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Prado LCDS, Giacchetto Felice A, Rodrigues TCV, Tiwari S, Andrade BS, Kato RB, Oliveira CJF, Silva MV, Barh D, Azevedo VADC, Jaiswal AK, Soares SDC. New putative therapeutic targets against Serratia marcescens using reverse vaccinology and subtractive genomics. J Biomol Struct Dyn 2022; 40:10106-10121. [PMID: 34192477 DOI: 10.1080/07391102.2021.1942211] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Gram-negative bacillus Serratia marcescens, a member of Enterobacteriaceae family, is an opportunistic nosocomial pathogen commonly found in hospital outbreaks that can cause infections in the urinary tract, bloodstream, central nervous system and pneumonia. Because S. marcescens strains are resistant to several antibiotics, it is critical the need for effective treatments, including new drugs and vaccines. Here, we applied reverse vaccinology and subtractive genomic approaches for the in silico prediction of potential vaccine and drug targets against 59 strains of S. marcescens. We found 759 core non-host homologous proteins, of which 87 are putative surface-exposed proteins, 183 secreted proteins, and 80 membrane proteins. From these proteins, we predicted seven candidates vaccine targets: a sn-glycerol-3-phosphate-binding periplasmic protein UgpB, a vitamin B12 TonB-dependent receptor, a ferrichrome porin FhuA, a divisome-associated lipoprotein YraP, a membrane-bound lytic murein transglycosylase A, a peptidoglycan lytic exotransglycosylase, and a DUF481 domain-containing protein. We also predicted two drug targets: a N(4)-acetylcytidine amidohydrolase, and a DUF1428 family protein. Using the molecular docking approach for each drug target, we identified and selected ZINC04259491 and ZINC04235390 molecules as the most favorable interactions with the target active site residues. Our findings may contribute to the development of vaccines and new drug targets against S. marcescens. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ligia Carolina da Silva Prado
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Andrei Giacchetto Felice
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Thaís Cristina Vilela Rodrigues
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, State University of Southwest of Bahia, Bahia, Brazil
| | - Rodrigo Bentes Kato
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carlo José Freire Oliveira
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Marcos Vinicius Silva
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, West Bengal, India
| | - Vasco Ariston de Carvalho Azevedo
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Arun Kumar Jaiswal
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Siomar de Castro Soares
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
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FitzGerald ES, Luz NF, Jamieson AM. Competitive Cell Death Interactions in Pulmonary Infection: Host Modulation Versus Pathogen Manipulation. Front Immunol 2020; 11:814. [PMID: 32508813 PMCID: PMC7248393 DOI: 10.3389/fimmu.2020.00814] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/08/2020] [Indexed: 12/12/2022] Open
Abstract
In the context of pulmonary infection, both hosts and pathogens have evolved a multitude of mechanisms to regulate the process of host cell death. The host aims to rapidly induce an inflammatory response at the site of infection, promote pathogen clearance, quickly resolve inflammation, and return to tissue homeostasis. The appropriate modulation of cell death in respiratory epithelial cells and pulmonary immune cells is central in the execution of all these processes. Cell death can be either inflammatory or anti-inflammatory depending on regulated cell death (RCD) modality triggered and the infection context. In addition, diverse bacterial pathogens have evolved many means to manipulate host cell death to increase bacterial survival and spread. The multitude of ways that hosts and bacteria engage in a molecular tug of war to modulate cell death dynamics during infection emphasizes its relevance in host responses and pathogen virulence at the host pathogen interface. This narrative review outlines several current lines of research characterizing bacterial pathogen manipulation of host cell death pathways in the lung. We postulate that understanding these interactions and the dynamics of intracellular and extracellular bacteria RCD manipulation, may lead to novel therapeutic approaches for the treatment of intractable respiratory infections.
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Affiliation(s)
| | | | - Amanda M. Jamieson
- Division of Biology and Medicine, Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, United States
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Konecka E, Mokracka J, Krzymińska S, Kaznowski A. Evaluation of The Pathogenic Potential of Insecticidal Serratia marcescens Strains to Humans. Pol J Microbiol 2019; 68:185-191. [PMID: 31257791 DOI: 10.21307/pjm-2019-018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 11/11/2022] Open
Abstract
We observed the death of insect caterpillars of Spodoptera exigua in the laboratory culture line and identified Serratia marcescens as the bacterial causative agent of the insect death. We confirmed that S. marcescens had insecticidal activity against S. exigua and caused high mortality of larvae. The LC50 values of S. marcescens CFU per 1 cm2 of insect diet surface were similar for all isolates. Our research reports novel strains with high pesticidal activity as candidates for future research on a new bioinsecticide. As bioinsecticides cannot be harmful to non-target organisms, we determined the pathogenic properties of S. marcescens to humans. We proved the ability of S. marcescens to damage mammalian epithelial cells. All strains had cytopathic effects to Vero cells with a cytotoxic index ranging from 51.2% ± 3.8% to 79.2% ± 4.1%. We found that all of the strains excreted catecholate siderophore - enterobactin. All isolates were resistant to sulfamethoxazole, tobramycin, gentamicin, cefepime, and aztreonam. We did not observe the ESBL phenotype and the integrons' integrase genes. Resistance to sulfamethoxazole was due to the presence of the sul1 or sul2 gene. The use of resistant S. marcescens strains that are pathogenic to humans in plant protection may cause infections difficult to cure and lead to the spread of resistance genes. The results of our study emphasize the necessity of determination of the safety to vertebrates of the bacteria that are proposed to serve as biocontrol agents. The novelty of our study lies in the demonstration of the indispensability of the bacteria verification towards the lack of hazardous properties to humans. We observed the death of insect caterpillars of Spodoptera exigua in the laboratory culture line and identified Serratia marcescens as the bacterial causative agent of the insect death. We confirmed that S. marcescens had insecticidal activity against S. exigua and caused high mortality of larvae. The LC50 values of S. marcescens CFU per 1 cm2 of insect diet surface were similar for all isolates. Our research reports novel strains with high pesticidal activity as candidates for future research on a new bioinsecticide. As bioinsecticides cannot be harmful to non-target organisms, we determined the pathogenic properties of S. marcescens to humans. We proved the ability of S. marcescens to damage mammalian epithelial cells. All strains had cytopathic effects to Vero cells with a cytotoxic index ranging from 51.2% ± 3.8% to 79.2% ± 4.1%. We found that all of the strains excreted catecholate siderophore – enterobactin. All isolates were resistant to sulfamethoxazole, tobramycin, gentamicin, cefepime, and aztreonam. We did not observe the ESBL phenotype and the integrons’ integrase genes. Resistance to sulfamethoxazole was due to the presence of the sul1 or sul2 gene. The use of resistant S. marcescens strains that are pathogenic to humans in plant protection may cause infections difficult to cure and lead to the spread of resistance genes. The results of our study emphasize the necessity of determination of the safety to vertebrates of the bacteria that are proposed to serve as biocontrol agents. The novelty of our study lies in the demonstration of the indispensability of the bacteria verification towards the lack of hazardous properties to humans.
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Affiliation(s)
- Edyta Konecka
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań , Poland
| | - Joanna Mokracka
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań , Poland
| | - Sylwia Krzymińska
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań , Poland
| | - Adam Kaznowski
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań , Poland
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Konecka E, Mokracka J, Krzymińska S, Kaznowski A. Evaluation of The Pathogenic Potential of Insecticidal Serratia marcescens Strains to Humans. Pol J Microbiol 2019. [PMID: 31257791 PMCID: PMC7260640 DOI: 10.33073/pjm-2019-018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We observed the death of insect caterpillars of Spodoptera exigua in the laboratory culture line and identified Serratia marcescens as the bacterial causative agent of the insect death. We confirmed that S. marcescens had insecticidal activity against S. exigua and caused high mortality of larvae. The LC50 values of S. marcescens CFU per 1 cm2 of insect diet surface were similar for all isolates. Our research reports novel strains with high pesticidal activity as candidates for future research on a new bioinsecticide. As bioinsecticides cannot be harmful to non-target organisms, we determined the pathogenic properties of S. marcescens to humans. We proved the ability of S. marcescens to damage mammalian epithelial cells. All strains had cytopathic effects to Vero cells with a cytotoxic index ranging from 51.2% ± 3.8% to 79.2% ± 4.1%. We found that all of the strains excreted catecholate siderophore – enterobactin. All isolates were resistant to sulfamethoxazole, tobramycin, gentamicin, cefepime, and aztreonam. We did not observe the ESBL phenotype and the integrons’ integrase genes. Resistance to sulfamethoxazole was due to the presence of the sul1 or sul2 gene. The use of resistant S. marcescens strains that are pathogenic to humans in plant protection may cause infections difficult to cure and lead to the spread of resistance genes. The results of our study emphasize the necessity of determination of the safety to vertebrates of the bacteria that are proposed to serve as biocontrol agents. The novelty of our study lies in the demonstration of the indispensability of the bacteria verification towards the lack of hazardous properties to humans.
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Affiliation(s)
- Edyta Konecka
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań , Poland
| | - Joanna Mokracka
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań , Poland
| | - Sylwia Krzymińska
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań , Poland
| | - Adam Kaznowski
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań , Poland
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Krzymińska S, Szczuka E, Dudzińska K, Kaznowski A. Virulence and the presence of aminoglycoside resistance genes of Staphylococcus haemolyticus strains isolated from clinical specimens. Antonie van Leeuwenhoek 2015; 107:857-68. [PMID: 25586730 PMCID: PMC4359711 DOI: 10.1007/s10482-015-0378-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/07/2015] [Indexed: 11/15/2022]
Abstract
We examined thirty methicillin-resistant Staphylococcus haemolyticus isolates cultured from clinical specimens for antibiotic resistance, various important interactions of the bacteria with epithelial cells and putative virulence determinants. All strains were resistant to oxacillin and carried the mecA gene. Aminocyclitol-3′-phosphotransferase (aph(3′)-IIIa) gene encoding nucleotidyltransferases was detected in 43 %, aminocyclitol-6′-acetyltransferase-aminocyclitol-2″-phosphotransferase (aac(6′)/aph(2″)) gene encoding bifunctional acetyltransferases/phosphotransferases in 33 %, aminocyclitol-4′-adenylyltransferase (ant(4′)-Ia) gene encoding phosphotransferases in 20 %. The coexistence of resistance to methicillin and aminoglycosides was investigated in multi-resistant strains. Coexisting (aac(6′)/aph(2″)) and (aph(3′)-IIIa) genes were detected in 33 % of isolates, whereas 63 % of isolates had at least one of these genes. All strains revealed adherence ability and most of them (63 %) were invasive to epithelial cells. Electron microscopy revealed that the bacteria were found in vacuoles inside the cells. We observed that the contact of the bacteria with host epithelial cells is a prerequisite to their cytotoxicity at 5 h-incubation. Culture supernatant of the strains induced a low effect of cytotoxicity at the same time of incubation. Cell-free supernatant of all isolates expressed cytotoxic activity which caused destruction of HEp-2 cells at 24 h. None of the strains was cytotonic towards CHO cells. Among thirty strains, 27 % revealed lipolytic activity, 43 % produced lecithinase and 20 % were positive for proteinase activity. Analyses of cellular morphology and DNA fragmentation exhibited typical characteristic features of those undergoing apoptosis. The Pearson linear test revealed positive correlations between the apoptotic index at 24 h and percentage of cytotoxicity. Our results provided new insights into the mechanisms contributing to the development of S. haemolyticus-associated infections. The bacteria adhered and invaded to non-professional phagocytes. The invasion of epithelial cells by S. haemolyticus could be similar to phagocytosis that requires polymerization of the actin cytoskeleton. The process is inhibited by cytochalasin D. Moreover, they survived within the cells by residing in membrane bound compartments and induced apoptotic cell death.
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Affiliation(s)
- Sylwia Krzymińska
- Department of Microbiology, Faculty of Biology, A.Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland,
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Petersen LM, Tisa LS. Friend or foe? A review of the mechanisms that driveSerratiatowards diverse lifestyles. Can J Microbiol 2013; 59:627-40. [DOI: 10.1139/cjm-2013-0343] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Found widespread around the globe, Serratia are Gram-negative bacteria capable of thriving in a diverse number of environments that include water, soil, and the digestive tracts of various animals. Known for their ability to produce a myriad of extracellular enzymes, these bacteria also produce various secondary metabolites that directly contribute to their survival. While the effects Serratia species have on other organisms range from parasitic to symbiotic, what these bacteria have in common is their ability to resist attack, respond appropriately to environmental conditions, and outcompete other microorganisms when colonizing their respective niche. This review highlights the mechanisms utilized by Serratia species that drive their ubiquitous nature, with emphasis on the latest findings. Also discussed is how secreted compounds drive these bacteria towards pathogenic, mutualistic, and antagonistic associations.
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Affiliation(s)
- Lauren M. Petersen
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824-2617, USA
| | - Louis S. Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824-2617, USA
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