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Investigation of Virulence Genes Detected in Antimicrobial-Resistance Pathogens Isolates for Five Countries across the World. Processes (Basel) 2020. [DOI: 10.3390/pr8121589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A large portion of annual deaths worldwide are due to infections caused by disease-causing pathogens. These pathogens contain virulence genes, which encode mechanisms that facilitate infection and microbial survival in hosts. More recently, antimicrobial resistance (AMR) genes, also found in these pathogens, have become an increasingly large issue. While the National Center for Biotechnology Information (NCBI) Pathogen Detection Isolates Browser (NPDIB) database has been compiling genes involved in microbial virulence and antimicrobial resistance through isolate samples, few studies have identified the genes primarily responsible for virulence and compared them to those responsible for AMR. This study performed the first multivariate statistical analysis of the multidimensional NPDIB data to identify the major virulence genes from historical pathogen isolates for Australia, China, South Africa, UK, and US—the largely populated countries from five of the six major continents. The important virulence genes were then compared with the AMR genes to study whether there is correlation between their occurrences. Among the significant genes and pathogens associated with virulence, it was found that the genes fdeC, iha, iss, iutA, lpfA, sslE, ybtP, and ybtQ are shared amongst all five countries. The pathogens E. coli and Shigella, Salmonella enterica, and Klebsiella pneumoniae mostly contained these genes and were common among four of the five studied countries. Additionally, the trend of virulence was investigated by plotting historical occurrences of gene and pathogen frequency in the annual samples. These plots showed that the trends of E. coli and Shigella and Salmonella enterica were similar to the trends of certain virulence genes, confirming the two pathogens do indeed carry important virulence genes. While the virulence genes in the five countries are not significantly different, the US and the UK share the largest amount of important virulence genes. The plots from principal component analysis and hierarchical clustering show that the important virulence and AMR genes were not significantly correlated, with only few genes from both types of genes clustered into the same groups.
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Inhibition of Protein Secretion in Escherichia coli and Sub-MIC Effects of Arylomycin Antibiotics. Antimicrob Agents Chemother 2019; 63:AAC.01253-18. [PMID: 30420476 DOI: 10.1128/aac.01253-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/04/2018] [Indexed: 12/31/2022] Open
Abstract
At sufficient concentrations, antibiotics effectively eradicate many bacterial infections. However, during therapy, bacteria are unavoidably exposed to lower antibiotic concentrations, and sub-MIC exposure can result in a wide variety of other effects, including the induction of virulence, which can complicate therapy, or horizontal gene transfer (HGT), which can accelerate the spread of resistance genes. Bacterial type I signal peptidase (SPase) is an essential protein that acts at the final step of the general secretory pathway. This pathway is required for the secretion of many proteins, including many required for virulence, and the arylomycins are a class of natural product antibiotics that target SPase. Here, we investigated the consequences of exposing Escherichia coli cultures to sub-MIC levels of an arylomycin. Using multidimensional protein identification technology mass spectrometry, we found that arylomycin treatment inhibits the proper extracytoplasmic localization of many proteins, both those that appear to be SPase substrates and several that do not. The identified proteins are involved in a broad range of extracytoplasmic processes and include a number of virulence factors. The effects of arylomycin on several processes required for virulence were then individually examined, and we found that, at even sub-MIC levels, the arylomycins potently inhibit flagellation, motility, biofilm formation, and the dissemination of antibiotic resistance via HGT. Thus, we conclude that the arylomycins represent promising novel therapeutics with the potential to eradicate infections while simultaneously reducing virulence and the dissemination of resistance.
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Jaiswal S, Jadhav PV, Jasrotia RS, Kale PB, Kad SK, Moharil MP, Dudhare MS, Kheni J, Deshmukh AG, Mane SS, Nandanwar RS, Penna S, Manjaya JG, Iquebal MA, Tomar RS, Kawar PG, Rai A, Kumar D. Transcriptomic signature reveals mechanism of flower bud distortion in witches'-broom disease of soybean (Glycine max). BMC PLANT BIOLOGY 2019; 19:26. [PMID: 30646861 PMCID: PMC6332543 DOI: 10.1186/s12870-018-1601-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 12/12/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Soybean (Glycine max L. Merril) crop is major source of edible oil and protein for human and animals besides its various industrial uses including biofuels. Phytoplasma induced floral bud distortion syndrome (FBD), also known as witches' broom syndrome (WBS) has been one of the major biotic stresses adversely affecting its productivity. Transcriptomic approach can be used for knowledge discovery of this disease manifestation by morpho-physiological key pathways. RESULTS We report transcriptomic study using Illumina HiSeq NGS data of FBD in soybean, revealing 17,454 differentially expressed genes, 5561 transcription factors, 139 pathways and 176,029 genic region putative markers single sequence repeats, single nucleotide polymorphism and Insertion Deletion. Roles of PmbA, Zn-dependent protease, SAP family and auxin responsive system are described revealing mechanism of flower bud distortion having abnormalities in pollen, stigma development. Validation of 10 randomly selected genes was done by qPCR. Our findings describe the basic mechanism of FBD disease, right from sensing of phytoplasma infection by host plant triggering molecular signalling leading to mobilization of carbohydrate and protein, phyllody, abnormal pollen development, improved colonization of insect in host plants to spread the disease. Study reveals how phytoplasma hijacks metabolic machinery of soybean manifesting FBD. CONCLUSIONS This is the first report of transcriptomic signature of FBD or WBS disease of soybean revealing morphological and metabolic changes which attracts insect for spread of disease. All the genic region putative markers may be used as genomic resource for variety improvement and new agro-chemical development for disease control to enhance soybean productivity.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012 India
| | - Pravin V. Jadhav
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012 India
| | - Prashant B. Kale
- National Research Centre on Plant Biotechnology, LBS Centre, PUSA Campus, New Delhi, 110012 India
| | - Snehal K. Kad
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Mangesh P. Moharil
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Mahendra S. Dudhare
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Jashminkumar Kheni
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat India
| | - Amit G. Deshmukh
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Shyamsundar S. Mane
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Ravindra S. Nandanwar
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Suprasanna Penna
- Nuclear Agriculture and Biotechnology Division, Homi Bhabha National Institute, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, 400 085 India
| | - Joy G. Manjaya
- Nuclear Agriculture and Biotechnology Division, Homi Bhabha National Institute, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, 400 085 India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012 India
| | - Rukam Singh Tomar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat India
| | - Prashant G. Kawar
- ICAR- Directorate of Floricultural Research, College of Agriculture, Pune, Maharashtra, 411 005, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012 India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012 India
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Orman M, Bodea S, Funk MA, Campo AMD, Bollenbach M, Drennan CL, Balskus EP. Structure-Guided Identification of a Small Molecule That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria. J Am Chem Soc 2018; 141:33-37. [PMID: 30557011 DOI: 10.1021/jacs.8b04883] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The anaerobic gut microbial pathway that converts choline into trimethylamine (TMA) is broadly linked to human disease. Here, we describe the discovery that betaine aldehyde inhibits TMA production from choline by human gut bacterial isolates and a complex gut community. In vitro assays and a crystal structure suggest betaine aldehyde targets the gut microbial enzyme choline TMA-lyase (CutC). In our system, we do not observe activity for the previously reported CutC inhibitor 3,3-dimethylbutanol (DMB). The workflow we establish for identifying and characterizing betaine aldehyde provides a framework for developing additional inhibitors of gut microbial choline metabolism, including therapeutic candidates.
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Affiliation(s)
- Marina Orman
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Smaranda Bodea
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | | | - Ana Martínez-Del Campo
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Maud Bollenbach
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | | | - Emily P Balskus
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
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Waldman AJ, Balskus EP. The Human Microbiota, Infectious Disease, and Global Health: Challenges and Opportunities. ACS Infect Dis 2018; 4:14-26. [PMID: 29207239 DOI: 10.1021/acsinfecdis.7b00232] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Despite significant advances in treating infectious diseases worldwide, morbidity and mortality associated with pathogen infection remains extraordinarily high and represents a critical scientific and global health challenge. Current strategies to combat these infectious agents include a combination of vaccines, small molecule drugs, increased hygiene standards, and disease-specific interventions. While these approaches have helped to drastically reduce the incidence and number of deaths associated with infection, continued investment in current strategies and the development of novel therapeutic approaches will be required to address these global health threats. Recently, human- and vector-associated microbiotas, the assemblages of microorganisms living on and within their hosts, have emerged as a potentially important factor mediating both infection risk and disease progression. These complex microbial communities are involved in intricate and dynamic interactions with both pathogens as well as the innate and adaptive immune systems of their hosts. Here, we discuss recent findings that have illuminated the importance of resident microbiotas in infectious disease, emphasizing opportunities for novel therapeutic intervention and future challenges for the field. Our discussion will focus on four major global health threats: tuberculosis, malaria, HIV, and enteric/diarrheal diseases. We hope this Perspective will highlight the many opportunities for chemists and chemical biologists in this field as well as inspire efforts to elucidate the mechanisms underlying established disease correlations, identify novel microbiota-based risk factors, and develop new therapeutic interventions.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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Paharik AE, Schreiber HL, Spaulding CN, Dodson KW, Hultgren SJ. Narrowing the spectrum: the new frontier of precision antimicrobials. Genome Med 2017; 9:110. [PMID: 29241446 PMCID: PMC5729598 DOI: 10.1186/s13073-017-0504-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Antibiotics have become the standard of care for bacterial infections. However, rising rates of antibiotic-resistant infections are outpacing the development of new antimicrobials. Broad-spectrum antibiotics also harm beneficial microbial communities inhabiting humans. To combat antibiotic resistance and protect these communities, new precision antimicrobials must be engineered to target specific pathogens.
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Affiliation(s)
- Alexandra E Paharik
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Henry L Schreiber
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Caitlin N Spaulding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.,Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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Innovative Solutions to Sticky Situations: Antiadhesive Strategies for Treating Bacterial Infections. Microbiol Spectr 2017; 4. [PMID: 27227305 DOI: 10.1128/microbiolspec.vmbf-0023-2015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial adherence to host tissue is an essential process in pathogenesis, necessary for invasion and colonization and often required for the efficient delivery of toxins and other bacterial effectors. As existing treatment options for common bacterial infections dwindle, we find ourselves rapidly approaching a tipping point in our confrontation with antibiotic-resistant strains and in desperate need of new treatment options. Bacterial strains defective in adherence are typically avirulent and unable to cause infection in animal models. The importance of this initial binding event in the pathogenic cascade highlights its potential as a novel therapeutic target. This article seeks to highlight a variety of strategies being employed to treat and prevent infection by targeting the mechanisms of bacterial adhesion. Advancements in this area include the development of novel antivirulence therapies using small molecules, vaccines, and peptides to target a variety of bacterial infections. These therapies target bacterial adhesion through a number of mechanisms, including inhibition of pathogen receptor biogenesis, competition-based strategies with receptor and adhesin analogs, and the inhibition of binding through neutralizing antibodies. While this article is not an exhaustive description of every advancement in the field, we hope it will highlight several promising examples of the therapeutic potential of antiadhesive strategies.
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Dhakal D, Sohng JK. Coalition of Biology and Chemistry for Ameliorating Antimicrobial Drug Discovery. Front Microbiol 2017; 8:734. [PMID: 28522993 PMCID: PMC5415603 DOI: 10.3389/fmicb.2017.00734] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/10/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
- Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea.,Department of BT-Convergent Pharmaceutical Engineering, Sun Moon UniversityAsan-si, South Korea
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9
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Small Molecules That Sabotage Bacterial Virulence. Trends Pharmacol Sci 2017; 38:339-362. [PMID: 28209403 DOI: 10.1016/j.tips.2017.01.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/01/2017] [Accepted: 01/06/2017] [Indexed: 02/08/2023]
Abstract
The continued rise of antibiotic-resistant bacterial infections has motivated alternative strategies for target discovery and treatment of infections. Antivirulence therapies function through inhibition of in vivo required virulence factors to disarm the pathogen instead of directly targeting viability or growth. This approach to treating bacteria-mediated diseases may have advantages over traditional antibiotics because it targets factors specific for pathogenesis, potentially reducing selection for resistance and limiting collateral damage to the resident microbiota. This review examines vulnerable molecular mechanisms used by bacteria to cause disease and the antivirulence compounds that sabotage these virulence pathways. By expanding the study of antimicrobial targets beyond those that are essential for growth, antivirulence strategies offer new and innovative opportunities to combat infectious diseases.
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Application of Chemical Genomics to Plant-Bacteria Communication: A High-Throughput System to Identify Novel Molecules Modulating the Induction of Bacterial Virulence Genes by Plant Signals. Methods Mol Biol 2017; 1610:297-314. [PMID: 28439871 DOI: 10.1007/978-1-4939-7003-2_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The life cycle of bacterial phytopathogens consists of a benign epiphytic phase, during which the bacteria grow in the soil or on the plant surface, and a virulent endophytic phase involving the penetration of host defenses and the colonization of plant tissues. Innovative strategies are urgently required to integrate copper treatments that control the epiphytic phase with complementary tools that control the virulent endophytic phase, thus reducing the quantity of chemicals applied to economically and ecologically acceptable levels. Such strategies include targeted treatments that weaken bacterial pathogens, particularly those inhibiting early infection steps rather than tackling established infections. This chapter describes a reporter gene-based chemical genomic high-throughput screen for the induction of bacterial virulence by plant molecules. Specifically, we describe a chemical genomic screening method to identify agonist and antagonist molecules for the induction of targeted bacterial virulence genes by plant extracts, focusing on the experimental controls required to avoid false positives and thus ensuring the results are reliable and reproducible.
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Walsh SI, Craney A, Romesberg FE. Not just an antibiotic target: Exploring the role of type I signal peptidase in bacterial virulence. Bioorg Med Chem 2016; 24:6370-6378. [PMID: 27769673 PMCID: PMC5279723 DOI: 10.1016/j.bmc.2016.09.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/17/2016] [Accepted: 09/19/2016] [Indexed: 01/23/2023]
Abstract
The looming antibiotic crisis has prompted the development of new strategies towards fighting infection. Traditional antibiotics target bacterial processes essential for viability, whereas proposed antivirulence approaches rely on the inhibition of factors that are required only for the initiation and propagation of infection within a host. Although antivirulence compounds have yet to prove their efficacy in the clinic, bacterial signal peptidase I (SPase) represents an attractive target in that SPase inhibitors exhibit broad-spectrum antibiotic activity, but even at sub-MIC doses also impair the secretion of essential virulence factors. The potential consequences of SPase inhibition on bacterial virulence have not been thoroughly examined, and are explored within this review. In addition, we review growing evidence that SPase has relevant biological functions outside of mediating secretion, and discuss how the inhibition of these functions may be clinically significant.
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Affiliation(s)
- Shawn I Walsh
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Arryn Craney
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Narrow-spectrum inhibitors of Campylobacter jejuni flagellar expression and growth. Antimicrob Agents Chemother 2015; 59:3880-6. [PMID: 25870073 DOI: 10.1128/aac.04926-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/09/2015] [Indexed: 01/16/2023] Open
Abstract
Campylobacter jejuni is a major cause of food-borne illness due to its ability to reside within the gastrointestinal tracts of chickens. Multiple studies have identified the flagella of C. jejuni as a major determinant of chicken colonization. An inhibitor screen of approximately 147,000 small molecules was performed to identify compounds that are able to inhibit flagellar expression in a reporter strain of C. jejuni. Several compounds that modestly inhibited motility of wild-type C. jejuni in standard assays were identified, as were a number of small molecules that robustly inhibited C. jejuni growth, in vitro. Examination of similar bacterial screens found that many of these small molecules inhibited only the growth of C. jejuni. Follow-up assays demonstrated inhibition of other strains of C. jejuni and Campylobacter coli but no inhibition of the closely related Helicobacter pylori. The compounds were determined to be bacteriostatic and nontoxic to eukaryotic cells. Preliminary results from a day-of-hatch chick model of colonization suggest that at least one of the compounds demonstrates promise for reducing Campylobacter colonization loads in vivo, although further medicinal chemistry may be required to enhance bioavailability.
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