1
|
Fagerlund A, Aspholm M, Węgrzyn G, Lindbäck T. High diversity in the regulatory region of Shiga toxin encoding bacteriophages. BMC Genomics 2022; 23:230. [PMID: 35331132 PMCID: PMC8951638 DOI: 10.1186/s12864-022-08428-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/28/2022] [Indexed: 12/26/2022] Open
Abstract
Background Enterohemorrhagic Escherichia coli (EHEC) is an emerging health challenge worldwide and outbreaks caused by this pathogen poses a serious public health concern. Shiga toxin (Stx) is the major virulence factor of EHEC, and the stx genes are carried by temperate bacteriophages (Stx phages). The switch between lysogenic and lytic life cycle of the phage, which is crucial for Stx production and for severity of the disease, is regulated by the CI repressor which maintain latency by preventing transcription of the replication proteins. Three EHEC phage replication units (Eru1-3) in addition to the classical lambdoid replication region have been described previously, and Stx phages carrying the Eru1 replication region were associated with highly virulent EHEC strains. Results In this study, we have classified the Eru replication region of 419 Stx phages. In addition to the lambdoid replication region and three already described Erus, ten novel Erus (Eru4 to Eru13) were detected. The lambdoid type, Eru1, Eru4 and Eru7 are widely distributed in Western Europe. Notably, EHEC strains involved in severe outbreaks in England and Norway carry Stx phages with Eru1, Eru2, Eru5 and Eru7 replication regions. Phylogenetic analysis of CI repressors from Stx phages revealed eight major clades that largely separate according to Eru type. Conclusion The classification of replication regions and CI proteins of Stx phages provides an important platform for further studies aimed to assess how characteristics of the replication region influence the regulation of phage life cycle and, consequently, the virulence potential of the host EHEC strain. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08428-5.
Collapse
Affiliation(s)
- Annette Fagerlund
- Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Marina Aspholm
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdañsk, Gdañsk, Poland
| | - Toril Lindbäck
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway.
| |
Collapse
|
2
|
Flowers LJ, Hu S, Shrestha A, Martinot AJ, Leong JM, Osburne MS. Citrobacter rodentium Lysogenized with a Shiga Toxin-Producing Phage: A Murine Model for Shiga Toxin-Producing E. coli Infection. Methods Mol Biol 2021; 2291:381-397. [PMID: 33704765 DOI: 10.1007/978-1-0716-1339-9_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Shiga toxin-producing E. coli (STEC) is a common foodborne pathogen in developed countries. STEC generates "attaching and effacing" (AE) lesions on colonic epithelium, characterized by effacement of microvilli and the formation of actin "pedestals" beneath intimately attached bacteria. In addition, STEC are lysogenized with a phage that, upon induction, can produce potent Shiga toxins (Stx), potentially leading to both hemorrhagic colitis and hemolytic uremic syndrome. Investigation of the pathogenesis of this disease has been challenging because STEC does not readily colonize conventional mice.Citrobacter rodentium (CR) is a related mouse pathogen that also generates AE lesions. Whereas CR does not produce Stx, a murine model for STEC utilizes CR lysogenized with an E. coli-derived Stx phage, generating CR(Φstx), which both colonizes conventional mice and readily gives rise to systemic disease. We present here key methods for the use of CR(Φstx) infection as a highly predictable murine model for infection and disease by STEC. Importantly, we detail CR(Φstx) inoculation by feeding, determination of pathogen colonization, production of phage and toxin, and assessment of intestinal and renal pathology. These methods provide a framework for studying STEC-mediated systemic disease that may aid in the development of efficacious therapeutics.
Collapse
Affiliation(s)
- Laurice J Flowers
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.,Tufts University Graduate School in Biomedical Sciences, Boston, MA, USA.,Department of Dermatology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shenglan Hu
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.,Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding, Guangzhou, China
| | - Anishma Shrestha
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Amanda J Martinot
- Department of Infectious Diseases and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - John M Leong
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Marcia S Osburne
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
| |
Collapse
|
3
|
Llarena AK, Aspholm M, O'Sullivan K, Wêgrzyn G, Lindbäck T. Replication Region Analysis Reveals Non-lambdoid Shiga Toxin Converting Bacteriophages. Front Microbiol 2021; 12:640945. [PMID: 33868197 PMCID: PMC8044961 DOI: 10.3389/fmicb.2021.640945] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/16/2021] [Indexed: 11/22/2022] Open
Abstract
Shiga toxin is the major virulence factor of enterohemorrhagic Escherichia coli (EHEC), and the gene encoding it is carried within the genome of Shiga toxin-converting phages (Stx phages). Numerous Stx phages have been sequenced to gain a better understanding of their contribution to the virulence potential of EHEC. The Stx phages are classified into the lambdoid phage family based on similarities in lifestyle, gene arrangement, and nucleotide sequence to the lambda phages. This study explores the replication regions of non-lambdoid Stx phages that completely lack the O and P genes encoding the proteins involved in initiating replication in the lambdoid phage genome. Instead, they carry sequences encoding replication proteins that have not been described earlier, here referred to as eru genes (after EHEC phage replication unit genes). This study identified three different types of Eru-phages, where the Eru1-type is carried by the highly pathogenic EHEC strains that caused the Norwegian O103:H25 outbreak in 2006 and the O104:H4 strain that caused the large outbreak in Europe in 2011. We show that Eru1-phages exhibit a less stable lysogenic state than the classical lambdoid Stx phages. As production of phage particles is accompanied by production of Stx toxin, the Eru1-phage could be associated with a high-virulence phenotype of the host EHEC strain. This finding emphasizes the importance of classifying Stx phages according to their replication regions in addition to their Stx-type and could be used to develop a novel strategy to identify highly virulent EHEC strains for improved risk assessment and management.
Collapse
Affiliation(s)
- Ann-Katrin Llarena
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Marina Aspholm
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Kristin O'Sullivan
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Grzegorz Wêgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdañsk, Gdañsk, Poland
| | - Toril Lindbäck
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| |
Collapse
|
4
|
Mohaisen MR, McCarthy AJ, Adriaenssens EM, Allison HE. The Site-Specific Recombination System of the Escherichia coli Bacteriophage Φ24 B. Front Microbiol 2020; 11:578056. [PMID: 33162958 PMCID: PMC7581858 DOI: 10.3389/fmicb.2020.578056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/15/2020] [Indexed: 11/13/2022] Open
Abstract
Stx bacteriophages are members of the lambdoid group of phages and are responsible for Shiga toxin (Stx) production and the dissemination of Shiga toxin genes (stx) across shigatoxigenic Escherichia coli (STEC). These toxigenic bacteriophage hosts can cause life-threatening illnesses, and Stx is the virulence determinant responsible for the severe nature of infection with enterohemorrhagic E. coli, a subset of pathogenic STEC. Stx phages are temperate, and in the present study, the identification of what is actually required for Stx phage Φ24B and bacterial DNA recombination was tested using both in vitro and in situ recombination assays. It is well established that phage λ, which underpins most of what we understand about lambdoid phage biology, requires its own encoded phage attachment site (attP) of 250 bp, a host-encoded attachment site (attB) of 21 bp, and a host-encoded DNA binding protein known as integration host factor (IHF). The assays applied in this study enabled the manipulation of the phage attachment site (attP) and the bacterial attachment site (attB) sequences and the inclusion or exclusion of a host-encoded accessory element known as integration host factor. We were able to demonstrate that the minimal attP sequence required by Φ24B phage is between 350 and 427 bp. Unlike phage λ, the minimal necessary flanking sequences for the attB site do not appear to be equal in size, with a total length between 62 and 93 bp. Furthermore, we identified that the Φ24B integrase does not require IHF to drive the integration and the recombination process. Understanding how this unusual Stx phage integrase works may enable exploitation of its promiscuous nature in the context of genetic engineering.
Collapse
Affiliation(s)
- Mohammed Radhi Mohaisen
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,College of Dentistry, University of Anbar, Ramadi, Iraq
| | - Alan John McCarthy
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | | | - Heather Elizabeth Allison
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
5
|
Long JZ, Xu YK, Duan GC, Liang WJ, Liu HY, Chen SY, Xi YL, Wang PF, Wang YF. [Association between phage-mediated shiga toxin and molecular distribution of CRISPR in Escherichia coli O26 ∶ H11 or NM]. Zhonghua Liu Xing Bing Xue Za Zhi 2017; 38:944-949. [PMID: 28738471 DOI: 10.3760/cma.j.issn.0254-6450.2017.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Objective: To investigate the association between phage-mediated shiga toxin and molecular distribution of CRISPR in Escherichia (E.) coli O26∶H11 or NM. Methods: A total of 135 E. coli O26 ∶ H11 or NM strains were collected from NCBI database. Software CRT and CRISPR Finder were used to extract CRISPR and Excel was used to assign the spacer of unique number and type CRISPR. And the relationship between CRISPR and stx phage was analyzed. Results: All the 135 E. coli O26 ∶ H11 or NM strains had the CRISPR. For CRISPR1, CRISPR2.1, CRISPR2.2 and CRISPR3-4, 19, 22, 1 and 1 subtypes were found, respectively. According to the four CRISPR sites, the strains could be divided into 40 subtypes. Stx-phage was only observed in the group C of CRISPR. Compared with E. coli of stx-phage negative, E. coli with stx-phage harbored more spacers. Conclusions: CRISPR loci was extensively existed in E. coli O26∶H11 or NM, and many subtypes were found in these strains. The presence of stx-phage was related to the molecular distribution of CRISPR in E. coli O26∶H11 or NM. CRISPR might be a valuable biomarker to identify strains with high virulent potential.
Collapse
Affiliation(s)
- J Z Long
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Y K Xu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - G C Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - W J Liang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - H Y Liu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - S Y Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Y L Xi
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - P F Wang
- University Health Service, Henan University of Science and Technology, Luoyang 471023, China
| | - Y F Wang
- Department of Preventive Medicine, Henan University of Science and Technology, Luoyang 471023, China
| |
Collapse
|
6
|
Cao D, Ji W, Fu Q, Lu C, Wang H, Sun J, Yan Y. Escherichia coli nfuA is essential for maintenance of Shiga toxin phage Min27 lysogeny under iron-depleted condition. FEMS Microbiol Lett 2015; 362:fnv149. [PMID: 26337151 DOI: 10.1093/femsle/fnv149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2015] [Indexed: 11/14/2022] Open
Abstract
It has been earlier hypothesized that lysogenic infection with Stx-encoding phages influences protein expression in the bacterial host, and therefore, some differentially expressed proteins could affect survival characteristics and pathogenicity. We compared the protein expression profiles of the host MG1655 and lysogens by 2D electrophoresis. Four different genes identified were all related to Fe/S subunit production, namely, nfuA, fdoH, sdhB and ftnA. To explore the role of nfuA in the biology of Stx prophage lysogeny, gene knockout experiments and phage lysogenic conversion were performed. The inactivation of nfuA caused the prophage to enter its lytic life cycle, especially under an iron-depleted condition. A similar activity was also detected in the Escherichia coli O157:H7 strain from which the Stx phage Min 27 was originally isolated. NfuA might be the positive regulator of genes controlling lysogenic cycle such as cI, cII and cIII since their transcriptional level was significantly reduced in nfuA deletion mutant as shown by qRT-PCR. We conclude that NfuA is essential for maintenance of Stx phage lysogeny in host's genetic reservoir under iron-deficient condition.
Collapse
Affiliation(s)
- Dongmei Cao
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Wenhui Ji
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Qiang Fu
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Chenping Lu
- Key Laboratory of Animal Disease Diagnosis and Immunology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China
| | - Hengan Wang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Jianhe Sun
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Yaxian Yan
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China;
| |
Collapse
|