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Suzuki Y, Shimizu H, Tamai S, Hoshiko Y, Maeda T, Nukazawa K, Iguchi A, Masago Y, Ishii S. Simultaneous detection of various pathogenic Escherichia coli in water by sequencing multiplex PCR amplicons. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:264. [PMID: 36600083 DOI: 10.1007/s10661-022-10863-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Waterborne diseases due to pathogen contamination in water are a serious problem all over the world. Accurate and simultaneous detection of pathogens in water is important to protect public health. In this study, we developed a method to simultaneously detect various pathogenic Escherichia coli by sequencing the amplicons of multiplex PCR. Our newly designed multiplex PCR amplified five genes for pathogenic E. coli (uidA, stx1, stx2, STh gene, and LT gene). Additional two PCR assays (for aggR and eae) were also designed and included in the amplicon sequencing analysis. The same assays were also used for digital PCR (dPCR). Strong positive correlations were observed between the sequence read count and the dPCR results for most of the genes targeted, suggesting that our multiplex PCR-amplicon sequencing approach could provide quantitative information. The method was also successfully applied to monitor the level of pathogenic E. coli in river water and wastewater samples. The approach shown here could be expanded by targeting genes for other pathogens.
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Affiliation(s)
- Yoshihiro Suzuki
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan.
| | - Hiroki Shimizu
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
| | - Shouichiro Tamai
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
| | - Yuki Hoshiko
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-ku, Kitakyushu, 808-0196, Japan
- Present address: Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, 67 Asahi-Machi, Kurume-City, Fukuoka, 830-0011, Japan
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-ku, Kitakyushu, 808-0196, Japan
| | - Kei Nukazawa
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
| | - Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Yoshifumi Masago
- Center for Climate Change Adaptation, National Institute for Environmental Studies, Ibaraki, Japan
| | - Satoshi Ishii
- Department of Soil, Water, and Climate, University of Minnesota, Falcon Heights, MN, USA
- Bio Technology Institute, University of Minnesota, Falcon Heights, MN, USA
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Fusco A, Savio V, Perfetto B, Mattina R, Donnarumma G. Antimicrobial peptide human β-defensin-2 improves in vitro cellular viability and reduces pro-inflammatory effects induced by enteroinvasive Escherichia coli in Caco-2 cells by inhibiting invasion and virulence factors’ expression. Front Cell Infect Microbiol 2022; 12:1009415. [PMID: 36310877 PMCID: PMC9606569 DOI: 10.3389/fcimb.2022.1009415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli is one of the commensal species most represented in the intestinal microbiota. However, there are some strains that can acquire new virulence factors that enable them to adapt to new intestinal niches. These include enteroinvasive E. coli (EIEC) that is responsible for the bacillary dysentery that causes severe diarrheal symptoms in both children and adults. Due to the increasing onset of antibiotic resistance phenomena, scientific research is focused on the study of other therapeutic approaches for the treatment of bacterial infections. A promising alternative could be represented by antimicrobial peptides (AMPs), that have received widespread attention due to their broad antimicrobial spectrum and low incidence of bacterial resistance. AMPs modulate the immune defenses of the host and regulate the composition of microbiota and the renewal of the intestinal epithelium. With the aim to investigate an alternative therapeutic approach, especially in the case of antibiotic resistance, in this work we created a line of intestinal epithelial cells able to express high concentrations of AMP human β-defensin-2 (HBD-2) in order to test its ability to interfere with the pathogenicity mechanisms of EIEC. The results showed that HBD-2 is able to significantly reduce the expression of the proinflammatory cytokines by intestinal epithelial cells, the invasiveness ability of EIEC and the expression of invasion-associated genes.
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Affiliation(s)
- Alessandra Fusco
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Vittoria Savio
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Brunella Perfetto
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Roberto Mattina
- Department of Biomedical Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Giovanna Donnarumma
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
- *Correspondence: Giovanna Donnarumma,
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Bai Z, Zhang S, Wang X, Aslam MZ, Wang W, Li H, Dong Q. Genotyping Based on CRISPR Loci Diversity and Pathogenic Potential of Diarrheagenic Escherichia coli. Front Microbiol 2022; 13:852662. [PMID: 35308371 PMCID: PMC8924505 DOI: 10.3389/fmicb.2022.852662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/26/2022] [Indexed: 11/23/2022] Open
Abstract
Diarrheagenic Escherichia coli (DEC) can cause epidemic diarrhea worldwide. The pathogenic potential of different strains is diverse and the continuous emergence of pathogenic strains has brought serious harm to public health. Accurately distinguishing and identifying DEC with different virulence is necessary for epidemiological surveillance and investigation. Clustered regularly interspaced short palindromic repeats (CRISPR) typing is a new molecular method that can distinguish pathogenic bacteria excellently and has shown great promise in DEC typing. The purpose of this study was to investigate the discrimination of CRISPR typing method for DEC and explore the pathogenicity potential of DEC based on CRISPR types (CT). The whole genome sequences of 789 DEC strains downloaded from the database were applied CRISPR typing and serotyping. The D value (Simpson’s index) with 0.9709 determined that CRISPR typing had a higher discrimination. Moreover, the same H antigen strains with different O seemed to share more identical spacers. Further analyzing the strains CRISPR types and the number of virulence genes, it was found that there was a significant correlation between the CRISPR types and the number of virulence genes (p < 0.01). The strains with the largest number of virulence genes concentrated in CT25 and CT56 and the number of virulence genes in CT264 was the least, indicating that the pathway potential of different CRISPR types was variable. Combined with the Caco-2 cell assay of the laboratory strains, the invasion capacity of STEC strains of different CRISPR types was different and there was no significant difference in the invasion rate between different CRISPR type strains (p > 0.05). In the future, with the increase of the number of strains that can be studied experimentally, the relationship between CRISPR types and adhesion and invasion capacities will be further clarified.
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Affiliation(s)
- Zhiye Bai
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Shiqin Zhang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiang Wang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Muhammad Zohaib Aslam
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, MOA Laboratory of Quality and Safety Risk Assessment for Agro-products (Hangzhou), Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongmei Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Qingli Dong
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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4
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Comprehensive study of common Enterogenic E. coli in Iran during 2010–2020: A systematic review. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Pakbin B, Brück WM, Rossen JWA. Virulence Factors of Enteric Pathogenic Escherichia coli: A Review. Int J Mol Sci 2021; 22:9922. [PMID: 34576083 PMCID: PMC8468683 DOI: 10.3390/ijms22189922] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 12/18/2022] Open
Abstract
Escherichia coli are remarkably versatile microorganisms and important members of the normal intestinal microbiota of humans and animals. This harmless commensal organism can acquire a mixture of comprehensive mobile genetic elements that contain genes encoding virulence factors, becoming an emerging human pathogen capable of causing a broad spectrum of intestinal and extraintestinal diseases. Nine definite enteric E. coli pathotypes have been well characterized, causing diseases ranging from various gastrointestinal disorders to urinary tract infections. These pathotypes employ many virulence factors and effectors subverting the functions of host cells to mediate their virulence and pathogenesis. This review summarizes new developments in our understanding of diverse virulence factors associated with encoding genes used by different pathotypes of enteric pathogenic E. coli to cause intestinal and extraintestinal diseases in humans.
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Affiliation(s)
- Babak Pakbin
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Switzerland;
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin 15315-3419, Iran
| | - Wolfram M. Brück
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Switzerland;
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
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Dolatyar Dehkharghani A, Haghighat S, Rahnamaye Farzami M, Douraghi M, Rahbar M. Subtyping β-lactamase-producing Escherichia coli strains isolated from patients with UTI by MLVA and PFGE methods. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:437-443. [PMID: 34094024 PMCID: PMC8143711 DOI: 10.22038/ijbms.2021.49790.11372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 03/07/2021] [Indexed: 12/03/2022]
Abstract
OBJECTIVES Strain subtyping is an important epidemiological tool to trace contamination, determine clonal relationships between different strains, and the cause of outbreaks. Current subtyping methods, however, yield less than optimal subtype discrimination. Pulsed-field gel electrophoresis is the gold standard method for Escherichia coli and Multiple-Locus Variable-number tandem repeat Analysis is a rapid PCR-based method. The purpose of this study was to evaluate MLVA and PFGE methods for subtyping β -lactamase-producing E. coli strains isolated from urinary tract infections. MATERIALS AND METHODS Overall, 230 E. coli isolates from patients with urinary tract infections were examined for antimicrobial susceptibility testing. 10-loci and 7-loci MLVA and PFGE methods were used for molecular typing of β -lactamase-producing E. coli isolates. RESULTS Out of 230 isolates, 130 (56.5%) β -lactamase-producing E. coli isolates were found in this study. The diversity indices of the VNTR loci showed an average diversity of 0.48 and 0.54 for 7-loci and 10-loci MLVA, respectively. The discriminatory power of PFGE showed a value of 0.87. The discordance between the methods was high. CONCLUSION Our study showed that PFGE is more discriminatory than MVLA. MLVA is a PCR- based method and can generate unmistakable data, in contrast to PFGE. Optimization of polymorphic VNTR is essential to improve the discriminatory power of MLVA based on geographical region.
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Affiliation(s)
- Alireza Dolatyar Dehkharghani
- Department of Microbiology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Setareh Haghighat
- Department of Microbiology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Marjan Rahnamaye Farzami
- Department of Microbiology, Research Center of Reference Health Laboratory, Ministry of Health and Medical Education, Tehran, Iran
| | - Masoumeh Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Rahbar
- Department of Microbiology, Research Center of Reference Health Laboratory, Ministry of Health and Medical Education, Tehran, Iran
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Jomehzadeh N, Ahmadi K, Javaherizadeh H, Afzali M. Distribution of genes encoding virulence factors of Shigella strains isolated from children with diarrhea in southwest Iran. Mol Biol Rep 2021; 48:1645-1649. [PMID: 33550574 DOI: 10.1007/s11033-021-06170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/15/2021] [Indexed: 10/22/2022]
Abstract
This study aimed to investigate the distribution of virulence factor genes in Shigella strains isolated from children with diarrhea in the southwest, Iran. In this cross-sectional study, 1530 diarrheal stool specimens were collected from children aged under 15 years. The Shigella strains were identified by biochemical methods and polymerase chain reaction (PCR). Subsequently, all Shigella isolates were evaluated by PCR for the presence of nine virulence genes ipaH (responsible for dissemination from cell to cell), ial (responsible for epithelial cell penetration), sat (displays cytopathic activity in several intestinal cell lines), sigA (toxic to epithelial cells), pic (associated with colonization), pet (cytotoxic for epithelial cells), sepA (contribute to intestinal inflammation and colonization), virF and invE (regulatory proteins). A total of 91 isolates including 47 S. flexneri, 36 S. sonnei, and 8 S. boydii were identified. All isolates were positive for the ipaH gene. The other genes include ial, virF, invE, sigA, sat, sepA, pic and pet found in 84.6%, 72.5%, 68.1%, 62.6%, 51.6%, 39.5%, 37.3% and 28.5% of the isolates, respectively. The results showed a high distribution of virulence genes among Shigella strains in our region. It seems that for different Shigella spp. different virulence factors contribute to pathogenesis. The current study provided insights into some baseline information about the distribution of some virulence genes of Shigella isolates in Southwest Iran.
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Affiliation(s)
- Nabi Jomehzadeh
- Department of Microbiology, Abadan Faculty of Medical Sciences, Abadan, Iran
| | - Khadijah Ahmadi
- Department of Microbiology, Abadan Faculty of Medical Sciences, Abadan, Iran
| | - Hazhir Javaherizadeh
- Alimentary Tract Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Afzali
- Department of Microbiology, Abadan Faculty of Medical Sciences, Abadan, Iran.
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