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Tiwari SK, van der Putten BCL, Fuchs TM, Vinh TN, Bootsma M, Oldenkamp R, La Ragione R, Matamoros S, Hoa NT, Berens C, Leng J, Álvarez J, Ferrandis-Vila M, Ritchie JM, Fruth A, Schwarz S, Domínguez L, Ugarte-Ruiz M, Bethe A, Huber C, Johanns V, Stamm I, Wieler LH, Ewers C, Fivian-Hughes A, Schmidt H, Menge C, Semmler T, Schultsz C. Genome-wide association reveals host-specific genomic traits in Escherichia coli. BMC Biol 2023; 21:76. [PMID: 37038177 PMCID: PMC10088187 DOI: 10.1186/s12915-023-01562-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/10/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Escherichia coli is an opportunistic pathogen which colonizes various host species. However, to what extent genetic lineages of E. coli are adapted or restricted to specific hosts and the genomic determinants of such adaptation or restriction is poorly understood. RESULTS We randomly sampled E. coli isolates from four countries (Germany, UK, Spain, and Vietnam), obtained from five host species (human, pig, cattle, chicken, and wild boar) over 16 years, from both healthy and diseased hosts, to construct a collection of 1198 whole-genome sequenced E. coli isolates. We identified associations between specific E. coli lineages and the host from which they were isolated. A genome-wide association study (GWAS) identified several E. coli genes that were associated with human, cattle, or chicken hosts, whereas no genes associated with the pig host could be found. In silico characterization of nine contiguous genes (collectively designated as nan-9) associated with the human host indicated that these genes are involved in the metabolism of sialic acids (Sia). In contrast, the previously described sialic acid regulon known as sialoregulon (i.e. nanRATEK-yhcH, nanXY, and nanCMS) was not associated with any host species. In vitro growth experiments with a Δnan-9 E. coli mutant strain, using the sialic acids 5-N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) as sole carbon source, showed impaired growth behaviour compared to the wild-type. CONCLUSIONS This study provides an extensive analysis of genetic determinants which may contribute to host specificity in E. coli. Our findings should inform risk analysis and epidemiological monitoring of (antimicrobial resistant) E. coli.
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Affiliation(s)
- Sumeet K Tiwari
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Program, Norwich Research Park, Norwich, UK
| | - Boas C L van der Putten
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Thilo M Fuchs
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Trung N Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Veterinary Medicine, College of Agriculture, Can Tho University, Can Tho, Vietnam
| | | | - Rik Oldenkamp
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Life and Environment, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Roberto La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Sebastien Matamoros
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ngo T Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Tropical medicine and global health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Microbiology- Parasitology Unit, Biomedical Research Center and Microbiology Department, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Christian Berens
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Joy Leng
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Julio Álvarez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | | | - Jenny M Ritchie
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Angelika Fruth
- Robert Koch Institute, Enteropathogenic Bacteria and Legionella, Wernigerode, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Lucas Domínguez
- Tropical medicine and global health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Microbiology- Parasitology Unit, Biomedical Research Center and Microbiology Department, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Charlotte Huber
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Vanessa Johanns
- Robert Koch Institute, Advanced Light and Electron Microscopy, Berlin, Germany
| | - Ivonne Stamm
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Kornwestheim, Germany
| | | | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Giessen, Germany
| | - Amanda Fivian-Hughes
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Herbert Schmidt
- Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, University of Hohenheim, Stuttgart, Germany
| | - Christian Menge
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Torsten Semmler
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany.
| | - Constance Schultsz
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
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Tran-Mai AP, Tran HDT, Mai QG, Huynh KQ, Tran TL, Tran-Van H, Tran-Van H. Flagellin from Salmonella enteritidis Enhances the Immune Response of Fused F18 from Enterotoxigenic Escherichia coli. Trop Life Sci Res 2022; 33:19-32. [PMID: 36545054 PMCID: PMC9747111 DOI: 10.21315/tlsr2022.33.3.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
F18 plays an important role in helping Enterotoxigenic Escherichia coli (ETEC) binds to specific receptors on small intestinal enterocytes, followed by secreting of toxins causing diarrhea in post-weaning piglets (post-weaning diarrhea, PWD). However, the F18 subunit vaccine is not sufficient to stimulate an immune response that can protect weaning pigs from F18-positive ETEC (F18+ETEC). Recently, a body of evidence shows that flagellin protein (FliC) helps to increase the immunity of fused proteins. Therefore, in this study, we combined FliC with F18 to enhance the immune response of F18. The f18 gene was obtained from F18+ETEC, then was fused with the fliC gene. The expression of recombinant FliC-F18 protein was induced by Isopropyl-beta-D-Thiogalactopyranoside (IPTG). The purified protein was tested in vivo in mouse models to evaluate the immunostimulation. Results showed that the fusion of FliC and F18 protein increased the production of anti-F18 antibodies. Besides, the anti-F18 antibody in the collected antiserum specifically identified F18+ETEC. This result provides proof-of-concept for the development of subunit vaccine to prevent PWD using F18 antigen.
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Affiliation(s)
- An-Phuc Tran-Mai
- Department of Molecular and Environmental Biotechnology, University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam,National Veterinary Joint Stock Company, 28 VSIP, Street no. 06, Vietnam-Singapore Industrial Park, Thuan An City, Binh Duong Province, Vietnam
| | - Hong-Diep Thi Tran
- Department of Molecular and Environmental Biotechnology, University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam,Vietnam National University, Vo Truong Toan Street, Linh Trung Ward, Thu Duc City, Ho Chi Minh City, Vietnam
| | - Quoc-Gia Mai
- Laboratory of Biosensors, University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
| | - Kien-Quang Huynh
- Department of Molecular and Environmental Biotechnology, University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam,Vietnam National University, Vo Truong Toan Street, Linh Trung Ward, Thu Duc City, Ho Chi Minh City, Vietnam
| | - Thuoc Linh Tran
- Department of Molecular and Environmental Biotechnology, University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam,Vietnam National University, Vo Truong Toan Street, Linh Trung Ward, Thu Duc City, Ho Chi Minh City, Vietnam
| | - Hieu Tran-Van
- Department of Molecular and Environmental Biotechnology, University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam,Vietnam National University, Vo Truong Toan Street, Linh Trung Ward, Thu Duc City, Ho Chi Minh City, Vietnam,Corresponding author:
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Barth SA, Bauerfeind R, Berens C, Menge C. Shiga Toxin-Producing E. coli in Animals: Detection, Characterization, and Virulence Assessment. Methods Mol Biol 2021; 2291:19-86. [PMID: 33704748 DOI: 10.1007/978-1-0716-1339-9_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cattle and other ruminants are primary reservoirs for Shiga toxin-producing Escherichia coli (STEC) strains which have a highly variable, but unpredictable, pathogenic potential for humans. Domestic swine can carry and shed STEC, but only STEC strains producing the Shiga toxin (Stx) 2e variant and causing edema disease in piglets are considered pathogens of veterinary medical interest. In this chapter, we present general diagnostic workflows for sampling livestock animals to assess STEC prevalence, magnitude, and duration of host colonization. This is followed by detailed method protocols for STEC detection and typing at genetic and phenotypic levels to assess the relative virulence exerted by the strains.
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Affiliation(s)
- Stefanie A Barth
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Rolf Bauerfeind
- Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University Gießen, Gießen, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Christian Menge
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany.
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4
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F4- and F18-Positive Enterotoxigenic Escherichia coli Isolates from Diarrhea of Postweaning Pigs: Genomic Characterization. Appl Environ Microbiol 2020; 86:AEM.01913-20. [PMID: 32948526 DOI: 10.1128/aem.01913-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/07/2020] [Indexed: 12/11/2022] Open
Abstract
This study aimed to characterize in silico enterotoxigenic Escherichia coli F4- and F18-positive isolates (n = 90) causing swine postweaning diarrhea, including pathogenic potential, phylogenetic relationship, antimicrobial and biocide resistance, prophage content, and metal tolerance rates. F4 strains belonged mostly to the O149 and O6 serogroups and ST100 and ST48 sequence types (STs). F18 strains were mainly assigned to the O8 and O147 serogroups and ST10, ST23, and ST42. The highest rates of antimicrobial resistance were found against streptomycin, sulfamethoxazole, tetracycline, trimethoprim, and ampicillin. No resistance was found toward ciprofloxacin, cefotaxime, ceftiofur, and colistin. Genes conferring tolerance to copper (showing the highest diversity), cadmium, silver, and zinc were predicted in all genomes. Enterotoxin genes (ltcA, 100% F4, 62% F18; astA, 100% F4, 38.1% F18; sta, 18.8% F4, 38.1% F18; stb, 100% F4, 76.2% F18) and fimbria-encoding genes typed as F4ac and F18ac were detected in all strains, in addition to up to 16 other virulence genes in individual strains. Phage analysis predicted between 7 and 20 different prophage regions in each strain. A highly diverse variety of plasmids was found; IncFII, IncFIB, and IncFIC were prevalent among F4 isolates, while IncI1 and IncX1 were dominant among F18 strains. Interestingly, F4 isolates from the early 1990s belonged to the same clonal group detected for most of the F4 strains from 2018 to 2019 (ONT:H10-A-ST100-CH27-0). The small number of single-nucleotide polymorphism differences between the oldest and recent F4 ST100 isolates suggests a relatively stable genome. Overall, the isolates analyzed in this study showed remarkably different genetic traits depending on the fimbria type.IMPORTANCE Diarrhea in the postweaning period due to enterotoxigenic E. coli (ETEC) is an economically relevant disease in pig production worldwide. In Denmark, prevention is mainly achieved by zinc oxide administration (to be discontinued by 2022). In addition, a breeding program has been implemented that aims to reduce the prevalence of this illness. Treatment with antimicrobials contributes to the problem of antimicrobial resistance (AMR) development. As a novelty, this study aims to deeply understand the genetic population structure and variation among diarrhea-associated isolates by whole-genome sequencing characterization. ST100-F4ac is the dominant clonal group circulating in Danish herds and showed high similarity to ETEC ST100 isolates from China, the United States, and Spain. High rates of AMR and high diversity of virulence genes were detected. The characterization of diarrhea-related ETEC is important for understanding the disease epidemiology and pathogenesis and for implementation of new strategies aiming to reduce the impact of the disease in pig production.
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Impedimetric DNA E-biosensor for multiplexed sensing of Escherichia coli and its virulent f17 strains. Mikrochim Acta 2020; 187:635. [DOI: 10.1007/s00604-020-04614-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/21/2020] [Indexed: 11/26/2022]
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6
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Baldo V, Salogni C, Giovannini S, D'Incau M, Boniotti MB, Birbes L, Pitozzi A, Formenti N, Grassi A, Pasquali P, Alborali GL. Pathogenicity of Shiga Toxin Type 2e Escherichia coli in Pig Colibacillosis. Front Vet Sci 2020; 7:545818. [PMID: 33062659 PMCID: PMC7530191 DOI: 10.3389/fvets.2020.545818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/12/2020] [Indexed: 11/24/2022] Open
Abstract
Shiga toxin type 2e (Stx2e) Escherichia coli is the causative factor of diarrhea and edema in swine. The aims of this study were to determine the prevalence of Stx2e-producing E. coli isolates and to characterize isolates from clinical cases of pig colibacillosis and healthy swine. During the 11 years of the study (2006–2017), a total of 233 Stx2e-producing isolates were detected−230 out of 2,060 (11.16%) E. coli isolated from diseased pigs and 3 out of 171 (1.75%) from healthy swine. Stx2e-producing isolates were indeed more present in clinical colibacillosis cases than in healthy pigs (p = 0.0002). The predominant serogroup was O139 (79.82%) and the most common fimbrial factor present in these isolates was F18 (177 isolates), followed by F6 (5 isolates). The enterotoxins LTI, STa, and STb were detected in 10.43, 41.73, and 48.26% of the isolates, respectively. The predominant virotypes F18-Stx2e and -STa-STb-Stx2e were similarly present in weaners (33.33 and 35.52%) and finishers (38.30 and 25.53%). Among isolates from diseased pigs, O139 and F18 were the more frequently identified serogroup and virulence factor, respectively. Of the tested 230 Stx2e-producing isolates isolated from diseased pigs, 29 (12.60%) harbored genes encoding ESBL, particularly TEM (79.30%), CTX-M1 (17.20%), and CMY-2 (3.40%). Antimicrobial resistance to tetracycline was the most common characteristic (98.25%), followed by ampicillin (93.91%), cephalotin (90.43%) and trimethoprim/sulfamethoxazole (82.17%). Our results showed that Stx2e-producing E. coli were more frequently associated with clinical forms of colibacillosis, with minimal probability to isolate these isolates from healthy pigs.
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Affiliation(s)
- Valentina Baldo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Cristian Salogni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Stefano Giovannini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Mario D'Incau
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Maria Beatrice Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Laura Birbes
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Alessandra Pitozzi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Nicoletta Formenti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Andrea Grassi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Paolo Pasquali
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Giovanni Loris Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
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7
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Santos ACDM, Santos FF, Silva RM, Gomes TAT. Diversity of Hybrid- and Hetero-Pathogenic Escherichia coli and Their Potential Implication in More Severe Diseases. Front Cell Infect Microbiol 2020; 10:339. [PMID: 32766163 PMCID: PMC7381148 DOI: 10.3389/fcimb.2020.00339] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/04/2020] [Indexed: 12/17/2022] Open
Abstract
Although extraintestinal pathogenic Escherichia coli (ExPEC) are designated by their isolation site and grouped based on the type of host and the disease they cause, most diarrheagenic E. coli (DEC) are subdivided into several pathotypes based on the presence of specific virulence traits directly related to disease development. This scenario of a well-categorized E. coli collapsed after the German outbreak of 2011, caused by one strain bearing the virulence factors of two different DEC pathotypes (enteroaggregative E. coli and Shiga toxin-producing E. coli). Since the outbreak, many studies have shown that this phenomenon is more frequent than previously realized. Therefore, the terms hybrid- and hetero-pathogenic E. coli have been coined to describe new combinations of virulence factors among the classic E. coli pathotypes. In this review, we provide an overview of these classifications and highlight the E. coli genomic plasticity that results in some mixed E. coli pathotypes displaying novel pathogenic strategies, which lead to a new symptomatology related to E. coli diseases. In addition, as the capacity for genome interrogation has grown in the last few years, it is clear that genes encoding some virulence factors, such as Shiga toxin, are found among different E. coli pathotypes to which they have not traditionally been associated, perhaps foreshowing their emergence in new and severe outbreaks caused by such hybrid strains. Therefore, further studies regarding hetero-pathogenic and hybrid-pathogenic E. coli isolates are necessary to better understand and control the spread of these pathogens.
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Affiliation(s)
- Ana Carolina de Mello Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda Fernandes Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rosa Maria Silva
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tânia Aparecida Tardelli Gomes
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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Abubakar RH, Madoroba E, Adebowale O, Fasanmi OG, Fasina FO. Antimicrobial usage in pig production: Effects on Escherichia coli virulence profiles and antimicrobial resistance. Onderstepoort J Vet Res 2019; 86:e1-e11. [PMID: 31714139 PMCID: PMC6852416 DOI: 10.4102/ojvr.v86i1.1743] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 02/05/2023] Open
Abstract
Antimicrobials (AM) are used for growth promotion and therapy in pig production. Its misuse has led to the development of resistant organisms. We evaluated Escherichia coli virulence genes, and compared phenotypic-genotypic antimicrobial resistance (AMR) patterns of faecal E. coli from pigs receiving routine farm treatment without antimicrobial agents against pigs treated routinely with AM over 70 days. Recovered E. coli were tested for AMR using disk diffusion and polymerase chain reaction. Virulence genes were detected in 24.8% of isolates from antimicrobial group and 43.5% from non-antimicrobial group (p = 0.002). The proportion of virulence genes heat-stable enterotoxins a b (STa, STb), enteroaggregative heat stable enterotoxin 1 [EAST1] and Shiga toxin type 2e [Stx2e]) were 18.1%, 0.0%, 78.7% and 3.0% for antimicrobial group and 14.8%, 8.5%, 85.1% and 12.7% for non-antimicrobial groups, respectively. Resistance to oxytetracycline was most common (p = 0.03) in samples collected between days 10 and 21. Resistance shifted to amoxicillin on days 56-70, and trimethoprim resistance was observed throughout. Seventeen phenotypic AMR combinations were observed and eight were multidrug resistant. At least one tetracycline resistance gene was found in 63.9% of the isolates. tet (A) (23.3%) was most common in the antimicrobial group, whereas tet (B) (43.5%) was prevalent in the non-antimicrobial group. Usage or non-usage of antimicrobial agents in growing pigs does not preclude virulence genes development and other complex factors may be involved as previously described. Heavily used AM correspond to the degree of resistance and tetracycline resistance genes were detected during the growth phase.
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Affiliation(s)
- Rukayya H Abubakar
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Sciences, University of Pretoria, Pretoria.
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9
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Do KH, Byun JW, Lee WK. Prevalence of O-serogroups, virulence genes, and F18 antigenic variants in Escherichia coli isolated from weaned piglets with diarrhea in Korea during 2008-2016. J Vet Sci 2019; 20:43-50. [PMID: 30481984 PMCID: PMC6351757 DOI: 10.4142/jvs.2019.20.1.43] [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] [Received: 08/06/2018] [Revised: 10/01/2018] [Accepted: 10/18/2018] [Indexed: 11/20/2022] Open
Abstract
To diagnose colibacillosis, detection of O-serogroups and virulence genes has been recommended worldwide. The prevalence of virulence factors can fluctuate over time. The objectives of this study were to determine the prevalence of O-serogroups, virulence genes, and F18 subtypes among pathogenic Escherichia coli isolated from weaned piglets with diarrhea in Korea. Between 2008 and 2016, 362 E. coli were isolated from weaned piglets with diarrhea. Hemolysis was determined in blood agar, and O-serogroups were identified using the slide agglutination technique. The genes for the toxins and fimbriae were amplified by polymerase chain reaction (PCR). Real-time PCR was conducted to discriminate between F18 subtypes. Although the most prevalent serogroup was O149 (11.3%) in the last 9 years, O139 (19.1%) became the most prevalent in recent years (2015–2016). The most predominant pathotype was enterotoxigenic E. coli (61.3%). The frequencies of Shiga-like toxin-producing E. coli (STEC) (23.4%), O139 (19.1%), Stx2e (35.1%), and F18ab (48.7%) increased over the most recent years. Although enterotoxigenic E. coli was the most predominant pathotype, the frequencies of O139, Stx2e, STEC, and F18ab have increased in recent years. These results demonstrate that there have been temporal changes in the predominant O-serogroups and virulence genes over the last decade in Korea. These findings can be practicable for use in epidemiology and control measures for enteric colibacillosis in Korean piggeries.
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Affiliation(s)
- Kyung-Hyo Do
- Laboratory of Veterinary Bacteriology and Infectious Diseases, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Jae-Won Byun
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Wan-Kyu Lee
- Laboratory of Veterinary Bacteriology and Infectious Diseases, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea
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García-Meniño I, García V, Mora A, Díaz-Jiménez D, Flament-Simon SC, Alonso MP, Blanco JE, Blanco M, Blanco J. Swine Enteric Colibacillosis in Spain: Pathogenic Potential of mcr-1 ST10 and ST131 E. coli Isolates. Front Microbiol 2018; 9:2659. [PMID: 30455680 PMCID: PMC6230658 DOI: 10.3389/fmicb.2018.02659] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/18/2018] [Indexed: 12/25/2022] Open
Abstract
This is a wide epidemiological study of 499 E. coli isolates recovered from 179 outbreaks of enteric colibacillosis from pig production farms in Spain during a period of 10 years. Most samples were of diarrheagenic cases occurred during the post-wean period (PWD) which showed to be significantly associated with ETEC (67%) followed by aEPEC (21.7%). On the contrary, aEPEC was more prevalent (60.3%) among diarrheas of suckling piglets, followed by ETEC (38.8%). STEC/ETEC or STEC were recovered in 11.3 and 0.9% of PWD and neonatal diarrhea, respectively. Detection of the F4 colonization factor was not significantly different between isolates recovered from neonatal pigs and those recovered post wean (40.5 versus 27.7%) while F18 was only present among PWD isolates (51.5% of ETEC, STEC, and STEC/ETEC isolates). We also found a high prevalence of resistance to colistin related to the presence of the mcr-1 gene (25.6% of the diarreagenic isolates). The characterization of 65 representative mcr-1 isolates showed that all were phenotypically resistant to colistin (>2 μg/ml), and most (61 of 65) multidrug-resistant (MDR). Six ETEC and one STEC mcr-1 isolates were also carriers of ESBL genes. In addition, other seven mcr-1 isolates harbored mcr-4 (three ETEC) and mcr-5 (two ETEC and two aEPEC) genes. In the phylogenetic analysis of the 65 mcr-1 diarrheagenic isolates we found that more than 50% (38 out of 65) belonged to A-ST10 Cplx and from those, 29 isolates showed the clonotype CH11-24. In this study, we also recovered 18 ST131 isolates including seven mcr-1 carriers. To the best of our knowledge, this would be the first report of ST131 mcr-1 isolation in pigs. Worryingly, the swine mcr-1 ST131 carriers also showed MDR, including to trimethoprim-sulfamethoxazole, tobramycin, gentamicin and ciprofloxacin. In the PFGE-macrorestriction comparison of clinical swine and human ST131, we found high similarities (≥85%) between two pig and two human ST131 isolates of virotype D5. Acquisition of mcr-1 by this specific clone means an increased risk due to its special feature of congregating virulence and resistance traits, together with its spread capability. Here we show a potential zoonotic swine source of ST131.
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Affiliation(s)
- Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Dafne Díaz-Jiménez
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Saskia C Flament-Simon
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - María Pilar Alonso
- Unidad de Microbiología, Hospital Universitario Lucus Augusti (HULA), Lugo, Spain
| | - Jesús E Blanco
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Miguel Blanco
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
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Wang W, Zijlstra RT, Gänzle MG. Identification and quantification of virulence factors of enterotoxigenic Escherichia coli by high-resolution melting curve quantitative PCR. BMC Microbiol 2017; 17:114. [PMID: 28506262 PMCID: PMC5433089 DOI: 10.1186/s12866-017-1023-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/05/2017] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Diagnosis of enterotoxigenic E. coli (ETEC) associated diarrhea is complicated by the diversity of E.coli virulence factors. This study developed a multiplex quantitative PCR assay based on high-resolution melting curves analysis (HRM-qPCR) to identify and quantify genes encoding five ETEC fimbriae related to diarrhea in swine, i.e. K99, F41, F18, F6 and K88. METHODS Five fimbriae expressed by ETEC were amplified in multiple HRM-qPCR reactions to allow simultaneous identification and quantification of five target genes. The assay was calibrated to allow quantification of the most abundant target gene, and validated by analysis of 30 samples obtained from piglets with diarrhea and healthy controls, and comparison to standard qPCR detection. RESULTS The five amplicons with melting temperatures (Tm) ranging from 74.7 ± 0.06 to 80.5 ± 0.15 °C were well-separated by HRM-qPCR. The area of amplicons under the melting peak correlated linearly to the proportion of the template in the calibration mixture if the proportion exceeded 4.8% (K88) or <1% (all other amplicons). The suitability of the method was evaluated using 30 samples from weaned pigs aged 6-7 weeks; 14 of these animals suffered from diarrhea in consequence of poor sanitary conditions. Genes encoding fimbriae and enterotoxins were quantified by HRM-qPCR and/or qPCR. The multiplex HRM-qPCR allowed accurate analysis when the total gene copy number of targets was more than 1 × 105 / g wet feces and the HRM curves were able to simultaneously distinguish fimbriae genes in the fecal samples. The relative quantification of the most abundant F18 based on melting peak area was highly correlated (P < 0.001; r2 = 0.956) with that of individual qPCR result but the correlation for less abundant fimbriae was much lower. CONCLUSIONS The multiplex HRM assay identifies ETEC virulence factors specifically and efficiently. It correctly indicated the predominant fimbriae type and additionally provides information of presence/ absence of other fimbriae types and it could find broad applications for pathogen diagnosis.
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Affiliation(s)
- Weilan Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Ag/For Centre, Edmonton, AB, T6G 2P5, Canada
| | - Ruurd T Zijlstra
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Ag/For Centre, Edmonton, AB, T6G 2P5, Canada
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Ag/For Centre, Edmonton, AB, T6G 2P5, Canada.
- College of Bioengineering and Food Science, Hubei University of Technology, Wuhan, Hubei, People's Republic of China.
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12
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Diseases of the Alimentary Tract. Vet Med (Auckl) 2017. [PMCID: PMC7167529 DOI: 10.1016/b978-0-7020-5246-0.00007-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Okello E, Moonens K, Erume J, De Greve H. Enterotoxigenic Escherichia coli strains are highly prevalent in Ugandan piggeries but disease outbreaks are masked by antibiotic prophylaxis. Trop Anim Health Prod 2014; 47:117-22. [DOI: 10.1007/s11250-014-0694-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 09/30/2014] [Indexed: 11/24/2022]
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Real-time PCR for differentiation of F18 variants among enterotoxigenic and Shiga toxin-producing Escherichia coli from piglets with diarrhoea and oedema disease. Vet J 2013; 198:538-40. [PMID: 23992871 DOI: 10.1016/j.tvjl.2013.07.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 07/08/2013] [Accepted: 07/14/2013] [Indexed: 11/20/2022]
Abstract
One-step real-time PCR using one set of primers and four probes was developed for differentiation of F18 variants (F18 common, F18ab, F18ac, F18new variant) of enterotoxigenic (ETEC) and Shiga toxin-producing (STEC) Escherichia coli from piglets with diarrhoea and oedema disease. The limits of detection for F18common, F18ab, F18ac, and F18new variant were 10(7), 10(7), 10(5) and 10(7)colony forming units/g faeces, respectively. Of 94 Korean isolates of E. coli encoding F18, 70 were F18ac (43 STEC/ETEC, 4 STEC and 23 ETEC), 15 were F18ab (all STEC) and nine were F18new variant (1 STEC/ETEC, 7 STEC, 1 ETEC).
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Zhou C, Liu Z, Jiang J, Yu Y, Zhang Q. Differential gene expression profiling of porcine epithelial cells infected with three enterotoxigenic Escherichia coli strains. BMC Genomics 2012; 13:330. [PMID: 22823589 PMCID: PMC3472312 DOI: 10.1186/1471-2164-13-330] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Accepted: 06/30/2012] [Indexed: 11/13/2022] Open
Abstract
Background Enterotoxigenic Escherichia coli (ETEC) is one of the most important pathogenic bacteria causing severe diarrhoea in human and pigs. In ETEC strains, the fimbrial types F4 and F18 are commonly found differently colonized within the small intestine and cause huge economic losses in the swine industry annually worldwide. To address the underlying mechanism, we performed a transcriptome study of porcine intestinal epithelial cells (IPEC-J2) with and without infection of three representative ETEC strains. Results A total 2443, 3493 and 867 differentially expressed genes were found in IPEC-J2 cells infected with F4ab ETEC (CF4ab), with F4ac ETEC (CF4ac) and with F18ac ETEC (CF18ac) compared to the cells without infection (control), respectively. The number of differentially expressed genes between CF4ab and CF4ac, CF4ab and CF18ac, and CF4ac and CF18ac were 77, 1446 and 1629, respectively. The gene ontology and pathway analysis showed that the differentially expressed genes in CF4abvs control are significantly involved in cell-cycle progress and amino acid metabolism, while the clustered terms of the differentially expressed genes in CF4acvs control comprise immune, inflammation and wounding response and apoptosis as well as cell cycle progress and proteolysis. Differentially expressed genes between CF18acvs control are mainly involved in cell-cycle progression and immune response. Furthermore, fundamental differences were observed in expression levels of immune-related genes among the three ETEC treatments, especially for the important pro-inflammatory molecules, including IL-6, IL-8, TNF-α, CCL20, CXCL2 etc. Conclusions The discovery in this study provides insights into the interaction of porcine intestinal epithelial cells with F4 ETECs and F18 ETEC, respectively. The genes induced by ETECs with F4 versus F18 fimbriae suggest why ETEC with F4 may be more virulent compared to F18 which seems to elicit milder effects.
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Affiliation(s)
- Chuanli Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193 Beijing, Peoples Republic of China
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