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Olymon K, Yadav M, Teronpi V, Kumar A. Unravelling the genomic secrets of bacterial fish pathogens: a roadmap to aquaculture sustainability. Mol Biol Rep 2024; 51:364. [PMID: 38407655 DOI: 10.1007/s11033-024-09331-w] [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: 10/24/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
In the field of aquaculture, bacterial pathogens pose significant challenges to fish health and production. Advancements in genomic technologies have revolutionized our understanding of bacterial fish pathogens and their interactions with their host species. This review explores the application of genomic approaches in the identification, classification, and characterization of bacterial fish pathogens. Through an extensive analysis of the literature, we have compiled valuable data on 79 bacterial fish pathogens spanning 13 different phyla, encompassing their whole genome sequences. By leveraging high-throughput sequencing techniques, researchers have gained valuable insights into the genomic makeup of these pathogens, enabling a deeper understanding of their virulence factors and mechanisms of host interaction. Furthermore, genomic approaches have facilitated the discovery of potential vaccine and drug targets, opening up new avenues for the development of effective interventions against fish pathogens. Additionally, the utilization of genomics in fish disease resistance and control in aquaculture has shown promising results, enabling the identification of genetic markers associated with disease resistance traits. This review highlights the significant contributions of genomics to the field of fish pathogen research and underscores its potential for improving disease management strategies and enhancing the sustainability of aquaculture practices.
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Affiliation(s)
- Kaushika Olymon
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Mohit Yadav
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Valentina Teronpi
- Department, of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, Assam, 784184, India.
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India.
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Liu C, Zhao C, Wang L, Du X, Zhu L, Wang J, Mo Kim Y, Wang J. Biodegradation mechanism of chlorpyrifos by Bacillus sp. H27: Degradation enzymes, products, pathways and whole genome sequencing analysis. ENVIRONMENTAL RESEARCH 2023; 239:117315. [PMID: 37805180 DOI: 10.1016/j.envres.2023.117315] [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: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Chlorpyrifos (CP) is a pesticide widely used in agricultural production. However, excessive use of CP is risky for human health and the ecological environment. Microbial remediation has become a research hotspot of environmental pollution control. In this study, the effective CP-degrading strain H27 (Bacillus cereus) was screened from farmland soil, and the degradation ratio was more than 80%. Then, the degradation mechanism was discussed in terms of enzymes, pathways, products and genes, and the mechanism was improved in terms of cell motility, secretory transport system and biofilm formation. The key CP-degrading enzymes were mainly intracellular enzymes (IE), and the degradation ratio reached 49.6% within 30 min. The optimal pH for IE was 7.0, and the optimal temperature was 25 °C. Using DFT and HPLC‒MS analysis, it was found that degradation mainly involved oxidation, hydrolysis and other reactions, and 3 degradation pathways and 14 products were identified, among which TCP (3,5,6-trichloro-2-pyridinol) was the main primary degradation product in addition to small molecules such as CO2 and H2O. Finally, the whole genome of strain H27 was sequenced, and the related degrading genes and enzymes were investigated to improve the metabolic pathways. Strain H27 had perfect genes related to flagellar assembly and chemotaxis and tended to tolerate CP. Moreover, it can secrete esterase, phosphatase and other substances, which can form biofilms and degrade CP in the environment. In addition, CP enters the cell under the action of permeases or transporters, and it is metabolized by IE. The degradation mechanism of CP by strain H27 is speculated in this study, which provided a theoretical basis for enriching CP-degrading bacteria resources, improving degradation metabolic pathways and mechanisms, and applying strain H27 to environmental pollution remediation.
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Affiliation(s)
- Changrui Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Changyu Zhao
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Lanjun Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Xiaomin Du
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Lusheng Zhu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Jun Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Jinhua Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
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Forecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches. mSystems 2022; 7:e0037822. [PMID: 35862809 PMCID: PMC9426533 DOI: 10.1128/msystems.00378-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major human and animal pathogen, colonizing diverse ecological niches within its hosts. Predicting whether an isolate will infect a specific host and its subsequent clinical fate remains unknown. In this study, we investigated the S. aureus pangenome using a curated set of 356 strains, spanning a wide range of hosts, origins, and clinical display and antibiotic resistance profiles. We used genome-wide association study (GWAS) and random forest (RF) algorithms to discriminate strains based on their origins and clinical sources. Here, we show that the presence of sak and scn can discriminate strains based on their host specificity, while other genes such as mecA are often associated with virulent outcomes. Both GWAS and RF indicated the importance of intergenic regions (IGRs) and coding DNA sequence (CDS) but not sRNAs in forecasting an outcome. Additional transcriptomic analyses performed on the most prevalent clonal complex 8 (CC8) clonal types, in media mimicking nasal colonization or bacteremia, indicated three RNAs as potential RNA markers to forecast infection, followed by 30 others that could serve as infection severity predictors. Our report shows that genetic association and transcriptomics are complementary approaches that will be combined in a single analytical framework to improve our understanding of bacterial pathogenesis and ultimately identify potential predictive molecular markers. IMPORTANCE Predicting the outcome of bacterial colonization and infections, based on extensive genomic and transcriptomic data from a given pathogen, would be of substantial help for clinicians in treating and curing patients. In this report, genome-wide association studies and random forest algorithms have defined gene combinations that differentiate human from animal strains, colonization from diseases, and nonsevere from severe diseases, while it revealed the importance of IGRs and CDS, but not small RNAs (sRNAs), in anticipating an outcome. In addition, transcriptomic analyses performed on the most prevalent clonal types, in media mimicking either nasal colonization or bacteremia, revealed significant differences and therefore potent RNA markers. Overall, the use of both genomic and transcriptomic data in a single analytical framework can enhance our understanding of bacterial pathogenesis.
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Gaidar D, Jonas A, Akulenko R, Ruffing U, Herrmann M, Helms V, von Müller L. Analysis of the dynamics of Staphylococcus aureus binding to white blood cells using whole blood assay and geno-to-pheno mapping. Int J Med Microbiol 2020; 310:151411. [DOI: 10.1016/j.ijmm.2020.151411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/02/2019] [Accepted: 02/03/2020] [Indexed: 12/28/2022] Open
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Giulieri SG, Tong SYC, Williamson DA. Using genomics to understand meticillin- and vancomycin-resistant Staphylococcus aureus infections. Microb Genom 2020; 6:e000324. [PMID: 31913111 PMCID: PMC7067033 DOI: 10.1099/mgen.0.000324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/12/2019] [Indexed: 12/15/2022] Open
Abstract
Resistance to meticillin and vancomycin in Staphylococcus aureus significantly complicates the management of severe infections like bacteraemia, endocarditis or osteomyelitis. Here, we review the molecular mechanisms and genomic epidemiology of resistance to these agents, with a focus on how genomics has provided insights into the emergence and evolution of major meticillin-resistant S. aureus clones. We also provide insights on the use of bacterial whole-genome sequencing to inform management of S. aureus infections and for control of transmission at the hospital and in the community.
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Affiliation(s)
- Stefano G. Giulieri
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Infectious Disease Department, Austin Health, Melbourne, Australia
| | - Steven Y. C. Tong
- Victorian Infectious Disease Service, Royal Melbourne Hospital, and Doherty Department University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Menzies School of Health Research, Darwin, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
- Microbiology, Royal Melbourne Hospital, Melbourne, Australia
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Ermert D, Ram S, Laabei M. The hijackers guide to escaping complement: Lessons learned from pathogens. Mol Immunol 2019; 114:49-61. [PMID: 31336249 DOI: 10.1016/j.molimm.2019.07.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 02/07/2023]
Abstract
Pathogens that invade the human host are confronted by a multitude of defence mechanisms aimed at preventing colonization, dissemination and proliferation. The most frequent outcome of this interaction is microbial elimination, in which the complement system plays a major role. Complement, an essential feature of the innate immune machinery, rapidly identifies and marks pathogens for efficient removal. Consequently, this creates a selective pressure for microbes to evolve strategies to combat complement, permitting host colonization and access to resources. All successful pathogens have developed mechanisms to resist complement activity which are intimately aligned with their capacity to cause disease. In this review, we describe the successful methods various pathogens use to evade complement activation, shut down inflammatory signalling through complement, circumvent opsonisation and override terminal pathway lysis. This review summarizes how pathogens undermine innate immunity: 'The Hijackers Guide to Complement'.
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Affiliation(s)
- David Ermert
- Department of Preclinical Research, BioInvent International AB, Lund, Sweden; Department of Translational Medicine, Division of Medical Protein Chemistry, Lund University, Malmö, Sweden
| | - Sanjay Ram
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Maisem Laabei
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
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7
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Ghosh S, Kanwar P, Jha G. Identification of candidate pathogenicity determinants of Rhizoctonia solani AG1-IA, which causes sheath blight disease in rice. Curr Genet 2017; 64:729-740. [PMID: 29196814 DOI: 10.1007/s00294-017-0791-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 01/04/2023]
Abstract
Sheath blight disease is one of the predominant diseases of rice and it is caused by the necrotrophic fungal pathogen Rhizoctonia solani. The mechanistic insight about its widespread success as a broad host range pathogen is limited. In this study, we endeavor to identify pathogenicity determinants of R. solani during infection process in rice. Through RNAseq analysis, we identified a total of 65 and 232 R. solani (strain BRS1) genes to be commonly upregulated in three different rice genotypes (PB1, Tetep, and TP309) at establishment and necrotrophic phase, respectively. The induction of genes encoding extracellular protease, ABC transporter, and transcription factors were notable during establishment phase. While during necrotrophic phase, several CAZymes, sugar transporters, cellular metabolism, and protein degradation-related genes were prominently induced. We have also identified few putative secreted effector encoding genes that were upregulated during pathogenesis. The qPCR analysis further validated the phase-specific expression dynamics of some selected putative effectors and pathogenicity-associated genes. Overall, the present study reports identification of key genes and processes that might be crucial for R. solani pathogenesis. The ability to effectively damage host cell wall and survive in hostile plant environment by managing oxidative stress, cytotoxic compounds, etc. is being proposed to be important for pathogenesis of R. solani in rice. The functional characterization of these genes would provide key insights about this important pathosystem and facilitate development of strategies to control this devastating disease.
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Affiliation(s)
- Srayan Ghosh
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Poonam Kanwar
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Buvelot H, Posfay-Barbe KM, Linder P, Schrenzel J, Krause KH. Staphylococcus aureus, phagocyte NADPH oxidase and chronic granulomatous disease. FEMS Microbiol Rev 2017; 41:139-157. [PMID: 27965320 DOI: 10.1093/femsre/fuw042] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2016] [Indexed: 11/14/2022] Open
Abstract
Dysfunction of phagocytes is a relevant risk factor for staphylococcal infection. The most common hereditary phagocyte dysfunction is chronic granulomatous disease (CGD), characterized by impaired generation of reactive oxygen species (ROS) due to loss of function mutations within the phagocyte NADPH oxidase NOX2. Phagocytes ROS generation is fundamental to eliminate pathogens and to regulate the inflammatory response to infection. CGD is characterized by recurrent and severe bacterial and fungal infections, with Staphylococcus aureus as the most frequent pathogen, and skin and lung abscesses as the most common clinical entities. Staphylococcus aureus infection may occur in virtually any human host, presumably because of the many virulence factors of the bacterium. However, in the presence of functional NOX2, staphylococcal infections remain rare and are mainly linked to breaches of the skin barrier. In contrast, in patients with CGD, S. aureus readily survives and frequently causes clinically apparent disease. Astonishingly, little is known why S. aureus, which possesses a wide range of antioxidant enzymes (e.g. catalase, SOD), is particularly sensitive to control through NOX2. In this review, we will evaluate the discovery of CGD and our present knowledge of the role of NOX2 in S. aureus infection.
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Affiliation(s)
- Helene Buvelot
- Division of General Internal Medicine, Geneva University Hospitals, CH-1211 Geneva 4, Switzerland
| | - Klara M Posfay-Barbe
- Paediatric Infectious Diseases Unit, Department of Paediatrics, University Hospitals of Geneva, 1205 Geneva and Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Patrick Linder
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Jacques Schrenzel
- Divisions of Infectious Diseases and Laboratory Medicine, Geneva University Hospitals, CH-1211 Geneva 4, Switzerland
| | - Karl-Heinz Krause
- Divisions of Infectious Diseases and Laboratory Medicine, Geneva University Hospitals, CH-1211 Geneva 4, Switzerland.,Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
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Fleury OM, McAleer MA, Feuillie C, Formosa-Dague C, Sansevere E, Bennett DE, Towell AM, McLean WHI, Kezic S, Robinson DA, Fallon PG, Foster TJ, Dufrêne YF, Irvine AD, Geoghegan JA. Clumping Factor B Promotes Adherence of Staphylococcus aureus to Corneocytes in Atopic Dermatitis. Infect Immun 2017; 85:e00994-16. [PMID: 28373353 PMCID: PMC5442637 DOI: 10.1128/iai.00994-16] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/21/2017] [Indexed: 12/31/2022] Open
Abstract
Staphylococcus aureus skin infection is a frequent and recurrent problem in children with the common inflammatory skin disease atopic dermatitis (AD). S. aureus colonizes the skin of the majority of children with AD and exacerbates the disease. The first step during colonization and infection is bacterial adhesion to the cornified envelope of corneocytes in the outer layer, the stratum corneum. Corneocytes from AD skin are structurally different from corneocytes from normal healthy skin. The objective of this study was to identify bacterial proteins that promote the adherence of S. aureus to AD corneocytes. S. aureus strains from clonal complexes 1 and 8 were more frequently isolated from infected AD skin than from the nasal cavity of healthy children. AD strains had increased ClfB ligand binding activity compared to normal nasal carriage strains. Adherence of single S. aureus bacteria to corneocytes from AD patients ex vivo was studied using atomic force microscopy. Bacteria expressing ClfB recognized ligands distributed over the entire corneocyte surface. The ability of an isogenic ClfB-deficient mutant to adhere to AD corneocytes compared to that of its parent clonal complex 1 clinical strain was greatly reduced. ClfB from clonal complex 1 strains had a slightly higher binding affinity for its ligand than ClfB from strains from other clonal complexes. Our results provide new insights into the first step in the establishment of S. aureus colonization in AD patients. ClfB is a key adhesion molecule for the interaction of S. aureus with AD corneocytes and represents a target for intervention.
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Affiliation(s)
- Orla M Fleury
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Maeve A McAleer
- Clinical Medicine, Trinity College Dublin, Dublin, Ireland
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
- Paediatric Dermatology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Cécile Feuillie
- Institute of Life Sciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Cécile Formosa-Dague
- Institute of Life Sciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Emily Sansevere
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Désirée E Bennett
- Epidemiology and Molecular Biology Unit, Temple Street Children's University Hospital, Dublin, Ireland
| | - Aisling M Towell
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - W H Irwin McLean
- Dermatology and Genetic Medicine, University of Dundee, Dundee, United Kingdom
| | - Sanja Kezic
- Coronel Institute of Occupational Health, Academic Medical Center, Amsterdam, The Netherlands
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Padraic G Fallon
- Clinical Medicine, Trinity College Dublin, Dublin, Ireland
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Timothy J Foster
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Yves F Dufrêne
- Institute of Life Sciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Wavre, Belgium
| | - Alan D Irvine
- Clinical Medicine, Trinity College Dublin, Dublin, Ireland
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
- Paediatric Dermatology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Joan A Geoghegan
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
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Cansizoglu MF, Toprak E. Fighting against evolution of antibiotic resistance by utilizing evolvable antimicrobial drugs. Curr Genet 2017; 63:973-976. [PMID: 28497241 DOI: 10.1007/s00294-017-0703-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/03/2017] [Accepted: 05/05/2017] [Indexed: 12/24/2022]
Abstract
Antibiotic resistance is a worldwide public health problem (Bush et al. in Nat Rev Microbiol 9:894-896, 2011). The lack of effective therapies against resistant bacteria globally leads to prolonged treatments, increased mortality, and inflating health care costs (Oz et al. in Mol Biol Evol 31:2387-2401, 2014; Martinez in Science 321:365-367, 2008; Lipsitch et al. in Proc Natl Acad Sci USA 97:1938-1943, 2000; Taubes in Science 321:356-361, 2008; Laxminarayan et al. in Lancet, 2016; Laxminarayan et al. in Lancet Infect Dis 13:1057-1098, 2013). Current efforts towards a solution of this problem can be boiled down to two main strategies: (1) developing of new antimicrobial agents and (2) searching for smart strategies that can restore or preserve the efficacy of existing antimicrobial agents. In this short review article, we discuss the need for evolvable antimicrobial agents, focusing on a new antimicrobial technology that utilizes peptide-conjugated phosphorodiamidate morpholino oligomers to inhibit the growth of pathogenic bacteria by targeting bacterial genes.
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Affiliation(s)
- Mehmet Fatih Cansizoglu
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Erdal Toprak
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Abstract
The community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) epidemic in the United States is largely attributable to the meteoric rise of a single clone, referred to as USA300. This strain not only spread across the United States in just a few years to become the predominant cause of staphylococcal disease, but it also appears to have increased the overall number of skin and soft-tissue infections (SSTIs), increasing the overall disease burden. While USA300 still constitutes a major public health burden, its prevalence may be decreasing in some parts of the United States. Other than an epidemic in South America due to a closely related strain, USA300 also seems to have been largely unable to establish itself as an endemic infection in other geographic locations. While there have been several hypotheses put forward to explain the enormous success of USA300, the reasons for its failures and its potential fall remain obscure. Far from being unique to USA300, the rise and fall of specific clones of S. aureus in human populations seems to be a common process that has occurred multiple times and in multiple locations. This review charts the rise of USA300 and the evidence that suggests that it may be in decline, and it considers how best to understand the future spread, containment, and possible extinction of CA-MRSA.
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Affiliation(s)
- Paul J Planet
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York.,Pediatric Infectious Disease Division, Children's Hospital of Philadelphia.,Perelman School of Medicine, University of Pennsylvania, Philadelphia
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12
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Garrido-Cardenas JA, Manzano-Agugliaro F. The metagenomics worldwide research. Curr Genet 2017; 63:819-829. [PMID: 28401295 DOI: 10.1007/s00294-017-0693-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/20/2022]
Abstract
Metagenomics is the technique, or set of techniques, whose main objective is to determine the microbial population that can be found in a determined environment, studied in the context of its community. For this, it uses the techniques of massive sequencing, or next generation sequencing, due to the difficulties presented by traditional techniques when trying to transfer all the microorganisms present in a given environment to the laboratory. Metagenomics is a newly created technique, which was born at the beginning of the twenty-first century, and since then the interest of the world scientific community in fields as diverse as medicine, biotechnology, agriculture or genetics has not left to grow. In this article, the authors make a historical review of the metagenomics, analyze and evaluate the different massive sequencing platforms used for metagenomic assays, review the current literature on this subject and advance future problems with which researchers who decide to go deeper in this field could find. In this way, the prior knowledge of the researcher will facilitate the approach of his research.
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13
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Bayliss SC, Verner-Jeffreys DW, Bartie KL, Aanensen DM, Sheppard SK, Adams A, Feil EJ. The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens. Front Microbiol 2017; 8:121. [PMID: 28217117 PMCID: PMC5290457 DOI: 10.3389/fmicb.2017.00121] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/17/2017] [Indexed: 01/23/2023] Open
Abstract
Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools.
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Affiliation(s)
- Sion C Bayliss
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath Bath, UK
| | | | - Kerry L Bartie
- Institute of Aquaculture, University of Stirling Stirling, UK
| | - David M Aanensen
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College LondonLondon, UK; The Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusCambridge, UK
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath Bath, UK
| | - Alexandra Adams
- Institute of Aquaculture, University of Stirling Stirling, UK
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath Bath, UK
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