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Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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2
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Applied Proteomics in 'One Health'. Proteomes 2021; 9:proteomes9030031. [PMID: 34208880 PMCID: PMC8293331 DOI: 10.3390/proteomes9030031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022] Open
Abstract
‘One Health’ summarises the idea that human health and animal health are interdependent and bound to the health of ecosystems. The purpose of proteomics methodologies and studies is to determine proteins present in samples of interest and to quantify changes in protein expression during pathological conditions. The objectives of this paper are to review the application of proteomics technologies within the One Health concept and to appraise their role in the elucidation of diseases and situations relevant to One Health. The paper develops in three sections. Proteomics Applications in Zoonotic Infections part discusses proteomics applications in zoonotic infections and explores the use of proteomics for studying pathogenetic pathways, transmission dynamics, diagnostic biomarkers and novel vaccines in prion, viral, bacterial, protozoan and metazoan zoonotic infections. Proteomics Applications in Antibiotic Resistance part discusses proteomics applications in mechanisms of resistance development and discovery of novel treatments for antibiotic resistance. Proteomics Applications in Food Safety part discusses the detection of allergens, exposure of adulteration, identification of pathogens and toxins, study of product traits and characterisation of proteins in food safety. Sensitive analysis of proteins, including low-abundant ones in complex biological samples, will be achieved in the future, thus enabling implementation of targeted proteomics in clinical settings, shedding light on biomarker research and promoting the One Health concept.
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3
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Zhang D, Hu Y, Zhu Q, Huang J, Chen Y. Proteomic interrogation of antibiotic resistance and persistence in Escherichia coli - progress and potential for medical research. Expert Rev Proteomics 2020; 17:393-409. [PMID: 32567419 DOI: 10.1080/14789450.2020.1784731] [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] [Indexed: 12/19/2022]
Abstract
Introduction Escherichia coli strains possess two survival strategies to endure lethal antibiotic exposure including antibiotic resistance and persistence, in which persistence can contribute to the emergence of antibiotic resistance and increasing the risk of multidrug resistance. Using high-throughput proteomics for the comprehensive understanding of mechanisms of antibiotic resistance and persistence is an effective strategy for development of target-based anti-bacterial therapies. Areas covered In this review, we summarize a comprehensive proteomic perspective of antibiotic resistance and persistence in E. coli, and overview of anti-antibiotic resistance and anti-persister molecules and strategies for the development of potential therapies. Expert opinion Proteomics allows us to globally identify the critical proteins and pathways involved in antibiotic resistance and persistence. Advancements in methodologies of proteomics and multi-omic strategies are required to overcome the limitations of proteomics and better understand mechanisms of antibiotic resistance and persistence in E. coli, and to open the possibility for identification of new targets for alternative strategies in therapeutics.
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Affiliation(s)
- Danfeng Zhang
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Yuanqing Hu
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Qiuqiang Zhu
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Jiafu Huang
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China.,Engineering Technological Center of Mushroom Industry , Zhangzhou, China
| | - Yiyun Chen
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
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4
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Palma E, Tilocca B, Roncada P. Antimicrobial Resistance in Veterinary Medicine: An Overview. Int J Mol Sci 2020; 21:E1914. [PMID: 32168903 PMCID: PMC7139321 DOI: 10.3390/ijms21061914] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance (AMR) represents one of the most important human- and animal health-threatening issues worldwide. Bacterial capability to face antimicrobial compounds is an ancient feature, enabling bacterial survival over time and the dynamic surrounding. Moreover, bacteria make use of their evolutionary machinery to adapt to the selective pressure exerted by antibiotic treatments, resulting in reduced efficacy of the therapeutic intervention against human and animal infections. The mechanisms responsible for both innate and acquired AMR are thoroughly investigated. Commonly, AMR traits are included in mobilizable genetic elements enabling the homogeneous diffusion of the AMR traits pool between the ecosystems of diverse sectors, such as human medicine, veterinary medicine, and the environment. Thus, a coordinated multisectoral approach, such as One-Health, provides a detailed comprehensive picture of the AMR onset and diffusion. Following a general revision of the molecular mechanisms responsible for both innate and acquired AMR, the present manuscript focuses on reviewing the contribution of veterinary medicine to the overall issue of AMR. The main sources of AMR amenable to veterinary medicine are described, driving the attention towards the indissoluble cross-talk existing between the diverse ecosystems and sectors and their cumulative cooperation to this warning phenomenon.
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Affiliation(s)
| | | | - Paola Roncada
- Department of Health Science, University “Magna Graecia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (E.P.); (B.T.)
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5
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Zhu W, Zhou S, Chu W. Comparative proteomic analysis of sensitive and multi-drug resistant Aeromonas hydrophila isolated from diseased fish. Microb Pathog 2019; 139:103930. [PMID: 31846742 DOI: 10.1016/j.micpath.2019.103930] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022]
Abstract
Bacterial hemorrhagic septicemia caused by multi-drug resistant (MDR) Aeromonas hydrophila has exponentially increased in the past decade, and reached an alarming rate making it a major concern in the aquaculture industry in China. The aim of this study was to investigate the difference in the regulation of proteins expression in multi-drug resistance and susceptible A. hydrophila strains isolated from diseased fish using two-dimensional electrophoresis (2-DE) combined with mass spectrometry. 28 isolates of A. hydrophila were successfully identified by biochemical tests. Antibiotic susceptibility test results showed that all the isolates have different drug resistant patterns. A total of 61 and 17 differently expressed proteins were identified in MDR and susceptible A. hydrophila, respectively, evidencing that biological processes related to carbon metabolism, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, cationic antimicrobial peptide (CAMP) resistance and propanoate metabolism were down-regulated in MDR strain, while proteins involved in biosynthesis of antibiotics, glycolysis/gluconeogenesis were highly expressed in the sensitive strain. The analysis of differentially expressed proteins from multi-drug resistance and susceptible strains suggests that a number of proteins are involved in several metabolic metabolism pathways plays an important role in A. hydrophila drug resistance. Our findings provide new insights about mechanisms involved in drug resistance and propose possible novel targets for developing alternative antibacterial drugs.
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Affiliation(s)
- Wei Zhu
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Shuxin Zhou
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Weihua Chu
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China.
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6
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Bottagisio M, Soggiu A, Piras C, Bidossi A, Greco V, Pieroni L, Bonizzi L, Roncada P, Lovati AB. Proteomic Analysis Reveals a Biofilm-Like Behavior of Planktonic Aggregates of Staphylococcus epidermidis Grown Under Environmental Pressure/Stress. Front Microbiol 2019; 10:1909. [PMID: 31551940 PMCID: PMC6743020 DOI: 10.3389/fmicb.2019.01909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/05/2019] [Indexed: 01/14/2023] Open
Abstract
Prosthetic joint replacement failure has a huge impact on quality of life and hospitalization costs. A leading cause of prosthetic joint infection is bacteria-forming biofilm on the surface of orthopedic devices. Staphylococcus epidermidis is an emergent, low-virulence pathogen implicated in chronic infections, barely indistinguishable from aseptic loosening when embedded in a mature matrix. The literature on the behavior of quiescent S. epidermidis in mature biofilms is scarce. To fill this gap, we performed comparative analysis of the whole proteomic profiles of two methicillin-resistant S. epidermidis strains growing in planktonic and in sessile form to investigate the molecular mechanisms underlying biofilm stability. After 72-h culture of biofilm-forming S. epidermidis, overexpression of proteins involved in the synthesis of nucleoside triphosphate and polysaccharides was observed, whereas planktonic bacteria expressed proteins linked to stress and anaerobic growth. Cytological analysis was performed to determine why planktonic bacteria unexpectedly expressed proteins typical of sessile culture. Images evidenced that prolonged culture under vigorous agitation can create a stressful growing environment that triggers microorganism aggregation in a biofilm-like matrix as a mechanism to survive harsh conditions. The choice of a unique late time point provided an important clue for future investigations into the biofilm-like behavior of planktonic cells. Our preliminary results may inform comparative proteomic strategies in the study of mature bacterial biofilm. Finally, there is an increasing number of studies on the aggregation of free-floating bacteria embedded in an extracellular matrix, prompting the need to gain further insight into this mode of bacterial growth.
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Affiliation(s)
- Marta Bottagisio
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, Milan, Italy
| | - Alessio Soggiu
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Cristian Piras
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Alessandro Bidossi
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, Milan, Italy
| | - Viviana Greco
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore Roma, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Luisa Pieroni
- Proteomics and Metabonomics Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Luigi Bonizzi
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Paola Roncada
- Department of Health Sciences, Università degli Studi "Magna Græcia", Catanzaro, Italy
| | - Arianna B Lovati
- IRCCS Istituto Ortopedico Galeazzi, Cell and Tissue Engineering Laboratory, Milan, Italy
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7
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Xu S, Yang J, Yin C, Zhao X. The dominance of bacterial genotypes leads to susceptibility variations under sublethal antibiotic pressure. Future Microbiol 2017; 13:165-185. [PMID: 29260580 DOI: 10.2217/fmb-2017-0070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
AIM To investigate the collective resistance of the bacteria population with resistant horizontal gene transfer under sublethal bactericide pressure. MATERIALS & METHODS By employing qualitative analysis of ordinary differential equations, particularly bifurcation theory and several numerical simulations, a modified 4D ordinary differential equation model describing antibiotic susceptibility variations induced by sublethal antibiotic pressure is analyzed in detail. RESULTS The long-term behaviors and collective resistance of different bacterial genotype populations in different sublethal bactericide concentration subintervals exhibit high levels of heterogeneity and are determined by the protection provided by resistant genes on chromosome or plasmid, their fitness costs, plasmid segregation rate and sublethal bactericide pressure. CONCLUSION First, the possible mechanism of antibiotic susceptibility variations is the dominance of different bacterial genotypes under sublethal bactericide pressure, rather than persistence, tolerance or resistance. Additionally, the combination of vertical genetic transfer, horizontal genetic transfer and plasmid segregation can lead to unique switch between two states of different bacterial genotypes.
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Affiliation(s)
- Shilian Xu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia.,Department of Mathematics, Zhejiang Normal University, Jinhua 321004, China
| | - Jiaru Yang
- Institute for Tropical Medicine, Kunming Medical University, Kunming, Yunnan Province 650500, China.,Macrophage-pathogen Interaction Lab, Infection & Immunity program, Department of Biochemistry & Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Chong Yin
- Bone Metabolism Lab, Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Xiaohua Zhao
- Department of Mathematics, Zhejiang Normal University, Jinhua 321004, China
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8
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Ramos S, Silva N, Hébraud M, Santos HM, Nunes-Miranda JD, Pinto L, Pereira JE, Capelo JL, Poeta P, Igrejas G. Proteomics for Drug Resistance on the Food Chain? Multidrug-Resistant Escherichia coli Proteomes from Slaughtered Pigs. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:362-74. [PMID: 27310477 DOI: 10.1089/omi.2016.0044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding global drug resistance demands an integrated vision, focusing on both human and veterinary medicine. Omics technologies offer new vistas to decipher mechanisms of drug resistance in the food chain. For example, Escherichia coli resistance to major antibiotics is increasing whereas multidrug resistance (MDR) strains are now commonly found in humans and animals. Little is known about the structural and metabolic changes in the cell that trigger resistance to antimicrobial agents. Proteomics is an emerging field that is used to advance our knowledge in global health and drug resistance in the food chain. In the present proteomic analysis, we offer an overview of the global protein expression of different MDR E. coli strains from fecal samples of pigs slaughtered for human consumption. A full proteomic survey of the drug-resistant strains SU60, SU62, SU76, and SU23, under normal growth conditions, was made by two-dimensional electrophoresis, identifying proteins by MALDI-TOF/MS. The proteomes of these four E. coli strains with different genetic profiles were compared in detail. Identical transport, stress response, or metabolic proteins were discovered in the four strains. Several of the identified proteins are essential in bacterial pathogenesis (GAPDH, LuxS, FKBPs), development of bacterial resistance (Omp's, TolC, GroEL, ClpB, or SOD), and potential antibacterial targets (FBPA, FabB, ACC's, or Fab1). Effective therapies against resistant bacteria are crucial and, to accomplish this, a comprehensive understanding of putative resistance mechanisms is essential. Moving forward, we suggest that multi-omics research will further improve our knowledge about bacterial growth and virulence on the food chain, especially under antibiotic stress.
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Affiliation(s)
- Sónia Ramos
- 1 Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal .,2 Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal .,3 Centre for Animal and Veterinary Science, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal .,4 Department of Veterinary Science, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal
| | - Nuno Silva
- 3 Centre for Animal and Veterinary Science, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal .,4 Department of Veterinary Science, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal
| | - Michel Hébraud
- 5 INRA (Institut National de la Recherche Agronomique), Centre Auvergne-Rhône-Alpes , UR454 Microbiologie, Saint-Genès Champanelle, France .,6 Plate-Forme d'Exploration du Métabolisme Composante Protéomique, UR370 QuaPA, Institut National de la Recherche Agronomique (INRA) , Centre Auvergne-Rhône-Alpes, Saint-Genès Champanelle, France
| | - Hugo M Santos
- 7 UCIBIO-REQUIMTE, Faculty of Technology and Science, University Nova de Lisboa , Caparica, Portugal
| | - Júlio Dinis Nunes-Miranda
- 1 Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal .,2 Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal
| | - Luís Pinto
- 1 Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal .,2 Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal .,3 Centre for Animal and Veterinary Science, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal .,4 Department of Veterinary Science, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal
| | - José E Pereira
- 4 Department of Veterinary Science, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal
| | - José-Luis Capelo
- 8 ProteoMass Scientific Society , Faculty of Sciences and Technology, Caparica, Portugal
| | - Patrícia Poeta
- 4 Department of Veterinary Science, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal .,7 UCIBIO-REQUIMTE, Faculty of Technology and Science, University Nova de Lisboa , Caparica, Portugal
| | - Gilberto Igrejas
- 1 Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal .,2 Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real, Portugal .,7 UCIBIO-REQUIMTE, Faculty of Technology and Science, University Nova de Lisboa , Caparica, Portugal
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9
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Kalule JB, Fortuin S, Calder B, Robberts L, Keddy KH, Nel AJM, Garnett S, Nicol M, Warner DF, Soares NC, Blackburn JM. Proteomic comparison of three clinical diarrhoeagenic drug-resistant Escherichia coli isolates grown on CHROMagar™STEC media. J Proteomics 2017; 180:25-35. [PMID: 28887208 DOI: 10.1016/j.jprot.2017.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 08/21/2017] [Accepted: 09/02/2017] [Indexed: 02/06/2023]
Abstract
Shiga-toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) are key diarrhoea-causing foodborne pathogens. We used proteomics to characterize the virulence and antimicrobial resistance protein profiles of three clinical pathogenic E. coli isolates (two EPEC [one resistant to ciprofloxacin] and one STEC) cultured on CHROMagar™STEC solid media after minimal laboratory passage. We identified 4767 unique peptides from 1630 protein group across all three clinical E. coli strains. Label-free proteomic analysis allowed the identification of virulence and drug resistance proteins that were unique to each of the clinical isolates compared in this study. The B subunit of Shiga toxin, ToxB, was uniquely detected in the STEC strain while several other virulence factors including SheA, OmpF, OmpC and OmpX were significantly more abundant in the STEC strain. The ciprofloxacin resistant EPEC isolate possessed reduced levels of key virulence proteins compared to the ciprofloxacin susceptible EPEC and STEC strains. Parallel reaction monitoring assays validated the presence of biologically relevant proteins across biologically-replicated cultures. Propagation of clinical isolates on a relevant solid medium followed by mass spectrometry analysis represents a convenient means to quantify virulence factors and drug resistance determinants that might otherwise be lost through extensive in vitro passage in enteropathogenic bacteria. SIGNIFICANCE Through the use of quantitative proteomics, we have characterized the virulence and antimicrobial resistance attributes of three clinically isolated, pathogenic E. coli strains cultured on solid media. Our results provide new, quantitative data on the expressed proteomes of these tellurite-resistant, diarrhoeagenic E. coli strains and reveal a subset of antimicrobial resistance and virulence proteins that are differentially abundant between these clinical strains. Our quantitative proteomics-based approach should thus have applicability in microbiological diagnostic labs for the identification of pathogenic/drug resistant E. coli in the future.
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Affiliation(s)
- John Bosco Kalule
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Suereta Fortuin
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Bridget Calder
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Lourens Robberts
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Karen H Keddy
- Bacteriology Division, Centre for Enteric Diseases, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew J M Nel
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Shaun Garnett
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark Nicol
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa
| | - Digby F Warner
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa; MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Nelson C Soares
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa.
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10
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Andjelković U, Šrajer Gajdošik M, Gašo-Sokač D, Martinović T, Josić D. Foodomics and Food Safety: Where We Are. Food Technol Biotechnol 2017; 55:290-307. [PMID: 29089845 PMCID: PMC5654429 DOI: 10.17113/ftb.55.03.17.5044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 05/31/2017] [Indexed: 12/21/2022] Open
Abstract
The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling.
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Affiliation(s)
- Uroš Andjelković
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, RS-11000 Belgrade, Serbia
| | - Martina Šrajer Gajdošik
- Department of Chemistry, J. J. Strossmayer University of Osijek, Cara Hadrijana 8/A, HR-31000 Osijek, Croatia
| | - Dajana Gašo-Sokač
- Faculty of Food Technology, J. J. Strossmayer University of Osijek, Franje Kuhača 20, HR-31000 Osijek, Croatia
| | - Tamara Martinović
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
| | - Djuro Josić
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Warren Alpert Medical School, Brown University, 222 Richmond St, Providence, RI 02903, USA
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11
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Proteomic analysis of food borne pathogens following the mode of action of the disinfectants based on pyridoxal oxime derivatives. Food Res Int 2017; 99:560-570. [DOI: 10.1016/j.foodres.2017.06.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/08/2017] [Accepted: 06/05/2017] [Indexed: 01/11/2023]
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12
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Piras C, Guo Y, Soggiu A, Chanrot M, Greco V, Urbani A, Charpigny G, Bonizzi L, Roncada P, Humblot P. Changes in protein expression profiles in bovine endometrial epithelial cells exposed to E. coli LPS challenge. MOLECULAR BIOSYSTEMS 2017; 13:392-405. [PMID: 28070584 DOI: 10.1039/c6mb00723f] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
E. coli is one of the most frequently involved bacteria in uterine diseases. Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria involved in pathogenic processes leading to post-partum metritis and endometritis in cattle. It also causes inflammation of the endometrium. The increase of cell proliferation by LPS is part of the inflammatory process. The aim of this study was to investigate possible changes in protein expression in relation to the proliferative response of bEECs after challenge with E. coli-LPS. In vitro culture of bEECs was performed from cow genital tracts collected at a slaughterhouse. In passage 5, bEECs from each of 9 cows (3 series of 3 cows) were exposed to 0, 8, and 16 μg ml-1 LPS for 72 h. At time 0 and 72 h later, attached cells/living cells were counted and for each time and LPS dosage, cells were frozen for proteomic analyses. All samples from the 3 series were analyzed by 2-D gel electrophoresis coupled to MALDI-TOF/TOF mass spectrometry. The samples from the first series were subjected to shotgun nLC-MS/MS analysis. From the whole differential proteomics analysis, 38 proteins were differentially expressed (p < 0.05 to p < 0.001) following exposure to LPS. Among them, twenty-eight were found to be up-regulated in the LPS groups in comparison to control groups and ten were down-regulated. Differentially expressed proteins were associated with cell proliferation and apoptosis, transcription, destabilization of cell structure, oxidative stress, regulation of histones, allergy and general cell metabolism pathways. The de-regulations induced by LPS were consistent with the proliferative phenotype and indicated strong alterations of several cell functions. In addition, some of the differentially expressed proteins relates to pathways activated at the time of implantation. The specific changes induced through those signals may have negative consequences for the establishment of pregnancy.
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Affiliation(s)
- Cristian Piras
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milano, Italy
| | - Yongzhi Guo
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, Sweden
| | - Alessio Soggiu
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milano, Italy
| | - Metasu Chanrot
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, Sweden and Rajamangala University of Srivijaya (RMUTSV), Thungyai, Thailand
| | - Viviana Greco
- Proteomics and Metabonomics Unit Fondazione Santa Lucia - IRCCS, Rome, Italy
| | - Andrea Urbani
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Roma, Italy
| | - Gilles Charpigny
- INRA, Biologie du Développement et Reproduction, 78350, Jouy en Josas, France
| | - Luigi Bonizzi
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milano, Italy
| | - Paola Roncada
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milano, Italy and Istituto Sperimentale Italiano L. Spallanzani, Milano and TechnologieS srl, via Celoria 10, 20133 Milano, Italy.
| | - Patrice Humblot
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, Sweden
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Ali L, Goraya MU, Arafat Y, Ajmal M, Chen JL, Yu D. Molecular Mechanism of Quorum-Sensing in Enterococcus faecalis: Its Role in Virulence and Therapeutic Approaches. Int J Mol Sci 2017; 18:ijms18050960. [PMID: 28467378 PMCID: PMC5454873 DOI: 10.3390/ijms18050960] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 04/26/2017] [Indexed: 12/22/2022] Open
Abstract
Quorum-sensing systems control major virulence determinants in Enterococcusfaecalis, which causes nosocomial infections. The E. faecalis quorum-sensing systems include several virulence factors that are regulated by the cytolysin operon, which encodes the cytolysin toxin. In addition, the E. faecalis Fsr regulator system controls the expression of gelatinase, serine protease, and enterocin O16. The cytolysin and Fsr virulence factor systems are linked to enterococcal diseases that affect the health of humans and other host models. Therefore, there is substantial interest in understanding and targeting these regulatory pathways to develop novel therapies for enterococcal infection control. Quorum-sensing inhibitors could be potential therapeutic agents for attenuating the pathogenic effects of E. faecalis. Here, we discuss the regulation of cytolysin, the LuxS system, and the Fsr system, their role in E. faecalis-mediated infections, and possible therapeutic approaches to prevent E. faecalis infection.
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Affiliation(s)
- Liaqat Ali
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan.
| | - Mohsan Ullah Goraya
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yasir Arafat
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Ajmal
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan.
| | - Ji-Long Chen
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China.
| | - Daojin Yu
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Antibiotic Resistance Determinant-Focused Acinetobacter baumannii Vaccine Designed Using Reverse Vaccinology. Int J Mol Sci 2017; 18:ijms18020458. [PMID: 28230771 PMCID: PMC5343991 DOI: 10.3390/ijms18020458] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 01/31/2017] [Accepted: 02/10/2017] [Indexed: 12/11/2022] Open
Abstract
As one of the most influential and troublesome human pathogens, Acinetobacter baumannii (A. baumannii) has emerged with many multidrug-resistant strains. After collecting 33 complete A. baumannii genomes and 84 representative antibiotic resistance determinants, we used the Vaxign reverse vaccinology approach to predict classical type vaccine candidates against A. baumannii infections and new type vaccine candidates against antibiotic resistance. Our genome analysis identified 35 outer membrane or extracellular adhesins that are conserved among all 33 genomes, have no human protein homology, and have less than 2 transmembrane helices. These 35 antigens include 11 TonB dependent receptors, 8 porins, 7 efflux pump proteins, and 2 fimbrial proteins (FilF and CAM87009.1). CAM86003.1 was predicted to be an adhesin outer membrane protein absent from 3 antibiotic-sensitive strains and conserved in 21 antibiotic-resistant strains. Feasible anti-resistance vaccine candidates also include one extracellular protein (QnrA), 3 RND type outer membrane efflux pump proteins, and 3 CTX-M type β-lactamases. Among 39 β-lactamases, A. baumannii CTX-M-2, -5, and -43 enzymes are predicted as adhesins and better vaccine candidates than other β-lactamases to induce preventive immunity and enhance antibiotic treatments. This report represents the first reverse vaccinology study to systematically predict vaccine antigen candidates against antibiotic resistance for a microbial pathogen.
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El-Kersh TA, Marie MA, Al-Sheikh YA, Al-Agamy MH, Al Bloushy AA. Prevalence and risk factors of early fecal carriage of Enterococcus faecalis and Staphylococcus spp and their antimicrobial resistant patterns among healthy neonates born in a hospital setting in central Saudi Arabia. Saudi Med J 2017; 37:280-7. [PMID: 26905350 PMCID: PMC4800892 DOI: 10.15537/smj.2016.3.13871] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Objectives: To investigate the prevalence, antibiotic resistant profiles, and risk factors of early fecal carriage of Enterococcus faecalis (E. faecalis) and staphylococci among 150 healthy Saudi neonates born in a hospital setting in central Saudi Arabia. Methods: This prospective study was conducted in Al-Bukayriyah General Hospital, Qassim, Saudi Arabia, between June 2012 and January 2013. The E. faecalis and Staphylococcus spp. isolates were identified manually, and Vitek2 system was used for identity confirmation at the species level and minimum inhibitory concentration-susceptibility testing. Results: Enterococcus faecalis (n=73) and Staphylococcus spp. (n=18) were recovered. Unlike staphylococci, E. faecalis colonization did not significantly vary from day one up to 7 days of life, regardless of the type of feeding, but it was relatively higher among vaginally versus cesarean delivery. Both Staphylococcus epidermidis (S. epidermidis) and Staphylococcus aureus carriage increase as the body weight increases, and this difference was significant (p=0.025) for S. epidermidis. High-level resistance in Gentamycin among E. faecalis isolates was 25% and 11% to Streptomycin. Thirty percent of S. epidermidis were resistant to oxacillin and exhibited multidrug-resistant (MDR) patterns of 5 resistant markers, which were also observed among 2/5 (40%) of Methicillin-resistant Staphylococcus aureus isolates. Conclusion: Enterococcus faecalis did not significantly vary in relation to type of delivery, age up to 7 days, and type of feeding. The neonatal fecal carriage of MDR isolates should be considered as a crucial reservoir to the further spread of antimicrobial resistance genes among hospitals, cross infections, and the community.
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Affiliation(s)
- Talat A El-Kersh
- Department of Clinical Laboratory Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia. E-mail.
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Adamus-Białek W, Lechowicz Ł, Kubiak-Szeligowska AB, Wawszczak M, Kamińska E, Chrapek M. A new look at the drug-resistance investigation of uropathogenic E. coli strains. Mol Biol Rep 2017; 44:191-202. [PMID: 28091786 PMCID: PMC5310551 DOI: 10.1007/s11033-017-4099-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 01/02/2017] [Indexed: 11/01/2022]
Abstract
Bacterial drug resistance and uropathogenic tract infections are among the most important issues of current medicine. Uropathogenic Escherichia coli strains are the primary factor of this issue. This article is the continuation of the previous study, where we used Kohonen relations to predict the direction of drug resistance. The characterized collection of uropathogenic E. coli strains was used for microbiological (the disc diffusion method for antimicrobial susceptibility testing), chemical (ATR/FT-IR) and mathematical (artificial neural networks, Ward's hierarchical clustering method, the analysis of distributions of inhibition zone diameters for antibiotics, Cohen's kappa measure of agreement) analysis. This study presents other potential tools for the epidemiological differentiation of E. coli strains. It is noteworthy that ATR/FT-IR technique has turned out to be useful for the quick and simple identification of MDR strains. Also, diameter zones of resistance of this E. coli population were compared to the population of E. coli strains published by EUCAST. We observed the bacterial behaviors toward particular antibiotics in comparison to EUCAST bacterial collections. Additionally, we used Cohen's kappa to show which antibiotics from the same class are closely related to each other and which are not. The presented associations between antibiotics may be helpful in selecting the proper therapy directions. Here we present an adaptation of interdisciplinary studies of drug resistance of E. coli strains for epidemiological and clinical investigations. The obtained results may be some indication in deciding on antibiotic therapy.
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Affiliation(s)
- Wioletta Adamus-Białek
- Institute of Medical Sciences, Jan Kochanowski University, IX Wieków Kielc 19A Av., 25-317, Kielce, Poland.
| | - Łukasz Lechowicz
- Department of Microbiology, Institute of Biology, Jan Kochanowski University, 15 Swietokrzyska St., 25-406, Kielce, Poland
| | | | - Monika Wawszczak
- Department of Microbiology, Institute of Biology, Jan Kochanowski University, 15 Swietokrzyska St., 25-406, Kielce, Poland
| | - Ewelina Kamińska
- Department of Microbiology, Institute of Biology, Jan Kochanowski University, 15 Swietokrzyska St., 25-406, Kielce, Poland
| | - Magdalena Chrapek
- Institute of Mathematics, Jan Kochanowski University, 15 Swietokrzyska St., 25-406, Kielce, Poland
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Sun L, Chen H, Lin W, Lin X. Quantitative proteomic analysis of Edwardsiella tarda in response to oxytetracycline stress in biofilm. J Proteomics 2017; 150:141-148. [DOI: 10.1016/j.jprot.2016.09.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/31/2016] [Accepted: 09/11/2016] [Indexed: 01/23/2023]
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18
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Magalhães S, Aroso M, Roxo I, Ferreira S, Cerveira F, Ramalheira E, Ferreira R, Vitorino R. Proteomic profile of susceptible and multidrug-resistant clinical isolates of Escherichia coli and Klebsiella pneumoniae using label-free and immunoproteomic strategies. Res Microbiol 2016; 168:222-233. [PMID: 28040467 DOI: 10.1016/j.resmic.2016.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 11/12/2016] [Accepted: 12/18/2016] [Indexed: 01/13/2023]
Abstract
Infectious diseases caused by multidrug-resistant (MDR) Enterobacteriaceae have exponentially increased in the past decade, and are a major concern in hospitals. In the first part of the work, we compared the proteome profile of MDR and susceptible clinical isolates of Escherichia coli and Klebsiella pneumoniae in order to identify possible biological processes associated with drug resistance and susceptible phenotypes, using a label-free approach. In the second part, we used an immunoproteomics approach to identify immunoreactive proteins in the same isolates. A total of 388 and 377 proteins were identified in MDR and susceptible E. coli, respectively, evidencing that biological processes related to translation are upregulated in E. coli MDR, while there is an upregulation of processes related to catalytic activity in K. pneumoniae MDR. Both MDR strains show downregulation of processes related to amino acid activation and tRNA amino-acylation. Our data also suggest that MDR strains have higher immunoreactivity than the susceptible strains. The application of high-throughput mass spectrometry (MS) and bioinformatics to the study of modulation of biological processes might shed light on the characterization of multidrug resistance in bacteria.
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Affiliation(s)
- Sandra Magalhães
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal; iBiMED - Institute for Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Miguel Aroso
- iBiMED - Institute for Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Inês Roxo
- Clinical Pathology, Centro Hospitalar do Baixo Vouga, Oliveira do Bairro, Portugal
| | - Sónia Ferreira
- Clinical Pathology, Centro Hospitalar do Baixo Vouga, Oliveira do Bairro, Portugal; Institute of Education and Citizenship, Oliveira do Bairro, Portugal
| | - Frederico Cerveira
- Clinical Pathology, Centro Hospitalar do Baixo Vouga, Oliveira do Bairro, Portugal
| | - Elmano Ramalheira
- Clinical Pathology, Centro Hospitalar do Baixo Vouga, Oliveira do Bairro, Portugal
| | - Rita Ferreira
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- iBiMED - Institute for Biomedicine, University of Aveiro, Aveiro, Portugal; Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal.
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Exploring the neural mechanisms of finasteride: a proteomic analysis in the nucleus accumbens. Psychoneuroendocrinology 2016; 74:387-396. [PMID: 27750143 DOI: 10.1016/j.psyneuen.2016.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 09/07/2016] [Accepted: 10/05/2016] [Indexed: 02/06/2023]
Abstract
The enzyme 5α-reductase (5αR) catalyzes the conversion of progesterone and testosterone into neuroactive steroids implicated in a wide array of behavioral functions. The prototypical 5αR inhibitor, finasteride (FIN), is clinically approved for the treatment of androgenic alopecia and benign prostatic hyperplasia. Recent evidence has shown that FIN, albeit generally well tolerated, can induce untoward psychological effects in a subset of patients; furthermore, this drug may have therapeutic efficacy for a number of different neuropsychiatric conditions, ranging from Tourette syndrome to schizophrenia. In rat models of these conditions, FIN has been shown to block the effects of dopamine receptors in the nucleus accumbens (NAcc), a key terminal of the dopamine mesolimbic system. The biological underpinnings of these effects, however, remain mostly elusive. To elucidate the neurochemical networks that may be responsible for the behavioral effects of FIN, we evaluated the proteomic profile of the NAcc following acute (100mg/kg, IP) and subchronic (7 days; 100mg/kg/day, IP) treatment with this drug, in comparison with vehicle treatment (n=5/group). Two-dimensional electrophoresis (2-DE) analysis coupled to mass spectrometry revealed significant changes in the expression of nine proteins (CRMP2, PSMD1, STX18, KCNC3, CYP255, GABRP, GABT, PRPS1, CYP2B3), which were further analyzed by ontological classification (PANTHER). These results point to a number of novel potential chemical targets of FIN, and may help elucidate the underpinnings of FIN's behavioral effects and therapeutic potential for neuropsychiatric disorders.
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Weiss SJ, Mansell TJ, Mortazavi P, Knight R, Gill RT. Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli. PLoS One 2016; 11:e0146916. [PMID: 26771672 PMCID: PMC4714920 DOI: 10.1371/journal.pone.0146916] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 12/23/2015] [Indexed: 12/26/2022] Open
Abstract
Chemical genomics expands our understanding of microbial tolerance to inhibitory chemicals, but its scope is often limited by the throughput of genome-scale library construction and genotype-phenotype mapping. Here we report a method for rapid, parallel, and deep characterization of the response to antibiotics in Escherichia coli using a barcoded genome-scale library, next-generation sequencing, and streamlined bioinformatics software. The method provides quantitative growth data (over 200,000 measurements) and identifies contributing antimicrobial resistance and susceptibility alleles. Using multivariate analysis, we also find that subtle differences in the population responses resonate across multiple levels of functional hierarchy. Finally, we use machine learning to identify a unique allelic and proteomic fingerprint for each antibiotic. The method can be broadly applied to tolerance for any chemical from toxic metabolites to next-generation biofuels and antibiotics.
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Affiliation(s)
- Sophie J. Weiss
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, Colorado, 80303, United States of America
| | - Thomas J. Mansell
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, Colorado, 80303, United States of America
| | - Pooneh Mortazavi
- Department of Computer Science, University of Colorado Boulder, 1111 Engineering Drive ECOT 717, Boulder, CO 80303, United States of America
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive, MC 0602, La Jolla, CA 92093, United States of America
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, MC 0404, La Jolla, CA 92093, United States of America
| | - Ryan T. Gill
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, Colorado, 80303, United States of America
- * E-mail:
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21
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Du XJ, Han R, Li P, Wang S. Comparative proteomic analysis of Cronobacter sakazakii isolates with different virulences. J Proteomics 2015; 128:344-51. [PMID: 26327241 DOI: 10.1016/j.jprot.2015.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 07/24/2015] [Accepted: 08/21/2015] [Indexed: 10/23/2022]
Abstract
UNLABELLED Cronobacter is a genus of widespread, opportunistic, foodborne pathogens that can result in serious illnesses in at-risk infants because of their immature immunity and high dependence on powdered formula, which is one of the foods most often contaminated by this pathogen. However, limited information is available regarding the pathogenesis and the specific virulence factors of this species. In this study, the virulences of 42 Cronobacter sakazakii isolates were analyzed by infecting neonatal SD rats. A comparison of the typing patterns of the isolates enabled groups with close relationships but that exhibited distinct pathogenesis to be identified. Among these groups, 2 strains belonging to the same group but showing distinct virulences were selected, and 2-DE was applied to identify differentially expressed proteins, focusing on virulence-related proteins. A total of 111 protein spots were identified using matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS), and 89 were successfully identified. Further analysis suggested that at least 11 of these proteins may be involved in the pathogenesis of this pathogen. Real-time PCR was carried out to further confirm the differential expression pattern of the genes, and the results indicated that the mRNA expression levels were consistent with the protein expression levels. BIOLOGICAL SIGNIFICANCE The virulence factors and pathogenesis of Cronobacter are largely unknown. In combination with animal toxicological experiments and subtyping results of C. sakazakii, comparative proteomics analysis was performed to comprehensively evaluate the differentially expressed proteins of two isolates that exhibited distinct virulence but were closely related. These procedures made it possible to identify the virulence-related of factors of Cronobacter. Among the 89 total identified proteins, at least 11 show virulence-related potential. This work provides comprehensive candidates for the further investigation of the pathogenesis of Cronobacter.
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Affiliation(s)
- Xin-jun Du
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ran Han
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ping Li
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China.
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Álvarez R, Frávega J, Rodas PI, Fuentes JA, Paredes-Sabja D, Calderón IL, Gil F. Participation of S. Typhimurium cysJIH Operon in the H2S-mediated Ciprofloxacin Resistance in Presence of Sulfate as Sulfur Source. Antibiotics (Basel) 2015. [PMCID: PMC4790288 DOI: 10.3390/antibiotics4030321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Ricardo Álvarez
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, República 217, Santiago 8370146, Chile; E-Mails: (R.A.); (J.F.); (I.L.C.)
| | - Jorge Frávega
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, República 217, Santiago 8370146, Chile; E-Mails: (R.A.); (J.F.); (I.L.C.)
| | - Paula I. Rodas
- Center for Integrative Medicine and Innovative Science, Facultad de Medicina, Universidad Andres Bello, Echaurren 183, Santiago 8370071, Chile; E-Mail:
| | - Juan A. Fuentes
- Laboratorio de Microbiología, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, República 217, Santiago 8370146, Chile; E-Mail:
| | - Daniel Paredes-Sabja
- Gut Microbiota and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, República 217, Santiago 837014, Chile; E-Mail:
| | - Iván L. Calderón
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, República 217, Santiago 8370146, Chile; E-Mails: (R.A.); (J.F.); (I.L.C.)
| | - Fernando Gil
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, República 217, Santiago 8370146, Chile; E-Mails: (R.A.); (J.F.); (I.L.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +56-2-2661-8664
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da Costa JP, Carvalhais V, Ferreira R, Amado F, Vilanova M, Cerca N, Vitorino R. Proteome signatures—how are they obtained and what do they teach us? Appl Microbiol Biotechnol 2015. [DOI: 10.1007/s00253-015-6795-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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24
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Piras C, Soggiu A, Greco V, Martino PA, Del Chierico F, Putignani L, Urbani A, Nally JE, Bonizzi L, Roncada P. Mechanisms of antibiotic resistance to enrofloxacin in uropathogenic Escherichia coli in dog. J Proteomics 2015; 127:365-76. [PMID: 26066767 DOI: 10.1016/j.jprot.2015.05.040] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 05/12/2015] [Accepted: 05/29/2015] [Indexed: 01/25/2023]
Abstract
Escherichia coli (E. coli) urinary tract infections (UTIs) are becoming a serious problem both for pets and humans (zoonosis) due to the close contact and to the increasing resistance to antibiotics. This study has been performed in order to unravel the mechanism of induced enrofloxacin resistance in canine E. coli isolates that represent a good tool to study this pathology. The isolated E. coli has been induced with enrofloxacin and studied through 2D DIGE and shotgun MS. Discovered differentially expressed proteins are principally involved in antibiotic resistance and linked to oxidative stress response, to DNA protection and to membrane permeability. Moreover, since enrofloxacin is an inhibitor of DNA gyrase, the overexpression of DNA starvation/stationary phase protection protein (Dsp) could be a central point to discover the mechanism of this clone to counteract the effects of enrofloxacin. In parallel, the dramatic decrease of the synthesis of the outer membrane protein W, which represents one of the main gates for enrofloxacin entrance, could explain additional mechanism of E. coli defense against this antibiotic. All 2D DIGE and MS data have been deposited into the ProteomeXchange Consortium with identifier PXD002000 and DOI http://dx.doi.org/10.6019/PXD002000. This article is part of a Special Issue entitled: HUPO 2014.
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Affiliation(s)
- Cristian Piras
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli studi di Milano, Milan, Italy
| | - Alessio Soggiu
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli studi di Milano, Milan, Italy
| | - Viviana Greco
- Fondazione Santa Lucia - IRCCS, Rome, Italy; Dipartimento di Medicina Sperimentale e Chirurgia, Università degli Studi di Roma "Tor Vergata", Italy
| | - Piera Anna Martino
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli studi di Milano, Milan, Italy
| | | | - Lorenza Putignani
- Parasitology and Metagenomics Units, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Urbani
- Fondazione Santa Lucia - IRCCS, Rome, Italy; Dipartimento di Medicina Sperimentale e Chirurgia, Università degli Studi di Roma "Tor Vergata", Italy
| | - Jarlath E Nally
- Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, United States
| | - Luigi Bonizzi
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli studi di Milano, Milan, Italy
| | - Paola Roncada
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli studi di Milano, Milan, Italy; Istituto Sperimentale Italiano L. Spallanzani, Milano, Italy.
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Kouidhi B, Al Qurashi YMA, Chaieb K. Drug resistance of bacterial dental biofilm and the potential use of natural compounds as alternative for prevention and treatment. Microb Pathog 2015; 80:39-49. [PMID: 25708507 DOI: 10.1016/j.micpath.2015.02.007] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 11/19/2022]
Abstract
Oral diseases, such as dental caries and periodontal disease are directly linked with the ability of bacteria to form biofilm. The development of dental caries involves acidogenic and aciduric Gram-positive bacteria colonizing the supragingival biofilm (Streptococcus, Lactobacillus and Actinomycetes). Periodontal diseases have been linked to anaerobic Gram-negative bacteria forming a subgingival plaque (Porphyromonas gingivalis, Actinobacillus, Prevotella and Fusobacterium). Cells embedded in biofilm are up to 1000-fold more resistant to antibiotics compared to their planctonic ones. Several mechanisms have been proposed to explain biofilms drug resistance. Given the increased bacterial resistance to antibiotics currently used in dentistry, a great importance is given to natural compounds for the prevention of oral bacterial growth, adhesion and colonization. Over the past decade, interest in drugs derived from medicinal plants has markedly increased. It has been well documented that medicinal plants and natural compounds confer considerable antibacterial activity against various microorganisms including cariogenic and periodontal pathogens. This paper provides a review of the literature focusing on the studies on (i) biofilm in the oral cavity, (ii) drug resistance of bacterial biofilm and (iii) the potential use of plant extracts, essential oils and natural compounds as biofilm preventive agents in dentistry, involving their origin and their mechanism of biofilm inhibition.
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Affiliation(s)
- Bochra Kouidhi
- College of Applied Medical Sciences, Medical Laboratory Department, Yanbu, Taibah University, Saudi Arabia.
| | | | - Kamel Chaieb
- College of Sciences, Biology Department, Yanbu, Taibah University, Saudi Arabia
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Piras C, Soggiu A, Bonizzi L, Greco V, Ricchi M, Arrigoni N, Bassols A, Urbani A, Roncada P. Identification of immunoreactive proteins of Mycobacterium avium subsp. paratuberculosis. Proteomics 2015; 15:813-23. [PMID: 25404104 DOI: 10.1002/pmic.201400276] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 10/23/2014] [Accepted: 11/13/2014] [Indexed: 11/10/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the cause of a chronic enteritis of ruminants (bovine paratuberculosis (PTB)--Johne's disease) that is associated with enormous worldwide economic losses for the animal production. Diagnosis is based on observation of clinical signs, the detection of antibodies in milk or serum, or evaluation of bacterial culture from feces. The limit of these methods is that they are not able to detect the disease in the subclinical stage and are applicable only when the disease is already advanced. For this reason, the main purpose of this study is to use the MAP proteome to detect novel immunoreactive proteins that may be helpful for PTB diagnoses. 2DE and 2D immunoblotting of MAP proteins were performed using sera of control cattle and PTB-infected cattle in order to highlight the specific immunoreactive proteins. Among the assigned identifiers to immunoreactive spots it was found that most of them correspond to surface-located proteins while three of them have never been described before as antigens. The identification of these proteins improves scientific knowledge that could be useful for PTB diagnoses. The sequence of the identified protein can be used for the synthesis of immunoreactive peptides that could be screened for their immunoreaction against bovine sera infected with MAP. All MS data have been deposited in the ProteomeXchange consortium with identifier PXD001159 and DOI 10.6019/PXD001159.
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Siroski PA, Russi NB, Ortega HH, Formentini EA. In vitro evaluation of synergistic activity between ciprofloxacin and broad snouted caiman serum against Escherichia coli. Res Vet Sci 2014; 98:98-105. [PMID: 25468795 DOI: 10.1016/j.rvsc.2014.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 09/04/2014] [Accepted: 11/06/2014] [Indexed: 11/15/2022]
Abstract
The in vitro synergistic activity between ciprofloxacin and serum of broad snouted caiman on Escherichia coli was studied. The estimated MIC value of ciprofloxacin was 0.0188 µg/ml, and two assays of kill curve during 5 hours were performed: the first one in a standard culture medium and the second one in the presence of caiman serum. Different concentrations of ciprofloxacin were tested. Ciprofloxacin showed higher values of bacterial elimination rate in the presence of caiman serum in all concentrations tested. The combined activity of sub-inhibitory concentrations of ciprofloxacin and the humoral immune factors present in caiman serum determined an increase in the bacterial elimination observed in this assay. We suggest that the antibacterial activity of complement and natural antibodies present in caiman serum, which can bind to both Gram-negative and Gram-positive bacteria and acting through the classical complement pathway, can inhibit bacterial growth of Escherichia coli by lysis.
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Affiliation(s)
- P A Siroski
- ICIVET-CONICET-Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P. Kreder 2805, CP S3080HOF Esperanza, Santa Fe, Argentina; Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC-UNL/MASPyMA) Departamento de ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral, Ciudad Universitaria -Paraje El Pozo, CP S3000 Santa Fe, Argentina.
| | - N B Russi
- Laboratorio de Bacteriología del Hospital de Salud Animal-Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P. Kreder 2805, CP S3080HOF Esperanza, Santa Fe, Argentina
| | - H H Ortega
- ICIVET-CONICET-Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P. Kreder 2805, CP S3080HOF Esperanza, Santa Fe, Argentina
| | - E A Formentini
- Cátedra de Farmacología-Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P. Kreder 2805, CP S3080HOF Esperanza, Santa Fe, Argentina
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Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts. J Biosci 2014; 39:631-42. [DOI: 10.1007/s12038-014-9453-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Zhang L, Wen Y, Li Y, Wei X, Yan X, Wen X, Wu R, Huang X, Huang Y, Yan Q, Liu M, Cao S. Comparative proteomic analysis of the membrane proteins of two Haemophilus parasuis strains to identify proteins that may help in habitat adaptation and pathogenesis. Proteome Sci 2014; 12:38. [PMID: 25057263 PMCID: PMC4107730 DOI: 10.1186/1477-5956-12-38] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/29/2014] [Indexed: 01/03/2023] Open
Abstract
Background Haemophilus parasuis is the causative agent of Glässer’s disease characterized by polyserositis, arthritis, and meningitis in pig, leading to serious economic loss. Despite many years of study, virulence factors and the mechanisms of the entire infection process remain largely unclear. So two-dimensional gel electrophoresis and mass spectrometry were used to search for distinctions at the membrane protein expression level between two H. parasuis isolates aimed at uncovering some proteins potentially involved in habitat adaption and pathogenesis. Results A comparative proteomic approach combining two-dimensional gel electrophoresis with mass spectrometry and tandem mass spectrometry was employed to explore the differences among membrane proteomes of a virulent Haemophilus parasuis strain isolated from the lung of a diseased pig and an avirulent strain isolated from the nasal swab of a healthy pig. Differentially expressed protein spots identified by mass spectrometry were annotated and analyzed by bioinformatic interpretation. The mRNA level was determined by quantitative real-time PCR. Proteins representing diverse functional activities were identified. Among them, the tonB-dependent siderophore receptor was a new discovery highlighted for its activity in iron uptake. In addition, periplasmic serine protease and putrescine/spermidine ABC transporter substrate-binding protein were given focus because of their virulence potential. This study revealed that the differentially expressed proteins were important in either the habitat adaption or pathogenesis of H. parasuis. Conclusions The outcome demonstrated the presence of some proteins which raise the speculation for their importance in helping in habitat adaption or pathogenesis within the host.
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Affiliation(s)
- Luhua Zhang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Yiping Wen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Ying Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Xingliang Wei
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Xuefeng Yan
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Xintian Wen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Rui Wu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Xiaobo Huang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Yong Huang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Qigui Yan
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Mafeng Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Sanjie Cao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
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Gonçalves A, Poeta P, Monteiro R, Marinho C, Silva N, Guerra A, Petrucci-Fonseca F, Rodrigues J, Torres C, Vitorino R, Domingues P, Igrejas G. Comparative proteomics of an extended spectrum β-lactamase producing Escherichia coli strain from the Iberian wolf. J Proteomics 2014; 104:80-93. [PMID: 24631823 DOI: 10.1016/j.jprot.2014.02.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/15/2014] [Accepted: 02/25/2014] [Indexed: 12/13/2022]
Abstract
UNLABELLED The Iberian wolf (Canis lupus signatus) is an endangered species native to the Iberian Peninsula. Due to their predatory and wild nature, these wolves serve as important indicators of environmental contamination by antimicrobial-resistant bacteria. β-Lactam antibiotics like cefotaxime are the most commonly used antibacterial agents. Bacterial resistance to these antibiotics occurs predominantly through enzymatic inactivation by extended-spectrum beta-lactamases. Escherichia coli strain WA57, isolated from Iberian wolf feces, is a cefotaxime-resistant strain that produces extended-spectrum beta-lactamases. In this study, using 2D-GE combined with MS and bioinformatics, we report significant differences in the abundance of 40 protein spots (p<0.01) from the extracellular, periplasmic, cytoplasmic, and membrane sub-proteomes and the whole-cell proteome of WA57 exposed and non-exposed to cefotaxime. A total of 315 protein spots were collected for protein identification. The comparative proteomics presented gives an overview of the complex changes in expression and metabolism that occur when WA57 is stressed with cefotaxime. Abundance of chaperone, porin and export proteins is particularly affected showing that the stress response and transport functions might directly influence the antibiotic resistance of this strain. BIOLOGICAL SIGNIFICANCE This study highlights the importance of proteomics in detecting protein expression changes in bacterial strains exposed to stress such as that caused by cefotaxime. This approach might help us understand which pathways form barriers for antibiotics. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- A Gonçalves
- Institute for Biotechnology and Bioengineering, Center of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Center for Animal Science and Veterinary, Vila Real, Portugal; Department of Veterinary Science, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - P Poeta
- Center for Animal Science and Veterinary, Vila Real, Portugal; Department of Veterinary Science, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - R Monteiro
- Institute for Biotechnology and Bioengineering, Center of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Center for Animal Science and Veterinary, Vila Real, Portugal; Department of Veterinary Science, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - C Marinho
- Institute for Biotechnology and Bioengineering, Center of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Center for Animal Science and Veterinary, Vila Real, Portugal; Department of Veterinary Science, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - N Silva
- Center for Animal Science and Veterinary, Vila Real, Portugal
| | - A Guerra
- Department of Animal Biology, Centre for Environmental Biology, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
| | - F Petrucci-Fonseca
- Department of Animal Biology, Centre for Environmental Biology, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
| | - J Rodrigues
- Center for Animal Science and Veterinary, Vila Real, Portugal; Department of Veterinary Science, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - C Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, Spain
| | - R Vitorino
- Chemistry Department, University of Aveiro, Aveiro, Portugal
| | - P Domingues
- Chemistry Department, University of Aveiro, Aveiro, Portugal
| | - G Igrejas
- Institute for Biotechnology and Bioengineering, Center of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.
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Panjkovich A, Gibert I, Daura X. antibacTR: dynamic antibacterial-drug-target ranking integrating comparative genomics, structural analysis and experimental annotation. BMC Genomics 2014; 15:36. [PMID: 24438389 PMCID: PMC3932961 DOI: 10.1186/1471-2164-15-36] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/11/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Development of novel antibacterial drugs is both an urgent healthcare necessity and a partially neglected field. The last decades have seen a substantial decrease in the discovery of novel antibiotics, which combined with the recent thrive of multi-drug-resistant pathogens have generated a scenario of general concern. The procedures involved in the discovery and development of novel antibiotics are economically challenging, time consuming and lack any warranty of success. Furthermore, the return-on-investment for an antibacterial drug is usually marginal when compared to other therapeutics, which in part explains the decrease of private investment. RESULTS In this work we present antibacTR, a computational pipeline designed to aid researchers in the selection of potential drug targets, one of the initial steps in antibacterial-drug discovery. The approach was designed and implemented as part of two publicly funded initiatives aimed at discovering novel antibacterial targets, mechanisms and drugs for a priority list of Gram-negative pathogens: Acinetobacter baumannii, Escherichia coli, Helicobacter pylori, Pseudomonas aeruginosa and Stenotrophomonas maltophilia. However, at present this list has been extended to cover a total of 74 fully sequenced Gram-negative pathogens. antibacTR is based on sequence comparisons and queries to multiple databases (e.g. gene essentiality, virulence factors) to rank proteins according to their potential as antibacterial targets. The dynamic ranking of potential drug targets can easily be executed, customized and accessed by the user through a web interface which also integrates computational analyses performed in-house and visualizable on-site. These include three-dimensional modeling of protein structures and prediction of active sites among other functionally relevant ligand-binding sites. CONCLUSIONS Given its versatility and ease-of-use at integrating both experimental annotation and computational analyses, antibacTR may effectively assist microbiologists, medicinal-chemists and other researchers working in the field of antibacterial drug-discovery. The public web-interface for antibacTR is available at 'http://bioinf.uab.cat/antibactr'.
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Affiliation(s)
| | | | - Xavier Daura
- Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain.
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Bernaschi P, Del Chierico F, Petrucca A, Argentieri A, Ciofi Degli Atti M, Ciliento G, Carletti M, Muraca M, Locatelli F, Putignani L. Microbial tracking of multidrug-resistant Klebsiella pneumoniae isolates in a pediatric hospital setting. Int J Immunopathol Pharmacol 2013; 26:463-72. [PMID: 23755761 DOI: 10.1177/039463201302600219] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We investigated the clonal relatedness of seven multi-drug-resistant (MDR) Klebsiella pneumoniae isolates, as well as three susceptible K. pneumoniae isolates collected during hospital outbreaks and outbreak-related microbiological surveillance, respectively. The relatedness among K. pneumoniae isolates was assessed by pulsed field gel electrophoresis (PFGE) and automated repetitive-sequence-based PCR (rep-PCR) genotyping and the results were compared to a proteomic phenotyping performed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). All typing methods agreed on the generation of three different clusters of K. pneumoniae isogenetic/related MDR strains. After strengthening hospital infection control measures, no other spreading events involving MDR-K. pneumoniae were reported until the end of the observation period. This preliminary investigation suggests that, in a hierarchical approach to bacterial typing, MALDI-TOF MS proteome profiling might offer a fast and valuable preliminary screening tool able to support microbiologists during nosocomial outbreak surveys.
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Affiliation(s)
- P Bernaschi
- Unit of Microbiology, Bambino Gesu Childrens Hospital, IRCCS, Rome, Italy
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Regev-Shoshani G, Church JS, Cook NJ, Schaefer AL, Miller C. Prophylactic nitric oxide treatment reduces incidence of bovine respiratory disease complex in beef cattle arriving at a feedlot. Res Vet Sci 2013; 95:606-11. [PMID: 23850382 DOI: 10.1016/j.rvsc.2013.06.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 04/05/2013] [Accepted: 06/18/2013] [Indexed: 11/16/2022]
Abstract
Bovine respiratory disease complex (BRDc), is a challenging multi-factorial health issue caused by viral/bacterial pathogens and stressors linked with the transport and mixing of cattle, negatively impacting the cattle feedlot industry. Nitric oxide (NO) is a naturally occurring molecule with antimicrobial attributes. This study tests whether NO can prevent the symptoms associated with BRDc. Eighty-five, crossbred, multiple-sourced, commingled commercial weaned beef calves were monitored and scored for temperature, white blood count, clinical score, hematology, cortisol levels and neutrophil/lymphocyte ratio. NO treatment or placebo were given once on arrival to the stockyard. After one week 87.5% of sick animals were from the control while 12.5% from treatment groups and after two weeks 72% and 28% respectively. Treatment was shown to be safe, causing neither distress nor adverse effects on the animals. These data show that NO treatment on arrival to the feedlot significantly decreased the incidence of BRDc in this study.
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Affiliation(s)
- G Regev-Shoshani
- Faculty of Medicine, Respiratory Division, University of British Columbia, Vancouver, British Columbia, Canada
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Gabani P, Prakash D, Singh OV. Emergence of antibiotic-resistant extremophiles (AREs). Extremophiles 2012; 16:697-713. [PMID: 22907125 DOI: 10.1007/s00792-012-0475-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 08/02/2012] [Indexed: 12/14/2022]
Abstract
Excessive use of antibiotics in recent years has produced bacteria that are resistant to a wide array of antibiotics. Several genetic and non-genetic elements allow microorganisms to adapt and thrive under harsh environmental conditions such as lethal doses of antibiotics. We attempt to classify these microorganisms as antibiotic-resistant extremophiles (AREs). AREs develop strategies to gain greater resistance to antibiotics via accumulation of multiple genes or plasmids that harbor genes for multiple drug resistance (MDR). In addition to their altered expression of multiple genes, AREs also survive by producing enzymes such as penicillinase that inactivate antibiotics. It is of interest to identify the underlying molecular mechanisms by which the AREs are able to survive in the presence of wide arrays of high-dosage antibiotics. Technologically, "omics"-based approaches such as genomics have revealed a wide array of genes differentially expressed in AREs. Proteomics studies with 2DE, MALDI-TOF, and MS/MS have identified specific proteins, enzymes, and pumps that function in the adaptation mechanisms of AREs. This article discusses the molecular mechanisms by which microorganisms develop into AREs and how "omics" approaches can identify the genetic elements of these adaptation mechanisms. These objectives will assist the development of strategies and potential therapeutics to treat outbreaks of pathogenic microorganisms in the future.
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Affiliation(s)
- Prashant Gabani
- Division of Biological and Health Sciences, University of Pittsburgh, 300 Campus Drive, Bradford, PA 16701, USA
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35
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Stepanenko AA, Kavsan VM. Evolutionary karyotypic theory of cancer versus conventional cancer gene mutation theory. ACTA ACUST UNITED AC 2012. [DOI: 10.7124/bc.000059] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- A. A. Stepanenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - V. M. Kavsan
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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