1
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Qin J, Hong Y, Totsika M. Determining glycosyltransferase functional order via lethality due to accumulated O-antigen intermediates, exemplified with Shigella flexneri O-antigen biosynthesis. Appl Environ Microbiol 2024; 90:e0220323. [PMID: 38747588 PMCID: PMC11218652 DOI: 10.1128/aem.02203-23] [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: 12/07/2023] [Accepted: 04/09/2024] [Indexed: 06/19/2024] Open
Abstract
The O antigen (OAg) polysaccharide is one of the most diverse surface molecules of Gram-negative bacterial pathogens. The structural classification of OAg, based on serological typing and sequence analysis, is important in epidemiology and the surveillance of outbreaks of bacterial infections. Despite the diverse chemical structures of OAg repeating units (RUs), the genetic basis of RU assembly remains poorly understood and represents a major limitation in assigning gene functions in polysaccharide biosynthesis. Here, we describe a genetic approach to interrogate the functional order of glycosyltransferases (GTs). Using Shigella flexneri as a model, we established an initial glycosyltransferase (IT)-controlled system, which allows functional order allocation of the subsequent GT in a 2-fold manner as follows: (i) first, by reporting the growth defects caused by the sequestration of UndP through disruption of late GTs and (ii) second, by comparing the molecular sizes of stalled OAg intermediates when each putative GT is disrupted. Using this approach, we demonstrate that for RfbF and RfbG, the GT involved in the assembly of S. flexneri backbone OAg RU, RfbG, is responsible for both the committed step of OAg synthesis and the third transferase for the second L-Rha. We also show that RfbF functions as the last GT to complete the S. flexneri OAg RU backbone. We propose that this simple and effective genetic approach can be also extended to define the functional order of enzymatic synthesis of other diverse polysaccharides produced both by Gram-negative and Gram-positive bacteria.IMPORTANCEThe genetic basis of enzymatic assembly of structurally diverse O antigen (OAg) repeating units (RUs) in Gram-negative pathogens is poorly understood, representing a major limitation in our understanding of gene functions for the synthesis of bacterial polysaccharides. We present a simple genetic approach to confidently assign glycosyltransferase (GT) functions and the order in which they act during assembly of the OAg RU. We employed this approach to determine the functional order of GTs involved in Shigella flexneri OAg assembly. This approach can be generally applied in interrogating GT functions encoded by other bacterial polysaccharides to advance our understanding of diverse gene functions in the biosynthesis of polysaccharides, key knowledge in advancing biosynthetic polysaccharide production.
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Affiliation(s)
- Jilong Qin
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Yaoqin Hong
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Max Planck Queensland Centre, Queensland University of Technology, Brisbane City, Queensland, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Max Planck Queensland Centre, Queensland University of Technology, Brisbane City, Queensland, Australia
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2
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Liu Y, Koudelka G. O-Polysaccharides of LPS Modulate E. coli Uptake by Acanthamoeba castellanii. Microorganisms 2023; 11:1377. [PMID: 37374879 DOI: 10.3390/microorganisms11061377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Protozoan grazing is a major cause of bacterial mortality and controls bacterial population size and composition in the natural environment. To enhance their survival, bacteria evolved many defense strategies to avoid grazing by protists. Cell wall modification is one of the defense strategies that helps bacteria escape from recognition and/or internalization by its predators. Lipopolysaccharide (LPS) is the major component of Gram-negative bacterial cell wall. LPS is divided into three regions: lipid A, oligosaccharide core and O-specific polysaccharide. O-polysaccharide as the outermost region of E. coli LPS provides protection against predation by Acanthamoeba castellanii; however, the characteristics of O-polysaccharide contribute to this protection remain unknown. Here, we investigate how length, structure and composition of LPS affect E. coli recognition and internalization by A. castellanii. We found that length of O-antigen does not play a significant role in regulating bacterial recognition by A. castellanii. However, the composition and structure of O-polysaccharide play important roles in providing resistance to A. castellanii predation.
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Affiliation(s)
- Ying Liu
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Gerald Koudelka
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
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3
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Liu B, Furevi A, Perepelov AV, Guo X, Cao H, Wang Q, Reeves PR, Knirel YA, Wang L, Widmalm G. Structure and genetics of Escherichia coli O antigens. FEMS Microbiol Rev 2020; 44:655-683. [PMID: 31778182 PMCID: PMC7685785 DOI: 10.1093/femsre/fuz028] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 11/22/2019] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli includes clonal groups of both commensal and pathogenic strains, with some of the latter causing serious infectious diseases. O antigen variation is current standard in defining strains for taxonomy and epidemiology, providing the basis for many serotyping schemes for Gram-negative bacteria. This review covers the diversity in E. coli O antigen structures and gene clusters, and the genetic basis for the structural diversity. Of the 187 formally defined O antigens, six (O31, O47, O67, O72, O94 and O122) have since been removed and three (O34, O89 and O144) strains do not produce any O antigen. Therefore, structures are presented for 176 of the 181 E. coli O antigens, some of which include subgroups. Most (93%) of these O antigens are synthesized via the Wzx/Wzy pathway, 11 via the ABC transporter pathway, with O20, O57 and O60 still uncharacterized due to failure to find their O antigen gene clusters. Biosynthetic pathways are given for 38 of the 49 sugars found in E. coli O antigens, and several pairs or groups of the E. coli antigens that have related structures show close relationships of the O antigen gene clusters within clades, thereby highlighting the genetic basis of the evolution of diversity.
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Affiliation(s)
- Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Axel Furevi
- Department of Organic Chemistry, Arrhenius Laboratory, Svante Arrhenius väg 16C, Stockholm University, S-106 91 Stockholm, Sweden
| | - Andrei V Perepelov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia
| | - Xi Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Hengchun Cao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Quan Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Peter R Reeves
- School of Molecular and Microbial Bioscience, University of Sydney, 2 Butilin Ave, Darlington NSW 2008, Sydney, Australia
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia
| | - Lei Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Svante Arrhenius väg 16C, Stockholm University, S-106 91 Stockholm, Sweden
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4
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Li Y, Huang J, Wang X, Xu C, Han T, Guo X. Genetic Characterization of the O-Antigen and Development of a Molecular Serotyping Scheme for Enterobacter cloacae. Front Microbiol 2020; 11:727. [PMID: 32411106 PMCID: PMC7198725 DOI: 10.3389/fmicb.2020.00727] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/27/2020] [Indexed: 11/13/2022] Open
Abstract
Enterobacter cloacae is a well-characterized opportunistic pathogen that is closely associated with various nosocomial infections. The O-antigen, which is one of the most variable constituents on the cell surface, has been used widely and traditionally for serological classification of many gram-negative bacteria. E. cloacae is divided into 30 serotypes, based on its O-antigen diversity. In this study, by using genomic and comparative-genomic approaches, we analyzed the O-antigen gene clusters of 26 E. cloacae serotypes in depth. We also identified the sero-specific gene for each serotype and developed a multiplex polymerase chain reaction (PCR) method. The sensitivity of the assay was 0.1 ng for genomic DNA and 103 colony forming units for pure cultures. The assay reliability was evaluated by double-blinded testing with 81 clinical strains. Furthermore, we established a valid, genome-based tool for in silico serotyping of E. cloacae. By screening 431 E. cloacae genomes deposited in GenBank, 304 were classified into current antigenic scheme, and 112 were allocated into 55 putative novel serotypes. Our results represent the first genetic basis of the O-antigen diversity and variation of E. cloacae, providing a rationale for studying the O-antigen associated evolution and pathogenesis of this bacterium. In addition, we extended the current serotyping system for E. cloacae, which is important for detection and epidemiological surveillance purposes for this important pathogen.
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Affiliation(s)
- Yayue Li
- The Third Central Hospital of Tianjin, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Junjie Huang
- Department of Vascular Surgery, Tianjin Hospital, Tianjin, China
| | - Xiaotong Wang
- Tianjin Children's Hospital, Third Central Clinical College of Tianjin Medical University, Tianjin, China
| | - Cong Xu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Tao Han
- The Third Central Hospital of Tianjin, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Xi Guo
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
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5
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Ooka T, Seto K, Ogura Y, Nakamura K, Iguchi A, Gotoh Y, Honda M, Etoh Y, Ikeda T, Sugitani W, Konno T, Kawano K, Imuta N, Yoshiie K, Hara-Kudo Y, Murakami K, Hayashi T, Nishi J. O-antigen biosynthesis gene clusters of Escherichia albertii: their diversity and similarity to Escherichia coli gene clusters and the development of an O-genotyping method. Microb Genom 2020; 5. [PMID: 31738701 PMCID: PMC6927306 DOI: 10.1099/mgen.0.000314] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Escherichia albertii is a recently recognized human enteropathogen that is closely related to Escherichia coli. In many Gram-negative bacteria, including E. coli, O-antigen variation has long been used for the serotyping of strains. In E. albertii, while eight O-serotypes unique to this species have been identified, some strains have been shown to exhibit genetic or serological similarity to known E. coli/Shigella O-serotypes. However, the diversity of O-serotypes and O-antigen biosynthesis gene clusters (O-AGCs) of E. albertii remains to be systematically investigated. Here, we analysed the O-AGCs of 65 E. albertii strains and identified 40 E. albertii O-genotypes (EAOgs) (named EAOg1–EAOg40). Analyses of the 40 EAOgs revealed that as many as 20 EAOgs exhibited significant genetic and serological similarity to the O-AGCs of known E. coli/Shigella O-serotypes, and provided evidence for the inter-species horizontal gene transfer of O-AGCs between E. albertii and E. coli. Based on the sequence variation in the wzx gene among the 40 EAOgs, we developed a multiplex PCR-based O-genotyping system for E. albertii (EAO-genotyping PCR) and verified its usefulness by genotyping 278 E. albertii strains from various sources. Although 225 (80.9 %) of the 278 strains could be genotyped, 51 were not assigned to any of the 40 EAOgs, indicating that further analyses are required to better understand the diversity of O-AGCs in E. albertii and improve the EAO-genotyping PCR method. A phylogenetic view of E. albertii strains sequenced so far is also presented with the distribution of the 40 EAOgs, which provided multiple examples for the intra-species horizontal transfer of O-AGCs in E. albertii.
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Affiliation(s)
- Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Kazuko Seto
- Osaka Institute of Public Health, 1-3-69 Nakamichi, Higasinari-ku, Osaka 537-0025, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-kibanadai-nishi, Miyazaki 889-2192, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mikiko Honda
- Fukuoka City Institute of Hygiene and the Environment, 2-1-34 Jigyohama, Chuo-ku, Fukuoka 810-0065, Japan
| | - Yoshiki Etoh
- Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka 818-0135, Japan
| | - Tetsuya Ikeda
- Hokkaido Institute of Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo 060-0819, Japan
| | - Wakana Sugitani
- Kumamoto City Environmental Research Institute, 404-1, Ezumachi Tokorojima, Higashi-ku, Kumamoto 862-0946, Japan
| | - Takayuki Konno
- Akita Prefectural Research Center for Public Health and Environment, 6-6 Senshu Kubota-machi, Akita 010-0874, Japan
| | - Kimiko Kawano
- Miyazaki Prefectural Institute for Public Health and Environment, 2-3-2 Gakuen-kibanadai-nishi, Miyazaki 889-2155, Japan
| | - Naoko Imuta
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Kiyotaka Yoshiie
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Yukiko Hara-Kudo
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki 210-9501, Japan
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-murayama, Tokyo 208-0011, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Junichiro Nishi
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
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6
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Sizova OV, Shashkov AS, Toukach PV, Knirel YA, Shaikhutdinova RZ, Ivanov SA, Kislichkina AA, Dentovskaya SV. Structure elucidation and gene cluster characterization of the O-antigen of Yersinia kristensenii С-134. Carbohydr Res 2019; 481:9-15. [PMID: 31220629 DOI: 10.1016/j.carres.2019.06.001] [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: 04/17/2019] [Revised: 05/24/2019] [Accepted: 06/01/2019] [Indexed: 11/26/2022]
Abstract
Mild acid degradation of the lipopolysaccharide of Yersinia kristensenii C-134 afforded a glycerol teichoic acid-like O-polysaccharide, which was studied by sugar analysis, O-deacetylation and dephosphorylation along with 1D and 2D NMR spectroscopy. The following structure of the O-polysaccharide was established: This structure is related to those of other Y. kristensenii O-polysaccharides studied earlier. The O-antigen gene cluster of Y. kristensenii С-134 was analyzed and found to be consistent with the O-polysaccharide structure established.
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Affiliation(s)
- Olga V Sizova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Philip V Toukach
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Rima Z Shaikhutdinova
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russian Federation
| | - Sergei A Ivanov
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russian Federation
| | - Angelina A Kislichkina
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russian Federation
| | - Svetlana V Dentovskaya
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russian Federation.
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7
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Shashkov AS, Senchenkova SN, Naumenko OI, Kalinchuk NA, Perepelov AV, Knirel YA. Escherichia coli O106, a new member of a group of enteric bacteria sharing an O-polysaccharide backbone structure. Russ Chem Bull 2018. [DOI: 10.1007/s11172-018-2253-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Zdorovenko EL, Wang Y, Shashkov AS, Chen T, Ovchinnikova OG, Liu B, Golomidova AK, Babenko VV, Letarov AV, Knirel YA. O-Antigens of Escherichia coli Strains O81 and HS3-104 Are Structurally and Genetically Related, Except O-Antigen Glucosylation in E. coli HS3-104. BIOCHEMISTRY (MOSCOW) 2018; 83:534-541. [PMID: 29738687 DOI: 10.1134/s0006297918050061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Glycerophosphate-containing O-specific polysaccharides (OPSs) were obtained by mild acidic degradation of lipopolysaccharides isolated from Escherichia coli type strain O81 and E. coli strain HS3-104 from horse feces. The structures of both OPSs and of the oligosaccharide derived from the strain O81 OPS by treatment with 48% HF were studied by monosaccharide analysis and one- and two-dimensional 1H- and 13C-NMR spectroscopy. Both OPSs had similar structures and differed only in the presence of a side-chain glucose residue in the strain HS3-104 OPS. The genes and the organization of the O-antigen biosynthesis gene cluster in both strains are almost identical with the exception of the gtr gene cluster responsible for glucosylations in the strain HS3-104, which is located elsewhere in the genome.
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Affiliation(s)
- E L Zdorovenko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Y Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China
| | - A S Shashkov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia
| | - T Chen
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China
| | - O G Ovchinnikova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia
| | - B Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.
| | - A K Golomidova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 117312, Russia
| | - V V Babenko
- Federal Research and Clinical Centre of Physico-Chemical Medicine, Moscow, 119435, Russia.
| | - A V Letarov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 117312, Russia.
| | - Y A Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia.
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9
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Full structure and insight into the gene cluster of the O-specific polysaccharide of Yersinia intermedia H9-36/83 (O:17). Carbohydr Res 2018. [PMID: 29524727 DOI: 10.1016/j.carres.2018.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Lipopolysaccharide was isolated from bacteria Yersinia intermedia H9-36/83 (O:17) and degraded with mild acid to give an O-specific polysaccharide, which was isolated by GPC on Sephadex G-50 and studied by sugar analysis and 1D and 2D NMR spectroscopy. The polysaccharide was found to contain 3-deoxy-3-[(R)-3-hydroxybutanoylamino]-d-fucose (d-Fuc3NR3Hb) and the following structure of the heptasaccharide repeating unit was established: The structure established is consistent with the gene content of the O-antigen gene cluster. The O-polysaccharide structure and gene cluster of Y. intermedia are related to those of Hafnia alvei 1211 and Escherichia coli O:103.
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10
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Iguchi A. A complete view of the Escherichia coli O-antigen biosynthesis gene cluster and the development of molecular-based O-serogrouping methods. Nihon Saikingaku Zasshi 2017; 71:209-215. [PMID: 27980292 DOI: 10.3412/jsb.71.209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Much of what we know about Escherichia coli populations and epidemiology is defined at some level by O serogroups. Moreover, in our collective knowledge, outbreak and disease reports and elsewhere, all information of pathogenic E. coli have O serogroup records. O-serogroup diversification shows a strong association with the genetic diversity of O-antigen biosynthesis genes, and O-serogroup-specific sequences can be used as genetic markers for identifying O serogroups. We sequenced all the known O-antigen biosynthesis gene clusters (O-AGCs) from the 184 E. coli defined O serogroups and determined their genetic makeup and diversity. Subsequently, based on a highly detailed analysis of O-AGCs, we developed comprehensive and practical molecular O-serogrouping platforms; PCR-based "E. coli O-genotuping PCR" and in silico-based "SerotypeFinder". These simple and exhaustive systems may integrate microbial typing, genomics and evolutionary analyses.
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Affiliation(s)
- Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki
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11
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Leonard SR, Mammel MK, Lacher DW, Elkins CA. Strain-Level Discrimination of Shiga Toxin-Producing Escherichia coli in Spinach Using Metagenomic Sequencing. PLoS One 2016; 11:e0167870. [PMID: 27930729 PMCID: PMC5145215 DOI: 10.1371/journal.pone.0167870] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/21/2016] [Indexed: 11/28/2022] Open
Abstract
Consumption of fresh bagged spinach contaminated with Shiga toxin-producing Escherichia coli (STEC) has led to severe illness and death; however current culture-based methods to detect foodborne STEC are time consuming. Since not all STEC strains are considered pathogenic to humans, it is crucial to incorporate virulence characterization of STEC in the detection method. In this study, we assess the comprehensiveness of utilizing a shotgun metagenomics approach for detection and strain-level identification by spiking spinach with a variety of genomically disparate STEC strains at a low contamination level of 0.1 CFU/g. Molecular serotyping, virulence gene characterization, microbial community analysis, and E. coli core gene single nucleotide polymorphism (SNP) analysis were performed on metagenomic sequence data from enriched samples. It was determined from bacterial community analysis that E. coli, which was classified at the phylogroup level, was a major component of the population in most samples. However, in over half the samples, molecular serotyping revealed the presence of indigenous E. coli which also contributed to the percent abundance of E. coli. Despite the presence of additional E. coli strains, the serotype and virulence genes of the spiked STEC, including correct Shiga toxin subtype, were detected in 94% of the samples with a total number of reads per sample averaging 2.4 million. Variation in STEC abundance and/or detection was observed in replicate spiked samples, indicating an effect from the indigenous microbiota during enrichment. SNP analysis of the metagenomic data correctly placed the spiked STEC in a phylogeny of related strains in cases where the indigenous E. coli did not predominate in the enriched sample. Also, for these samples, our analysis demonstrates that strain-level phylogenetic resolution is possible using shotgun metagenomic data for determining the genomic relatedness of a contaminating STEC strain to other closely related E. coli.
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Affiliation(s)
- Susan R. Leonard
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Mark K. Mammel
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - David W. Lacher
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
| | - Christopher A. Elkins
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, United States of America
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12
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Phenotypic H-Antigen Typing by Mass Spectrometry Combined with Genetic Typing of H Antigens, O Antigens, and Toxins by Whole-Genome Sequencing Enhances Identification of Escherichia coli Isolates. J Clin Microbiol 2016; 54:2162-8. [PMID: 27307455 PMCID: PMC4963523 DOI: 10.1128/jcm.00422-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022] Open
Abstract
Mass spectrometry-based phenotypic H-antigen typing (MS-H) combined with whole-genome-sequencing-based genetic identification of H antigens, O antigens, and toxins (WGS-HOT) was used to type 60 clinical Escherichia coli isolates, 43 of which were previously identified as nonmotile, H type undetermined, or O rough by serotyping or having shown discordant MS-H and serotyping results. Whole-genome sequencing confirmed that MS-H was able to provide more accurate data regarding H antigen expression than serotyping. Further, enhanced and more confident O antigen identification resulted from gene cluster based typing in combination with conventional typing based on the gene pair comprising wzx and wzy and that comprising wzm and wzt The O antigen was identified in 94.6% of the isolates when the two genetic O typing approaches (gene pair and gene cluster) were used in conjunction, in comparison to 78.6% when the gene pair database was used alone. In addition, 98.2% of the isolates showed the existence of genes for various toxins and/or virulence factors, among which verotoxins (Shiga toxin 1 and/or Shiga toxin 2) were 100% concordant with conventional PCR based testing results. With more applications of mass spectrometry and whole-genome sequencing in clinical microbiology laboratories, this combined phenotypic and genetic typing platform (MS-H plus WGS-HOT) should be ideal for pathogenic E. coli typing.
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Shashkov AS, Zhang Y, Sun Q, Guo X, Senchenkova SN, Perepelov AV, Knirel YA. Structure and gene cluster of the O-antigen of Escherichia coli O133. Carbohydr Res 2016; 430:82-84. [PMID: 27203746 DOI: 10.1016/j.carres.2016.04.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
Abstract
The O-specific polysaccharide (O-antigen) of Escherichia coli O133 was obtained by mild acid hydrolysis of the lipopolysaccharide of E. coli O133. The structure of the hexasaccharide repeating unit of the polysaccharide was elucidated by (1)H and (13)C NMR spectroscopy, including a two-dimensional (1)H-(1)H ROESY experiment: Functions of genes in the O-antigen gene cluster were putatively identified by comparison with sequences in the available databases and, particularly, an encoded predicted multifunctional glycosyltransferase was assigned to three α-l-rhamnosidic linkages.
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Affiliation(s)
- Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Yuanyuan Zhang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457 Tianjin, China
| | - Qiangzheng Sun
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China
| | - Xi Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457 Tianjin, China
| | - Sof'ya N Senchenkova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Andrei V Perepelov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation.
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
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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: 101] [Impact Index Per Article: 11.2] [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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Zhou D, Chen C, Xu L, Utkina N, Danilov L, Torgov V, Veselovsky V, Liu B, Feng L. Mass spectrometric characterization of a two-glycosyltransferase tandem reaction for assembly of tetrasaccharide repeating unit of Escherichia coli O77 O-antigen. Carbohydr Res 2016; 424:24-9. [PMID: 26963608 DOI: 10.1016/j.carres.2016.02.007] [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: 12/31/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 11/28/2022]
Abstract
The wbaD gene and wbaC gene from Escherichia coli O77 O-antigen gene cluster encoding mannosyltransferases were functionally characterized in vitro. A synthetic acceptor P(1)-(11-phenoxyundecyl)-P(2)-(2-acetamido-2-deoxy-α-D-glucopyranosyl) diphosphate (GlcNAc-PP-PhU) was used as an acceptor and GDP-Man as a donor substrate; the activities of WbaD and WbaC were confirmed by detailed structural characterization of their lipooligosacharide enzyme products using high-sensitivity negative-ion electrospray ionization (ESI) collision-induced dissociation tandem mass spectrometry (CID) MS-MS. The extensive fragmentation unequivocally demonstrated that the Man(1-3)-GlcNAc linkage in WbaD catalyzed reaction product and two Man(1-2)-Man linkages in tandem WbaD/WbaC catalyzed reaction product are present, respectively. This study provided valuable information for the understanding of diversified glycosyltransferase (GT) functions and the two GTs characterized can serve as additional enzyme sources for possible pharmaceutical related applications.
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Affiliation(s)
- Dawei Zhou
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Chao Chen
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Lingling Xu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Natalia Utkina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp., 47, 119991 Moscow, Russia
| | - Leonid Danilov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp., 47, 119991 Moscow, Russia
| | - Vladimir Torgov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp., 47, 119991 Moscow, Russia
| | - Vladimir Veselovsky
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp., 47, 119991 Moscow, Russia
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Lu Feng
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China.
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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: 70] [Impact Index Per Article: 7.8] [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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17
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Novel microarray design for molecular serotyping of shiga toxin- producing Escherichia coli strains isolated from fresh produce. Appl Environ Microbiol 2015; 80:4677-4682. [PMID: 24837388 DOI: 10.1128/aem.01049-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serotyping Escherichia coli is a cumbersome and complex procedure due to the existence of large numbers of O- and H-antigen types. It can also be unreliable, as many Shiga toxin-producing E. coli (STEC) strains isolated from fresh produce cannot be typed by serology or have only partial serotypes. The FDA E. coli identification (FDA-ECID) microarray, designed for characterizing pathogenic E. coli, contains a molecular serotyping component, which was evaluated here for its efficacy. Analysis of a panel of 75 reference E. coli strains showed that the array correctly identified the O and H types in 97% and 98% of the strains, respectively. Comparative analysis of 73 produce STEC strains showed that serology and the array identified 37% and 50% of the O types, respectively, and that the array was able to identify 16 strains that could not be O serotyped. Furthermore, the array identified the H types of 97% of the produce STEC strains compared to 65% by serology, including six strains that were mistyped by serology. These results show that the array is an effective alternative to serology in serotyping environmental E. coli isolates.
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18
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Related structures of the O-polysaccharides of Cronobacter dublinensis G3983 and G3977 containing 3-(N-acetyl-l-alanyl)amino-3,6-dideoxy-d-galactose. Carbohydr Res 2015; 404:132-7. [DOI: 10.1016/j.carres.2014.11.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/10/2014] [Accepted: 11/12/2014] [Indexed: 11/21/2022]
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19
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Iguchi A, Iyoda S, Kikuchi T, Ogura Y, Katsura K, Ohnishi M, Hayashi T, Thomson NR. A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster. DNA Res 2014; 22:101-7. [PMID: 25428893 PMCID: PMC4379981 DOI: 10.1093/dnares/dsu043] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The O antigen constitutes the outermost part of the lipopolysaccharide layer in Gram-negative bacteria. The chemical composition and structure of the O antigen show high levels of variation even within a single species revealing itself as serological diversity. Here, we present a complete sequence set for the O-antigen biosynthesis gene clusters (O-AGCs) from all 184 recognized Escherichia coli O serogroups. By comparing these sequences, we identified 161 well-defined O-AGCs. Based on the wzx/wzy or wzm/wzt gene sequences, in addition to 145 singletons, 37 serogroups were placed into 16 groups. Furthermore, phylogenetic analysis of all the E. coli O-serogroup reference strains revealed that the nearly one-quarter of the 184 serogroups were found in the ST10 lineage, which may have a unique genetic background allowing a more successful exchange of O-AGCs. Our data provide a complete view of the genetic diversity of O-AGCs in E. coli showing a stronger association between host phylogenetic lineage and O-serogroup diversification than previously recognized. These data will be a valuable basis for developing a systematic molecular O-typing scheme that will allow traditional typing approaches to be linked to genomic exploration of E. coli diversity.
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Affiliation(s)
- Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Taisei Kikuchi
- Division of Parasitology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Keisuke Katsura
- Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Tetsuya Hayashi
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Nicholas R Thomson
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Rojas-Macias MA, Stahle J, Lutteke T, Widmalm G. Development of the ECODAB into a relational database for Escherichia coli O-antigens and other bacterial polysaccharides. Glycobiology 2014; 25:341-7. [DOI: 10.1093/glycob/cwu116] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Structural studies and biosynthetic aspects of the O-antigen polysaccharide from Escherichia coli O42. Carbohydr Res 2014; 403:174-81. [PMID: 24909379 DOI: 10.1016/j.carres.2014.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/06/2014] [Accepted: 05/10/2014] [Indexed: 01/31/2023]
Abstract
The structure of the O-antigen polysaccharide (PS) from Escherichia coli O42 has been investigated by NMR spectroscopy as the main method, which was complemented with sugar analysis, mass spectrometry, and analysis of biosynthetic information. The O-specific chain of the O-deacylated lipopolysaccharide (LPS-OH) consists of branched tetrasaccharide-glycerol repeating units joined by phosphodiester linkages. The lipid-free polysaccharide contains 0.8equiv of O-acetyl groups per repeating unit and has the following teichoic acid-like structure: Based on biosynthetic aspects, this should also be the biological repeating unit. This O-antigen structure is remarkably similar to that of E. coli O28ac, differing only in the presence or absence, respectively, of a glucose residue at the branching point. The structural similarity explains the serological cross-reactivity observed between strains of these two serogroups, and also their almost identical O-antigen gene cluster sequences.
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Tall BD, Chen Y, Yan Q, Gopinath GR, Grim CJ, Jarvis KG, Fanning S, Lampel KA. Cronobacter: an emergent pathogen causing meningitis to neonates through their feeds. Sci Prog 2014; 97:154-72. [PMID: 25108996 PMCID: PMC10365370 DOI: 10.3184/003685014x13994743930498] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The recognition of Cronobacter as a public health concern was raised when powdered infant formula (PIF) was linked to several neonatal meningitis outbreaks. It is an opportunistic pathogen that causes necrotising enterocolitis, infantile septicaemia, and meningitis which carries a high mortality rate among neonates. It has been also linked with cases of infection in adults and elderly. Over the past decade, much focus has been made on developing sensitive and specific characterisation, detection, and isolation methods to ascertain the quality of foods, notably contamination of PIF with Cronobacter and to understand its ability to cause disease. Whole genome sequencing has unveiled several putative virulence factors, yet the full capacity of the pathogenesis of Cronobacter has not yet been elucidated.
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Affiliation(s)
- Ben D. Tall
- Center for Food Safety and Applied Nutrition, Food and Drug Administration in Laurel, Maryland
| | - Yi Chen
- FDA in College Park, Maryland
| | | | - Gopal R. Gopinath
- Center for Food Safety and Applied Nutrition, FDA, in Laurel, Maryland
| | | | - Karen G. Jarvis
- Center for Food Safety and Applied Nutrition, FDA, in Laurel, Maryland
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Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN, Reeves PR, Wang L. Structural diversity in Salmonella O antigens and its genetic basis. FEMS Microbiol Rev 2013; 38:56-89. [PMID: 23848592 DOI: 10.1111/1574-6976.12034] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 05/15/2013] [Accepted: 07/05/2013] [Indexed: 11/30/2022] Open
Abstract
This review covers the structures and genetics of the 46 O antigens of Salmonella, a major pathogen of humans and domestic animals. The variation in structures underpins the serological specificity of the 46 recognized serogroups. The O antigen is important for the full function and virulence of many bacteria, and the considerable diversity of O antigens can confer selective advantage. Salmonella O antigens can be divided into two major groups: those which have N-acetylglucosamine (GlcNAc) or N-acetylgalactosamine (GalNAc) and those which have galactose (Gal) as the first sugar in the O unit. In recent years, we have determined 21 chemical structures and sequenced 28 gene clusters for GlcNAc-/GalNAc-initiated O antigens, thus completing the structure and DNA sequence data for the 46 Salmonella O antigens. The structures and gene clusters of the GlcNAc-/GalNAc-initiated O antigens were found to be highly diverse, and 24 of them were found to be identical or closely related to Escherichia coli O antigens. Sequence comparisons indicate that all or most of the shared gene clusters were probably present in the common ancestor, although alternative explanations are also possible. In contrast, the better-known eight Gal-initiated O antigens are closely related both in structures and gene cluster sequences.
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Affiliation(s)
- Bin Liu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China
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Jarvis KG, Yan QQ, Grim CJ, Power KA, Franco AA, Hu L, Gopinath G, Sathyamoorthy V, Kotewicz ML, Kothary MH, Lee C, Sadowski J, Fanning S, Tall BD. Identification and Characterization of Five New Molecular Serogroups of Cronobacter spp. Foodborne Pathog Dis 2013; 10:343-52. [DOI: 10.1089/fpd.2012.1344] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Karen G. Jarvis
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
| | - Qiong Q. Yan
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference, and Training on Cronobacter, UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
| | - Karen A. Power
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference, and Training on Cronobacter, UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Augusto A. Franco
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
| | - Lan Hu
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
| | - Gopal Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
| | - Venugopal Sathyamoorthy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
| | - Michael L. Kotewicz
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
| | - Mahendra H. Kothary
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
| | - Chloe Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
| | - Jennifer Sadowski
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
| | - Seamus Fanning
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference, and Training on Cronobacter, UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Ben D. Tall
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
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Structure and genetics of the O-antigen of Cronobacter sakazakii G2726 (serotype O3) closely related to the O-antigen of C. muytjensii 3270. Carbohydr Res 2012; 355:50-5. [DOI: 10.1016/j.carres.2012.02.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 02/24/2012] [Accepted: 02/27/2012] [Indexed: 11/23/2022]
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Abstract
Lipopolysaccharide on the surface of Escherichia coli constitutes the O antigens which are important virulence factors that are targets of both the innate and adaptive immune systems and play a major role in host-pathogen interactions. O antigens are responsible for antigenic specificity of the strain and determine the O serogroup. The designation of O serogroups is important for classifying E. coli strains, for epidemiological studies, in tracing the source of outbreaks of gastrointestinal or other illness, and for linking the source to the infection. For conventional serogroup identification, serotyping by agglutination reactions against antisera developed for each of the O serogroups has been used. In the last decade, many O-antigen gene clusters that encode for the enzymes responsible for the synthesis of the variable oligosaccharide region on the surface of the bacteria have been sequenced and characterized. Unique gene sequences within the O-antigen gene clusters have been targeted for identification and detection of many O groups using the polymerase chain reaction and microarrays. This review summarizes current knowledge on the DNA sequences of the O-antigen gene clusters, genetic-based methods for O-group determination and detection of pathogenic E. coli based on O-antigen and virulence gene detection, and provides perspectives on future developments in the field.
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27
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Perepelov AV, Liu B, Guo D, Senchenkova SN, Shahskov AS, Feng L, Wang L, Knirel YA. Structure elucidation of the O-Antigen of Salmonella enterica O51 and its structural and genetic relation to the O-Antigen of Escherichia coli O23. BIOCHEMISTRY (MOSCOW) 2012; 76:774-9. [PMID: 21999538 DOI: 10.1134/s0006297911070078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The O-polysaccharide (O-antigen) of Salmonella enterica O51 was isolated by mild acid degradation of the lipopolysaccharide and its structure was established using sugar analysis and NMR spectroscopy. The O-antigen of Escherichia coli O23, whose structure was elucidated earlier, possesses a similar structure and differs only in the presence of an additional lateral α-D-Glcp residue at position 6 of the GlcNAc residue in the main chain. Sequencing of the O-antigen gene clusters of S. enterica O51 and E. coli O23 revealed the same genes with a high-level similarity. By comparison with opened gene databases, all genes expected for the synthesis of the common structure of the two O-antigens were assigned functions. It is suggested that the gene clusters of both bacteria originated from a common ancestor, whereas the O-antigen modification in E. coli O23, which, most probably, is induced by prophage genes outside the gene cluster, could be introduced after the species divergence.
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Affiliation(s)
- A V Perepelov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow.
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Kumirska J, Dziadziuszko H, Czerwicka M, Lubecka EA, Kunikowska D, Siedlecka EM, Stepnowski P. Heterogeneous structure of O-antigenic part of lipopolysaccharide of Salmonella telaviv (Serogroup O:28) containing 3-acetamido-3,6-dideoxy-D-glucopyranose. BIOCHEMISTRY (MOSCOW) 2011; 76:780-90. [DOI: 10.1134/s000629791107008x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Dziadziuszko H, Kumirska J, Muża S, Czerwicka M, Lubecka EA, Stepnowski P, Kunikowska D. Immunochemical studies of Salmonella Dakar and Salmonella Telaviv O-antigens (serogroup O:28). FEMS Microbiol Lett 2011; 326:55-61. [PMID: 22092663 DOI: 10.1111/j.1574-6968.2011.02431.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 10/04/2011] [Accepted: 10/04/2011] [Indexed: 11/29/2022] Open
Abstract
Salmonella Dakar and Salmonella Telaviv bacteria belong to serogroup O:28, which represents 107 serovars and possesses only the epitope O28. Salmonella Telaviv has the subfactors O28(1) and O28(2) , whereas S. Dakar has O28(1) and O28(3) . So far, only limited serological and immunological information for this serogroup is available in the literature. Knowledge of the structures of their O-polysaccharides and the immunochemical investigations performed in this work allowed to reveal the nature of subfactor O28(1) as attributed to the presence of 3-linked (or 3,4-disubstituted) α-d-GalpNAc in the main chains of S. Dakar and S. Telaviv O-polysaccharides. An explanation for the cross-reactions between Salmonella enterica O28 O-antigens and other Salmonella O-polysaccharides and their structural similarity to Escherichia coli O-serogroups is also given.
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Affiliation(s)
- Halina Dziadziuszko
- Department of Molecular Microbiology and Serology, National Salmonella Centre, Medical University of Gdańsk, Gdańsk, Poland
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30
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MacLean LL, Vinogradov E, Pagotto F, Perry MB. Characterization of the lipopolysaccharide O-antigen of Cronobacter turicensis HPB3287 as a polysaccharide containing a 5,7-diacetamido-3,5,7,9-tetradeoxy-D-glycero-D-galacto-non-2-ulosonic acid (legionaminic acid) residue. Carbohydr Res 2011; 346:2589-94. [PMID: 21963342 DOI: 10.1016/j.carres.2011.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/01/2011] [Accepted: 09/03/2011] [Indexed: 01/08/2023]
Abstract
Cronobacter turicensis, previously known as Enterobacter sakazakii, is a Gram-negative opportunistic food-borne pathogen that has been reported as a cause of life-threatening neonatal infections. From chemical and physical analyses involving composition analysis, methylation, two-dimensional high-resolution nuclear magnetic resonance, and mass spectrometry methods, the antigenic O-polysaccharide in the smooth-type lipopolysaccharide of C. turicensis (strain HPB 3287) was determined to be a high molecular mass polymer of a repeating pentasaccharide unit composed of D-galactose, D-glucose, 2-acetamido-2-deoxy-D-galactose, and 5,7-diacetamido-3,5,7,9-tetradeoxy-D-glycero-D-galacto-non-2-ulosonic acid (legionaminic acid), in a molar ratio 2:1:1:1, and having the structure: [see formula in text].
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Affiliation(s)
- Leann L MacLean
- Institute for Biological Sciences, National Research Council, Ottawa, ON, Canada K1A 0R6
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31
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Perepelov AV, Liu B, Senchenkova SN, Guo D, Shevelev SD, Feng L, Shashkov AS, Wang L, Knirel YA. O-antigen structure and gene clusters of Escherichia coli O51 and Salmonella enterica O57; another instance of identical O-antigens in the two species. Carbohydr Res 2011; 346:828-32. [DOI: 10.1016/j.carres.2011.02.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 02/17/2011] [Accepted: 02/21/2011] [Indexed: 11/17/2022]
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32
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Molecular characterization of Cronobacter lipopolysaccharide O-antigen gene clusters and development of serotype-specific PCR assays. Appl Environ Microbiol 2011; 77:4017-26. [PMID: 21531829 DOI: 10.1128/aem.00162-11] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cronobacter (formerly Enterobacter sakazakii) is a recently defined genus consisting of six species, C. sakazakii, C. malonaticus, C. dublinensis, C. muytjensii, C. turicensis, and Cronobacter genomospecies 1. In this study, MboII restriction fragment length polymorphism (RFLP) patterns of O-antigen gene clusters, located between galF and gnd, were used to identify serotypes in Cronobacter spp. Seven O-antigen RFLP clusters were generated, including three C. sakazakii clusters, previously identified as serotypes O1, O2, and O3. The O-antigen regions of six strains with unique RFLP patterns, including two C. sakazakii strains, two C. malonaticus strains, one C. turicensis strain, and one C. muytjensii strain, revealed three O-antigen gene clusters shared among Cronobacter species. PCR assays were developed, targeting the wzx O-antigen polymerase gene, and used to screen 231 Cronobacter strains to determine the frequency of these newly identified serotypes.
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Li Y, Perepelov AV, Guo D, Shevelev SD, Senchenkova SN, Shahskov AS, Liu B, Wang L, Knirel YA. Structural and genetic relationships of two pairs of closely related O-antigens ofEscherichia coliandSalmonella enterica:E. coliO11/S. entericaO16 andE. coliO21/S. entericaO38. ACTA ACUST UNITED AC 2011. [DOI: 10.1111/j.1574-695x.2010.00771.x (2011)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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34
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Li Y, Perepelov AV, Guo D, Shevelev SD, Senchenkova SN, Shahskov AS, Liu B, Wang L, Knirel YA. Structural and genetic relationships of two pairs of closely related O-antigens ofEscherichia coliandSalmonella enterica:E. coliO11/S. entericaO16 andE. coliO21/S. entericaO38. ACTA ACUST UNITED AC 2011; 61:258-68. [DOI: 10.1111/j.1574-695x.2010.00771.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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MacLean LL, Liu Y, Vinogradov E, Perry MB. The structural characterization of the O-polysaccharide antigen of the lipopolysaccharide of Escherichia coli serotype O118 and its relation to the O-antigens of Escherichia coli O151 and Salmonella enterica O47. Carbohydr Res 2010; 345:2664-9. [DOI: 10.1016/j.carres.2010.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 09/30/2010] [Accepted: 10/02/2010] [Indexed: 10/18/2022]
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36
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Liu B, Perepelov AV, Guo D, Shevelev SD, Senchenkova SN, Feng L, Shashkov AS, Wang L, Knirel YA. Structural and genetic relationships between the O-antigens ofEscherichia coliO118 and O151. ACTA ACUST UNITED AC 2010; 60:199-207. [DOI: 10.1111/j.1574-695x.2010.00738.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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37
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Ristl R, Steiner K, Zarschler K, Zayni S, Messner P, Schäffer C. The s-layer glycome-adding to the sugar coat of bacteria. Int J Microbiol 2010; 2011:127870. [PMID: 20871840 PMCID: PMC2943079 DOI: 10.1155/2011/127870] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 06/29/2010] [Indexed: 11/29/2022] Open
Abstract
The amazing repertoire of glycoconjugates present on bacterial cell surfaces includes lipopolysaccharides, capsular polysaccharides, lipooligosaccharides, exopolysaccharides, and glycoproteins. While the former are constituents of Gram-negative cells, we review here the cell surface S-layer glycoproteins of Gram-positive bacteria. S-layer glycoproteins have the unique feature of self-assembling into 2D lattices providing a display matrix for glycans with periodicity at the nanometer scale. Typically, bacterial S-layer glycans are O-glycosidically linked to serine, threonine, or tyrosine residues, and they rely on a much wider variety of constituents, glycosidic linkage types, and structures than their eukaryotic counterparts. As the S-layer glycome of several bacteria is unravelling, a picture of how S-layer glycoproteins are biosynthesized is evolving. X-ray crystallography experiments allowed first insights into the catalysis mechanism of selected enzymes. In the future, it will be exciting to fully exploit the S-layer glycome for glycoengineering purposes and to link it to the bacterial interactome.
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Affiliation(s)
- Robin Ristl
- Department of NanoBiotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Kerstin Steiner
- Department of NanoBiotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
- Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
| | - Kristof Zarschler
- Department of NanoBiotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
- Institute of Genetics, General Genetics, Dresden University of Technology, Zellescher Weg 20b, 01217 Dresden, Germany
| | - Sonja Zayni
- Department of NanoBiotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Paul Messner
- Department of NanoBiotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Christina Schäffer
- Department of NanoBiotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
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Maclean LL, Vinogradov E, Pagotto F, Farber JM, Perry MB. The structure of the O-antigen of Cronobacter sakazakii HPB 2855 isolate involved in a neonatal infection. Carbohydr Res 2010; 345:1932-7. [PMID: 20684949 DOI: 10.1016/j.carres.2010.06.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 06/07/2010] [Accepted: 06/29/2010] [Indexed: 11/24/2022]
Abstract
Strains of Cronobactersakazakii (previously known as Enterobactersakazakii) are medically recognized important Gram-negative bacterial pathogens that cause enterocolitis, septicemia, and meningitis, with a high mortality rate in neonates. The structure of their O-antigens, that form part of their somatic lipopolysaccharide (LPS) components, is of interest for their chemical and serological identification and their relationship to virulence. The O-polysaccharide (O-PS) of C.sakazakii HPB 2855 (SK 81), a strain isolated from an infant at the Hospital for Sick Children in Toronto in 1981, was shown to be a polymer of a partially O-acetylated-repeating hexasaccharide unit composed of d-glucose, d-galacturonic acid, 2-acetamido-2-deoxy-d-galactose, and l-rhamnose (1:1:1:3). From composition and methylation analysis, and the application of 1D and 2D (1)H and (13)C NMR spectroscopy, the O-PS was determined to be a polymer of a repeating oligosaccharide unit having the structure:
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Affiliation(s)
- Leann L Maclean
- Institute for Biological Sciences, National Research Council, Ottawa, Canada
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Liu B, Perepelov AV, Li D, Senchenkova SN, Han Y, Shashkov AS, Feng L, Knirel YA, Wang L. Structure of the O-antigen of Salmonella O66 and the genetic basis for similarity and differences between the closely related O-antigens of Escherichia coli O166 and Salmonella O66. Microbiology (Reading) 2010; 156:1642-1649. [DOI: 10.1099/mic.0.037325-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
O-antigen is a component of the outer membrane of Gram-negative bacteria and is one of the most variable cell surface constituents, leading to major antigenic variability. The O-antigen forms the basis for bacterial serotyping. In this study, the O-antigen structure of Salmonella O66 was established, which differs from the known O-antigen structure of Escherichia coli O166 only in one linkage (most likely the linkage between the O-units) and O-acetylation. The O-antigen gene clusters of Salmonella O66 and E. coli O166 were found to have similar organizations, the only exception being that in Salmonella O66, the wzy gene is replaced by a non-coding region. The function of the wzy gene in E. coli O166 was confirmed by the construction and analysis of deletion and trans-complementation mutants. It is proposed that a functional wzy gene located outside the O-antigen gene cluster is involved in Salmonella O66 O-antigen biosynthesis, as has been reported previously in Salmonella serogroups A, B and D1. The sequence identity for the corresponding genes between the O-antigen gene clusters of Salmonella O66 and E. coli O166 ranges from 64 to 70 %, indicating that they may originate from a common ancestor. It is likely that after the species divergence, Salmonella O66 got its specific O-antigen form by inactivation of the wzy gene located in the O-antigen gene cluster and acquisition of two new genes (a wzy gene and a prophage gene for O-acetyl modification) both residing outside the O-antigen gene cluster.
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Affiliation(s)
- Bin Liu
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China
- TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, PR China
| | - Andrei V. Perepelov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Dan Li
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China
- TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, PR China
| | - Sof'ya N. Senchenkova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Yanfang Han
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China
- TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, PR China
| | - Alexander S. Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Lu Feng
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China
- TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, PR China
| | - Yuriy A. Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Lei Wang
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China
- TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, PR China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, PR China
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China
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40
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Perepelov AV, Dan Li, Bin Liu, Senchenkova SN, Dan Guo, Shashkov AS, Lu Feng, Knirel YA, Lei Wang. Structural and genetic characterization of the closely related O-antigens of Escherichia coli O85 and Salmonella enterica O17. Innate Immun 2010; 17:164-73. [DOI: 10.1177/1753425910369270] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
O-Antigen is a part of the lipopolysaccharide present in the outer membrane of Gram-negative bacteria, which confers major antigenic variability to the cell surface. In this study, we report on a previously undefined pair of Escherichia coli and Salmonella enterica with closely related O-antigens. The O-polysaccharides were isolated from the lipopolysaccharides of E. coli O85 and S. enterica O17 by mild acid degradation and studied by sugar analysis and NMR spectroscopy. The following structure was established for the O-unit of the E. coli O85-polysaccharide: The S. enterica O17-polysaccharide has the same carbohydrate backbone and, in addition, contains an O-acetyl group at position 2 of ~80% β-Galf residues. The O-antigen gene cluster of E. coli O85 was found to be closely related to that of S. enterica O17. Screening of type strains of all E. coli and S. enterica O-serogroups revealed two genes specific to the E. coli O85 O-antigen gene cluster, which can be used for development of PCR-based assays for identification and detection of E. coli O85 strains.
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Affiliation(s)
- Andrei V. Perepelov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation,
| | - Dan Li
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China
| | - Bin Liu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China
| | - Sof'ya N. Senchenkova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Dan Guo
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China
| | - Alexander S. Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Lu Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China, Tianjin Research Center for Functional Genomics and Biochip, Tianjin, P. R. China
| | - Yuriy A. Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China, Tianjin Research Center for Functional Genomics and Biochip, Tianjin, P. R. China, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, P. R. China
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Hu B, Perepelov AV, Liu B, Shevelev SD, Guo D, Senchenkova SN, Shashkov AS, Feng L, Knirel YA, Wang L. Structural and genetic evidence for the close relationship between Escherichia coli O71 and Salmonella enterica O28 O-antigens. ACTA ACUST UNITED AC 2010; 59:161-9. [PMID: 20482625 DOI: 10.1111/j.1574-695x.2010.00676.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
O-antigen is the most variable cell wall constituent of Gram-negative bacteria. Escherichia coli and Salmonella enterica are closely related species. In this work, we present structural and genetic evidence for the close relationship between O-antigens of E. coli O71 and S. enterica O28. The E. coli O71 O-antigen was found to consist of tetrasaccharide-repeating units containing d-GalpNAc, d-Galp, l-Rhap, and d-Quip3NAc, with multiple O-acetyl lateral groups. It is very similar to the known structure of the S. enterica O28 O-antigen, which has the same backbone units, but with a lateral Glc residue instead of O-acetyl groups. The O-antigen gene clusters of E. coli O71 and S. enterica O28 were sequenced and found to contain the same genes with high-level similarity. All of the genes expected for the synthesis of the common backbone structure of the two O-antigens were identified based on homology. It is proposed that the two gene clusters had originated from the same ancestor, and diverged by acquiring prophage genes to carry out side-chain modifications. This is a new pair of the closely related E. coli and S. enterica O-serogroups. The serogroup-specific genes of E. coli O71 and S. enterica O28 were also identified.
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Affiliation(s)
- Bo Hu
- Nankai University, Tianjin, China
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42
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Liu B, Perepelov AV, Svensson MV, Shevelev SD, Guo D, Senchenkova SN, Shashkov AS, Weintraub A, Feng L, Widmalm G, Knirel YA, Wang L. Genetic and structural relationships of Salmonella O55 and Escherichia coli O103 O-antigens and identification of a 3-hydroxybutanoyltransferase gene involved in the synthesis of a Fuc3N derivative. Glycobiology 2010; 20:679-88. [PMID: 20147450 DOI: 10.1093/glycob/cwq015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
O-antigen (O-polysaccharide), a part of the outer membrane of Gram-negative bacteria, is one of the most variable cell constituents and is related to bacterial virulence. O-antigen diversity is almost entirely due to genetic variations in O-antigen gene clusters. In this study, the O-polysaccharide structures of Salmonella O55 and Escherichia coli O103 were elucidated by chemical analysis and nuclear magnetic resonance spectroscopy. It was found that the O-polysaccharides have similar pentasaccharide O-units, which differ only in one sugar (glucose versus N-acetylglucosamine) and in the N-acyl group (acetyl versus 3-hydroxybutanoyl) on 3-amino-3,6-dideoxy-d-galactose (d-Fuc3N). The Salmonella O55 antigen gene cluster was sequenced and compared with the E. coli O103 antigen gene cluster reported previously. The two gene clusters were found to share high-level similarity (DNA identity ranges from 53% to 76%), except for two putative acyl transferase genes (fdtC in Salmonella O55 and fdhC in E. coli O103) which show no similarity. Replacement of the fdtC gene in Salmonella O55 with the fdhC gene from E. coli O103 resulted in production of a modified O-antigen, which contains a 3-hydroxybutanoyl derivative of Fuc3N in place of 3-acetamido-3,6-dideoxygalactose. This finding strongly suggests that fdhC is a 3-hydroxybutanoyltransferase gene. The sequence similarity level suggested that the O-antigen gene clusters of Salmonella O55 and E. coli O103 originate from a common ancestor, and this evolutionary relationship is discussed.
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Affiliation(s)
- Bin Liu
- TEDA School of Biological Sciences and Biotechnology, Tianjin, China
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43
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Abstract
The O antigen, consisting of many repeats of an oligosaccharide unit, is part of the lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria. It is on the cell surface and appears to be a major target for both immune system and bacteriophages, and therefore becomes one of the most variable cell constituents. The variability of the O antigen provides the major basis for serotyping schemes of Gram-negative bacteria. The genes responsible for the synthesis of O antigen are usually in a single cluster known as O antigen gene cluster, and their location on the chromosome within a species is generally conserved. Three O antigen biosynthesis pathways including Wzx/Wzy, ABC-transporter and Synthase have been discovered. In this chapter, the traditional and molecular O serotyping schemes are compared, O antigen structures and gene clusters of well-studied species are described, processes for formation and distribution of the variety of O antigens are discussed, and finally, the role of O antigen in bacterial virulence.
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Affiliation(s)
- Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China.
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44
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MacLean LL, Perry MB. Characterization of the antigenic O-polysaccharide produced by Escherichia coli serotype O:70. Carbohydr Res 2009; 345:644-8. [PMID: 20110088 DOI: 10.1016/j.carres.2009.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 11/17/2009] [Accepted: 11/18/2009] [Indexed: 10/20/2022]
Abstract
The structure of the antigenic O-polysaccharide (O-PS) produced by Escherichia coli serotype O:70 was determined by analysis of the chromatographically purified O-PS polymer prepared by mild hydrolysis of its aqueous phenol-extracted smooth-type somatic lipopolysaccharide. The O-PS is composed of D-glucose, D-galactose, D-fucose, 2-acetamido-2-deoxy-D-galactose, and 3-acetamido-3-deoxy-D-quinovose in a ratio of 1:1:1:1:1. From the use of DOC-PAGE, methylation, Smith-type periodate oxidation, and (1)H and (13)C NMR spectroscopy, including 2D experiments, the O-PS was shown to be a polymer of a branched repeating pentasaccharide unit having the structure: [structure: see the text]
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Affiliation(s)
- Leann L MacLean
- Institute for Biological Sciences, National Research Council, Ottawa, ON, Canada K1A 0R6
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Clark CG, Kropinski AM, Parolis H, Grant CCR, Trout-Yakel KM, Franklin K, Ng LK, Paramonov NA, Parolis LAS, Rahn K, Tabor H. Escherichia coli O123 O antigen genes and polysaccharide structure are conserved in some Salmonella enterica serogroups. J Med Microbiol 2009; 58:884-894. [DOI: 10.1099/jmm.0.007187-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The serotyping of O and H antigens is an important first step in the characterization of Salmonella enterica. However, serotyping has become increasingly technically demanding and expensive to perform. We have therefore sequenced additional S. enterica O antigen gene clusters to provide information for the development of DNA-based serotyping methods. Three S. enterica isolates had O antigen gene clusters with homology to the Escherichia coli O123 O antigen region. O antigen clusters from two serogroup O58 S. enterica strains had approximately 85 % identity with the E. coli O123 O antigen region over their entire length, suggesting that these Salmonella and E. coli O antigen regions evolved from a common ancestor. The O antigen cluster of a Salmonella serogroup O41 isolate had a lower level of identity with E. coli O123 over only part of its O antigen DNA cluster sequence, suggesting a different and more complex evolution of this gene cluster than those in the O58 strains. A large part of the Salmonella O41 O antigen DNA cluster had very close identity with the O antigen cluster of an O62 strain. This region of DNA homology included the wzx and wzy genes. Therefore, molecular serotyping tests using only the O41 or O62 wzx and wzy genes would not differentiate between the two serogroups. The E. coli O123 O-antigenic polysaccharide and its repeating unit were characterized, and the chemical structure for E. coli O123 was entirely consistent with the O antigen gene cluster sequences of E. coli O123 and the Salmonella O58 isolates. An understanding of both the genetic and structural composition of Salmonella and E. coli O antigens is necessary for the development of novel molecular methods for serotyping these organisms.
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Affiliation(s)
- Clifford G. Clark
- Department of Medical Microbiology, 510 Medical Sciences Building, University of Manitoba, 730 William Avenue, Winnipeg, MB R3T 2N2, Canada
- Enteric Diseases Program, Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Andrew M. Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada
| | - Haralambos Parolis
- School of Pharmaceutical Sciences, Rhodes University, Grahamstown 6140, South Africa
| | - Christopher C. R. Grant
- Enteric Diseases Program, Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Keri M. Trout-Yakel
- Enteric Diseases Program, Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Kristyn Franklin
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada
| | - Lai-King Ng
- Department of Medical Microbiology, 510 Medical Sciences Building, University of Manitoba, 730 William Avenue, Winnipeg, MB R3T 2N2, Canada
- Enteric Diseases Program, Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Nikolay A. Paramonov
- School of Pharmaceutical Sciences, Rhodes University, Grahamstown 6140, South Africa
| | - Lesley A. S. Parolis
- School of Pharmaceutical Sciences, Rhodes University, Grahamstown 6140, South Africa
| | - Kris Rahn
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada
| | - Helen Tabor
- Enteric Diseases Program, Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
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Molecular analysis of the Enterobacter sakazakii O-antigen gene locus. Appl Environ Microbiol 2008; 74:3783-94. [PMID: 18441119 DOI: 10.1128/aem.02302-07] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleotide polymorphism associated with the O-antigen-encoding locus, rfb, in Enterobacter sakazakii was determined by PCR-restriction fragment length polymorphism analysis. Based on the analysis of these DNA profiles, 12 unique banding patterns were detected among a collection of 62 strains from diverse origins. Two common profiles were identified and were designated serotypes O:1 and O:2. DNA sequencing of the 12,500-bp region flanked by galF and gnd identified 11 open reading frames, all with the same transcriptional direction. Analysis of the proximal region of both sequences demonstrated remarkable heterogeneity. A PCR assay targeting genes specific for the two prominent serotypes was developed and applied for the identification of these strains recovered from food, environmental, and clinical samples.
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Olsson U, Weintraub A, Widmalm G. Structural determination of the O-antigenic polysaccharide from the verocytotoxin-producing Escherichia coli O176. Carbohydr Res 2008; 343:805-9. [DOI: 10.1016/j.carres.2008.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Revised: 01/03/2008] [Accepted: 01/07/2008] [Indexed: 11/30/2022]
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Determination of glycosyltransferase specificities for the Escherichia coli O111 O antigen by a generic approach. Appl Environ Microbiol 2007; 74:1294-8. [PMID: 18156323 DOI: 10.1128/aem.02660-07] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe a bacterial strain developed to facilitate the determination of glycosyltransferase (GT) specificities for O antigens of known structure and gene cluster sequence. For proof of principle for the approach, the strain was used to determine the specificity of the Escherichia coli O111 O-antigen GT genes.
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Structure of the O-polysaccharide of Escherichia coli O112ab containing L-iduronic acid. Carbohydr Res 2007; 343:571-5. [PMID: 18062946 DOI: 10.1016/j.carres.2007.10.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 10/17/2007] [Indexed: 11/20/2022]
Abstract
An acidic O-polysaccharide was isolated by mild acid degradation of the lipopolysaccharide of Escherichia coli O112ab and studied by sugar analysis along with (1)H and (13)C NMR spectroscopy. The O-polysaccharide was found to contain a rarely occurring sugar component, L-iduronic acid (L-IdoA), and the following structure of the branched pentasaccharide repeating unit was established: [structure: see text].
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