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Qureshi H, Basheer A, Sajjad W, Faheem M, Babar Jamal S. An integrated in-silico approach for drug target identification in human pathogen Shigella dysenteriae. PLoS One 2024; 19:e0303048. [PMID: 38753867 PMCID: PMC11098424 DOI: 10.1371/journal.pone.0303048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
Shigella dysenteriae, is a Gram-negative bacterium that emerged as the second most significant cause of bacillary dysentery. Antibiotic treatment is vital in lowering Shigella infection rates, yet the growing global resistance to broad-spectrum antibiotics poses a significant challenge. The persistent multidrug resistance of S. dysenteriae complicates its management and control. Hence, there is an urgent requirement to discover novel therapeutic targets and potent medications to prevent and treat this disease. Therefore, the integration of bioinformatics methods such as subtractive and comparative analysis provides a pathway to compute the pan-genome of S. dysenteriae. In our study, we analysed a dataset comprising 27 whole genomes. The S. dysenteriae strain SD197 was used as the reference for determining the core genome. Initially, our focus was directed towards the identification of the proteome of the core genome. Moreover, several filters were applied to the core genome, including assessments for non-host homology, protein essentiality, and virulence, in order to prioritize potential drug targets. Among these targets were Integration host factor subunit alpha and Tyrosine recombinase XerC. Furthermore, four drug-like compounds showing potential inhibitory effects against both target proteins were identified. Subsequently, molecular docking analysis was conducted involving these targets and the compounds. This initial study provides the list of novel targets against S. dysenteriae. Conclusively, future in vitro investigations could validate our in-silico findings and uncover potential therapeutic drugs for combating bacillary dysentery infection.
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Affiliation(s)
- Hurria Qureshi
- Department of Biological Sciences, National University of Medical Sciences, Islamabad, Pakistan
| | - Amina Basheer
- Department of Biological Sciences, National University of Medical Sciences, Islamabad, Pakistan
| | - Wasim Sajjad
- Department of Biological Sciences, National University of Medical Sciences, Islamabad, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Islamabad, Pakistan
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, ND, United States of America
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Islamabad, Pakistan
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2
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Song Y, Sun M, Mu G, Tuo Y. Exopolysaccharide secreted by Lactiplantibacillus plantarum Y12 showed inhibitory effect on the pathogenicity of Shigella flexneri in vitro and in vivo. Int J Biol Macromol 2024; 261:129478. [PMID: 38237822 DOI: 10.1016/j.ijbiomac.2024.129478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
Shigella flexneri is a prevalent foodborne and waterborne pathogen that threatens human health. Our previous research indicated that the Lactiplantibacillus plantarum Y12 exopolysaccharide (L-EPS) potentially inhibited the pathogenicity of S. flexneri. The in vitro results of this study demonstrated that L-EPS effectively mitigated the symptoms induced by S. flexneri in HT-29 cells, including inhibited gene expression levels of IL-1β, IL-6, IL-8, TNF-α, TLR 2/4, and NOD1/2; decreased apoptosis ratio; and alleviated damage degree of intestinal barrier function (Zona occludens 1, Occludin, and Claudin-1). The in vivo results demonstrated that S. flexneri treated with L-EPS elicited mild adverse physiological manifestations, an inflammatory response, and tissue damage. The infection of S. flexneri caused significant alterations in the abundance of phylum (Firmicutes, Bacteroidota, Actinobacteriota, and Proteobacteria), family (Lachnospiraceae, Muribaculaceae, Rikenellaceae, Prevotellaceaea, Ruminococcaceae, and Lactobaillaceae), and genus (Escherichia Shigella and Lachnospirillaceae NK4A136 group) within the cecal microbiota. These changes were accompanied by perturbations in taurine and hypotaurine metabolism, tricarboxylic acid (TCA) cycle activity, arginine biosynthesis, and histidine metabolic pathways. However, intervention with L-EPS attenuated the dysbiosis of cecal microbiota and metabolic disturbances. In summary, our research suggested a potential application of L-EPS as a functional food additive for mitigating S. flexneri infection.
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Affiliation(s)
- Yinglong Song
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China
| | - Mengying Sun
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China
| | - Guangqing Mu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China; Dalian Probiotics Function Research Key Laboratory, Dalian Polytechnic University, Dalian 116034, PR China.
| | - Yanfeng Tuo
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China.
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Vaja MD, Chokshi HA, Jansari JJ, Dixit OS, Savaliya SS, Patel DP, Patel FS. Study of Antimicrobial Resistance (AMR) in Shigella spp. in India. RECENT ADVANCES IN ANTI-INFECTIVE DRUG DISCOVERY 2024; 19:182-196. [PMID: 38317464 DOI: 10.2174/0127724344268156231129095108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/11/2023] [Accepted: 11/20/2023] [Indexed: 02/07/2024]
Abstract
Antimicrobial agents are essential in reducing illness and mortality brought on by infectious diseases in both humans and animals. However, the therapeutic effect of antibiotics has diminished due to an increase in antimicrobial drug resistance (AMR). This article provides a retrospective analysis of AMR in Shigella infections in India, showing a rise in resistance that has contributed to a global burden. Shigella spp. are widespread and the second-leading cause of diarrheal death in people of all ages. The frequency and mortality rates of Shigella infections are decreased by antibiotic treatment. However, the growth of broad-spectrum antibiotic resistance is making it more difficult to treat many illnesses. Reduced cell permeability, efflux pumps, and the presence of enzymes that break down antibiotics are the causes of resistance. AMR is a multifaceted and cross-sectoral problem that affects humans, animals, food, and the environment. As a result, there is a growing need for new therapeutic approaches, and ongoing surveillance of Shigella spp. infections which should definitely be improved for disease prevention and management. This review emphasizes on the epidemiological data of India, and antimicrobial resistance in Shigella spp.
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Affiliation(s)
- Maulikkumar D Vaja
- Department of Pharmaceutical Chemistry, Saraswati Institute of Pharmaceutical Sciences, Near Hotel Anjali Inn, Dhanap, India
| | - Heenaben A Chokshi
- Department of Pharmacology and Pharmacy Practice, Saraswati Institute of Pharmaceutical Sciences, Near Hotel Anjali Inn, Dhanap, India
| | - Janak J Jansari
- Department of Pharmacology and Pharmacy Practice, Saraswati Institute of Pharmaceutical Sciences, Near Hotel Anjali Inn, Dhanap, India
| | - Om S Dixit
- Department of Pharmacology and Pharmacy Practice, Saraswati Institute of Pharmaceutical Sciences, Near Hotel Anjali Inn, Dhanap, India
| | - Shubham S Savaliya
- Department of Pharmacology and Pharmacy Practice, Saraswati Institute of Pharmaceutical Sciences, Near Hotel Anjali Inn, Dhanap, India
| | - Deepak P Patel
- Department of Pharmacology and Pharmacy Practice, Saraswati Institute of Pharmaceutical Sciences, Near Hotel Anjali Inn, Dhanap, India
| | - Fenil S Patel
- Department of Pharmacology and Pharmacy Practice, Saraswati Institute of Pharmaceutical Sciences, Near Hotel Anjali Inn, Dhanap, India
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Song Y, Sun M, Mu G, Tuo Y. Exopolysaccharide produced by Lactiplantibacillus plantarum Y12 exhibits inhibitory effect on the Shigella flexneri genes expression related to biofilm formation. Int J Biol Macromol 2023; 253:127048. [PMID: 37748596 DOI: 10.1016/j.ijbiomac.2023.127048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
Shigella is a specific enteric pathogen in humans, causing symptoms of bacterial dysentery. The biofilm formation of S. flexneri contributes to the emergence of multidrug resistance and facilitates the establishment of persistent chronic infections. This study investigated the regulatory effects of Lactiplantibacillus plantarum Y12 exopolysaccharide (L-EPS) on gene expression and its spatial hindrance effects in inhibiting the biofilm formation of S. flexneri. The transcriptome analysis revealed a significant impact of L-EPS on the gene expression profile of S. flexneri, with a total of 968 genes showing significant changes (507 up-regulated and 461 down-regulated). The significantly down-regulated KEGG metabolic pathway enriched in phosphotransferase system, Embden-Meyerhf-Parnas, Citrate cycle, Lipopolysaccharide biosynthesis, Cationic antimicrobial peptide resistance, Two-component system. Moreover, L-EPS significantly down-regulated the gene expression levels of fimbriae synthesis (fimF), lipopolysaccharide synthesis (lptE, lptB), anchor protein repeat domain (arpA), virulence factor (lpp, yqgB), antibiotic resistance (marR, cusB, mdtL, mdlB), heavy metal resistance (zraP), and polysaccharide synthesis (mtgA, mdoB, mdoC). The expression of biofilm regulator factor (bssS) and two-component system suppressor factor (mgrB) were significantly up-regulated. The RT-qPCR results indicated that a major component of L-EPS (L-EPS 2-1) exhibited the gene regulatory effect on the S. flexneri biofilm formation. Furthermore, electrophoresis and isothermal microtitration calorimetry demonstrated that the interaction between L-EPS 2-1 and eDNA is electrostatic dependent on the change in environmental pH, disrupting the stable spatial structure of S. flexneri biofilm. In conclusion, L-EPS inhibited the biofilm formation of S. flexneri through gene regulation and spatial obstruction effects.
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Affiliation(s)
- Yinglong Song
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China
| | - Mengying Sun
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China
| | - Guangqing Mu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China; Dalian Probiotics Function Research Key Laboratory, Dalian Polytechnic University, Dalian 116034, PR China.
| | - Yanfeng Tuo
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China.
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Kenneth MJ, Koner S, Hsu GJ, Chen JS, Hsu BM. A review on the effects of discharging conventionally treated livestock waste to the environmental resistome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122643. [PMID: 37775024 DOI: 10.1016/j.envpol.2023.122643] [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: 06/09/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.
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Affiliation(s)
- Mutebi John Kenneth
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Doctoral Program in Science, Technology, Environment and Mathematics, National Chung Cheng University, Chiayi County, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Gwo-Jong Hsu
- Division of Infectious Diseases, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan.
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Miljkovic M, Lozano S, Castellote I, de Cózar C, Villegas-Moreno AI, Gamallo P, Jimenez-Alfaro Martinez D, Fernández-Álvaro E, Ballell L, Garcia GA. Novel inhibitors that target bacterial virulence identified via HTS against intra-macrophage survival of Shigella flexneri. mSphere 2023; 8:e0015423. [PMID: 37565760 PMCID: PMC10597453 DOI: 10.1128/msphere.00154-23] [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: 03/24/2023] [Accepted: 06/02/2023] [Indexed: 08/12/2023] Open
Abstract
Shigella flexneri is a facultative intracellular pathogen that causes shigellosis, a human diarrheal disease characterized by the destruction of the colonic epithelium. Novel antimicrobial compounds to treat infections are urgently needed due to the proliferation of bacterial antibiotic resistance and lack of new effective antimicrobials in the market. Our approach to find compounds that block the Shigella virulence pathway has three potential advantages: (i) resistance development should be minimized due to the lack of growth selection pressure, (ii) no resistance due to environmental antibiotic exposure should be developed since the virulence pathways are not activated outside of host infection, and (iii) the normal intestinal microbiota, which do not have the targeted virulence pathways, should be unharmed. We chose to utilize two phenotypic assays, inhibition of Shigella survival in macrophages and Shigella growth inhibition (minimum inhibitory concentration), to interrogate the 1.7 M compound screening collection subset of the GlaxoSmithKline drug discovery chemical library. A number of secondary assays on the hit compounds resulting from the primary screens were conducted, which, in combination with chemical, structural, and physical property analyses, narrowed the final hit list to 44 promising compounds for further drug discovery efforts. The rapid development of antibiotic resistance is a critical problem that has the potential of returning the world to a "pre-antibiotic" type of environment, where millions of people will die from previously treatable infections. One relatively newer approach to minimize the selection pressures for the development of resistance is to target virulence pathways. This is anticipated to eliminate any resistance selection pressure in environmental exposure to virulence-targeted antibiotics and will have the added benefit of not affecting the non-virulent microbiome. This paper describes the development and application of a simple, reproducible, and sensitive assay to interrogate an extensive chemical library in high-throughput screening format for activity against the survival of Shigella flexneri 2457T-nl in THP-1 macrophages. The ability to screen very large numbers of compounds in a reasonable time frame (~1.7 M compounds in ~8 months) distinguishes this assay as a powerful tool in further exploring new compounds with intracellular effect on S. flexneri or other pathogens with similar pathways of pathogenesis. The assay utilizes a luciferase reporter which is extremely rapid, simple, relatively inexpensive, and sensitive and possesses a broad linear range. The assay also utilized THP-1 cells that resemble primary monocytes and macrophages in morphology and differentiation properties. THP-1 cells have advantages over human primary monocytes or macrophages because they are highly plastic and their homogeneous genetic background minimizes the degree of variability in the cell phenotype (1). The intracellular and virulence-targeted selectivity of our methodology, determined via secondary screening, is an enormous advantage. Our main interest focuses on hits that are targeting virulence, and the most promising compounds with adequate physicochemical and drug metabolism and pharmacokinetic (DMPK) properties will be progressed to a suitable in vivo shigellosis model to evaluate the therapeutic potential of this approach. Additionally, compounds that act via a host-directed mechanism could be a promising source for further research given that it would allow a whole new, specific, and controlled approach to the treatment of diseases caused by some pathogenic bacteria.
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Affiliation(s)
- Marija Miljkovic
- Department of Medical Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
- GSK Global Health Unit, Madrid, Spain
| | | | | | | | | | | | | | | | | | - George A. Garcia
- Department of Medical Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
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Ararsa T, Wolde D, Alemayehu H, Bizuwork K, Eguale T. Prevalence and Antimicrobial Susceptibility Profile of Salmonella and Shigella among Diarrheic Patients Attending Selected Health Facilities in Addis Ababa, Ethiopia. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:6104416. [PMID: 37867502 PMCID: PMC10590268 DOI: 10.1155/2023/6104416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/24/2023]
Abstract
Diarrhea is one of the important public health problems in developing countries. Salmonella and Shigella species are the major bacterial causal agents of diarrhea. The increasing burden of antimicrobial resistance is posing difficulty in the treatment of these pathogens. This study aimed to assess the occurrence of Salmonella and Shigella in the feces of diarrheic patients receiving health services in Addis Ababa, Ethiopia, and to determine their antimicrobial susceptibility profile. A cross-sectional study involving 13 health centers was conducted where 428 diarrheic patients were recruited. Standard microbiology techniques were used to isolate Salmonella and Shigella from stool samples. In addition, Salmonella isolates were confirmed by polymerase chain reaction (PCR). The Kirby-Bauer disc diffusion method was employed to assess susceptibility to 11 antimicrobials for each of the Salmonella and Shigella isolates. The prevalence of Salmonella and Shigella spp. among diarrheic patients was 8.4%; n = 36 and 5.6%; n = 24, respectively. Thirty (83.3%) of Salmonella isolates were susceptible to all antimicrobials tested, whereas 4 (10.8%) of isolates were resistant to 2 or more antimicrobials and 2 (5.6%) were multidrug resistant. Resistance to ampicillin was recorded in only one (2.7%) of Salmonella isolates; however, resistance to ampicillin was recorded in 12 (50%) of the Shigella isolates. Half of the Shigella isolates (n = 12) were resistant to 2 or more antimicrobials while 5 (20.8%) of them were resistant to 3 or more antimicrobials. The overall rate of resistance to antimicrobials was more common in Shigella compared to Salmonella isolates. In conclusion, Salmonella and Shigella were isolated from the feces of diarrheic patients, with a higher rate of antimicrobial resistance in Shigella isolates, which could make the treatment of shigellosis challenging. Therefore, increasing hygienic practices during food preparation to reduce the burden of Salmonella and Shigella infection and prudent use of antimicrobials are recommended to limit the spread of antimicrobial resistant strains.
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Affiliation(s)
- Tiruneh Ararsa
- Tikur Anbesssa Specialized Hospital, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Deneke Wolde
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Wachemo University, Hossana, Ethiopia
| | - Haile Alemayehu
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ketema Bizuwork
- Tikur Anbesssa Specialized Hospital, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tadesse Eguale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- The Ohio State University, Global One Health LLC, Addis Ababa, Ethiopia
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Zhang G, Liu J, He Y, Du Y, Xu L, Chen T, Guo Y, Fu H, Li A, Tian Y, Hu Y, Yang C, Lu M, Deng X, Wang J, Lu N. Modifying Escherichia coli to mimic Shigella for medical microbiology laboratory teaching: a new strategy to improve biosafety in class. Front Cell Infect Microbiol 2023; 13:1257361. [PMID: 37780843 PMCID: PMC10533986 DOI: 10.3389/fcimb.2023.1257361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Laboratory teaching of medical microbiology involves highly pathogenic microorganisms, thus posing potential biosafety risks to the students and the teacher. To address these risks, non/low-pathogenic microorganisms were modified to mimic highly pathogenic ones or highly pathogenic microorganisms were attenuated directly using the CRISPR/Cas9 technology. This study describes the modification of Escherichia coli DH5α to mimic Shigella and its evaluation as a safe alternative for medical laboratory teaching. Methods To generate E. coli DH5α△FliC△tnaA2a, the tnaA and FliC genes in E. coli DH5α were knocked out using CRISPR/Cas9 technology; a plasmid bearing the O-antigen determinant of S. flexneri 2a was then constructed and transformed. Acid tolerance assays and guinea pig eye tests were used to assess the viability and pathogenicity, respectively. Questionnaires were used to analyze teaching effectiveness and the opinions of teachers and students. Results The survey revealed that most teachers and students were inclined towards real-time laboratory classes than virtual classes or observation of plastic specimens. However, many students did not abide by the safety regulations, and most encountered potential biosafety hazards in the laboratory. E. coli DH5α△FliC△tnaA2a was biochemically and antigenically analogous to S. flexneri 2a and had lower resistance to acid than E. coli. There was no toxicity observed in guinea pigs. Most of teachers and students were unable to distinguish E. coli DH5α△FliC△tnaA2a from pure S. flexneri 2a in class. Students who used E. coli DH5α△FliC△tnaA2a in their practice had similar performance in simulated examinations compared to students who used real S. flexneri 2a, but significantly higher than the virtual experimental group. Discussion This approach can be applied to other high-risk pathogenic microorganisms to reduce the potential biosafety risks in medical laboratory-based teaching and provide a new strategy for the development of experimental materials.
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Affiliation(s)
- Guangyuan Zhang
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
- Chongqing Medical University, Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing, China
| | - Jia Liu
- Chongqing Medical University, Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing, China
| | - Yonglin He
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
| | - Yuheng Du
- Department for Rehabilitation Medicine, The Second College of Clinical Medicine of Chongqing Medical University, Chongqing, China
| | - Lei Xu
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
| | - Tingting Chen
- Chongqing Medical University, Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing, China
| | - Yanan Guo
- Chongqing Medical University, International Medical College, Chongqing, China
| | - Huichao Fu
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
| | - Anlong Li
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
| | - Yunbo Tian
- Chongqing Blood Center, Quality Management Section, Chongqing, China
| | - Yan Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Chun Yang
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
| | - Mingqi Lu
- Chongqing Medical University, Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing, China
| | - Xichuan Deng
- Chongqing Medical University, Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing, China
| | - Jingsong Wang
- R&D Department, Chongqing Kebilong Biotechnology Co., Ltd., Chongqing, China
| | - Nan Lu
- Chongqing Medical University, Basic Medical School, Department of Pathogen Biology, Chongqing, China
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Haidar-Ahmad N, Manigat FO, Silué N, Pontier SM, Campbell-Valois FX. A Tale about Shigella: Evolution, Plasmid, and Virulence. Microorganisms 2023; 11:1709. [PMID: 37512882 PMCID: PMC10383432 DOI: 10.3390/microorganisms11071709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Shigella spp. cause hundreds of millions of intestinal infections each year. They target the mucosa of the human colon and are an important model of intracellular bacterial pathogenesis. Shigella is a pathovar of Escherichia coli that is characterized by the presence of a large invasion plasmid, pINV, which encodes the characteristic type III secretion system and icsA used for cytosol invasion and cell-to-cell spread, respectively. First, we review recent advances in the genetic aspects of Shigella, shedding light on its evolutionary history within the E. coli lineage and its relationship to the acquisition of pINV. We then discuss recent insights into the processes that allow for the maintenance of pINV. Finally, we describe the role of the transcription activators VirF, VirB, and MxiE in the major virulence gene regulatory cascades that control the expression of the type III secretion system and icsA. This provides an opportunity to examine the interplay between these pINV-encoded transcriptional activators and numerous chromosome-encoded factors that modulate their activity. Finally, we discuss novel chromosomal genes icaR, icaT, and yccE that are regulated by MxiE. This review emphasizes the notion that Shigella and E. coli have walked the fine line between commensalism and pathogenesis for much of their history.
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Affiliation(s)
- Nathaline Haidar-Ahmad
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - France Ourida Manigat
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Navoun Silué
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Stéphanie M Pontier
- Centre de Recherche Santé Environnementale et Biodiversité de l'Outaouais (SEBO), CEGEP de l'Outaouais, Gatineau, QC J8Y 6M4, Canada
| | - François-Xavier Campbell-Valois
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Centre for Infection, Immunity and Inflammation, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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Pakbin B, Brück WM, Brück TB. Molecular Mechanisms of Shigella Pathogenesis; Recent Advances. Int J Mol Sci 2023; 24:ijms24032448. [PMID: 36768771 PMCID: PMC9917014 DOI: 10.3390/ijms24032448] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Shigella species are the main cause of bacillary diarrhoea or shigellosis in humans. These organisms are the inhabitants of the human intestinal tract; however, they are one of the main concerns in public health in both developed and developing countries. In this study, we reviewed and summarised the previous studies and recent advances in molecular mechanisms of pathogenesis of Shigella Dysenteriae and non-Dysenteriae species. Regarding the molecular mechanisms of pathogenesis and the presence of virulence factor encoding genes in Shigella strains, species of this bacteria are categorised into Dysenteriae and non-Dysenteriae clinical groups. Shigella species uses attachment, invasion, intracellular motility, toxin secretion and host cell interruption mechanisms, causing mild diarrhoea, haemorrhagic colitis and haemolytic uremic syndrome diseases in humans through the expression of effector delivery systems, protein effectors, toxins, host cell immune system evasion and iron uptake genes. The investigation of these genes and molecular mechanisms can help us to develop and design new methods to detect and differentiate these organisms in food and clinical samples and determine appropriate strategies to prevent and treat the intestinal and extraintestinal infections caused by these enteric pathogens.
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Affiliation(s)
- Babak Pakbin
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenberg Str. 4, 85748 Garching bei München, Germany
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion, Switzerland
| | - Wolfram Manuel Brück
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion, Switzerland
- Correspondence: (W.M.B.); (T.B.B.)
| | - Thomas B. Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenberg Str. 4, 85748 Garching bei München, Germany
- Correspondence: (W.M.B.); (T.B.B.)
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Abstract
Enteric bacterial infections contribute substantially to global disease burden and mortality, particularly in the developing world. In vitro 2D monolayer cultures have provided critical insights into the fundamental virulence mechanisms of a multitude of pathogens, including Salmonella enterica serovars Typhimurium and Typhi, Vibrio cholerae, Shigella spp., Escherichia coli and Campylobacter jejuni, which have led to the identification of novel targets for antimicrobial therapy and vaccines. In recent years, the arsenal of experimental systems to study intestinal infections has been expanded by a multitude of more complex models, which have allowed to evaluate the effects of additional physiological and biological parameters on infectivity. Organoids recapitulate the cellular complexity of the human intestinal epithelium while 3D bioengineered scaffolds and microphysiological devices allow to emulate oxygen gradients, flow and peristalsis, as well as the formation and maintenance of stable and physiologically relevant microbial diversity. Additionally, advancements in ex vivo cultures and intravital imaging have opened new possibilities to study the effects of enteric pathogens on fluid secretion, barrier integrity and immune cell surveillance in the intact intestine. This review aims to present a balanced and updated overview of current intestinal in vitro and ex vivo methods for modeling of enteric bacterial infections. We conclude that the different paradigms are complements rather than replacements and their combined use promises to further our understanding of host-microbe interactions and their impacts on intestinal health.
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Affiliation(s)
- Nayere Taebnia
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- CONTACT Ute Römling Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Volker M. Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- Volker M. Lauschke Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
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Yousaf Kazmi S. The etymology of microbial nomenclature and the diseases these cause in a historical perspective. Saudi J Biol Sci 2022; 29:103454. [PMID: 36248774 PMCID: PMC9562425 DOI: 10.1016/j.sjbs.2022.103454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/20/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
When the hunter-gatherers finally started settling down as farmers, infectious diseases started scourging them. The earlier humans could differentiate sporadic diseases like tooth decay, tumors, etc., from the infectious diseases that used to cause outbreaks and epidemics. The earliest comprehension of infectious diseases was primarily based on religious background and myths, but as human knowledge grew, the causes of these diseases were being probed. Similarly, the taxonomy of infectious diseases gradually changed from superstitious prospects, like influenza, signifying disease infliction due to the "influence of stars" to more scientific ones like tuberculosis derived from the word "tuberculum" meaning small swellings seen in postmortem human tissue specimens. From a historical perspective, we identified five categories for the basis of the microbial nomenclature, namely phenotypic characteristics of microbe, disease name, eponym, body site of isolation, and toponym. This review article explores the etymology of common infectious diseases and microorganisms' nomenclature in a historical context.
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Affiliation(s)
- Syed Yousaf Kazmi
- Department of Basic Medical Sciences, College of Medicine, Majmaah University, P.O. Box 66, Post code 11952, Al Majmaah, Saudi Arabia
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13
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Torrez Lamberti MF, Terán LC, Lopez FE, de Las Mercedes Pescaretti M, Delgado MA. Genomic and proteomic characterization of two strains of Shigella flexneri 2 isolated from infants' stool samples in Argentina. BMC Genomics 2022; 23:495. [PMID: 35804311 PMCID: PMC9264714 DOI: 10.1186/s12864-022-08711-5] [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: 02/22/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022] Open
Abstract
Background Shigella specie is a globally important intestinal pathogen disseminated all over the world. In this study we analyzed the genome and the proteomic component of two Shigella flexneri 2a clinical isolates, collected from pediatric patients with gastroenteritis of the Northwest region of Argentina (NWA) in two periods of time, with four years of difference. Our goal was to determine putative changes at molecular levels occurred during these four years, that could explain the presence of this Shigella`s serovar as the prevalent pathogen in the population under study. Results As previously reported, our findings support the idea of Shigella has a conserved “core” genome, since comparative studies of CI133 and CI172 genomes performed against 80 genomes obtained from the NCBI database, showed that there is a large number of genes shared among all of them. However, we observed that CI133 and CI172 harbors a small number of strain-specific genes, several of them present in mobile genetic elements, supporting the hypothesis that these isolates were established in the population by horizontal acquisition of genes. These differences were also observed at proteomic level, where it was possible to detect the presence of certain secreted proteins in a culture medium that simulates the host environment. Conclusion Great similarities were observed between the CI133 and CI172 strains, confirming the high percentage of genes constituting the “core” genome of S. flexneri 2. However, numerous strain specific genes were also determined. The presence of the here identified molecular elements into other strain of our culture collation, is currently used to develop characteristic markers of local pathogens. In addition, the most outstanding result of this study was the first description of a S. flexneri 2 producing Colicin E, as one of the characteristics that allows S. flexneri 2 to persist in the microbial community. These findings could also contribute to clarify the mechanism and the evolution strategy used by this pathogen to specifically colonize, survive, and cause infection within the NWA population. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08711-5.
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Affiliation(s)
- Mónica F Torrez Lamberti
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, 5Q7R+96, San Miguel de Tucumán, Argentina
| | - Lucrecia C Terán
- Centro de Referencia Para Lactobacilos (CERELA-CONICET), Chacabuco 145, 5Q9R+3J, San Miguel de Tucumán, Argentina
| | - Fabián E Lopez
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, 5Q7R+96, San Miguel de Tucumán, Argentina.,Universidad Nacional de Chilecito (UNdeC), 9 de Julio 22, F5360CKB, Chilecito, La Rioja, Argentina
| | - María de Las Mercedes Pescaretti
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, 5Q7R+96, San Miguel de Tucumán, Argentina.
| | - Mónica A Delgado
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, 5Q7R+96, San Miguel de Tucumán, Argentina.
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Imported Infectious Diseases, Tropical Diseases and Local Endemic Infectious Diseases in Japan. Pediatr Infect Dis J 2022; 41:e275-e282. [PMID: 35421047 DOI: 10.1097/inf.0000000000003541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We aimed to describe the historical perspectives and the current epidemiology of tropical, imported and local endemic infectious diseases in Japan in this review. Public health legislation for infectious diseases and immigration statistics were overviewed to provide the background of the infectious disease situation in Japan. Many tropical diseases were successfully controlled and eliminated in the latter half of the 20th century and the majority of those diseases are imported today. The trend of the main 15 imported infectious diseases before the advent of COVID-19 was summarized as well as local endemic infectious diseases in Japan. Transmission risks of traditional cuisines, lifestyles and nature exposures in Japan are introduced to guide clinicians for travel advice to prevent those local infectious diseases.
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Zhao Z, Yang M, Lv J, Hu Q, Chen Q, Lei Z, Wang M, Zhang H, Zhai X, Zhao B, Su Y, Chen Y, Zhang XS, Cui JA, Frutos R, Chen T. Shigellosis seasonality and transmission characteristics in different areas of China: A modelling study. Infect Dis Model 2022; 7:161-178. [PMID: 35662902 PMCID: PMC9144056 DOI: 10.1016/j.idm.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
Objective In China, the burden of shigellosis is unevenly distributed, notably across various ages and geographical areas. Shigellosis temporal trends appear to be seasonal. We should clarify seasonal warnings and regional transmission patterns. Method This study adopted a Logistic model to assess the seasonality and a dynamics model to compare the transmission in different areas. The next-generation matrix was used to calculate the effective reproduction number (Reff) to quantify the transmissibility. Results In China, the rate of shigellosis fell from 35.12 cases per 100,000 people in 2005 to 7.85 cases per 100,000 people in 2017, peaking in June and August. After simulation by the Logistic model, the ‘peak time’ is mainly concentrated from mid-June to mid-July. China's ‘early warning time’ is primarily focused on from April to May. We predict the ‘peak time’ of shigellosis is the 6.30th month and the ‘early warning time’ is 3.87th month in 2021. According to the dynamics model results, the water/food transfer pathway has been mostly blocked off. The transmissibility of different regions varies greatly, such as the mean Reff of Longde County (3.76) is higher than Xiamen City (3.15), higher than Chuxiong City (2.52), and higher than Yichang City (1.70). Conclusion The ‘early warning time’ for shigellosis in China is from April to May every year, and it may continue to advance in the future, such as the early warning time in 2021 is in mid-March. Furthermore, we should focus on preventing and controlling the person-to-person route of shigellosis and stratified deploy prevention and control measures according to the regional transmission.
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Affiliation(s)
- Zeyu Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China
- CIRAD, UMR 17, Intertryp, Montpellier, France
| | - Meng Yang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China
| | - Jinlong Lv
- Department of Mathematics, School of Science, Beijing University of Civil Engineering and Architecture, Beijing, 102616, People's Republic of China
| | - Qingqing Hu
- Division of Public Health, School of Medicine, University of Utah, 201 Presidents Circle, Salt Lake City, 84112, Utah, USA
| | | | - Zhao Lei
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China
| | - Mingzhai Wang
- Xiamen Center for Disease Control and Prevention, Xiamen City, Fujian Province, People's Republic of China
| | - Hao Zhang
- Yichang Center for Disease Control and Prevention, Yichang City, Hubei Province, People's Republic of China
| | - Xiongjie Zhai
- Longde County Center for Disease Control and Prevention, Guyuan City, Ningxia Hui Autonomous Region, People's Republic of China
| | - Benhua Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China
| | - Yanhua Su
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China
| | - Yong Chen
- Department of Stomatology, School of Medicine, Xiamen University People's Republic of China
| | | | - Jing-An Cui
- Department of Mathematics, School of Science, Beijing University of Civil Engineering and Architecture, Beijing, 102616, People's Republic of China
| | - Roger Frutos
- CIRAD, UMR 17, Intertryp, Montpellier, France
- Corresponding author. CIRAD, Intertryp, Montpellier, France.
| | - Tianmu Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China
- Corresponding author. State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, 4221-117, South Xiang'an Road, Xiang'an District, Xiamen City, Fujian Province, People's Republic of China.
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Herrera CM, Schmitt JS, Chowdhry EI, Riddle MS. From Kiyoshi Shiga to Present-Day Shigella Vaccines: A Historical Narrative Review. Vaccines (Basel) 2022; 10:645. [PMID: 35632401 PMCID: PMC9145194 DOI: 10.3390/vaccines10050645] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/20/2022] [Accepted: 04/18/2022] [Indexed: 02/06/2023] Open
Abstract
We are at an exciting moment in time with the advancement of many vaccines, including a shigella vaccine for the world. It is instructive to look at the long road that some vaccines have traveled to recognize the remarkable accomplishments of those who were pioneers, appreciate the evolution of scientific and applied technology, and inform the future history of a vaccine that would have great potential for global health. To achieve this valuable retrospective, a narrative historical literature review was undertaken utilizing PubMed and Embase databases with relevant search terms. Retrieved articles were reviewed and information was organized into historical themes, landmark discoveries, and important vaccine development parallels. The literature reviewed was synthesized into major eras of shigella vaccine development from pathogen discovery and first attempts to empirical approaches of killed whole-cell and live-attenuated approaches, and a modern era that applied recombinant DNA engineering and structural vaccinology. The history of shigella vaccine development has largely followed the evolutionary path of vaccine development over the last 120 years, but with important lessons learned that should be considered as we embark on the future chapters of bringing to the world a safe and effective vaccine for global health.
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Affiliation(s)
| | | | | | - Mark S. Riddle
- Reno School of Medicine, University of Nevada, Reno, NV 89557, USA; (C.M.H.); (J.S.S.); (E.I.C.)
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Henrique IDM, Sacerdoti F, Ferreira RL, Henrique C, Amaral MM, Piazza RMF, Luz D. Therapeutic Antibodies Against Shiga Toxins: Trends and Perspectives. Front Cell Infect Microbiol 2022; 12:825856. [PMID: 35223548 PMCID: PMC8866733 DOI: 10.3389/fcimb.2022.825856] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 12/22/2022] Open
Abstract
Shiga toxins (Stx) are AB5-type toxins, composed of five B subunits which bind to Gb3 host cell receptors and an active A subunit, whose action on the ribosome leads to protein synthesis suppression. The two Stx types (Stx1 and Stx2) and their subtypes can be produced by Shiga toxin-producing Escherichia coli strains and some Shigella spp. These bacteria colonize the colon and induce diarrhea that may progress to hemorrhagic colitis and in the most severe cases, to hemolytic uremic syndrome, which could lead to death. Since the use of antibiotics in these infections is a topic of great controversy, the treatment remains supportive and there are no specific therapies to ameliorate the course. Therefore, there is an open window for Stx neutralization employing antibodies, which are versatile molecules. Indeed, polyclonal, monoclonal, and recombinant antibodies have been raised and tested in vitro and in vivo assays, showing differences in their neutralizing ability against deleterious effects of Stx. These molecules are in different phases of development for which we decide to present herein an updated report of these antibody molecules, their source, advantages, and disadvantages of the promising ones, as well as the challenges faced until reaching their applicability.
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Affiliation(s)
| | - Flavia Sacerdoti
- Laboratorio de Fisiopatogenia, Instituto de Fisiología y Biofísica Bernardo Houssay (IFIBIO Houssay-CONICET), Departamento de Fisiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Camila Henrique
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Maria Marta Amaral
- Laboratorio de Fisiopatogenia, Instituto de Fisiología y Biofísica Bernardo Houssay (IFIBIO Houssay-CONICET), Departamento de Fisiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Roxane Maria Fontes Piazza
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
- *Correspondence: Roxane Maria Fontes Piazza, ; Daniela Luz,
| | - Daniela Luz
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
- *Correspondence: Roxane Maria Fontes Piazza, ; Daniela Luz,
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He P, Wang H, Yan Y, Zhu G, Chen Z. Development and Application of a Multiplex Fluorescent PCR for Shigella Detection and Species Identification. J Fluoresc 2022; 32:707-713. [PMID: 35044573 DOI: 10.1007/s10895-021-02876-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 12/17/2021] [Indexed: 11/25/2022]
Abstract
This study was to develop a multiplex fluorescent PCR for Shigella detection and species identification. Five primer pairs for Shigella detection and species identification were designed by Primer Premier 5.0. The multiplex fluorescent PCR was optimized by varying single parameter while other parameters were maintained. The multiplex fluorescent PCR assay could correctly detect Shigella and identify four Shigella species with a detection limits of 10 pg genomic DNA per reaction. Testing different strains and clinical samples confirmed the sensitivity and specificity of the multiplex fluorescent PCR. The newly developed multiplex fluorescent PCR assay is simple, sensitive and specific for Shigella detection and species identification. It has a potential to be used in routine Shigella detection and species identification in clinical laboratories.
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Affiliation(s)
- Peiyan He
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Zhejiang, Jiaxing, 314050, China
| | - Henghui Wang
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Zhejiang, Jiaxing, 314050, China
| | - Yong Yan
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Zhejiang, Jiaxing, 314050, China
| | - Guoying Zhu
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Zhejiang, Jiaxing, 314050, China
| | - Zhongwen Chen
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Zhejiang, Jiaxing, 314050, China.
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Nowicki D, Krause K, Karczewska M, Szalewska-Pałasz A. Evaluation of the Anti-Shigellosis Activity of Dietary Isothiocyanates in Galleria mellonella Larvae. Nutrients 2021; 13:nu13113967. [PMID: 34836222 PMCID: PMC8625812 DOI: 10.3390/nu13113967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Cruciferous vegetables, widely present in daily diets, are a rich source of organosulfur compounds with proven health benefits, especially chemopreventive or antioxidative effects. Isothiocyanate derivatives (ITCs) exhibit a broad spectrum of biological and pharmacological activity and recently, their antibacterial properties have been of particular importance. Here, we have focused on the anti-shigellosis activity of sulforaphane (SFN) and phenethyl ITC (PEITC). The genus Shigella causes gastroenteritis in humans, which constitutes a threat to public health. Production of a potent Stx toxin by S. dysenteriae type 1 results not only in more severe symptoms but also in serious sequela, including the hemolytic uremic syndrome. Here, we present evidence that two aliphatic and aromatic ITCs derivatives, SFN and PEITC, have an effective antibacterial potency against S. dysenteriae, also negatively regulating the stx gene expression. The molecular mechanism of this effect involves induction of the global stress-induced stringent response. ITCs also inhibit bacterial virulence against the Vero and HeLa cells. We present evidence for the therapeutic effect of sulforaphane and phenethyl ITC against a S. dysenteriae infection in the Galleria mellonella larvae model. Thus, our results indicate that isothiocyanates can be effectively used to combat dangerous bacterial infections.
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Halimeh FB, Rafei R, Osman M, Kassem II, Diene SM, Dabboussi F, Rolain JM, Hamze M. Historical, current, and emerging tools for identification and serotyping of Shigella. Braz J Microbiol 2021; 52:2043-2055. [PMID: 34524650 PMCID: PMC8441030 DOI: 10.1007/s42770-021-00573-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
The Shigella genus includes serious foodborne disease etiologic agents, with 4 species and 54 serotypes. Identification at species and serotype levels is a crucial task in microbiological laboratories. Nevertheless, the genetic similarity between Shigella spp. and Escherichia coli challenges the correct identification and serotyping of Shigella spp., with subsequent negative repercussions on surveillance, epidemiological investigations, and selection of appropriate treatments. For this purpose, multiple techniques have been developed historically ranging from phenotype-based methods and single or multilocus molecular techniques to whole-genome sequencing (WGS). To facilitate the selection of the most relevant method, we herein provide a global overview of historical and emerging identification and serotyping techniques with a particular focus on the WGS-based approaches. This review highlights the excellent discriminatory power of WGS to more accurately elucidate the epidemiology of Shigella spp., disclose novel promising genomic targets for surveillance methods, and validate previous well-established methods.
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Affiliation(s)
- Fatima Bachir Halimeh
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14850, USA
| | - Issmat I Kassem
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, 1109 Experiment Street, Griffin, GA, 30223-1797, USA
| | - Seydina M Diene
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Jean-Marc Rolain
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
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Pakbin B, Didban A, Monfared YK, Mahmoudi R, Peymani A, Modabber MR. Antibiotic susceptibility and genetic relatedness of Shigella species isolated from food and human stool samples in Qazvin, Iran. BMC Res Notes 2021; 14:144. [PMID: 33865447 PMCID: PMC8052664 DOI: 10.1186/s13104-021-05554-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/02/2021] [Indexed: 01/25/2023] Open
Abstract
Objective The aim of this study was to investigate the genetic relatedness and antimicrobial resistance among Shigella species isolated from food and stool samples. Using cross sectional study method, Shigella spp. were isolated from food and clinical samples using culture-based, biochemical and serological methods. Antimicrobial susceptibility and genetic relatedness among the isolates were evaluated using disk diffusion and RAPD-PCR methods respectively. Results The prevalence of Shigella spp. were 4.84 and 7.7% in food and stool samples respectively. All food isolates were Sh. sonnei. 91.42% of the Shigella stool isolates were Sh. sonnei. 62.5% of food isolates were resistant to tetracycline. 46.8, 50 and 65.8% of clinical isolates were resistant to imipenem, amikacin and azithromycin respectively. 50 and 85.7% of the food and clinical isolates respectively were MDR. Dendrogram generated by RAPD-PCR showed that the isolates from food and stool samples were categorized in a same group. Close genetic relatedness between MDR Shigella isolates from food and clinical samples indicate that foods can be considered as one of the main vehicles for transmission of MDR Shigella to human causing acute diseases. Survey of MDR Shigella among food and clinical samples is strongly suggested to be implemented.
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Affiliation(s)
- Babak Pakbin
- Children Growth Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Bahonar Blvd., P.O. Box: 34185-754, Qazvin, Iran.,Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Abdollah Didban
- Children Growth Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Bahonar Blvd., P.O. Box: 34185-754, Qazvin, Iran.
| | | | - Razzagh Mahmoudi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amir Peymani
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohammad Reza Modabber
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
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22
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Bajunaid W, Haidar-Ahmad N, Kottarampatel AH, Ourida Manigat F, Silué N, F. Tchagang C, Tomaro K, Campbell-Valois FX. The T3SS of Shigella: Expression, Structure, Function, and Role in Vacuole Escape. Microorganisms 2020; 8:microorganisms8121933. [PMID: 33291504 PMCID: PMC7762205 DOI: 10.3390/microorganisms8121933] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022] Open
Abstract
Shigella spp. are one of the leading causes of infectious diarrheal diseases. They are Escherichia coli pathovars that are characterized by the harboring of a large plasmid that encodes most virulence genes, including a type III secretion system (T3SS). The archetypal element of the T3SS is the injectisome, a syringe-like nanomachine composed of approximately 20 proteins, spanning both bacterial membranes and the cell wall, and topped with a needle. Upon contact of the tip of the needle with the plasma membrane, the injectisome secretes its protein substrates into host cells. Some of these substrates act as translocators or effectors whose functions are key to the invasion of the cytosol and the cell-to-cell spread characterizing the lifestyle of Shigella spp. Here, we review the structure, assembly, function, and methods to measure the activity of the injectisome with a focus on Shigella, but complemented with data from other T3SS if required. We also present the regulatory cascade that controls the expression of T3SS genes in Shigella. Finally, we describe the function of translocators and effectors during cell-to-cell spread, particularly during escape from the vacuole, a key element of Shigella’s pathogenesis that has yet to reveal all of its secrets.
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Affiliation(s)
- Waad Bajunaid
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Nathaline Haidar-Ahmad
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Anwer Hasil Kottarampatel
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - France Ourida Manigat
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Navoun Silué
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Caetanie F. Tchagang
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Kyle Tomaro
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - François-Xavier Campbell-Valois
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Correspondence:
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23
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Tardón A, Bataller E, Llobat L, Jiménez-Trigos E. Bacteria and antibiotic resistance detection in fractures of wild birds from wildlife rehabilitation centres in Spain. Comp Immunol Microbiol Infect Dis 2020; 74:101575. [PMID: 33260016 DOI: 10.1016/j.cimid.2020.101575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/23/2020] [Accepted: 11/03/2020] [Indexed: 12/29/2022]
Abstract
Anatomic adaptations make birds more prone to open fractures with exposed bone parts losing vascularization. As a result of this exposure, fractures are colonized by different microorganisms, including different types of bacteria, both aerobic and anaerobic, causing osteomyelitis in many cases. For this reason, antibiotic treatment is common. However, carrying out antibiotic treatment without carrying out a previous antibiogram may contribute to increased resistance against antibiotics, especially in migratory wild birds. In this paper, bacterial counts regarding fracture type, bacterial identification and antibiotic resistance have been analysed in wild birds from wildlife rehabilitation centres in Spain. The results obtained showed that open fractures had higher bacterial counts (CFU/mL) than closed ones. Bacteria in family Enterobacteriaceae, identified were Escherichia spp., Enterobacter spp., Shigella spp., Hafnia alvei, Proteus mirabilis, Leclercia adecarboxylata and Pantoea agglomerans. Other bacteria present in wild birds' fractures were Aeromonas spp., Enterococcus spp. Bacillus wiedmannii and Staphylococcus sciuri. All species found presented resistance to at least one of the antibiotics used. Wild birds can be implicated in the introduction, maintenance and global spreading of antibiotic resistant bacteria and represent an emerging public health concern. Results obtained in this paper support the idea that it is necessary to take this fact into account before antibiotic administration to wild animals, since it could increase the number of bacteria resistant to antibiotics.
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Affiliation(s)
- A Tardón
- CREW Foundation (Conservation and Research for Endangered Wildlife), Lleida, Spain
| | - E Bataller
- Research Group Microbiological Agents Associated With Animal Reproduction (PROVAGINBIO), Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology (PASAPTA) Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Spain
| | - L Llobat
- Research Group Microbiological Agents Associated With Animal Reproduction (PROVAGINBIO), Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology (PASAPTA) Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Spain.
| | - E Jiménez-Trigos
- Research Group Microbiological Agents Associated With Animal Reproduction (PROVAGINBIO), Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology (PASAPTA) Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Spain.
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24
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Ranganathan S, Smith EM, Foulke-Abel JD, Barry EM. Research in a time of enteroids and organoids: how the human gut model has transformed the study of enteric bacterial pathogens. Gut Microbes 2020; 12:1795492. [PMID: 32795243 PMCID: PMC7524385 DOI: 10.1080/19490976.2020.1795389] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 02/03/2023] Open
Abstract
Enteric bacterial pathogens cause significant morbidity and mortality globally. Studies in tissue culture and animal models shaped our initial understanding of these host-pathogen interactions. However, intrinsic shortcomings in these models limit their application, especially in translational applications like drug screening and vaccine development. Human intestinal enteroid and organoid models overcome some limitations of existing models and advance the study of enteric pathogens. In this review, we detail the use of human enteroids and organoids to investigate the pathogenesis of invasive bacteria Shigella, Listeria, and Salmonella, and noninvasive bacteria pathogenic Escherichia coli, Clostridium difficile, and Vibrio cholerae. We highlight how these studies confirm previously identified mechanisms and, importantly, reveal novel ones. We also discuss the challenges for model advancement, including platform engineering to integrate environmental conditions, innate immune cells and the resident microbiome, and the potential for pre-clinical testing of recently developed antimicrobial drugs and vaccines.
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Affiliation(s)
- Sridevi Ranganathan
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emily M. Smith
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jennifer D. Foulke-Abel
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eileen M. Barry
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
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25
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Nguyen KH, Operario DJ, Nyathi ME, Hill CL, Smith JA, Guerrant RL, Samie A, Dillingham RA, Bessong PO, Rogawski McQuade ET. Seasonality of drinking water sources and the impact of drinking water source on enteric infections among children in Limpopo, South Africa. Int J Hyg Environ Health 2020; 231:113640. [PMID: 33115698 DOI: 10.1016/j.ijheh.2020.113640] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023]
Abstract
Enteric infections and water-related illnesses are more frequent during times of relative water abundance, especially in regions that experience bimodal rainfall patterns. However, it is unclear how seasonal changes in water availability and drinking water source types affect enteric infections in young children. This study investigated seasonal shifts in primary drinking water source type and the effect of water source type on enteric pathogen prevalence in stool samples from 404 children below age 5 in rural communities in Limpopo Province, South Africa. From wet to dry season, 4.6% (n = 16) of households switched from a source with a higher risk of contamination to a source with lower risk, with the majority switching to municipal water during the dry season. In contrast, 2.6% (n = 9) of households switched from a source with a lower risk of contamination to a source with higher risk. 74.5% (n = 301) of the total households experienced interruptions in their water supply, regardless of source type. There were no significant differences in enteric pathogen prevalence between drinking water sources. Intermittent municipal water distribution and household water use and storage practices may have a larger impact on enteric infections than water source type. The limited differences in enteric pathogen prevalence in children by water source could also be due to other exposure pathways in addition to drinking water, for example through direct contact and food-borne transmission.
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Affiliation(s)
- Kathy H Nguyen
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
| | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA
| | - Mzwakhe E Nyathi
- Department of Animal Science, University of Venda, Limpopo Province, Thohoyandou, 0950, South Africa
| | - Courtney L Hill
- Department of Engineering Systems and Environment, University of Virginia, Charlottesville, VA, 22904, USA
| | - James A Smith
- Department of Engineering Systems and Environment, University of Virginia, Charlottesville, VA, 22904, USA
| | - Richard L Guerrant
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA
| | - Amidou Samie
- Department of Microbiology, University of Venda, Limpopo Province, Thohoyandou, 0950, South Africa
| | - Rebecca A Dillingham
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA
| | - Pascal O Bessong
- Department of Microbiology, University of Venda, Limpopo Province, Thohoyandou, 0950, South Africa
| | - Elizabeth T Rogawski McQuade
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA; Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA.
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26
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Shigella sonnei: virulence and antibiotic resistance. Arch Microbiol 2020; 203:45-58. [PMID: 32929595 PMCID: PMC7489455 DOI: 10.1007/s00203-020-02034-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 12/21/2022]
Abstract
Shigella sonnei is the emerging pathogen globally, as it is the second common infectious species of shigellosis (bloody diarrhoea) in low- and middle-income countries (LMICs) and the leading one in developed world. The multifactorial processes and novel mechanisms have been identified in S. sonnei, that are collectively playing apart a substantial role in increasing its prevalence, while replacing the S. flexneri and other Gram-negative gut pathogens niche occupancy. Recently, studies suggest that due to improvement in sanitation S. sonnei has reduced cross-immunization from Plesiomonas shigelliodes (having same O-antigen as S. sonnei) and also found to outcompete the two major species of Enterobacteriaceae family (Shigella flexneri and Escherichia coli), due to encoding of type VI secretion system (T6SS). This review aimed to highlight S. sonnei as an emerging pathogen in the light of recent research with pondering aspects on its epidemiology, transmission, and pathogenic mechanisms. Additionally, this paper aimed to review S. sonnei disease pattern and related complications, symptoms, and laboratory diagnostic techniques. Furthermore, the available treatment reigns and antibiotic-resistance patterns of S. sonnei are also discussed, as the ciprofloxacin and fluoroquinolone-resistant S. sonnei has already intensified the global spread and burden of antimicrobial resistance. In last, prevention and controlling strategies are briefed to limit and tackle S. sonnei and possible future areas are also explored that needed more research to unravel the hidden mysteries surrounding S. sonnei.
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27
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Newly Emerged Serotype 1c of Shigella flexneri: Multiple Origins and Changing Drug Resistance Landscape. Genes (Basel) 2020; 11:genes11091042. [PMID: 32899396 PMCID: PMC7565858 DOI: 10.3390/genes11091042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/04/2022] Open
Abstract
Bacillary dysentery caused by Shigella flexneri is a major cause of under-five mortality in developing countries, where a novel S. flexneri serotype 1c has become very common since the 1980s. However, the origin and diversification of serotype 1c remain poorly understood. To understand the evolution of serotype 1c and their antimicrobial resistance, we sequenced and analyzed the whole-genome of 85 clinical isolates from the United Kingdom, Egypt, Bangladesh, Vietnam, and Japan belonging to serotype 1c and related serotypes of 1a, 1b and Y/Yv. We identified up to three distinct O-antigen modifying genes in S. flexneri 1c strains, which were acquired from three different bacteriophages. Our analysis shows that S. flexneri 1c strains have originated from serotype 1a and serotype 1b strains after the acquisition of bacteriophage-encoding gtrIc operon. The maximum-likelihood phylogenetic analysis using core genes suggests two distinct S. flexneri 1c lineages, one specific to Bangladesh, which originated from ancestral serotype 1a strains and the other from the United Kingdom, Egypt, and Vietnam originated from ancestral serotype 1b strains. We also identified 63 isolates containing multiple drug-resistant genes in them conferring resistance against streptomycin, sulfonamide, quinolone, trimethoprim, tetracycline, chloramphenicol, and beta-lactamase. Furthermore, antibiotic susceptibility assays showed 83 (97.6%) isolates as either complete or intermediate resistance to the WHO-recommended first- and second-line drugs. This changing drug resistance pattern demonstrates the urgent need for drug resistance surveillance and renewed treatment guidelines.
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28
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Sanada TJ, Hosomi K, Shoji H, Park J, Naito A, Ikubo Y, Yanagisawa A, Kobayashi T, Miwa H, Suda R, Sakao S, Mizuguchi K, Kunisawa J, Tanabe N, Tatsumi K. Gut microbiota modification suppresses the development of pulmonary arterial hypertension in an SU5416/hypoxia rat model. Pulm Circ 2020; 10:2045894020929147. [PMID: 32922743 PMCID: PMC7457673 DOI: 10.1177/2045894020929147] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/01/2020] [Indexed: 02/06/2023] Open
Abstract
The pathogenesis of pulmonary arterial hypertension is closely associated with dysregulated inflammation. Recently, abnormal alterations in gut microbiome composition and function were reported in a pulmonary arterial hypertension experimental animal model. However, it remains unclear whether these alterations are a result or the cause of pulmonary arterial hypertension. The purpose of this study was to investigate whether alterations in the gut microbiome affected the hemodynamics in SU5416/hypoxia rats. We used the SU5416/hypoxia rat model in our study. SU5416/hypoxia rats were treated with a single SU5416 injection (30 mg/kg) and a three-week hypoxia exposure (10% O2). Three SU5416/hypoxia rats were treated with a combination of four antibiotics (SU5416/hypoxia + ABx group) for four weeks. Another group was exposed to hypoxia (10% O2) without the SU5416 treatment, and control rats received no treatment. Fecal samples were collected from each animal, and the gut microbiota composition was analyzed by 16S rRNA sequencing. The antibiotic treatment significantly suppressed the vascular remodeling, right ventricular hypertrophy, and increase in the right ventricular systolic pressure in SU5416/hypoxia rats. 16S rRNA sequencing analysis revealed gut microbiota modification in SU5416/hypoxia + ABx group. The Firmicutes-to-Bacteroidetes ratio in SU5416/hypoxia rats was significantly higher than that in control and hypoxia rats. Compared with the control microbiota, 14 bacterial genera, including Bacteroides and Akkermansia, increased, whereas seven bacteria, including Rothia and Prevotellaceae, decreased in abundance in SU5416/hypoxia rats. Antibiotic-induced modification of the gut microbiota suppresses the development of pulmonary arterial hypertension. Dysbiosis may play a causal role in the development and progression of pulmonary arterial hypertension.
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Affiliation(s)
- Takayuki J. Sanada
- Department of Respirology, Graduate School of
Medicine, Chiba, Japan
- Department of Pulmonology, Institute for
Cardiovascular Research (ICaR-VU)/VU University Medical Center, Amsterdam, the
Netherlands
| | - Koji Hosomi
- Center for Vaccine and Adjuvant Research and
Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation,
Health, and Nutrition, Osaka, Japan
| | - Hiroki Shoji
- Department of Respirology, Graduate School of
Medicine, Chiba, Japan
| | - Jonguk Park
- Artificial Intelligence Center for Health and
Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition,
Osaka, Japan
| | - Akira Naito
- Department of Respirology, Graduate School of
Medicine, Chiba, Japan
| | - Yumiko Ikubo
- Department of Respirology, Graduate School of
Medicine, Chiba, Japan
| | - Asako Yanagisawa
- Department of Respirology, Graduate School of
Medicine, Chiba, Japan
| | | | - Hideki Miwa
- Department of Respirology, Graduate School of
Medicine, Chiba, Japan
| | - Rika Suda
- Department of Respirology, Graduate School of
Medicine, Chiba, Japan
| | - Seiichiro Sakao
- Department of Respirology, Graduate School of
Medicine, Chiba, Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and
Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition,
Osaka, Japan
- Institute for Protein Research,
Osaka
University, Osaka, Japan
| | - Jun Kunisawa
- Center for Vaccine and Adjuvant Research and
Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation,
Health, and Nutrition, Osaka, Japan
| | - Nobuhiro Tanabe
- Department of Respirology, Graduate School of
Medicine, Chiba, Japan
- Department of Respirology,
Chibaken
Saiseikai Narashino Hospital, Narashino, Japan
| | - Koichiro Tatsumi
- Department of Respirology, Graduate School of
Medicine, Chiba, Japan
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29
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Lu H, Yan P, Xiong W, Wang J, Liu X. Genomic characterization of a novel virulent phage infecting Shigella fiexneri and isolated from sewage. Virus Res 2020; 283:197983. [PMID: 32325115 DOI: 10.1016/j.virusres.2020.197983] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/15/2020] [Accepted: 04/15/2020] [Indexed: 11/24/2022]
Abstract
Shigella fiexneri phage SGF2 is a novel lytic phage isolated from a sewage sample. Morphological characterization indicates that phage SGF2 is a member of the Podoviridae family, producing virions with an isometric head (82.6 ± 8 nm diameter) and a short non-contractile tail (length 52 ± 8 nm). This phage specifically infected the Shigella fiexneri. One-step growth curves indicated that the burst period of phage SGF2 is 30 min, with an approximate burst size of 38. The full-length genome was sequenced and potential virulence genes were detected. We will discuss the potential application of phage SGF2 in phage therapy.
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Affiliation(s)
- Han Lu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Peihan Yan
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Wenbin Xiong
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Jingwei Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China.
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30
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Zhao ZY, Chen Q, Zhao B, Hannah MN, Wang N, Wang YX, Xuan XF, Rui J, Chu MJ, Yu SS, Wang Y, Liu XC, An R, Pan LL, Chiang YC, Su YH, Zhao BH, Chen TM. Relative transmissibility of shigellosis among male and female individuals: a modeling study in Hubei Province, China. Infect Dis Poverty 2020; 9:39. [PMID: 32299485 PMCID: PMC7162736 DOI: 10.1186/s40249-020-00654-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/30/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Developing countries exhibit a high disease burden from shigellosis. Owing to the different incidences in males and females, this study aims to analyze the features involved in the transmission of shigellosis among male (subscript m) and female (subscript f) individuals using a newly developed sex-based model. METHODS The data of reported shigellosis cases were collected from the China Information System for Disease Control and Prevention in Hubei Province from 2005 to 2017. A sex-based Susceptible-Exposed-Infectious/Asymptomatic-Recovered (SEIAR) model was applied to explore the dataset, and a sex-age-based SEIAR model was applied in 2010 to explore the sex- and age-specific transmissions. RESULTS From 2005 to 2017, 130 770 shigellosis cases (including 73 981 male and 56 789 female cases) were reported in Hubei Province. The SEIAR model exhibited a significant fitting effect with the shigellosis data (P < 0.001). The median values of the shigellosis transmission were 2.3225 × 108 for SARmm (secondary attack rate from male to male), 2.5729 × 108 for SARmf, 2.7630 × 10-8 for SARfm, and 2.1061 × 10-8 for SARff. The top five mean values of the transmission relative rate in 2010 (where the subscript 1 was defined as male and age ≤ 5 years, 2 was male and age 6 to 59 years, 3 was male and age ≥ 60 years, 4 was female and age ≤ 5 years, 5 was female and age 6 to 59 years, and 6 was male and age ≥ 60 years) were 5.76 × 10-8 for β61, 5.32 × 10-8 for β31, 4.01 × 10-8 for β34, 7.52 × 10-9 for β62, and 6.04 × 10-9 for β64. CONCLUSIONS The transmissibility of shigellosis differed among male and female individuals. The transmissibility between the genders was higher than that within the genders, particularly female-to-male transmission. The most important route in children (age ≤ 5 years) was transmission from the elderly (age ≥ 60 years). Therefore, the greatest interventions should be applied in females and the elderly.
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Affiliation(s)
- Ze-Yu Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China
| | - Qi Chen
- Hubei Provincial Center for Disease Control and Prevention, Wuhan City, Hubei Province, People's Republic of China
| | - Bin Zhao
- Laboratory Department, Xiang'an Hospital of Xiamen University, State Key Laboratory of Molecular Vaccinology and Molecular Diagnosis, Xiamen, Fujian, People's Republic of China
| | - Mikah Ngwanguong Hannah
- Medical College, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Ning Wang
- Respiratory Department, Shanghai General Hospital, Shanghai, People's Republic of China
| | - Yu-Xin Wang
- Department of Nephrology, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian, People's Republic of China
| | - Xian-Fa Xuan
- Department of Nephrology, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian, People's Republic of China
| | - Jia Rui
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China
| | - Mei-Jie Chu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China
| | - Shan-Shan Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China
| | - Yao Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China
| | - Xing-Chun Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China
| | - Ran An
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China
| | - Li-Li Pan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China
| | - Yi-Chen Chiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China
| | - Yan-Hua Su
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China.
| | - Ben-Hua Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China.
| | - Tian-Mu Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, 4221-117 South Xiang'an Road, Xiang'an District, Xiamen, Fujian Province, People's Republic of China.
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Hendriks ACA, Reubsaet FAG, Kooistra-Smid AMDM, Rossen JWA, Dutilh BE, Zomer AL, van den Beld MJC. Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity. BMC Genomics 2020; 21:138. [PMID: 32041522 PMCID: PMC7011524 DOI: 10.1186/s12864-020-6555-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/04/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND We investigated the association of symptoms and disease severity of shigellosis patients with genetic determinants of infecting Shigella and entero-invasive Escherichia coli (EIEC), because determinants that predict disease outcome per individual patient could be used to prioritize control measures. For this purpose, genome wide association studies (GWAS) were performed using presence or absence of single genes, combinations of genes, and k-mers. All genetic variants were derived from draft genome sequences of isolates from a multicenter cross-sectional study conducted in the Netherlands during 2016 and 2017. Clinical data of patients consisting of binary/dichotomous representation of symptoms and their calculated severity scores were also available from this study. To verify the suitability of the methods used, the genetic differences between the genera Shigella and Escherichia were used as control. RESULTS The isolates obtained were representative of the population structure encountered in other Western European countries. No association was found between single genes or combinations of genes and separate symptoms or disease severity scores. Our benchmark characteristic, genus, resulted in eight associated genes and > 3,000,000 k-mers, indicating adequate performance of the algorithms used. CONCLUSIONS To conclude, using several microbial GWAS methods, genetic variants in Shigella spp. and EIEC that can predict specific symptoms or a more severe course of disease were not identified, suggesting that disease severity of shigellosis is dependent on other factors than the genetic variation of the infecting bacteria. Specific genes or gene fragments of isolates from patients are unsuitable to predict outcomes and cannot be used for development, prioritization and optimization of guidelines for control measures of shigellosis or infections with EIEC.
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Affiliation(s)
- Amber C A Hendriks
- Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Frans A G Reubsaet
- Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - A M D Mirjam Kooistra-Smid
- Department of Medical Microbiology, Certe, Groningen, the Netherlands
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Maaike J C van den Beld
- Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Han R, Pang D, Wen L, You L, Huang R, Kulikouskaya V. In vitro digestibility and prebiotic activities of a sulfated polysaccharide from Gracilaria Lemaneiformis. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103652] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Han SR, Kim DW, Kim B, Chi YM, Kang S, Park H, Jung SH, Lee JH, Oh TJ. Complete genome sequencing of Shigella sp. PAMC 28760: Identification of CAZyme genes and analysis of their potential role in glycogen metabolism for cold survival adaptation. Microb Pathog 2019; 137:103759. [PMID: 31560973 DOI: 10.1016/j.micpath.2019.103759] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 11/17/2022]
Abstract
Shigella sp. PAMC 28760 (isolated from Himantormia sp. lichen in Antarctica) is a gram-negative, non-sporulating bacterium that has cellulolytic and amylolytic characteristics as well as glycogen metabolic pathways. In this study, we isolated S. sp. PAMC 28760 from Antarctic lichen, and present the complete genome sequence with annotations describing its unique features. The genome sequence has 58.85% GC content, 4,278 coding DNA sequences, 85 tRNAs, and 22 rRNA operons. 16S rRNA gene sequence analyses revealed strain PAMC 28760 as a potentially new species of genus Shigella, showing various differences from pathogenic bacteria reported previously. dbCAN2 analyses revealed 91 genes related to carbohydrate-metabolizing enzymes. S. sp. PAMC 28760 likely degrades polysaccharide starch to obtain glucose for energy conservation. This study provides a foundation for understanding Shigella survival adaptation mechanisms under extremely cold Antarctic conditions.
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Affiliation(s)
- So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea
| | - Do Wan Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea
| | - Young Min Chi
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Seunghyun Kang
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Sang-Hee Jung
- Department of Dental Hygiene, Gangneung Yeongdong University, Gangneung, South Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, South Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea; Genome-based BioIT Convergence Institute, Asan, South Korea; Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, South Korea.
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Draft Genome Sequences of 72 Isolates from All Four Species of Shigella. Microbiol Resour Announc 2018; 7:MRA01399-18. [PMID: 30533843 PMCID: PMC6284731 DOI: 10.1128/mra.01399-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/07/2018] [Indexed: 11/20/2022] Open
Abstract
Shigella is a genus of Gram-negative enteric pathogenic bacteria which has four species, Shigella dysenteriae, S. flexneri, S. boydii, and S. sonnei. Shigella species are clinically important bacteria because they cause shigellosis or dysentery. Here we report the genome sequences of 72 Shigella isolates from these four species.
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Evaluation of a Culture-Dependent Algorithm and a Molecular Algorithm for Identification of Shigella spp., Escherichia coli, and Enteroinvasive E. coli. J Clin Microbiol 2018; 56:JCM.00510-18. [PMID: 30021824 PMCID: PMC6156305 DOI: 10.1128/jcm.00510-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/11/2018] [Indexed: 12/13/2022] Open
Abstract
Identification of Shigella spp., Escherichia coli, and enteroinvasive E. coli (EIEC) is challenging because of their close relatedness. Distinction is vital, as infections with Shigella spp. are under surveillance of health authorities, in contrast to EIEC infections. In this study, a culture-dependent identification algorithm and a molecular identification algorithm were evaluated. Discrepancies between the two algorithms and original identification were assessed using whole-genome sequencing (WGS). After discrepancy analysis with the molecular algorithm, 100% of the evaluated isolates were identified in concordance with the original identification. However, the resolution for certain serotypes was lower than that of previously described methods and lower than that of the culture-dependent algorithm. Although the resolution of the culture-dependent algorithm is high, 100% of noninvasive E. coli, Shigella sonnei, and Shigella dysenteriae, 93% of Shigella boydii and EIEC, and 85% of Shigella flexneri isolates were identified in concordance with the original identification. Discrepancy analysis using WGS was able to confirm one of the used algorithms in four discrepant results. However, it failed to clarify three other discrepant results, as it added yet another identification. Both proposed algorithms performed well for the identification of Shigella spp. and EIEC isolates and are applicable in low-resource settings, in contrast to previously described methods that require WGS for daily diagnostics. Evaluation of the algorithms showed that both algorithms are capable of identifying Shigella species and EIEC isolates. The molecular algorithm is more applicable in clinical diagnostics for fast and accurate screening, while the culture-dependent algorithm is more suitable for reference laboratories to identify Shigella spp. and EIEC up to the serotype level.
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