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Im H, Hwang SH, Kim BS, Choi SH. Pathogenic potential assessment of the Shiga toxin-producing Escherichia coli by a source attribution-considered machine learning model. Proc Natl Acad Sci U S A 2021; 118:e2018877118. [PMID: 33986113 PMCID: PMC8157976 DOI: 10.1073/pnas.2018877118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Instead of conventional serotyping and virulence gene combination methods, methods have been developed to evaluate the pathogenic potential of newly emerging pathogens. Among them, the machine learning (ML)-based method using whole-genome sequencing (WGS) data are getting attention because of the recent advances in ML algorithms and sequencing technologies. Here, we developed various ML models to predict the pathogenicity of Shiga toxin-producing Escherichia coli (STEC) isolates using their WGS data. The input dataset for the ML models was generated using distinct gene repertoires from positive (pathogenic) and negative (nonpathogenic) control groups in which each STEC isolate was designated based on the source attribution, the relative risk potential of the isolation sources. Among the various ML models examined, a model using the support vector machine (SVM) algorithm, the SVM model, discriminated between the two control groups most accurately. The SVM model successfully predicted the pathogenicity of the isolates from the major sources of STEC outbreaks, the isolates with the history of outbreaks, and the isolates that cannot be assessed by conventional methods. Furthermore, the SVM model effectively differentiated the pathogenic potentials of the isolates at a finer resolution. Permutation importance analyses of the input dataset further revealed the genes important for the estimation, proposing the genes potentially essential for the pathogenicity of STEC. Altogether, these results suggest that the SVM model is a more reliable and broadly applicable method to evaluate the pathogenic potential of STEC isolates compared with conventional methods.
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Affiliation(s)
- Hanhyeok Im
- National Research Laboratory of Molecular Microbiology and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Center for Food Safety and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea
| | - Seung-Ho Hwang
- National Research Laboratory of Molecular Microbiology and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Center for Food Safety and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea
| | - Byoung Sik Kim
- Department of Food Science and Engineering, Ewha Womans University, 03760 Seoul, Republic of Korea
| | - Sang Ho Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea;
- Department of Agricultural Biotechnology and Center for Food Safety and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, 08826 Seoul, Republic of Korea
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Romão FT, Martins FH, Hernandes RT, Ooka T, Santos FF, Yamamoto D, Bonfim-Melo A, Jones N, Hayashi T, Elias WP, Sperandio V, Gomes TAT. Genomic Properties and Temporal Analysis of the Interaction of an Invasive Escherichia albertii With Epithelial Cells. Front Cell Infect Microbiol 2020; 10:571088. [PMID: 33392102 PMCID: PMC7772469 DOI: 10.3389/fcimb.2020.571088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/03/2020] [Indexed: 12/17/2022] Open
Abstract
Diarrhea is one of the main causes of infant mortality worldwide, mainly in the developing world. Among the various etiologic agents, Escherichia albertii is emerging as an important human enteropathogen. E. albertii promote attaching and effacing (AE) lesions due to the presence of the locus of enterocyte effacement (LEE) that encodes a type three secretion system (T3SS), the afimbrial adhesin intimin and its translocated receptor, Tir, and several effector proteins. We previously showed that E. albertii strain 1551-2 invades several epithelial cell lineages by a process that is dependent on the intimin-Tir interaction. To understand the contribution of T3SS-dependent effectors present in E. albertii 1551-2 during the invasion process, we performed a genetic analysis of the LEE and non-LEE genes and evaluated the expression of the LEE operons in various stages of bacterial interaction with differentiated intestinal Caco-2 cells. The kinetics of the ability of the 1551-2 strain to colonize and form AE lesions was also investigated in epithelial HeLa cells. We showed that the LEE expression was constant during the early stages of infection but increased at least 4-fold during bacterial persistence in the intracellular compartment. An in silico analysis indicated the presence of a new tccP/espFU subtype, named tccP3. We found that the encoded protein colocalizes with Tir and polymerized F-actin during the infection process in vitro. Moreover, assays performed with Nck null cells demonstrated that the 1551-2 strain can trigger F-actin polymerization in an Nck-independent pathway, despite the fact that TccP3 is not required for this phenotype. Our study highlights the importance of the T3SS during the invasion process and for the maintenance of E. albertii 1551-2 inside the cells. In addition, this work may help to elucidate the versatility of the T3SS for AE pathogens, which are usually considered extracellular and rarely reach the intracellular environment.
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Affiliation(s)
- Fabiano T Romão
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo (EPM-UNIFESP), São Paulo, Brazil.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Fernando H Martins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Rodrigo T Hernandes
- Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, Brazil
| | - Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Fernanda F Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Denise Yamamoto
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo (EPM-UNIFESP), São Paulo, Brazil.,Universidade Santo Amaro, São Paulo, Brazil
| | - Alexis Bonfim-Melo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Nina Jones
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Waldir P Elias
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Vanessa Sperandio
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Tânia A T Gomes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo (EPM-UNIFESP), São Paulo, Brazil
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EspFu-Mediated Actin Assembly Enhances Enteropathogenic Escherichia coli Adherence and Activates Host Cell Inflammatory Signaling Pathways. mBio 2020; 11:mBio.00617-20. [PMID: 32291304 PMCID: PMC7157822 DOI: 10.1128/mbio.00617-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
EPEC is among the leading causes of diarrheal disease worldwide. The colonization of the gut mucosa by EPEC results in actin pedestal formation at the site of bacterial attachment. These pedestals are referred to as attaching and effacing (AE) lesions. Here, we exploit the different molecular mechanisms used by EPEC to induce AE lesions on epithelial cells, showing that the effector EspFu is associated with increased bacterial attachment and enhanced epithelial colonization compared to the Tir-Nck pathway. Moreover, we also showed that actin pedestal formation can counterbalance the anti-inflammatory activity induced by EPEC, especially when driven by EspFu. Collectively, our findings provide new insights into virulence mechanisms employed by EPEC to colonize epithelial cells, as well as the host response to this enteric pathogen. The translocation of effectors into the host cell through type 3 secretion systems (T3SS) is a sophisticated strategy employed by pathogenic bacteria to subvert host responses and facilitate colonization. Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) utilize the Tir and EspFu (also known as TccP) effectors to remodel the host cytoskeleton, culminating in the formation of attaching and effacing (AE) lesions on enterocytes. While some EPEC strains require tyrosine phosphorylation of Tir and recruitment of the host Nck to trigger actin polymerization, EHEC and certain EPEC strains, whose Tir is not phosphorylated, rely on the effector EspFu for efficient actin remodeling. Here, we investigated the role played by Tir-Nck and Tir-EspFu actin polymerization pathways during the infection of epithelial cells, as well as the host transcriptional response to the AE lesion formation induced by EPEC. We found that EspFu-mediated actin assembly promotes bacterial attachment and epithelial colonization more efficiently than Tir-Nck. Moreover, we showed that both actin polymerization mechanisms can activate inflammatory pathways and reverse the anti-inflammatory response induced by EPEC in epithelial cells. However, this activity is remarkably more evident in infections with EspFu-expressing EPEC strains. This study demonstrates the complex interactions between effector-mediated actin remodeling and inflammation. Different strains carry different combinations of these two effectors, highlighting the plasticity of pathogenic E. coli enteric infections.
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Vieira MA, Dias RCB, Dos Santos LF, Rall VLM, Gomes TAT, Hernandes RT. Diversity of strategies used by atypical enteropathogenic Escherichia coli to induce attaching and effacing lesion in epithelial cells. J Med Microbiol 2019; 68:940-951. [PMID: 31107199 DOI: 10.1099/jmm.0.000998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE This study aimed to characterize 82 atypical enteropathogenic Escherichia coli (aEPEC) isolates, obtained from patients with diarrhea in Brazil, regarding their adherence patterns on HeLa cells and attaching and effacing (AE) lesion pathways. METHODOLOGY The adherence and fluorescence-actin staining (FAS) assays were performed using HeLa cells. AE lesion pathways were determined through the detection of tyrosine residue 474 (Y474) phosphorylation in the Tir protein, after its translocation to host cells, and by PCR assays for tir genotyping and detection of Tir-cytoskeleton coupling protein (tccP) genes. RESULTS Regarding the adherence pattern, determined in the presence of d-mannose, 12 isolates (14.6 %) showed the localized adherence (LA)-like pattern, 3 (3.7 %) the aggregative adherence pattern and 4 (4.9 %) a hybrid LA/diffuse adherence pattern. In addition, 36 (43.9 %) isolates displayed an undefined adherence, and 26 (31.7 %) were non-adherent (NA), while one (1.2 %) caused cell detachment. Among the 26 NA aEPEC isolates, 11 showed a type 1 pilus-dependent adherence in assays performed without d-mannose, while 15 remained NA. Forty-eight (58.5 %) aEPEC were able to trigger F-actin accumulation underneath adherent bacteria (FAS-positive), which is an important feature of AE lesions. The majority (58.3 %) of these used the Tir-Nck pathway, while 39.6 % may use both Tir-Nck and Tir-TccP pathways to induce AE lesions. CONCLUSION Our results reveal the diversity of strategies used by aEPEC isolates to interact with and damage epithelial host cells, thereby causing diarrheal diseases.
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Affiliation(s)
- Melissa A Vieira
- 1 Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Botucatu, SP, Brazil
| | - Regiane C B Dias
- 1 Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Botucatu, SP, Brazil
| | - Luís F Dos Santos
- 2 Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), São Paulo SP, Brazil
| | - Vera L M Rall
- 1 Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Botucatu, SP, Brazil
| | - Tânia A T Gomes
- 3 Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo SP, Brazil
| | - Rodrigo T Hernandes
- 1 Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Botucatu, SP, Brazil
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Arais LR, Barbosa AV, Andrade JRC, Gomes TAT, Asensi MD, Aires CAM, Cerqueira AMF. Zoonotic potential of atypical enteropathogenic Escherichia coli (aEPEC) isolated from puppies with diarrhoea in Brazil. Vet Microbiol 2018; 227:45-51. [PMID: 30473351 DOI: 10.1016/j.vetmic.2018.10.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 10/10/2018] [Accepted: 10/23/2018] [Indexed: 02/02/2023]
Abstract
Recent studies point atypical enteropathogenic Escherichia coli (aEPEC) to be an important agent in childhood diarrhoea in Brazil. aEPEC are commonly found in various animal species, including dogs. Although the true zoonotic risk remains unknown, some strains recovered from dogs present the same serotypes and carry the same virulence genes implicated in human disease. In this study, we compared the virulence and genetic relationship among a set of aEPEC strains previously isolated from diarrheic faeces from companion dogs and humans. A total of 17 strains, 12 from puppies and five from children, were studied. The strains were assessed for: (i) presence of virulence-associated genes (a total of 31 genes) using PCR assays; (ii) genetic relationship by Random Amplified Polymorphic DNA (RAPD), Multilocus Sequence Typing (MLST) and Pulsed-field Gel Electrophoresis (PFGE); and (iii) adherence pattern in intestinal Caco-2 cells. The occurrence of virulence genes was similar between the canine and human isolates presenting the same serotype. The fimbrial genes ecpA and fimH were the most frequently detected, followed by hcpA, tccP, tccP2, lpfA1, lpfA2, astA and toxB genes. Several nle genes were also detected, with one canine strain (O156:H- / ST327) showing all PAI O-122 genes investigated (efa-1, nleB, nleE and ent/espL2). Canine and human strains of the same serotype were grouped into a single cluster by RAPD and PFGE, in which the ST10 and ST206 were identified. Additionally, most of the strains exhibited a localized adherence-like phenotype when interacting with Caco-2 cells. The results showed that some canine aEPEC strains share virulence genes commonly found in human pathogenic strains. Moreover, strains of the same serotype, isolated from dogs and children, share virulence genes and are phylogenetically close, suggesting a potential zoonotic risk.
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Affiliation(s)
- Lavicie R Arais
- Laboratório de Enteropatógenos, Microbiologia Veterinária e de Alimentos, Universidade Federal Fluminense, Professor Hernani Melo Street, 101, Niterói, RJ, 24210-130, Brazil
| | - André V Barbosa
- Laboratório de Enteropatógenos, Microbiologia Veterinária e de Alimentos, Universidade Federal Fluminense, Professor Hernani Melo Street, 101, Niterói, RJ, 24210-130, Brazil.
| | - João R C Andrade
- Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade do Estado do Rio de Janeiro. Prof., Manuel de Abreu Avenue, 444, Rio de Janeiro, RJ, 20550-170, Brazil
| | - Tânia A T Gomes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Botucatu Street, 862, São Paulo, SP, 04023-062, Brazil
| | - Marise D Asensi
- Laboratório de Pesquisa em Infecção Hospitalar, Fundação Oswaldo Cruz, Brasil Avenue, 4365, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Caio A M Aires
- Laboratório de Pesquisa em Infecção Hospitalar, Fundação Oswaldo Cruz, Brasil Avenue, 4365, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Aloysio M F Cerqueira
- Laboratório de Enteropatógenos, Microbiologia Veterinária e de Alimentos, Universidade Federal Fluminense, Professor Hernani Melo Street, 101, Niterói, RJ, 24210-130, Brazil
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