a main regulator of the glutamate system of the acid response, was reduced under these conditions. However, expression of rpoS and recA, which are involved in the establishment of stress responses, and Shiga toxin genes was not significantly different under the same conditions.
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Affiliation(s)
- T Slanec
- Department of Food Microbiology, Institute of Food Science and Biotechnology, Garbenstraße 28, University of Hohenheim, 70599 Stuttgart, Germany
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31
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Crépin S, Chekabab SM, Le Bihan G, Bertrand N, Dozois CM, Harel J. The Pho regulon and the pathogenesis of Escherichia coli. Vet Microbiol 2011; 153:82-8. [PMID: 21700403 DOI: 10.1016/j.vetmic.2011.05.043] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 05/18/2011] [Accepted: 05/25/2011] [Indexed: 11/18/2022]
Abstract
During the course of infection, bacteria must coordinately regulate gene expression in response to environmental stimuli. The phosphate (Pho) regulon is controlled by the two component-regulatory system PhoBR. PhoBR is activated during starvation and regulates genes involved in phosphate homeostasis. Several studies have highlighted the importance of the Pho regulon in bacterial pathogenesis, showing how induction of PhoBR, in addition to regulating genes participating in phosphate metabolism, leads to modulation of many cellular processes. The pleiotropic effects of Pho regulon activation include attenuated virulence and alteration of many virulence traits, including adhesion to host cells and resistance to cationic antimicrobial peptides, acidity and oxidative stresses. This review provides an overview of the relationship between the Pho regulon and virulence in Escherichia coli and illustrates that, in addition to regulating phosphate homeostasis, the Pho regulon plays a key role in regulating stress responses and virulence.
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Affiliation(s)
- Sébastien Crépin
- INRS-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, Québec, Canada H7V 1B7
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Peng S, Tasara T, Hummerjohann J, Stephan R. An overview of molecular stress response mechanisms in Escherichia coli contributing to survival of Shiga toxin-producing Escherichia coli during raw milk cheese production. J Food Prot 2011; 74:849-64. [PMID: 21549061 DOI: 10.4315/0362-028x.jfp-10-469] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ability of foodborne pathogens to survive in certain foods mainly depends on stress response mechanisms. Insight into molecular properties enabling pathogenic bacteria to survive in food is valuable for improvement of the control of pathogens during food processing. Raw milk cheeses are a potential source for human infections with Shiga toxin-producing Escherichia coli (STEC). In this review, we focused on the stress response mechanisms important for allowing STEC to survive raw milk cheese production processes. The major components and regulation pathways for general, acid, osmotic, and heat shock stress responses in E. coli and the implications of these responses for the survival of STEC in raw milk cheeses are discussed.
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Affiliation(s)
- Silvio Peng
- Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, 8057 Zürich, Switzerland
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Solute transport proteins and the outer membrane protein NmpC contribute to heat resistance of Escherichia coli AW1.7. Appl Environ Microbiol 2011; 77:2961-7. [PMID: 21398480 DOI: 10.1128/aem.01930-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study aimed to elucidate determinants of heat resistance in Escherichia coli by comparing the composition of membrane lipids, as well as gene expression, in heat-resistant E. coli AW1.7 and heat-sensitive E. coli GGG10 with or without heat shock. The survival of E. coli AW1.7 at late exponential phase was 100-fold higher than that of E. coli GGG10 after incubation at 60°C for 15 min. The cytoplasmic membrane of E. coli AW1.7 contained a higher proportion of saturated and cyclopropane fatty acids than that of E. coli GGG10. Microarray hybridization of cDNA libraries obtained from exponentially growing or heat-shocked cultures was performed to compare gene expression in these two strains. Expression of selected genes from different functional groups was quantified by quantitative PCR. DnaK and 30S and 50S ribosomal subunits were overexpressed in E. coli GGG10 relative to E. coli AW1.7 upon heat shock at 50°C, indicating improved ribosome stability. The outer membrane porin NmpC and several transport proteins were overexpressed in exponentially growing E. coli AW1.7. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of membrane properties confirmed that NmpC is present in the outer membrane of E. coli AW1.7 but not in that of E. coli GGG10. Expression of NmpC in E. coli GGG10 increased survival at 60°C 50- to 1,000-fold. In conclusion, the outer membrane porin NmpC contributes to heat resistance in E. coli AW1.7, but the heat resistance of this strain is dependent on additional factors, which likely include the composition of membrane lipids, as well as solute transport proteins.
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den Besten HMW, Arvind A, Gaballo HMS, Moezelaar R, Zwietering MH, Abee T. Short- and long-term biomarkers for bacterial robustness: a framework for quantifying correlations between cellular indicators and adaptive behavior. PLoS One 2010; 5:e13746. [PMID: 21060783 PMCID: PMC2966415 DOI: 10.1371/journal.pone.0013746] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 10/05/2010] [Indexed: 01/01/2023] Open
Abstract
The ability of microorganisms to adapt to changing environments challenges the prediction of their history-dependent behavior. Cellular biomarkers that are quantitatively correlated to stress adaptive behavior will facilitate our ability to predict the impact of these adaptive traits. Here, we present a framework for identifying cellular biomarkers for mild stress induced enhanced microbial robustness towards lethal stresses. Several candidate-biomarkers were selected by comparing the genome-wide transcriptome profiles of our model-organism Bacillus cereus upon exposure to four mild stress conditions (mild heat, acid, salt and oxidative stress). These candidate-biomarkers--a transcriptional regulator (activating general stress responses), enzymes (removing reactive oxygen species), and chaperones and proteases (maintaining protein quality)--were quantitatively determined at transcript, protein and/or activity level upon exposure to mild heat, acid, salt and oxidative stress for various time intervals. Both unstressed and mild stress treated cells were also exposed to lethal stress conditions (severe heat, acid and oxidative stress) to quantify the robustness advantage provided by mild stress pretreatment. To evaluate whether the candidate-biomarkers could predict the robustness enhancement towards lethal stress elicited by mild stress pretreatment, the biomarker responses upon mild stress treatment were correlated to mild stress induced robustness towards lethal stress. Both short- and long-term biomarkers could be identified of which their induction levels were correlated to mild stress induced enhanced robustness towards lethal heat, acid and/or oxidative stress, respectively, and are therefore predictive cellular indicators for mild stress induced enhanced robustness. The identified biomarkers are among the most consistently induced cellular components in stress responses and ubiquitous in biology, supporting extrapolation to other microorganisms than B. cereus. Our quantitative, systematic approach provides a framework to search for these biomarkers and to evaluate their predictive quality in order to select promising biomarkers that can serve to early detect and predict adaptive traits.
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Affiliation(s)
- Heidy M. W. den Besten
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Aarathi Arvind
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Heidi M. S. Gaballo
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Roy Moezelaar
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Food and Biobased Research, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Marcel H. Zwietering
- Laboratory of Food Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Tjakko Abee
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
- * E-mail:
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Allen K, Lepp D, McKellar R, Griffiths M. Targeted microarray analysis of stationary phase Escherichia coli O157:H7 subjected to disparate nutrient conditions. J Appl Microbiol 2010; 109:2118-27. [DOI: 10.1111/j.1365-2672.2010.04843.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Parry-Hanson AA, Jooste PJ, Buys EM. Relative gene expression in acid-adapted Escherichia coli O157:H7 during lactoperoxidase and lactic acid challenge in Tryptone Soy Broth. Microbiol Res 2010; 165:546-56. [DOI: 10.1016/j.micres.2009.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 11/02/2009] [Accepted: 11/07/2009] [Indexed: 11/24/2022]
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Jetter M, Spaniol V, Troller R, Aebi C. Down-regulation of porin M35 in Moraxella catarrhalis by aminopenicillins and environmental factors and its potential contribution to the mechanism of resistance to aminopenicillins. J Antimicrob Chemother 2010; 65:2089-96. [PMID: 20801781 PMCID: PMC2941675 DOI: 10.1093/jac/dkq312] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Objectives The outer membrane protein M35 of Moraxella catarrhalis is an antigenically conserved porin. Knocking out M35 significantly increases the MICs of aminopenicillins. The aim of this study was to determine the biological mechanism of this potentially new antimicrobial resistance mechanism of M. catarrhalis and the behaviour of M35 in general stress situations. Methods PCR using m35-specific primers was used to detect the m35 gene in clinical isolates. The m35 mRNA expression of strains 300, O35E and 415 after exposure to amoxicillin and different stress conditions was measured by real-time PCR and normalized in relation to their 16S rRNA expression. The expression of M35 protein was analysed by SDS-PAGE and western blotting. Results Screening of 52 middle ear isolates resulted in positive PCR products for all tested strains. The analysis of m35 mRNA expression after amoxicillin treatment showed 24%–85% down-regulation compared with the respective amoxicillin-free controls in all three strains tested. Also, analysis of protein concentrations revealed lower M35 expression after growth with amoxicillin. Investigation of M35 during general stress responses showed down-regulation of the porin with growth at 26°C and 42°C, under hyperosmolar stress and under iron restriction. Conclusions The reduced expression of M35 after aminopenicillin exposure indicates a novel resistance mechanism against aminopenicillins in M. catarrhalis, which may be relevant in vivo. The differences in expression after different stress treatments demonstrate that M35 is involved in general stress responses.
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Affiliation(s)
- Marion Jetter
- Institute for Infectious Diseases, University of Bern, CH-3010 Bern, Switzerland
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Olesen I, Jespersen L. Relative gene transcription and pathogenicity of enterohemorrhagic Escherichia coli after long-term adaptation to acid and salt stress. Int J Food Microbiol 2010; 141:248-53. [DOI: 10.1016/j.ijfoodmicro.2010.05.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 05/18/2010] [Accepted: 05/21/2010] [Indexed: 02/02/2023]
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Lopez-Velasco G, Davis M, Boyer RR, Williams RC, Ponder MA. Alterations of the phylloepiphytic bacterial community associated with interactions of Escherichia coli O157:H7 during storage of packaged spinach at refrigeration temperatures. Food Microbiol 2010; 27:476-86. [DOI: 10.1016/j.fm.2009.12.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 12/21/2009] [Accepted: 12/22/2009] [Indexed: 11/25/2022]
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40
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The LysR-type transcriptional regulator QseD alters type three secretion in enterohemorrhagic Escherichia coli and motility in K-12 Escherichia coli. J Bacteriol 2010; 192:3699-712. [PMID: 20494990 DOI: 10.1128/jb.00382-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 responds to the host-produced epinephrine and norepinephrine, and bacterially produced autoinducer 3 (AI-3), through two-component systems. Further integration of multiple regulatory signaling networks, involving regulators such as the LysR-type transcriptional regulator (LTTR) QseA, promotes effective regulation of virulence factors. These include the production of flagella, a phage-encoded Shiga toxin, and genes within the locus of enterocyte effacement (LEE) responsible for attaching and effacing (AE) lesion formation. Here, we describe a new member of this signaling cascade, an LTTR heretofore renamed QseD (quorum-sensing E. coli regulator D). QseD is present in all enterobacteria but exists almost exclusively in O157:H7 isolates as a helix-turn-helix (HTH) truncated isoform. This "short" isoform (sQseD) is still able to regulate gene expression through a different mechanism than the full-length K-12 E. coli "long" QseD isoform (lQseD). The EHEC Delta qseD mutant exhibits increased expression of all LEE operons and deregulation of AE lesion formation. The loss of qseD in EHEC does not affect motility, but the K-12 Delta qseD mutant is hypermotile. While the lQseD directly binds to the ler promoter, encoding the LEE master regulator, to repress LEE transcription, the sQseD isoform does not. LTTRs bind to DNA as tetramers, and these data suggest that sQseD regulates ler by forming heterotetramers with another LTTR. The LTTRs known to regulate LEE transcription, QseA and LrhA, do not interact with sQseD, suggesting that sQseD acts as a dominant-negative partner with a yet-unidentified LTTR.
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Affiliation(s)
- M Begley
- Food for Health Ireland, University College Cork, Cork, Ireland
| | - Colin Hill
- Food for Health Ireland, University College Cork, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland; ,
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Palonen E, Lindström M, Korkeala H. Adaptation of enteropathogenic Yersinia to low growth temperature. Crit Rev Microbiol 2010; 36:54-67. [PMID: 20088683 DOI: 10.3109/10408410903382581] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Yersinia enterocolitica and Yersinia pseudotuberculosis are important foodborne pathogens that cause infections through contaminated refrigerated food. Their cold tolerance mechanisms are therefore of special interest. Adaptation to cold involves changes in protein synthesis and in cell membranes to overcome diminished transcriptional and translational efficiency and reduced fluidity of cell membranes. Studies of low temperature adaptation mechanisms have mainly been performed on mesophilic bacteria, while most modern food hygiene risks are caused by psychrotrophs. Understanding low temperature adaptation of psychrotrophs would help to control these pathogens. This review demonstrates that more studies on cold tolerance mechanisms of psychrotrophs are needed.
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Affiliation(s)
- Eveliina Palonen
- Department of Food and Environmental Hygiene, University of Helsinki, Finland.
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Kyle JL, Parker CT, Goudeau D, Brandl MT. Transcriptome analysis of Escherichia coli O157:H7 exposed to lysates of lettuce leaves. Appl Environ Microbiol 2010; 76:1375-87. [PMID: 20061451 PMCID: PMC2832375 DOI: 10.1128/aem.02461-09] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 12/28/2009] [Indexed: 01/04/2023] Open
Abstract
Harvesting and processing of leafy greens inherently cause plant tissue damage, creating niches on leaves that human pathogens can exploit. We previously demonstrated that Escherichia coli O157:H7 (EcO157) multiplies more rapidly on shredded leaves than on intact leaves (M. T. Brandl, Appl. Environ. Microbiol. 74:5285-5289, 2008). To investigate how EcO157 cells adapt to physicochemical conditions in injured lettuce tissue, we used microarray-based whole-genome transcriptional profiling to characterize gene expression patterns in EcO157 after 15- and 30-min exposures to romaine lettuce lysates. Multiple carbohydrate transport systems that have a role in the utilization of substrates known to be prevalent in plant cells were activated in EcO157. This indicates the availability to the human pathogen of a variety of carbohydrates released from injured plant cells that may promote its extensive growth in leaf lysates and, thus, in wounded leaf tissue. In addition, microarray analysis revealed the upregulation of numerous genes associated with EcO157 attachment and virulence, with oxidative stress and antimicrobial resistance (including the OxyR and Mar regulons), with detoxification of noxious compounds, and with DNA repair. Upregulation of oxidative stress and antimicrobial resistance genes in EcO157 was confirmed on shredded lettuce by quantitative reverse transcription-PCR. We further demonstrate that this adaptation to stress conditions imparts the pathogen with increased resistance to hydrogen peroxide and calcium hypochlorite. This enhanced resistance to chlorinated sanitizers combined with increased expression of virulence determinants and multiplication at sites of injury on the leaves may help explain the association of processed leafy greens with outbreaks of EcO157.
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Affiliation(s)
- Jennifer L. Kyle
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710
| | - Craig T. Parker
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710
| | - Danielle Goudeau
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710
| | - Maria T. Brandl
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710
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Bergholz TM, Vanaja SK, Whittam TS. Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice. Appl Environ Microbiol 2009; 75:3542-53. [PMID: 19346340 PMCID: PMC2687279 DOI: 10.1128/aem.02841-08] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 03/27/2009] [Indexed: 01/05/2023] Open
Abstract
Escherichia coli O157:H7 has caused serious outbreaks of food-borne illness via transmission in a variety of food vehicles, including unpasteurized apple juice, dried salami, and spinach. To understand how this pathogen responds to the multiple stresses of the food environment, we compared global transcription patterns before and after exposure to model apple juice. Transcriptomes of mid-exponential- and stationary-phase cells were evaluated after 10 min in model apple juice (pH 3.5) using microarrays probing 4,886 open reading frames. A total of 331 genes were significantly induced upon exposure of cells to model apple juice, including genes involved in the acid, osmotic, and oxidative stress responses as well as the envelope stress response. Acid and osmotic stress response genes, including asr, osmC, osmB, and osmY, were significantly induced in response to model apple juice. Multiple envelope stress responses were activated as evidenced by increased expression of CpxR and Rcs phosphorelay-controlled genes. Genes controlled by CpxR (cpxP, degP, and htpX) were significantly induced 2- to 15-fold upon exposure to apple juice. Inactivation of CpxRA resulted in a significant decrease in survival of O157:H7 in model apple juice compared to the isogenic parent strain. Of the 331 genes induced in model apple juice, 104 are O157-specific genes, including those encoding type three secretion effectors (espJ, espB, espM2, espL3, and espZ). Elucidating the response of O157:H7 to acidic foods provides insight into how this pathogen is able to survive in food matrices and how exposure to foods influences subsequent transmission and virulence.
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Affiliation(s)
- Teresa M Bergholz
- National Food Safety and Toxicology Center, Michigan State University, East Lansing, 48824, USA.
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45
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Hu Y, Lu P, Wang Y, Ding L, Atkinson S, Chen S. OmpR positively regulates urease expression to enhance acid survival of Yersinia pseudotuberculosis. MICROBIOLOGY-SGM 2009; 155:2522-2531. [PMID: 19443542 DOI: 10.1099/mic.0.028381-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Yersinia pseudotuberculosis is an enteric bacterium which must overcome the acidic stress in host organs for successful colonization, but how this bacterium survives in acidic conditions remains largely unknown. In the present study, the importance of OmpR in acid survival of Y. pseudotuberculosis YpIII was confirmed by the fact that mutation of ompR (strain DeltaompR) greatly reduced cell survival at pH 4.5 or lower. To characterize the regulatory role of OmpR in this acid survival process, proteomic analysis was carried out to compare YpIII at pH 7.0 and pH 4.5 with DeltaompR at pH 7.0, and urease components were revealed to be the main targets for OmpR regulation. Addition of urea to the culture medium also enhanced acid survival of YpIII but not DeltaompR and urease activity was significantly induced by acid in YpIII but not in DeltaompR. Each of the seven components of the YpIII urease gene cluster was fused to a lacZ reporter and their expression was dramatically decreased in a DeltaompR background; this supports the notion that OmpR positively regulates urease expression. Furthermore, gel shift analysis revealed that OmpR binds to the deduced promoter regions of three polycistronic transcriptional units (ureABC, ureEF and ureGD) in the urease cluster, suggesting that the regulation of OmpR to urease components is direct. Taken together, these data strongly suggest that OmpR activates urease expression to enhance acid survival in Y. pseudotuberculosis.
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Affiliation(s)
- Yangbo Hu
- Graduate School of the Chinese Academy of Sciences, Beijing 100049, PR China
- Wuhan Institute of Virology, The Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Pei Lu
- Graduate School of the Chinese Academy of Sciences, Beijing 100049, PR China
- Wuhan Institute of Virology, The Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Yao Wang
- Wuhan Institute of Virology, The Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Lisha Ding
- Graduate School of the Chinese Academy of Sciences, Beijing 100049, PR China
- Wuhan Institute of Virology, The Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Steve Atkinson
- Institute of Infection, Immunity and Inflammation, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Shiyun Chen
- Wuhan Institute of Virology, The Chinese Academy of Sciences, Wuhan 430071, PR China
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