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Campanero-Rhodes MA, Palma AS, Menéndez M, Solís D. Microarray Strategies for Exploring Bacterial Surface Glycans and Their Interactions With Glycan-Binding Proteins. Front Microbiol 2020; 10:2909. [PMID: 32010066 PMCID: PMC6972965 DOI: 10.3389/fmicb.2019.02909] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022] Open
Abstract
Bacterial surfaces are decorated with distinct carbohydrate structures that may substantially differ among species and strains. These structures can be recognized by a variety of glycan-binding proteins, playing an important role in the bacteria cross-talk with the host and invading bacteriophages, and also in the formation of bacterial microcolonies and biofilms. In recent years, different microarray approaches for exploring bacterial surface glycans and their recognition by proteins have been developed. A main advantage of the microarray format is the inherent miniaturization of the method, which allows sensitive and high-throughput analyses with very small amounts of sample. Antibody and lectin microarrays have been used for examining bacterial glycosignatures, enabling bacteria identification and differentiation among strains. In addition, microarrays incorporating bacterial carbohydrate structures have served to evaluate their recognition by diverse host/phage/bacterial glycan-binding proteins, such as lectins, effectors of the immune system, or bacterial and phagic cell wall lysins, and to identify antigenic determinants for vaccine development. The list of samples printed in the arrays includes polysaccharides, lipopoly/lipooligosaccharides, (lipo)teichoic acids, and peptidoglycans, as well as sequence-defined oligosaccharide fragments. Moreover, microarrays of cell wall fragments and entire bacterial cells have been developed, which also allow to study bacterial glycosylation patterns. In this review, examples of the different microarray platforms and applications are presented with a view to give the current state-of-the-art and future prospects in this field.
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Affiliation(s)
- María Asunción Campanero-Rhodes
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Angelina Sa Palma
- UCIBIO, Department of Chemistry, Faculty of Science and Technology, NOVA University of Lisbon, Lisbon, Portugal
| | - Margarita Menéndez
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Dolores Solís
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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Abstract
AbstractO-antigens present on the surface ofEscherichia coliprovide antigenic specificity for the strain and are the main components for O-serogroup designation. Serotyping using O-group-specific antisera for the identification ofE. coliO-serogroups has been traditionally the gold-standard for distinguishingE. colistrains. Knowledge of the O-group is important for determining pathogenic lineage, classifyingE. colifor epidemiological studies, for determining virulence, and for tracing outbreaks of diseases and sources of infection. However, serotyping has limitations, as the antisera generated against each specific O-group may cross-react, many strains are non-typeable, and others can autoagglutinate or be rough (lacking an O-antigen). Currently, the nucleotide sequences are available for most of the 187 designatedE. coliO-groups. Public health and other laboratories are considering whole genome sequencing to develop genotypic methods to determine O-groups. These procedures require instrumentation and analysis that may not be accessible and may be cost-prohibitive at this time. In this review, we have identified unique gene sequences within the O-antigen gene clusters and have targeted these genes for identification of O-groups using the polymerase chain reaction. This information can be used to distinguish O-groups by developing other platforms forE. colidiagnostics in the future.
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Fratamico PM, DebRoy C, Liu Y, Needleman DS, Baranzoni GM, Feng P. Advances in Molecular Serotyping and Subtyping of Escherichia coli. Front Microbiol 2016; 7:644. [PMID: 27199968 PMCID: PMC4853403 DOI: 10.3389/fmicb.2016.00644] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/18/2016] [Indexed: 01/25/2023] Open
Abstract
Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract. E. coli have traditionally been serotyped using antisera against the ca. 186 O-antigens and 53 H-flagellar antigens. Phenotypic methods, including bacteriophage typing and O- and H- serotyping for differentiating and characterizing E. coli have been used for many years; however, these methods are generally time consuming and not always accurate. Advances in next generation sequencing technologies have made it possible to develop genetic-based subtyping and molecular serotyping methods for E. coli, which are more discriminatory compared to phenotypic typing methods. Furthermore, whole genome sequencing (WGS) of E. coli is replacing established subtyping methods such as pulsed-field gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. A variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers.
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Affiliation(s)
- Pina M. Fratamico
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Chitrita DebRoy
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University ParkPA, USA
| | - Yanhong Liu
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - David S. Needleman
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Gian Marco Baranzoni
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Peter Feng
- Division of Microbiology, U.S. Food and Drug Administration, College ParkMD, USA
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DebRoy C, Fratamico PM, Yan X, Baranzoni G, Liu Y, Needleman DS, Tebbs R, O'Connell CD, Allred A, Swimley M, Mwangi M, Kapur V, Raygoza Garay JA, Roberts EL, Katani R. Comparison of O-Antigen Gene Clusters of All O-Serogroups of Escherichia coli and Proposal for Adopting a New Nomenclature for O-Typing. PLoS One 2016; 11:e0147434. [PMID: 26824864 PMCID: PMC4732683 DOI: 10.1371/journal.pone.0147434] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 01/03/2016] [Indexed: 01/27/2023] Open
Abstract
Escherichia coli strains are classified based on O-antigens that are components of the lipopolysaccharide (LPS) in the cell envelope. O-antigens are important virulence factors, targets of both the innate and adaptive immune system, and play a role in host-pathogen interactions. Because they are highly immunogenic and display antigenic specificity unique for each strain, O-antigens are the biomarkers for designating O-types. Immunologically, 185 O-serogroups and 11 OX-groups exist for classification. Conventional serotyping for O-typing entails agglutination reactions between the O-antigen and antisera generated against each O-group. The procedure is labor intensive, not always accurate, and exhibits equivocal results. In this report, we present the sequences of 71 O-antigen gene clusters (O-AGC) and a comparison of all 196 O- and OX-groups. Many of the designated O-types, applied for classification over several decades, exhibited similar nucleotide sequences of the O-AGCs and cross-reacted serologically. Some O-AGCs carried insertion sequences and others had only a few nucleotide differences between them. Thus, based on these findings, it is proposed that several of the E. coli O-groups may be merged. Knowledge of the O-AGC sequences facilitates the development of molecular diagnostic platforms that are rapid, accurate, and reliable that can replace conventional serotyping. Additionally, with the scientific knowledge presented, new frontiers in the discovery of biomarkers, understanding the roles of O-antigens in the innate and adaptive immune system and pathogenesis, the development of glycoconjugate vaccines, and other investigations, can be explored.
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Affiliation(s)
- Chitrita DebRoy
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Pina M. Fratamico
- Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Xianghe Yan
- Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - GianMarco Baranzoni
- Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Yanhong Liu
- Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - David S. Needleman
- Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Robert Tebbs
- Animal Health & Food Safety, Life Sciences Solutions, Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Catherine D. O'Connell
- Animal Health & Food Safety, Life Sciences Solutions, Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Adam Allred
- Animal Health & Food Safety, Life Sciences Solutions, Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Michelle Swimley
- Animal Health & Food Safety, Life Sciences Solutions, Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Michael Mwangi
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Vivek Kapur
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Juan A. Raygoza Garay
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Elisabeth L. Roberts
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Robab Katani
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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Bai X, Wang H, Xin Y, Wei R, Tang X, Zhao A, Sun H, Zhang W, Wang Y, Xu Y, Zhang Z, Li Q, Xu J, Xiong Y. Prevalence and characteristics of Shiga toxin-producing Escherichia coli isolated from retail raw meats in China. Int J Food Microbiol 2015; 200:31-8. [DOI: 10.1016/j.ijfoodmicro.2015.01.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/31/2014] [Accepted: 01/24/2015] [Indexed: 12/19/2022]
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Tang Y, Kim H, Singh AK, Aroonnual A, Bae E, Rajwa B, Fratamico PM, Bhunia AK. Light scattering sensor for direct identification of colonies of Escherichia coli serogroups O26, O45, O103, O111, O121, O145 and O157. PLoS One 2014; 9:e105272. [PMID: 25136836 PMCID: PMC4138183 DOI: 10.1371/journal.pone.0105272] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/18/2014] [Indexed: 12/16/2022] Open
Abstract
Background Shiga-toxin producing Escherichia coli (STEC) have emerged as important foodborne pathogens, among which seven serogroups (O26, O45, O103, O111, O121, O145, O157) are most frequently implicated in human infection. The aim was to determine if a light scattering sensor can be used to rapidly identify the colonies of STEC serogroups on selective agar plates. Methodology/Principal Findings Initially, a total of 37 STEC strains representing seven serovars were grown on four different selective agar media, including sorbitol MacConkey (SMAC), Rainbow Agar O157, BBL CHROMagarO157, and R&F E. coli O157:H7, as well as nonselective Brain Heart Infusion agar. The colonies were scanned by an automated light scattering sensor, known as BARDOT (BActerial Rapid Detection using Optical scattering Technology), to acquire scatter patterns of STEC serogroups, and the scatter patterns were analyzed using an image classifier. Among all of the selective media tested, both SMAC and Rainbow provided the best differentiation results allowing multi-class classification of all serovars with an average accuracy of more than 90% after 10–12 h of growth, even though the colony appearance was indistinguishable at that early stage of growth. SMAC was chosen for exhaustive scatter image library development, and 36 additional strains of O157:H7 and 11 non-O157 serovars were examined, with each serogroup producing unique differential scatter patterns. Colony scatter images were also tested with samples derived from pure and mixed cultures, as well as experimentally inoculated food samples. BARDOT accurately detected O157 and O26 serovars from a mixed culture and also from inoculated lettuce and ground beef (10-h broth enrichment +12-h on-plate incubation) in the presence of natural background microbiota in less than 24 h. Conclusions BARDOT could potentially be used as a screening tool during isolation of the most important STEC serovars on selective agar plates from food samples in less than 24 h.
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Affiliation(s)
- Yanjie Tang
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, Indiana, United States of America
| | - Huisung Kim
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Atul K. Singh
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, Indiana, United States of America
| | - Amornrat Aroonnual
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, Indiana, United States of America
| | - Euiwon Bae
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States of America
| | - Pina M. Fratamico
- USDA-ARS, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Arun K. Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, Indiana, United States of America
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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