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Bonardi S, Conter M, Andriani L, Bacci C, Magagna G, Rega M, Lamperti L, Loiudice C, Pierantoni M, Filipello V. Emerging of Shiga toxin-producing Escherichia coli O177:H11 and O177:H25 from cattle at slaughter in Italy. Int J Food Microbiol 2024; 423:110846. [PMID: 39079448 DOI: 10.1016/j.ijfoodmicro.2024.110846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/18/2024]
Abstract
Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens frequently carried by cattle, responsible in humans of mild to bloody diarrhoea, haemolytic uraemic syndrome (HUS) and even death. In 2023-2024, a study on STEC contamination of hide and carcasses of dairy cattle at slaughter was planned in Emilia-Romagna region (northern Italy). When the study was still in progress and 60 animals were sampled, the detection of STEC O177 isolates reached high rates and gained our attention. A total of five O177 STEC strains were detected, namely four from three carcasses (5.0 %) and one from a hide sample (1.7 %). The isolates were typed by WGS as following: 1) STEC O177:H11 sequence type (ST) 765 (stx2a+, eae+), detected from one carcass; 2) STEC O177:H25 ST659 (stx2c+, eae+) detected from three carcasses and one hide sample. One carcass was contaminated by both STEC serotypes. The isolates carried other virulence determinants often found in STEC strains associated with HUS, namely the exha, astA and espP genes, together with genes for adhesion to the epithelial cells of the gut (lpfA, fdeC, fimH) and non-Locus for Enterocyte Effacement (LEE) effector protein genes (nleA, nleB). The STEC O177:H11 isolate harboured antimicrobial resistance (AMR) genes to β-lactams (blaTEM-1A), aminoglycosides (aadA1, aph(3″)-Ib, aph(6)-Id), trimethoprim (dfrA1), sulphonamides (sul1, sul2), tetracyclines (tetA), (tetB), streptothricin (sat2), and quaternary ammonium compounds (qacEdelta1). On the contrary, the STEC O177:H25 isolates carried no AMR genes. Persistent carriage of STEC O177:H25 ST659 (stx2c+, eae+) at farm level was assessed by testing animals of the same herd sent to slaughter. Interestingly, the colonies of STEC O177:H11 and STEC O177:H25 had different morphology on CHROMagar™ STEC plates, being mauve and colourless, respectively. Since mauve is the colour STEC colonies commonly have on the CHROMagar™ STEC medium, our findings can help microbiologists in the selection of uncommon serotypes. To the best of our knowledge, this is the first detection of STEC O177 from carcasses and hides of dairy cattle at slaughter. Noteworthy, the STEC-positive hide was classified as "very dirty" thus stressing the need of clean animals entering the slaughter chain, as required by Regulation (EC) No 853/2004. Since STEC O177 has been responsible of HUS in Europe, our data could add information on the source of uncommon serogroups in human infections.
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Affiliation(s)
- Silvia Bonardi
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy.
| | - Mauro Conter
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - Laura Andriani
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - Cristina Bacci
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - Giulia Magagna
- Department of Food Safety, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Via Bianchi 9, 25124 Brescia, Italy
| | - Martina Rega
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - Luca Lamperti
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - Carlo Loiudice
- National Veterinary Service, Via Vasari 13/A, 43126 Parma, Italy
| | - Marco Pierantoni
- National Veterinary Service, Via Vasari 13/A, 43126 Parma, Italy
| | - Virginia Filipello
- Department of Food Safety, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Via Bianchi 9, 25124 Brescia, Italy
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Szulc N, Gąsior-Głogowska M, Żyłka P, Szefczyk M, Wojciechowski JW, Żak AM, Dyrka W, Kaczorowska A, Burdukiewicz M, Tarek M, Kotulska M. Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124094. [PMID: 38503257 DOI: 10.1016/j.saa.2024.124094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
The most studied functional amyloid is the CsgA, major curli subunit protein, which is produced by numerous strains of Enterobacteriaceae. Although CsgA sequences are highly conserved, they exhibit species diversity, which reflects the specific evolutionary and functional adaptability of the major curli subunit. Herein, we performed bioinformatics analyses to uncover the differences in the amyloidogenic properties of the R4 fragments in Escherichia coli and Salmonella enterica and proposed four mutants for more detailed studies: M1, M2, M3, and M4. The mutated sequences were characterized by various experimental techniques, such as circular dichroism, ATR-FTIR, FT-Raman, thioflavin T, transmission electron microscopy and confocal microscopy. Additionally, molecular dynamics simulations were performed to determine the role of buffer ions in the aggregation process. Our results demonstrated that the aggregation kinetics, fibril morphology, and overall structure of the peptide were significantly affected by the positions of charged amino acids within the repeat sequences of CsgA. Notably, substituting glycine with lysine resulted in the formation of distinctive spherically packed globular aggregates. The differences in morphology observed are attributed to the influence of phosphate ions, which disrupt the local electrostatic interaction network of the polypeptide chains. This study provides knowledge on the preferential formation of amyloid fibrils based on charge states within the polypeptide chain.
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Affiliation(s)
- Natalia Szulc
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland; CNRS, University of Lorraine, F-5400 Nancy, France; Department of Physics and Biophysics, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paweł Żyłka
- Department of Electrical Engineering Fundamentals, Faculty of Electrical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jakub W Wojciechowski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej M Żak
- Institute of Advanced Materials, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Witold Dyrka
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Aleksandra Kaczorowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland; Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Michał Burdukiewicz
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Campus Universitat Autònoma de Barcelona Plaça Cívica Bellaterra, s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain; Clinical Research Centre, Medical University of Bialystok, Jana Kilinskiego 1, 15-089 Bialystok, Poland
| | - Mounir Tarek
- CNRS, University of Lorraine, F-5400 Nancy, France.
| | - Malgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
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Wojciechowski JW, Szczurek W, Szulc N, Szefczyk M, Kotulska M. PACT - Prediction of amyloid cross-interaction by threading. Sci Rep 2023; 13:22268. [PMID: 38097650 PMCID: PMC10721876 DOI: 10.1038/s41598-023-48886-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Amyloid proteins are often associated with the onset of diseases, including Alzheimer's, Parkinson's and many others. However, there is a wide class of functional amyloids that are involved in physiological functions, e.g., formation of microbial biofilms or storage of hormones. Recent studies showed that an amyloid fibril could affect the aggregation of another protein, even from a different species. This may result in amplification or attenuation of the aggregation process. Insight into amyloid cross-interactions may be crucial for better understanding of amyloid diseases and the potential influence of microbial amyloids on human proteins. However, due to the demanding nature of the needed experiments, knowledge of such interactions is still limited. Here, we present PACT (Prediction of Amyloid Cross-interaction by Threading) - the computational method for the prediction of amyloid cross-interactions. The method is based on modeling of a heterogeneous fibril formed by two amyloidogenic peptides. The resulting structure is assessed by the structural statistical potential that approximates its plausibility and energetic stability. PACT was developed and first evaluated mostly on data collected in the AmyloGraph database of interacting amyloids and achieved high values of Area Under ROC (AUC=0.88) and F1 (0.82). Then, we applied our method to study the interactions of CsgA - a bacterial biofilm protein that was not used in our in-reference datasets, which is expressed in several bacterial species that inhabit the human intestines - with two human proteins. The study included alpha-synuclein, a human protein that is involved in Parkinson's disease, and human islet amyloid polypeptide (hIAPP), which is involved in type 2 diabetes. In both cases, PACT predicted the appearance of cross-interactions. Importantly, the method indicated specific regions of the proteins, which were shown to play a central role in both interactions. We experimentally confirmed the novel results of the indicated CsgA fragments interacting with hIAPP based on the kinetic characteristics obtained with the ThT assay. PACT opens the possibility of high-throughput studies of amyloid interactions. Importantly, it can work with fairly long protein fragments, and as a purely physicochemical approach, it relies very little on scarce training data. The tool is available as a web server at https://pact.e-science.pl/pact/ . The local version can be downloaded from https://github.com/KubaWojciechowski/PACT .
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Affiliation(s)
- Jakub W Wojciechowski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland.
| | - Witold Szczurek
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland
| | - Natalia Szulc
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland
- Department of Physics and Biophysics, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375, Wrocław, Poland
- LPCT, CNRS, Université de Lorraine, F-54000, Nancy, France
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, 50-370, Wrocław, Poland
| | - Malgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland.
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Cámara-Almirón J, Domínguez-García L, El Mammeri N, Lends A, Habenstein B, de Vicente A, Loquet A, Romero D. Molecular characterization of the N-terminal half of TasA during amyloid-like assembly and its contribution to Bacillus subtilis biofilm formation. NPJ Biofilms Microbiomes 2023; 9:68. [PMID: 37739955 PMCID: PMC10516879 DOI: 10.1038/s41522-023-00437-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
Biofilms are bacterial communities that result from a cell differentiation process leading to the secretion of an extracellular matrix (ECM) by part of the population. In Bacillus subtilis, the main protein component of the ECM is TasA, which forms a fiber-based scaffold that confers structure to the ECM. The N-terminal half of TasA is strongly conserved among Bacillus species and contains a protein domain, the rigid core (RcTasA), which is critical for the structural and functional properties of the recombinant protein. In this study, we demonstrate that recombinantly purified RcTasA in vitro retains biochemical properties previously observed for the entire protein. Further analysis of the RcTasA amino acid sequence revealed two aggregation-prone stretches and a region of imperfect amino acid repeats, which are known to contribute to functional amyloid assembly. Biochemical characterization of these stretches found in RcTasA revealed their amyloid-like capacity in vitro, contributing to the amyloid nature of RcTasA. Moreover, the study of the imperfect amino acid repeats revealed the critical role of residues D64, K68 and D69 in the structural function of TasA. Experiments with versions of TasA carrying the substitutions D64A and K68AD69A demonstrated a partial loss of function of the protein either in the assembly of the ECM or in the stability of the core and amyloid-like properties. Taken together, our findings allow us to better understand the polymerization process of TasA during biofilm formation and provide knowledge into the sequence determinants that promote the molecular behavior of protein filaments in bacteria.
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Affiliation(s)
- Jesús Cámara-Almirón
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, Lausanne, Switzerland
| | - Laura Domínguez-García
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
| | - Nadia El Mammeri
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV, 1006, Latvia
| | - Birgit Habenstein
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
| | - Antonio de Vicente
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
| | - Diego Romero
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain.
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Basha S, Mukunda DC, Rodrigues J, Gail D'Souza M, Gangadharan G, Pai AR, Mahato KK. A comprehensive review of protein misfolding disorders, underlying mechanism, clinical diagnosis, and therapeutic strategies. Ageing Res Rev 2023; 90:102017. [PMID: 37468112 DOI: 10.1016/j.arr.2023.102017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
INTRODUCTION Proteins are the most common biological macromolecules in living system and are building blocks of life. They are extremely dynamic in structure and functions. Due to several modifications, proteins undergo misfolding, leading to aggregation and thereby developing neurodegenerative and systemic diseases. Understanding the pathology of these diseases and the techniques used to diagnose them is therefore crucial for their effective management . There are several techniques, currently being in use to diagnose them and those will be discussed in this review. AIM/OBJECTIVES Current review aims to discuss an overview of protein aggregation and the underlying mechanisms linked to neurodegeneration and systemic diseases. Also, the review highlights protein misfolding disorders, their clinical diagnosis, and treatment strategies. METHODOLOGY Literature related to neurodegenerative and systemic diseases was explored through PubMed, Google Scholar, Scopus, and Medline databases. The keywords used for literature survey and analysis are protein aggregation, neurodegenerative disorders, Alzheimer's disease, Parkinson's disease, systemic diseases, protein aggregation mechanisms, etc. DISCUSSION /CONCLUSION: This review summarises the pathogenesis of neurodegenerative and systemic disorders caused by protein misfolding and aggregation. The clinical diagnosis and therapeutic strategies adopted for the management of these diseases are also discussed to aid in a better understanding of protein misfolding disorders. Many significant concerns about the role, characteristics, and consequences of protein aggregates in neurodegenerative and systemic diseases are not clearly understood to date. Regardless of technological advancements, there are still great difficulties in the management and cure of these diseases. Therefore, for better understanding, diagnosis, and treatment of neurodegenerative and systemic diseases, more studies to identify novel drugs that may aid in their treatment and management are required.
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Affiliation(s)
- Shaik Basha
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | | | - Jackson Rodrigues
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Meagan Gail D'Souza
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Gireesh Gangadharan
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Aparna Ramakrishna Pai
- Department of Neurology, Kasturba Medical College - Manipal, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Krishna Kishore Mahato
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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Zhao D, Peng Z, Fang J, Fang Z, Zhang J. Programmable and low-cost biohybrid membrane for efficient heavy metal removal from water. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2022.122751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sivaranjani M, Hansen EG, Perera SR, Flores PA, Tükel Ç, White AP. Purification of the Bacterial Amyloid "Curli" from Salmonella enterica Serovar Typhimurium and Detection of Curli from Infected Host Tissues. Bio Protoc 2022; 12:e4419. [PMID: 35813019 PMCID: PMC9183970 DOI: 10.21769/bioprotoc.4419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/04/2022] [Accepted: 04/24/2022] [Indexed: 12/29/2022] Open
Abstract
Microbiologists are learning to appreciate the importance of "functional amyloids" that are produced by numerous bacterial species and have impacts beyond the microbial world. These structures are used by bacteria to link together, presumably to increase survival, protect against harsh conditions, and perhaps to influence cell-cell communication. Bacterial functional amyloids are also beginning to be appreciated in the context of host-pathogen interactions, where there is evidence that they can trigger the innate immune system and are recognized as non-self-molecular patterns. The characteristic three-dimensional fold of amyloids renders them similar across the bacterial kingdom and into the eukaryotic world, where amyloid proteins can be undesirable and have pathological consequences. The bacterial protein curli, produced by pathogenic Salmonella enterica and Escherichia coli strains, was one of the first functional amyloids discovered. Curli have since been well characterized in terms of function, and we are just starting to scratch the surface about their potential impact on eukaryotic hosts. In this manuscript, we present step-by-step protocols with pictures showing how to purify these bacterial surface structures. We have described the purification process from S. enterica, acknowledging that the same method can be applied to E. coli. In addition, we describe methods for detection of curli within animal tissues (i.e., GI tract) and discuss purifying curli intermediates in a S. enterica msbB mutant strain as they are more cytotoxic than mature curli fibrils. Some of these methods were first described elsewhere, but we wanted to assemble them together in more detail to make it easier for researchers who want to purify curli for use in biological experiments. Our aim is to provide methods that are useful for specialists and non-specialists as bacterial amyloids become of increasing importance.
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Affiliation(s)
- Murugesan Sivaranjani
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan, Canada
,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Elizabeth G. Hansen
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan, Canada
,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sumudu R. Perera
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan, Canada
,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Pamela A. Flores
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan, Canada
,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Çagla Tükel
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Aaron P. White
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan, Canada
,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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*For correspondence:
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